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LAMA version %s. Cannot determine type of input file Note - the two input files have different types of data. Minimal length of reported alignments %3d Score cutoff is %.1f Z score units (in the top %.1e percentile of chance scores) %s alignment Z-score expected number for block 1 from:to block 2 from:to length searching %d blocks %sBLIMPS_DIRdefault.amino.frq%s/docs/%sTrying %s... Comparisons skipped !Block matrix %s shorter (%d) than narrowest width allowed (%d) Comparison skipped ! %s%.1e%-10s %3d : %3d and %-10s %3d : %3d (%2d) score %3.0f (%4.1f %s)No hits found above score cutoff %.1f.Output written in file %s. Error in reading first file name from first argument !Error in reading second file name from first argument ! Enter name of a file with blocks or block matrices: The blocks/matrices in this file will be intercompared.If you wish to compare them against blocks/matrices inanother file enter that file name (else just hit ).r Enter name of output file: w Cannot open file "%s" Minimal alignment width can not be negative !The value given (%d) is out of range. Minimal alignment width can not be less than narrowest allowed blocks (%d). Cutoff score should be specified as a Z score (mean+Z*std).The Z score must be positive (corresponding to the 50 percentile or higher).A negative cutoff score (%f) was specified, default value (%.2f) used. Column scores for %s and %s - %6.3f S matrix for %s and %s - Column scores for optimal alignment of %s and %s - %3d,%2d %-10s %3d %3d %-10s %3d %3d %2d Prpo %6.2f (%4.1f) Error ! Extrapolated mean of shuffled PSSMs requested for a block too narrow (%d). Error ! Extrapolated variance of shuffled PSSMs requested for a block too narrow (%d). BL MA Error. variable db_type (%c) is of unknown type ! Unable to recover enough memory to continue. Aborting. Error ! Problem in format of ProDom entry description -line%s%s;%s%s%s; ProDom_mulError ! Problem in format of ProDom entry description-lineError ! Problem in ProDom entry %s second word in description line doesn't begin with a (second word in description line doesn't end with a )Error ! Problem in format of ProDom entry %s A non-digit in the number-of-sequences field "%s" Error ! Number of sequences in ProDom entry %s (%d) is less than 2 Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d. not enough residues to fill the sequence.Filling the rest of the sequence with blanks.read_a_prodom_entry(): Error reading sequence %s in block %s,Undocumented return value, %d, from read_sequence(). Error ! Not enough sequences (%d) in ProDom entry %s Error ! Actual number of sequences in ProDom entry %s different than what the entry reportsError ! Problem in format of ProDom entry %s sequence-line %d A non-digit in the sequence start position %s Error ! Problem in format of ProDom entry sequence-line %d Sequence %s has length of %d instead of expected %d distance from previous block=(%d,%d)adapted from ProDom entry; width=%d; seqs=%d; |% 4d %4d--+----%c |aInformation: %s Warning: %s Serious: %s Program Error: %s Fatal Error: %s Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked. See the errors.c source code for programming details. Aborting due to the SIGABRT signal. BLOCK; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method. All weights in the block were less than or equal to zero.Computing position-based sequence weights. , .+-0123456789convert: Block is too wide, unable to continue (max=%d). Qij matrix missing, unable to continue. %s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue. pb_weights:%d ignored for %s %s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction. dirichlet(): Cannot open dirichlet file %s dirichlet(): OUT OF MEMORY Mixture=Alpha== ID AC DE MATRIX on ID line; not a BLOCKnone; BLOCKError in block file format. Invalid ID line:CC Error in block file format. No ID line. block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format. Invalid AC line:Error in block file format. No AC line. noneError in block file format. Invalid DE line:Error in block file format. No DE line. motifwidth=width=%d;No width field for block %sSetting width to zero seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format. Invalid BL line:Error in block file format. No BL line. No space allocated for sequence %s in block %s.Allocating more space (%d)%d)%d more residues in the sequence than the expected %d.Resetting block width to %d. Filling the rest of the sequence with blanks. next_cluster(): Unknown sequence type, assuming an amino acid sequence. next_cluster(): Error reading sequence %s in block %s, Undocumented return value, %d, from read_sequence(). %lgNumber of sequences in block %s read from file as %d but is %d Allocating more space for sequences in block %s. Allocating more space for clusters in block %s. --- block ---ID %s AC %s DE %s BL %s motif: %s width=%d; 99.5%%=%d; strength=%d; num sequences: %d num clusters: %d %s ( %d:%d, AA) NA) ??) --- ----- ---Unknown output type: %d, using integer output ID %s AC %s DE %s width=%d; seqs=%d; 99.5%%=%d; strength=%d BL %s%-20s (%4d) %3d %f // idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s Error in matrix file format. No ID line. Error in matrix file format. No AC line. Error in matrix file format. No DE line. No width field for matrix %sError in matrix file format. No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed. %fresize_matrix() not finished. Exiting. % 6.4fMA %s %c * - %3d %3d % 6.4f % 6.4f Unknown output style: %d, using integer output Unknown sequence type: %d, using amino acid %c %c * - * - A C G T A C G T % 9.4f % 9.4f load_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c load_frequencies: Read a frequency of value of %f for: not a residue load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect. Unable to open codon usage fileload_codons: Setting all codon usages to 1. load_codons: Read a codon usage value of %f for: %c %s/docs/default.amino.frq%s/docs/default.qijdefault.qijGenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s Ran out of room for sequence %s. Allocating more space. read_sequence(): Unknown sequence type, asumming amino acid sequence translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d. Returning the original sequence. Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type. Not all of the database formats were handled. Decided it is not a GCG database format of %s.Could not figure out database format. Decided on %s database format. >--- sequence --->%s ( %d:%d, >--- -------- --->%s %s untranslate_sequence(): Not an amino acid sequence, not untranslating.Reclaim space function is not defined. 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Cx|"HACxK8a@Dx8H>x8exH?/A$| H>р |exxH@/@8yd8@8dH>8Vc@|X" /A$cxH>/@x8exH?1/@$cxH>/@x8exH? 8+ADcxH>/@48exxH>8exxH>x8exH>cxH>U |`x8!p|N |a|~x!|#x|#xH=̀x@xHEÀfxxH=||~̀h8!`a|N |B?|}x<|``87x!xH>E8`K]8B]Ѐ}H>|~y@(H/@|``<8,H>8`KX8!P|N |aB! ;a@}x/A<<_|~x_|tT`:|\./AH@1};/@88a@H->. :@U:H,|^ c|w|H1%~xH19||xCxH1/@uU8ExH1/A|>x}H0|exuUH3 /@LAH@LuU<8,H4-/A,<8,H4/A<8,H4/@ /b@<CxH4-+~cx@ 8a@K8!aa|}a N |Ba|}x<8c-!H/8}dH/<x8c-(H.<8c-0H.<8c-8H.݀/@X<8c&H.8` H.};@<_SP]|;|||ctH.MAH/@X<8c& H.i8` H.!;@<_SL]|;|||ctH-AHT<8c&H.8` H-̀;@0<_SP]|;|||ctH-A8` H-h<8!`|8c-@aH.l|B||x|#x<8+Ĕ!cxx8dH-Հ/@;@l<_?@"QcZ\;dx||y|ctH/|Жp||.p|P<@8` dxH/xAH/@;@<_?@"QcZ\;dx||y|ctH/)|Жp||.p|P<@8` dxH.xAH|;@l<_?@"QcZ;|Жp||.p|P<@8` dxH.\dx|x|y|ctH.}Ah8!`dx8` |H.T|ܐB!|zx/A@?<}O8)H-8`K偀}O<8(H-8`KiCxH$8`H.I||y@,H%/@<<cO8tH-8`K)z8cH*|yy@,H/@<<cO8tH-A8`KZ8:DxBԑ<x\;d\:dH/%x~xH/;z@0=x|{x88H;;ADx8dxH+ix~x8dH+Y<xx8!p|N |B<_Q!/AX8!P}|N <<cNd8(H,)8`KрX8!P8`|N |~y|B!@ <<cM8(,H+8`K}X<_8!PQ,|N |B=?<_9)M;|M}#Kxxx<8M=8 9M|P| G&|BtT:TB:|J|Bb(T:b|@J}dC'8 BTB:})th|@PU):TB:})b|KP 8B9|B8@h8c@TN +|B|A,+A$+AT:|*T:|2|cHX+A+A +@<_BLbcH0?_$ L  ;`}yB|EB+B|FB"T:j`IJx|ZT:||@}Cx}cx}Cx}Cx}Cx|E}9b9IX|خT&6@|E~ݳx Lƺ|E}&bI9 | `|tT:|T >@,^|HH| |C @9)PA9xA;{Jx~xAP|#xN Tc>|+B}H|ASearch ErrorYou need to enter a block to search with by writing or pasting a block in the query block window.

%s/%d.LAMA_Qblock_errorsw%s // There seems to be an error in the format of query block number %d:

No blocks were read from the query.Sorry, you can not compare more than %d query blocks in each run.
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No blocks were read from the target data.Sorry, you can not compare more than %d target blocks in each run. date/usr/bin/nice -5 %s %s,%s %s 0 %d 0 %f > /dev/null 2>&1An error occured during the search.Please try your search again at a later time.If it fails again contact the maintainer of these pagesand describe what caused the problem with an example.

Error opening LAMA output file.%s/htmlize-blimps.pl %s | %s/htmlize-LAMA %s %s - -Error opening pipeLAMA Search Results

LAMA Search Results (%s)

../help/LAMA_help.html?%s %s "/usr/bin/nice -10 %s %s,%s %s 0 %d 0 %f > /dev/null 2>&1"%s %s '(cat %s) | /usr/bin/mailx -s "LAMA Results" -r "blocks@fhcrc.org" %s'%s %s 'rm -f %s/%d.*'LAMA Search Submitted

LAMA Search Submitted

Your search has been submitted.You will receive the results via email to the address you gave ("%s"). %dC.html%s %s %s %s./cyrcaLama.pl5.6CYRCA results /blocks/icons/cyrcashLogo.gifContent-type: text/html REQUEST_METHODPOSTThis script should be referenced with a METHOD of POST.If you don't understand this, see this forms overview.%c

What could have happened is that you just reloaded this page rather than redoing the search.

If you use NETSCAPE it has a tendency to try to reload a page when you go back to it. This may be why you have this error.CONTENT_TYPEapplication/x-www-form-urlencodedThis script can only be used to decode form results. umask 006&;`'"|*?~<>^()[]{}$\Unable to recover enough memory to continue. Aborting. ID AC DE BL ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format. Invalid ID line:CC Error in block file format. No ID line. block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format. Invalid AC line:Error in block file format. No AC line. noneError in block file format. Invalid DE line:Error in block file format. No DE line. motifwidth=width=%d;No width field for block %sSetting width to zero seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format. Invalid BL line:Error in block file format. No BL line. No space allocated for sequence %s in block %s.Allocating more space (%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d. not enough residues to fill the sequence.Filling the rest of the sequence with blanks. next_cluster(): Unknown sequence type, assuming an amino acid sequence. next_cluster(): Error reading sequence %s in block %s, Undocumented return value, %d, from read_sequence(). %lgNumber of sequences in block %s read from file as %d but is %d Allocating more space for sequences in block %s. Allocating more space for clusters in block %s. --- block ---ID %s AC %s DE %s BL %s motif: %s width=%d; 99.5%%=%d; strength=%d; num sequences: %d num clusters: %d %s ( %d:%d, AA) NA) ??) --- ----- ---Unknown output type: %d, using integer output ID %s AC %s DE %s width=%d; seqs=%d; 99.5%%=%d; strength=%d BL %s%-20s (%4d) %3d %f idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s aInformation: %s Warning: %s Serious: %s Program Error: %s Fatal Error: %s Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked. See the errors.c source code for programming details. Aborting due to the SIGABRT signal. GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s Ran out of room for sequence %s. Allocating more space. read_sequence(): Unknown sequence type, asumming amino acid sequence translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d. Returning the original sequence. Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type. Not all of the database formats were handled. Decided it is not a GCG database format of %s.Could not figure out database format. Decided on %s database format. >--- sequence --->%s ( %d:%d, >--- -------- --->%s %s untranslate_sequence(): Not an amino acid sequence, not untranslating.Reclaim space function is not defined. 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8`A8`HP|~y@,H)/@<<ceL88HQa8`H88@8`^~xCxK9/@xHN8`Hl|/ACxxKHLx~x8HN/~@,H/@<<ceL88HP8`HMl8~x|`HN|}y@,HE/@<<ceL88HP}8`H ~x8HNi/~@,H/@<<ceL88HP=8`Hɀx;@l9@^W:l|J́>l}*J Ѐ^l>|\}*J9J|]Il>|;|| I.^xA8~8HM/~@,HA/@<<ceL88HOy8`H|;>.?; :@^; <_eHHT{eP<8;\8HR/A {eP<8;8HR/@ 8.x@}ePHM!+@}eP8(HP/A䀾<}eP8I,|8@8xHQaxHO=8a@HLŀl=xA0<ceL<8I<|8HNU8`Hl9@@@~x~ȳx|GP>|BtTB:}=J|BBi| Q9J^lAЀ~;;9|c|dx8cdHN@0CxHMy/@ {eP8Ex}xHO/@x8!a|}p N |B}H|dx|~H>X8!Px|H>8c8H?|@&|АA;!B|zx; @<_.T~ճx~Գx8` H@ /c@<8c<8ci<8c~x<dx8c@A8` H<<8c<8-H>x@h@\~x]W8<;TB:8c<|B"|H.9k|H.9k@D!@H>1@A;98` ;H@,^|HH| |C @9)PA9xA;{Jx~xAP|#xN Tc>|+B}H|A = input blocks = fasta format sequences = output file = processing option blks = add sequences to blocks & output blocks seqs = add sequences to blocks & output sequences simi = add sequences to blocks & do similarity analysis Enter name of file containing blocks: r Cannot open file %s Enter name of sequence file: Enter name of output seqs file: wseqssimiBLIMPS_DIR%s/docs/default.amino.frqdefault.qijNo blocks found in %s . FRAGMENT%s already in block out of order %d, previous end %d pad1=%d bestpos=%d endpos=%d seqlen=%d pad2=%d bestpos=%d endpos=%d seqlen=%d bad bestpos=%d endpos=%d seqlen=%d No sequences found in %s . Query added to %s %d sequences added addseqs.data%s %d %d %d %d %s %s calibrated best score = %5d at %d (,)Median TP score = %d, TPabove = %d 99.5 TN score = %d %s; distance from previous block=(%d,%d)Cannot write %s of length %d from %d to %d >%s %s from %d to %d WARNING: sequence segments are of different lengths%s %d : %s %d Mean dissimilarity distance = %.2f %s %.0f %.2f |_BLOCK; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method. All weights in the block were less than or equal to zero.Computing position-based sequence weights. Unable to recover enough memory to continue. Aborting. , .+-0123456789convert: Block is too wide, unable to continue (max=%d). Qij matrix missing, unable to continue. %s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue. pb_weights:%d ignored for %s %s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction. dirichlet(): Cannot open dirichlet file %s dirichlet(): OUT OF MEMORY Mixture=Alpha== GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID DE SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN Ran out of room for sequence %s. Allocating more space. read_sequence(): Unknown sequence type, asumming amino acid sequence translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d. Returning the original sequence. Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type. Not all of the database formats were handled. Decided it is not a GCG database format of %s.Could not figure out database format. Decided on %s database format. >--- sequence --->%s ( %d:%d, AA) NA) ??) >--- -------- --->%s %s untranslate_sequence(): Not an amino acid sequence, not untranslating.load_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c load_frequencies: Read a frequency of value of %f for: not a residue load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect. %lgUnable to open codon usage fileload_codons: Setting all codon usages to 1. load_codons: Read a codon usage value of %f for: %c %s/docs/default.amino.frq%s/docs/default.qijAC BL MATRIX on ID line; not a BLOCKnone; BLOCKError in block file format. Invalid ID line:%s CC Error in block file format. No ID line. block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format. Invalid AC line:Error in block file format. No AC line. noneError in block file format. Invalid DE line:Error in block file format. No DE line. motif%swidth=width=%d;No width field for block %sSetting width to zero seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format. Invalid BL line:Error in block file format. No BL line. No space allocated for sequence %s in block %s.Allocating more space (%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d. not enough residues to fill the sequence.Filling the rest of the sequence with blanks. next_cluster(): Unknown sequence type, assuming an amino acid sequence. next_cluster(): Error reading sequence %s in block %s, Undocumented return value, %d, from read_sequence(). Number of sequences in block %s read from file as %d but is %d Allocating more space for sequences in block %s. Allocating more space for clusters in block %s. --- block ---ID %s AC %s DE %s BL %s motif: %s width=%d; 99.5%%=%d; strength=%d; num sequences: %d num clusters: %d %s ( %d:%d, --- ----- ---Unknown output type: %d, using integer output ID %s AC %s DE %s width=%d; seqs=%d; 99.5%%=%d; strength=%d BL %s%-20s (%4d) %3d %f // idacde ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s Information: %s Warning: %s Serious: %s Program Error: %s Fatal Error: %s Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked. See the errors.c source code for programming details. Aborting due to the SIGABRT signal. Error in matrix file format. No ID line. Error in matrix file format. No AC line. Error in matrix file format. No DE line. No width field for matrix %sError in matrix file format. No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed. %fresize_matrix() not finished. Exiting. |% 4d --+----%c |% 6.4fMA %s %c * - %3d %3d % 6.4f % 6.4f Unknown output style: %d, using integer output Unknown sequence type: %d, using amino acid %c %c * - * - A C G T A C G T % 9.4f % 9.4f Reclaim space function is not defined. No memory will be reclaimed. |B}h=k|}N |B}h=k|}N |B}h=k|p}N |B}h=k|T}N |B}h=k|8}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|t}N |B}h=k|X}N |B}h=k|<}N |B}h=k| }N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|x}N |B}h=k|\}N |B}h=k|@}N |B}h=k|$}N |B}h=k|}N |B}h=k|}N |B}h=k|\}N |B}h=k|}N |B}h=k|}N |B}h=k|x}N |B}h=k|\}N |B}h=k|@}N |B}h=k|$}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k||}N |B}h=k|`}N |B}h=k|D}N |B}h=k|(}N |B}h=k| }N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N MATRIX A.?@YC0@@?@ =pA.@I@4@5@D@38?@?R@Ç3333Ç3333@X@?333333&%H$d    -ARNDCQEGHILKMFPSTWYVBZX*- A$R(N,D0C4Q8E x~x|8`8(Hs|`x@^@x^@|^@8(@8`-HsA}8`-@Hs!|N |B}=|9r}N |B}=|9r}N |B}=|9r}N |!|> x~x|8H8`-Hr~@8@D^D/@Hx^DBBx@L^DBB|@4^DH>D^H ^H/(AHqр^DB8DK|8`-@HqрH/A4^H /A^H ~H| x}N!~HHqU!|N |B}=|9q4}N |B}=|9qT}N |B}=|9q}N |B}=|9q4}N |!|> xBHp<_Bx@@/A^@T>+@H<_bvHp!<_bvHo!|N |B}=|9o}N |B}=|9o}N |B}=|9o}N |B<?!8c[HrYHr5<<}<c8[8[Hq<<<c8[8\Hq<<<c8\8\HqX<<<8!Pc|8\$8\Hq|BA<8c[l!Hq<8c[|?_Hq;ZHq)<_a@;ƒ;?H\{8@8&xHѐ~H~H ~8=H<~8[8Hp/@;;@/A{Hp/Ax8!pxA|N |B<_B,?!<}<8Z8ZpHpaX}8!P|Ho|BA?;!<I|t/@$<8cZlHoe<8cZ|HoY8`H<_?B<{<8Z8ZHoɀ{H+m\" |t/At?<}8ZHn\<|~x8ZHn}<x888cZHnExHn}<;8ZHni|~xH{<8Z;HnM||yAt<8cZlHny<x8cZHm<8c[0Hn]<_‚H~|ctHmExHm]|`t~/@<8c[8HmaxHmyH\xH/@h/A <8cZlHm<8c[@HmH(/ @,<8cZlHm<8c[X8 HlK8`Hmh8!`xA|Hlh8!`A|N |B<_?"q<_Bq<<<_B<8Ypƀ9`} t/A4}"KxA,|CY9k|^X|@t/A@H^/8|YA 9k|^X9 H|^X/|^I9k9)@X8!P|N ||zx<``c!|#x|+x?`Hjc{|~x;;CxHj|~@$|^==x8;iHja|~x\8B\|^|@tA$CxHiy/@/@|^|@tA;H ;Kx8x|鮀h8!`|N C|ix|@t/@@TB8B|CtH 8|t Tb 6|Ct|t/@@p|C8BH |C8B|CtN |||x!;/A8;/%|@xKe;||;;/@8|鮀X8!P|N /M 8@ /+@C/M K||~x!|#xHi%/8cA$||bx|tA/8c@8@X8!P|Cx|N |a|}x!|+x;d;xHhu|}|/ @xHh]|}||t/A/ AA ;K8x|HgA0C||xh8!`|aN ||}x!|#xxHg|~txHf/@xxHgK؀X8!P|N |ix8@/A$|t|Cx M 8B| /@8`N |Ba|}x!Hg||x;/Ad;`\<|t8cUK/A88|@ |P|C| 8BB}||x;;|/@h8!`a|N A|{y|B!8`A08`Hf|~y@,H>/@<<cx8UDHe8`H!88@8`^~xcxxH/@xHc)8`H^l8/A$??_=x8<_y:yH\<_?_8By;y|\x|He/}@,H> /@<<cx8UDHe8`H ?cxxHzyxAHbyxh8!`A|N |B|@&; |{x?|#xAex!:$,:$X$l$p$t$x$|$$$$8~wdH~wd8exHb}~wd<88T$Hc/Ah~wd<8T,8Hc/AL~wd<8T48Hc/A0~wd<8T<8Hcu/AcxHc/AtcxHcu/8`@~wd<8T$8Hc5/@wd|t/ Al<x8TDHf)/@08|; H":||xH"Cxx8dHeH<<cwh8TPHc!8`H8`H <_?8BTp}whb<8T|":zHb8`H}wh<x8OXHb8`H~wd8exH`~wd<88THb5/AHL8H<_<8BTpcwhb<8T":zHbI8`H~wd<8T,8Ha.|xx@䃞wd|t/ AL8|:dH!5; ||xH!}x8d~óx:HdxH"||xHb|||t/;@xHb||;x8d;xHd5xxHd xHba/ |}x@ ; /@h<_}=w`;|tT`1@Tb:|B4TH8Hc0C|/@;;@ /A~wd~ijxHcu~wd<8THc/Ap<88T8Hc HX<8)8T?8zdHb̀}wh<8U$H`8`H]}wh<x8OXH`y8`HA~wd8exH^~wd<88TH_/AH<<8)8T8zdHbM<8cwh<8UTH`8`Hـ~wd<8T48H_/@ԃwd|t/ @/@ /A0~wd; 8cH||xH9x8z8dHbAHT<_?8BU}wh"<8U:̐H_q8`H9}wh<x8OXH_U8`H~wd8exH]}~wd<88TH^/AH8<_<8BUcwh"<8U:̐H^8`H~wd<8T<8H^u/@wd|t/ @/@ /APwd; 8}H||xHx8d8z,Ha!<8UxHa1||yA<8|8N8XH`<x8UHa||yA<8l8UH`mH@?<}wh88VH^8`Hـ}wh<8VH]8`Hl~wd<8V4H`/A(<8|8V|KI.xAЀh8!`cxx|88AH|B>;o!p|#x<|vxo ~|+x~ųx|3xHY~óxHZx/; A; ~|t//@|t//@; <_?n$;o>><_:o n ~x}{xxHx;\Hx|}x@Dwn0<x88MHZ8`Hawn0<8MHZ8`HIcxH{x8d|cH\8`H}|}yA$|t/A<8MH 8`HM/A<8M|8H\A8`H%8|}x{8x|cH"||y@<wn08|8MHY8`H[wn0<|^|Ѐ8NHY8`HYl[cx|P|^l|PH[wn0<|^8NHHYE8`H {x8|c8H"-H|E@Psn0<88MHX8`Hsn0<8NhHX8`Hsn0<8NHX8`H{|^Z}i[x/@Dx@}{x|^J "| 8c;|^JAH/@Hx@}sx|^Z*b}+8c|^| xAHsn0<8NHX 8`HՀx|^@l}kxB |8c|^AH@@JIؐi;o~~ųx\xHUi~óxHV/A; ~|t//@|t//@; |A$r<8J8HVm/A; xH/@/AH /A8{8HT/{@,H/]/@<<cn08JHVY8`H!|AD<<cn08O8xHV)8`H|H~óxdx8xK;V"8|Pp|I.;|Z|BJ8!|N |B?|~x<|hp8J!8HU8`H]^x8B^xx~HU|}y@(H.M/@|hp<8DHUM8`Hlx^|!րbHU|}y@(H./@؀|hp<8DHU8`H̀^x~T:HUe|}y@(H-/@|hp<8DHT8`Hx9@h8^U :l|Ǵ>l^}(Iր|G8|J>l^}(Iց~9|J| Y.^xA9@P>9@^U 8}+J|BRI| x| H./@| 9JB9AX8!P|N |B?|}x<|fx8HP!8HS8`He]8B]}T8HS|~y@(H,U/@|fx<8BHSU8`HX8!P|N ||}x!cHP}HP]bHP}HPX8!Px|HP/@ |@!8bN /AHT8`N |B!|{x<8cGl!;HQ<dx8cG|HQ<8d8cGHQ <88cGHP<8,8cGHP<8X8cGHP݀lp<t8cGHP<|8cG̀HP@<_=?eLieH~x[W8; x|.@~x~ux~Wx;|Z<8cG|ȀHPE;}:JI|\/@x<8cHHP{;}:ZI|\@8~ڳx}=ZI|\"| ;|z|ctHO{}=ZI|\AH/@x<8cHHO{;}:ZI|\@~x}=ZI|\"| ;|z|ctHO{}=ZI|\AHt<8cHHO-{;}:ZI|\@H~x}=ZI|\"| ;|z|ctHN{}=ZI|\A8` ;9HN}[;x|.AD8` ;HNYA<8!8cH|!HO08H|@&+|BaA|+x!|zx|#x@4<<cbh8E0HO}8`H ECx$x8KH <|ex8E`#xHNM<8El8d#xHN9<;,8Ex8#xHN!xHO<|}x8@xHQ|{yA<x;8a@HQm,cxHO8@PxxHP,l<|8Ep8a@t:HN8@xHPU<#x8ExHM@<_-bbT:@8` $xHNZV8;|.x@=?N ~x~wxS$;`|@8a@|HP8a@HN+@08@9`~x| |t/|A4BA8| YZ<8E#x|\8@";};JHLz|\Z}j[x"};J @P~x}^~~>X>tp~~8HII/~@,H$/@<<c^8;`HJ8`Hŀ^~x8HI/~@,H#/@<<c^8;`HJ8`H}^l8~x|`HH|}y@,H#i/@<<c^8;`HJe8`H-~x8HHq/~@,H#)/@<<c^8;`HJ%8`Hx8@t^l}(JÌl>|8}(J| ^~|H9"}*Y.xAX8!Px|N |BA?|}x!|#x;@\(H~\(<888HH/@xHJ|zxHl~\(<888HH/@P8|dx8HJ]/8`A`8|dx8HJA/@xDx8HJ 8`H0xHHy/@~\(8xHF/@H8`h8!`A|N |@&|zy|BA! 8`A8`HI |~y@,H!)/@<<c[87HH%8`H88@8`^~xCxK9/@xHE8`Hl|/ACxxKHLx~x8HE/~@,H /@<<c[87HG8`HMl8~x|`HE|}y@,H E/@<<c[87HGA8`H ~x8HEM/~@,H /@<<c[87HG8`Hɀx;@l9@^W:l|J́>l}*J Ѐ^l>|\}*J9J|]Il>|;|| I.^xA8~8HD/~@,HA/@<<c[87HF=8`H|;>.?; :@^; <_[HT{[<8>8HE/A {[<878HEi/@ 8.x@}[HF+@}[8(HF/A䀾<}[8>|8@8xHGxHFY=8a@HF)l=xA0<c[<8>|8HE8`Hl9@@@~x~ȳx|GP>|BtTB:}=J|BBi| Q9J^lAЀ~;;9|c|dx8cdHG)@0CxHD]/@ {[8Ex}xHB/@x8!a|}p N |B}H|dx|8`K<_8BP?_`8`88@-. ^~;ZS|x>Ԑ̐<8cSK/@(<8cSH?I @|xHxH> /@<88cSxH|ex<8cSH?i/@|Ax@H<<8cS89DH@/AX<89LH@/AD<89TH@}/A0xh8!`a!|}a N |B<_/ 8B7<"|#x|+x!|{xd|3x%h%A?8@;OA@A@/A(|3x8exH;UxKA8|~x>8N}H=ɀ|exxH>9/Ax8exH;/@cxH8VN|Xb|zK9|}y@ <_8B7D"9H$H<+d@ 8dx#xH>I8N8}@H=/@<#xH<}|Cx|"H> CxK <87L8a@ExH;mxH|H<=|exxH->. :@A8:H,|^ c|w|H/~xH-||xCxH,/@uA88ExH+/A|>x}H-|exuA8H. /@LAH@LuA8<8((H/M/A,<8(0H/9/A<8(8H/%/@ /b@<CxH/M+~cx@ 8a@K8!aa|}a N |Ba|}x<8c(t!H+U8}dH+M<x8c(H*}<8c(H*m<8c(H*]/@X<8c!dH*E8` H);@<_>]|;|||ctH)̀AH/@X<8c!lH)8` H);@<_>]|;|||ctH)qAHT<8c!tH)8` H)M;@0<_>]|;|||ctH)A8` H) h<8!`|8c(aH)|B||x|#x<8'$!cxx8dH)U/@;@l<_?@"= cZ\;dx||y|ctH*m|Жp||.p|P<@8` dxH*AxAH/@;@<_?@"=cZ\;dx||y|ctH)|Жp||.p|P<@8` dxH)xAH|;@l<_?@"= cZ;|Жp||.p|P<@8` dxH)Y\dx|x|y|ctH)=Ah8!`dx8` |H)|ܐB!|zx/A@?<};T8%PH(y8`KA};T<8#|H(a8`K)CxH$8`H) ||y@,H%/@<<c;T8H(!8`Kz8cH&)|yy@,H/@<<c;T8H'8`K㩀Z8:DxBԑ<x\;d\:dH*%x~xH*;z@0=x|{x88H;;ADx8dxH)x~x8dH)ٓ<xx8!p|N |B<_=!/AX8!P}|N <<c98$H&8`K⑀X8!P8`|N |~y|B!@ <<c9H8#H&u8`K=X<_8!P<|N |B=?<_9)8;|8}#Kxxx<88=8 98|P| G&|BtT:TB:|J|Bb(T:b|@J}dC'8 BTB:})th|@PU):TB:})b|KP 8B9|B8@h8c@TN +|B|A,+A$+AT:|*T:|2|cHX+A+A +@<_B7bcH0?_$ 8   ;`}yB|EB+B|FB"T:j`IJx|ZT:||@}Cx}cx}Cx}Cx}Cx|E}9b9IX|خT&6@|E~ݳx 8 ƺ|E}&bI9 | `|tT:|T >@,^|HH| |C @9)PA9xA;{Jx~xAP|#xN Tc>|+B}H|AErrorYou need to enter a block by writing or pasting a block in the window.

%s/%d.block_errorsw%s // rThere seems to be an error in the format of block number %d:

No blocks were read.Sorry, you can not check more than %d blocks each time.
%s %s %f %f %d > %s 2>&1
Program Error
An error occured during the execution.Please try again at a later time.If it fails again contact the maintainer of these pagesand describe what caused the problem with an example.
Biassed Blocks Results
Biassed Blocks Results
Error opening program output file.Content-type: text/html

REQUEST_METHODPOSTThis script should be referenced with a METHOD of POST.If you don't understand this, see this forms overview.%c
What could have happened is that you just reloaded this page rather than redoing the search.
If you use NETSCAPE it has a tendency to try to reload a page when you go back to it.  This may be why you have this error.CONTENT_TYPEapplication/x-www-form-urlencodedThis script can only be used to decode form results. umask 006&;`'"|*?~<>^()[]{}$\Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motifwidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.Reclaim space function is not defined.  No memory will be reclaimed.
|B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|x}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|p}N |B}h=k|T}N |B}h=k|8}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|t}N |B}h=k|X}N |B}h=k|<}N |B}h=k| }N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|x}N |B}h=k|\}N  	

???333333C0)4'&	

	

-ARNDCQEGHILKMFPSTWYVBZX*-|pA|tR|xN||D|C|Q|E|G|H|I|L|K|M|F|P|S|T|W|Y|V|B|Z|X|*|?j~#?/v?
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/@/jx8@AL@|t/AA,/CA$/GA/TA/UA/N@8B
/@lB<C0liA!<_ɂX<_ɡ`(`($X@8`H8`8!a|N ||3y!BC|#x%P;@b*8`A/|t@`/A@8<_Bf->.	:@]:H,|^ c|w|HK~xHG||xCxHKA/@u]8ExHKi/A|>x}HGQ|exu]HIa/@LAH@Lu]<8AHJ/A,<8AHJ/A<8AHJ/@/b@<CxHK+~cx@8a@K8!aa|}a N |Ba|}x<8cA!HH	8}dHH<x8cBHH<8cBHH<8cBHG/@X<8c7HG8`
HF;@<_[d]|;|||ctHEAH/@X<8c7HG}8`
HE;@<_[`]|;|||ctHEAHT<8c7HG)8`
HEa;@0<_[d]|;|||ctHE1A8`
HEh<8!`|8cB aHF|B||x|#x<8@!cxx8dHGɀ/@;@l<_?@"YcZ\;dx||y|ctHGA|Жp||.p|P<@8`
dxHGxAH/@;@<_?@"YcZ\;dx||y|ctHF|Жp||.p|P<@8`
dxHFxAH|;@l<_?@"YcZ;|Жp||.p|P<@8`
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|HE|ܐB!|zx/A@?<}X8>HC-8`KA}X<8|{|t/;@cxH>m8|{dx8|8HAx8xHBAH,<8cT<8<|hH>=8`KQT|t/D@H|t/E@88}K|{xKdx8|8PHAQxx8HAH(<8cT<8<_P@,^|HH||C @9)PA9xA;{Jx~xAP|#xN Tc>|+B}H|A [-p|s|f|m|h|q|g] [width]          p=Posfai style, s=short style, f=fasta style,          m=MSF style, h=STOCKHOLM style, q=ungapped STOCKHOLM,          g=giant block          defaults are short style, width = 66
Enter name of file of blocks: r
Cannot open file %s
>%s %s
ERROR in block %s: %d sequences found but  %d expected
%d sequences are included in %d blocks

posfai_seqs: OUT OF MEMORY .%5d 
%20s 
short_seqs: OUT OF MEMORY
            %s%s, width = %d (%4d) 
fasta_seqs: OUT OF MEMORY>%s|%d              from %10.10s blocks

msf_seqs: OUT OF MEMORY//%-s/%d
%-28s 
giant: OUT OF MEMORY
stockholm_seqs: OUT OF MEMORY# STOCKHOLM 1.0Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motifwidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
//
idacde ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
BLOCKInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
 ,
.+-0123456789convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
pb_weights:%d ignored for %s
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
dirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 aInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.Reclaim space function is not defined.  No memory will be reclaimed.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
No width field for matrix %sError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
%fresize_matrix() not finished.  Exiting.
  |% 4d    --+----%c |% 6.4fMA   %s
 %c   *   -
%3d %3d
% 6.4f % 6.4f
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
% 9.4f % 9.4f
|B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|p}N |B}h=k|T}N |B}h=k|8}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|t}N |B}h=k|X}N |B}h=k|<}N |B}h=k| }N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N MATRIX 	

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~cx8xH}/A8a@~dxHH:a8@~cxH|[.<b8T|sH|dxaH}||yA(;<X8pL8a@H:/@<8a@8\H/AP;/@0P/@ <8|J8p8H/@;.A<~x8chxH0A4/8BA4A;xHx~cxHx~dxH/@<8H<8xH<x8cHu<x8H|ty@<<x8cHM8`H<~xx8cH1<8cH%8+AT|[.;!@~cx|"H~cxHY+K@8
KJAD<~x8~exHH,|[.;!@<b8P|yH|dx8a H<_:A ~Ox}kxH$+AA8a@~xH;~xHP||tT`1@Tb:|B4TH8H0C|/A\L8B\L;8a@Hq@AH|[.bHY|[.|ex8a@H/@p~CxH5|}x8a@H)+AP~Dx~cxH<8P~cxH|[.~cx|"H<8~cxH~Cx~dxHp/@l<8a@88H/@P<8aI8H}/A8<8`8He|dyA |t/ @88|=H|[.bHU|[.|ex8a@H/@t<}{x8p}{xHE/@<}{x8\H-/A8Px~cxHq~cxH+K@KA<~x8~exHe}kxH|[.<8b|yHe/AA|[.~x|"H%|[.~xHP||tT`1@Tb:|B4TH8HI0C|/A\L8B\L;8a@H!@AxHq/@D8a@8xH9/A,|[.bH|[.|ex8a@HQ/@xH!/@l8a@8xH/AT|[.bH|[.|ex8a@H/A,|[.bHm|[.|ex8a@H/@lA0/A~xH@ZbH)Z|ex8a@H/@\<8a@8H<8P8a@H~cx8xH/A$~dx8a@HH8a@8xHxH
/@Aa48!a|}a N |B!#t|#x/A<999@X/@<#x8
L8He/#xA$x8a@H<88a@H;@|}yA@;a;/	A|{x;Z;~HM<8`8H|}y@~xH/x|vx@:x~x~ųx}{xH8<}{x8HQ}kx|}yADx:@}sx:!@<x8
PAHa||y@8axxH)|XB;@~x~7x~ux~xxH/A(|t/Ax8aH/@~x~x~x~ųxH8;;;`H4|X|t/|@/@;Hb~ܳx;xH
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BLASTDAT: (C) Copyright 1992-2000, Fred Hutchinson Cancer Research Center
Enter name of BLASTP results file: r
Reading %s...
Enter name of file containing list of sequences: 
Cannot open file %s
No list of sequences will be checked.
%ld IDs in %s
.tnswt# True negative sequences for %s

%d total scores
.mis# Sequences missed for %s

%d missed sequences written to %s.fnd
Cannot open file %s
# Sequences found for %s

%d found sequences written to %s%ld true positives (%ld of them fragments), %ld in block
 Default 99.9th rank = %ld
QuerySearchingBLASTP%sSequences producing 

%lg
TP:Rank %.3d=%.20s, score=%d, P=%g
 BLOCK:Rank %.3d=%.20s, score=%d, P=%g%-20s       P=%g
  1st TN score=%g
  TN:%dth other score=%g
  TN:%dth score(99.9)=%g
  TN:Rank %.3d=%.20s, score=%d, P=%g
%d/%ld TP scores found, %d TN scores
%d/%ld fragments found, %d/%ld of sequences in block found
%d/%ld true positive scores above 99.9 percentile true negative score=%g
%d = Pearson equivalence number (%ld/%ld)
%f = ROC areablastdat.data
Cannot open file blastdat.dat
No statistics will be saved.%s %d %ld %ld %ld %ld %d %d %d %d %d %d %d %d %f  PS=%s  LENGTH=%-6d  FRAGMENT  BLOCK  LSTARNDCQEGHILKMFPSTWYVX.*rtprotomat.stpSCORE ,	
Could not open %s, using default BLOSUM scoring matrix
HIGH
Using scoring matrix from %s
+-0123456789
Using BLOSUM62 scoring matrix.GENBANK//LOCUSDEFINITIONACCESSIONORIGINPROCLASSPIRENTRYTITLESEQUENCE///EMBLIDDEACSQUNI>VMSPCF_ACPCF_DEPCS_ID

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directory 	
FRAGMENTBLOCKLSTPS=LENGTH=
Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.  
	
fragment
%d. Entry %s found....dna.proCreating %sw+t
Cannot open %s

%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P>%sDR   PIR;.

>%s
ARNDCQEGHILKMFPSTWYVBZXactg-_|B}h=k|	\}N |B}h=k|	@}N |B}h=k|	$}N |B}h=k|	}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k||}N |B}h=k|`}N |B}h=k|D}N |B}h=k|(}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|0}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N ?PbMC0A@"C0?| 
		
	
					
			

			
	

	
			
							
	
			


		
		
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%d = Pearson equivalence number (%ld/%ld)
%f = ROC areablastdat.data
Cannot open file blastdat.dat
No statistics will be saved.%s %d %ld %ld %ld %ld %d %d %d %blimps-3.9/bin/OSX/bldist000075500001460000012000001524401062461240000155770ustar00jorjastaff00000400000027
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Pƺ|E}&bI9 |`|tT:|T>@,^|HH||C @9)PA9xA;{Jx~xAP|#xN Tc>|+B}H|A      = file of fasta multiple alignments (blocks)    = substitution matrix      = output distance matrix     = output matrix type:			S=similarity			D=dissimilarity			P=dissimilarity in protdist format			C=correlation
Enter name of file of fasta multiple alignments: rCannot open file %s
WARNING: Sequences appear to be DNA but will be treated as proteinBLIMPS_DIR
Enter name of file containing substitution matrix: %s/docs/%s%s/docs/default.iijUsing %s

Enter name of output file: w
Enter type (S=similarity, D=dissimilarity, C=correlation): Writing similarity dissimilarity correlation protdist matrix to %s
WARNING: sequence segments are of different lengths%s %d : %s %d
Mean dissimilarity distance = %.2f
%d
%s %.0f %.2f %.5f GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleUnable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUNKNOWN Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, AA) 	NA) 	??) 	>--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.BLOCK; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
 ,
.+-0123456789convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
pb_weights:%d ignored for %s
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
dirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 aInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
%fresize_matrix() not finished.  Exiting.
  |% 4d    --+----%c |% 6.4fID   %s
AC   %s
DE   %s
MA   %s
 %c   *   -
%3d %3d
% 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
% 9.4f % 9.4f
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Unable to read block for scoring against the sequences.Not scoring the block.
Searching block %s against the sequence database.
Scoring vs sequence %s.
Scoring sequence %s vs block %s.
Unable to read the sequence for scoring against the matrices.Not scoring the sequence.
Searching sequence %s against the matrices database.
Scoring vs matrix %s.
Unable to read matrix for scoring against the sequences.Not scoring the matrix.
Searching matrix %s against the sequence database.
Scoring sequence %s vs matrix %s.
Records Searched:   %d
Scores Done:        %16.0f
Alignments Done:    %16.0f
BLIMPS (BLocks IMProved Searcher)3.82006/04(C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center

Usage: %s config_file
BLIMPS_DIR%s/docs/default.codon.frqdefault.amino.frqUsing frequencies from %s.
Error loading frequencies.
default.qijaltsUsing default.qij
rCannot open 'alts' file "%s".  Exiting...
Using pseudo-count parameters %f and %s.
Unknown genetic code %d.  Setting to Standard code (0).Using genetic code %d; %s.
wUnable to open output file "%s" for writing, aborting.Unable to open output file "%s" for writing.Not outputing the matrix output.
main(): SearchType variable corrupted, possible memory problems.        Should never have reached this part of the program.        The rest of the run may be invalid.        Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
Probe Sequence: %s %s
Probe Size: %d Base Pairs
Probe Size: %d Amino Acids
Probe Sequence: NO SEQUENCE
Probe Size: UNKNOWN
Probe File: %s
Target File (s) : %s
                  %s
AC#         Description                                         Strength  Score RF    AA#
Block File: %s
Matrix File: %s
AC#                    Description                                                Score RF  AA# Length
Block File (s) :    %s
                   %s
Matrix File (s) :    %s
Sequence File (s) : %s
aInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
default_scoring_method(): matrix %s has length <= 0default_scoring_method(): sequence %s has length (amino acids) <= 0default_scoring_method(): Not scoring the sequence.
enter_score(): Error placing matrix score into list
Unable to recover enough memory to continue.  Aborting.
Histogram:
   %5d - %-5d : %d
   %5d -       : %d
Unable to recover memory.
Decreasing the NumberToReport from saving all (%d currently) to %d.Ran out of memory (1), fewer scores will be reported.
Decreasing the number of saved nodes in the list.The saved nodes level of the list has been reduced to %d.The list saved nodes cannot be reduced any more.
The saved nodes level of the list has been reduced to %d.
Decreasing the NumberToReport from %d to %d.Ran out of memory (2), fewer scores will be reported.
blimps_reclaim_space(): NumInSL(Scores) is greater than NumberToReport.                 NumInSL(Scores) is supposed to be maintained                 less than or equal to the NumberToReport.                 NumberToReport = %d, NumInSL(Scores) = %d.                 Ran out of memory, removing the excess scores                 in the Scores list.
BLOCK; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
 ,
.+-0123456789convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
pb_weights:%d ignored for %s
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
dirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 ID   AC   DE   BL   MATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
//
idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
No width field for matrix %sError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
%fresize_matrix() not finished.  Exiting.
  |% 4d    --+----%c |% 6.4fMA   %s
 %c   *   -
%3d %3d
% 6.4f % 6.4f
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
% 9.4f % 9.4f
GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.get_file_list(): Unknown file group %d.insert_file(): Bad file list, not entering filename "%s"               into a file list
Already have a frequency file: %sThe file %s will be ignored.
get_file(): Bad file list, unable to open a file
Unable to open block file: %s
Unable to read sequence file: %s
Unable to read pattern file: %s
get_file(): Unknown file group            Unable to open a file
Unknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Assuming there is no title and just sequence.
Unable to read sequence file: %s to determine the type of database
Unable to open matrix file: %s
Unable to open database file: %s
Unable to open frequency file: %s
Unable to read sequence file: %sUnable to read pattern file: %srewind_file(): Bad file group, unable to rewind file list
get_current_file_name(): Bad file group, unable to return a file name
get_current_file_name(): No files in the file group                         Unable to return a file name
get_file_name(): Bad file group, unable to return a file name
get_file_name(): No files in the file groupget_file_name(): Requested file out of the range of the files                 in the file group                 Unable to return a file name
number_of_files(): Bad file group, unable to report number of files
close_file() : Bad file group, unable to rewind file list
Reclaim space function is not defined.  No memory will be reclaimed.
load_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
%s/docs/default.amino.frq%s/docs/default.qijscore_and_enter(): Tried to score a sequence that is not an                   amino acid sequence.  Not scoring the                   sequence %s
Invalid matrix-sequence scoring method specified, %d.Setting the method to the default value and using thedefault scoring method.
No pattern for matrix %s, Scoring the entire matrix
%-11.11s %-50.50s      %4d   %4d %2d %6d %s
%-20.20s %-62.62s %4d %2d %5d %6d %s
%-8s vs %-7s   %-20s... & %-20s... %4d %4d %2d %6d %6d %s
%-8s %4u %-45s      %4d   %4d %2d %6d %s
-------------------------------------------------------- score ---	Score: %d
	Position: %d
	Frame: %d
	Mat Num: %s
	Seq Num: %s
	Mat Desc: %s
	Seq Desc: %s
	Consensus: %s
S:% 6d	P:% 6d	F:% 6d
%s   Version %s (%s)  %s%s
%s   Version %s  %s%s
Unknown configuration file key: %s
MA field already used.  Cannot have both the BL and the MAfields.  Ignoring the BL line.
Using the PAttern switch causes the REpeats switch to be ignored.Alignments reported will include repeats.
%dTRUEYES0BL field already used.  Cannot have both the MA and the BLfields.  Ignoring the MA line.
Old style configuration file.New style does not use the SE field.
MATRIXUnknown search type: %s
DNAAAConfiguration file "%s" not found.  Exiting
New style uses the ST field instead of P4.
New style uses the RE field instead of P5.
New style uses the NU field instead of P9.
No block file (BL) or sequence file (SQ) given, aborting.
No sequence file (SQ) or block file (BL) given, aborting.
Configuration file has SQ, BL, and DB entries.Unable to determine the type of search.Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
Missing either the BL or SQ field, aborting.
Configuration file has SQ and BL entries.No sequence files given for the sequence database, aborting.
No DB field given, assuming data is in the SQ field.
No block file given (BL field), aborting.
No block files given for the block database, aborting.
No DB field given, assuming data is in the BL field.
No sequence file given (SQ field), aborting.
Unknown search type given, assuming SQ vs BL search.
read_config_file_end(): SearchType variable corrupted.                        Should never have reached this part of the program.                        Possible memory problems.                        The rest of the run may be invalid.                        Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
%s:%u: failed assertion `%s'
sl.cp->key != NULLUnable to find pattern for PSSM %s
pattern.cpat_file != NULLNumInSL(residue_list) == 0%d: (null);(%d, [%s]) |B}h=k| }N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|x}N |B}h=k|\}N |B}h=k|@}N |B}h=k|$}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|4}N |B}h=k|\}N |B}h=k|@}N |B}h=k|$}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k||}N |B}h=k|`}N |B}h=k|D}N |B}h=k|(}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N MATRIX.err 	

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H);@<_:Ā]|;|||ctH)AHT<8c@,^|HH||C @9)PA9xA;{Jx~xAP|#xN Tc>|+B}H|A           = input file of protein sequences         = input file of blocks from sequences         = output file for motomat
Enter name of file containing sequences: r
Cannot open file %s

No sequences found in file %s

Enter name of blocks file: BL   
No blocks found in file %s

Enter name of new motomat file: wb 	
Couldn't allocate Seq[%d]
MOTIFJ=[[,]motif=[gibbsfreq==dups=mots=score=d1=d2=Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
//
idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.Reclaim space function is not defined.  No memory will be reclaimed.
|B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k||}N |B}h=k|`}N |B}h=k|D}N |B}h=k|(}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|D}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N  	

@QC0??333333@\	

	

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Enter name of BLOCKS input file: r
Cannot open file %s

Enter name of PSSM output file: w
Enter PSSM format type (B=blimps, M=mast, G=Gribskov, P=Psi-Blast) [B]:  Using type %d
%s Invalid type %d, using type %d
ALPHABET= ARNDCQEGHILKMFPSTWYVBZX
log-odds matrix: alength= 23 w= %d
% 6.3f (Peptide) Length: %d
COBBLER Profile for %s %s
Cons      %cdmin=%f
%c    %6d BLOCK; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
 ,
.+-0123456789convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
pb_weights:%d ignored for %s
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
dirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 ID   AC   DE   BL   MATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
//
idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
No width field for matrix %sError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
%fresize_matrix() not finished.  Exiting.
  |% 4d    --+----%c |% 6.4fMA   %s
 %c   *   -
%3d %3d
% 6.4f % 6.4f
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
% 9.4f % 9.4f
load_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqdefault.qijaInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.|B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|H}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|p}N |B}h=k|T}N |B}h=k|8}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|t}N |B}h=k|X}N |B}h=k|<}N |B}h=k| }N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N MATRIX 	

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|H>P|ܐB!|zx/A@?<}b87H:8`Ku}b<86 H:8`K]CxH$8`H;E||y@,Ky/@<<cb8 H:]8`Kz8cH8|yy@,K9/@<<cb8 H:8`K݀Z8:DxBԑ<x\;d\:dH;x~xH;Հ;z@0=x|{x88H;;ADx8dxH:ex~x8dH:U<xx8!p|N |B=?<_9)`l;|a}#Kxxx<8`l=8
9`l|P|	G&|BtT:TB:|J|Bb(T:b|@J}dC'8 BTB:})th|@PU):TB:})b|KP	8B9|B8@h8c@TN +|B|A,+A$+AT:|*T:|2|cHX+A+A+@<_B`(bcH0?_$`D;`}yB|EB+B|FB"T:j`IJx|ZT:||@}Cx}cx}Cx}Cx}Cx|E}9b9IX|خT&6@|E~ݳx
`Dƺ|E}&bI9 |`|tT:|T>@,^|HH||C @9)PA9xA;{Jx~xAP|#xN Tc>|+B}H|A   [-H n -E n -C n -mast|-rank -sum|-gff -stats]           = number of hits to report, use 0 for default     = blimps search output file     = blocks database searched by blimpsOR:    blkprob      = name of blimps configuration fileOther options    -H n            maximum number of hits to report    -E n            cutoff expected value for anchor blocks    -C n            min cutoff raw score for anchor blocks    -mast           order results by MAST-type e-values    -rank           order results by RANK-statistic e-values    -sum            output summary only (one line per hit)    -gff		  Sanger Center's GFF output    -stats          produces .dat statistics file    -S filename     header file (default=blkprob.stp)
Enter number of hits to report or blimps configuration file name [%d]: r
BLKPROB: Cannot open configuration file %s

Enter name of file containing blocks search results: 
Enter name of blocks database searched: -mast-rank-stats-sum-gff-E-H-C-S
BLKPROB: Cannot open file blimps file %s

Query=%s
Size=%ld Amino AcidsBase PairsBlocks Searched=%d
Blocks searched is negative, cannot use for statistics.Alignments Done=%16.0f
Alignments done is negative, cannot use for statistics.Cutoff combined expected value for hits=%3.0f
Cutoff block expected value for repeats/other=%3.0f

Results: OUT OF MEMORY

hits: OUT OF MEMORY
No hits found
%d possible hits reported
 	
 	
;OUDB//%sblkprob.stpblkprob.stp
===============================================================================
Here are your search results from the BLOCKS searcher.%sVersion 3.2.5Version 3.2.4Version 3.2.3Probe Sequence:Size:Base Pair: 

Size TargetRecordsAlignmentsAC#
BLKPROB: Cannot open blocks file %sDatabase=%s
blksort.stn%sblksort.stn%d %frepeats.dat%srepeats.dat%s %dblksort.bias%sblksort.biasassemble_hits(): OUT OF MEMORY
blksort.data==============================================================================                                                             CombinedFamily                                       Strand  Blocks   E-value                                                           RankFamily                                       Strand  Blocks   P-value%-10s %s  % 2d  %2d of %-2d %8.2g
%d %s %s %d %d %g %g %g %g

==============================================================================>%s %d/%d blocks Combined E-value=%8.2g: %s
Block    Frame    Location (bp)      Block E-value (aa)      Block E-value%-10s % 1d     %6ld-%-6ld        %8.2g       **biased**%s	BLOCKS	similarity	%ld	%ld	%8.2g -	%d	+	%d	%s  **biased** (hit) %s	"%d"
Up to %d repeats expected:
%-10s % 1d     %6ld-%-6ld        %8.2g
%s BLOCKS similarity %ld %ld %8.2g - %d + %d (repeat) %s
Other reported alignments:(other) %s

------------------------------------------------------------------------------
                         |---%5d amino acids---|
%20s           <->
%s
%s
%ld%d
pvalue_rank(): OUT OF MEMORY

closest_seq: Unable to allocate pair structure!maxscore is too big, increase MAXSCORE from %d
BLOCK; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
 ,
.+-0123456789convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
pb_weights:%d ignored for %s
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
dirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 ID   AC   DE   BL   MATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motifwidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
//
idacde ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
No width field for matrix %sError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
%fresize_matrix() not finished.  Exiting.
  |% 4d    --+----%c |% 6.4fMA   %s
 %c   *   -
%3d %3d
% 6.4f % 6.4f
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
% 9.4f % 9.4f
load_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqdefault.qijX.rtprotomat.stpSCORE ,	
Could not open %s, using default BLOSUM scoring matrix
HIGH
Using scoring matrix from %s
+-0123456789
Using BLOSUM62 scoring matrix.

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directoryFRAGMENTLSTPS=LENGTH=Information: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWNRan out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.|B}h=k|*}N |B}h=k|*x}N |B}h=k|*\}N |B}h=k|*@}N |B}h=k|*$}N |B}h=k|*}N |B}h=k|)}N |B}h=k|)}N |B}h=k|)}N |B}h=k|)}N |B}h=k|)|}N |B}h=k|)`}N |B}h=k|)D}N |B}h=k|)(}N |B}h=k|)}N |B}h=k|(}N |B}h=k|(}N |B}h=k|(}N |B}h=k|(}N |B}h=k|(}N |B}h=k|(d}N |B}h=k|(H}N |B}h=k|(,}N |B}h=k|(}N |B}h=k|'}N |B}h=k|'}N |B}h=k|'}N |B}h=k|'}N |B}h=k|'}N |B}h=k|'h}N |B}h=k|'L}N |B}h=k|'0}N |B}h=k|'}N |B}h=k|&h}N |B}h=k|&}N |B}h=k|&}N |B}h=k|&}N |B}h=k|&}N |B}h=k|&h}N |B}h=k|&L}N |B}h=k|&0}N |B}h=k|&}N |B}h=k|%}N |B}h=k|%}N |B}h=k|%}N |B}h=k|%}N |B}h=k|%}N |B}h=k|%l}N |B}h=k|%P}N |B}h=k|%4}N |B}h=k|%}N |B}h=k|$}N |B}h=k|$}N |B}h=k|$}N |B}h=k|$}N |B}h=k|$}N MATRIX| 
	 	

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BLKSORT Version %s
COPYRIGHT 1992-8 Fred Hutchinson Cancer Research CenterUSAGE: blksort    [-stats]           = number of hits to report, use 0 for default     = blimps search output file     = blocks database searched by blimps    -stats          produces blksort.dat statistics fileOR:    blksort      = name of blimps configuration file
Enter number of hits to report or blimps configuration file name [%d]: r
BLKSORT: Cannot open configuration file %s

Enter name of file containing blocks search results: 
Enter name of blocks database searched: -stats
Query=%s, 
 Size=%ld Amino AcidsBase Pairs
Blocks Searched=%d

%d possible hits reported
 	
 	
;OUDB//blksort.stp%sblksort.stp
===============================================================================
Here are your search results from the BLOCKS searcher.
Please report problems to webmaster@blocks.fhcrc.org, include your query
and this output. To obtain help, send the word HELP on a single line to
blocks@blocks.fhcrc.org
Copyright (c) 1992-6 by the Fred Hutchinson Cancer Research Center
If you use BLOCKS in your research, please cite:
Steven Henikoff and Jorja G. Henikoff, Protein Family Classification Based
on Searching a Database of Blocks, Genomics 19:97-107 (1994).
Each numbered result consists of one or more blocks from a PROSITE or PRINTS
group found in the query sequence. One set of the highest-scoring blocks that
are in the correct order and separated by distances comparable to the BLOCKS
database is selected for analysis. If this set includes multiple blocks
the probability that the lower scoring blocks support the highest scoring
block is reported. Maps of the database blocks and query sequence are shown:
  < indicates the sequence has been truncated to fit the page
  : indicates the minimum distance between blocks in the database
  . indicates the maximum distance
The maps are aligned on the highest scoring block. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database
is shown. Upper case in the query sequence indicates at least one
occurrence of the residue in that column of the block.%s
BLKSORT: Cannot open file blimps file %s
Version 3.2.5Version 3.2.4Version 3.2.3Probe Sequence:Size:Base Pair: 

Size TargetRecordsAC#
BLKSORT: Cannot open blocks file %sDatabase=%s
blksort.stn%sblksort.stn%d %frepeats.dat%srepeats.dat%s %dblksort.bias%sblksort.bias
OUT OF MEMORY
blksort.datablksort.rep
%d.------------------------------------------------------------------------
Block     Rank Frame Score Strength   Location (bp) Description
Block     Rank Frame Score Strength   Location (aa) Description%-8s %5d  % 2d   %4d  %4d     %7ld-%7ld %s
AC   ; 

	(,)BL   strength==

 

	 (biased) 
%d=%.2fth percentile of anchor block scores for shuffled queries
P<%6.2g for 
              %sin support of %s
P not calculated for single block %s (biased)%s %s %s 1 %d %d %6.2g %.16f %d %d %d %d %d %ld %.2f

Maximum number of repeats (from Prosite MAX-REPEAT) = %d
%d non-overlapping repeats in support of %s%s %s %s 2 %d %d %6.2g %.16f

                         |---%5d amino acids---|
%20s         <->
%s
%s
%d
cluster_seqs: Unable to allocate pair structure!ARNDCQEGHILKMFPSTWYVX.*rtprotomat.stpSCORE ,	
Could not open %s, using default BLOSUM scoring matrix
HIGH
Using scoring matrix from %s
+-0123456789
Using BLOSUM62 scoring matrix.GENBANKLOCUSDEFINITIONACCESSIONORIGINPROCLASSPIRENTRYTITLESEQUENCE///EMBLIDDEACSQUNI>VMSPCF_ACPCF_DEPCS_ID/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directoryFRAGMENTBLOCKLSTPS=LENGTH=
Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments. 
	
fragment
%d. Entry %s found....dna.proCreating %sw+t
Cannot open %s

%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P>%sDR   PIR;.

>%s
ARNDCQEGHILKMFPSTWYVBZXactg-_|B}h=k|
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	12/23/06.1gDfff4e	
	
					
			

			
	

	
			
							
	
			


		
		
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d2__picsymbolstub1__TEXTL< __DATAP@__data__DATAP@@__nl_symbol_ptr__DATAP@8@@__la_symbol_ptr__DATAPxl@x)__dyld__DATAP@__common__DATAPL8__LINKEDIT`P/usr/lib/dyld4FZX/usr/lib/libSystem.B.dylibP]UP7= TDT\ (%P|:x8!T!48!z8;cW{:|H	|<@!= |#x|yx|+x!bPP<@P$/}"Kx@8= 9)BH<|i|lxN!HX//A8BH9"}"Kx|t/@<@fx"PH8/@<@;FBP@B/A|I|LxN!<@BPHB/A|I|LxN!H<@BP/A|I|LxN!<`8<8cBHI<|	|xN!<`8@8cBH)<`888cBH<`8H8cBH	<`8L8cCH<`8P8cC(HA@/A,8/A H/AL/AP/A|I|Lx?;;CLN!|~xHԀ8x|	|xN!H//A8BH8b|bx|t/@=`9 9kCD|t/A |	9k|t@`9)K؀Hx|	|xN!/A<Lx8|	|xN!/AP|	|xN!,@;@A,<`8D8cCXHaD/AH-<@8xexBPDFx#xH!H=aB`}N =a@}N =aB}N =a(}N =aBp}N =P}=9N =`kP}iN |!|>x~x|8`8(H$|`x@^@x^@|^@8(@8`-H$a}8`-@H$1!|N |B}=|9$}N |B}=|9$}N |B}=|9$}N |!|>x~x|8H8`-H#~@8@D^D/@Hx^DBBx@L^DBB|@4^DH>D^H	^H/(AH"^DB8DK|8`-@H"H/A4^H/A^H~H|x}N!~HH"u!|N |B}=|9"T}N |B}=|9"t}N |B}=|9"4}N |B}=|9"T}N |!|>xBH!<_B$@@/A^@T>+@H<_b$H!A<_b$H!!|N |B}=|9 }N |B}=|9 }N |B}=|9 }N |B}H|Hq~|HA/A8~Hq88`Ke/A\<<8H=?<_ixx}A$<x8L8H/@</>@0]<x8T808,949%HH0]<x8d8@809,9&49FHy샾},cpHŐ}8<8cxK
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|t/-A~H!Wx/@`8`K-/AP<_D/A$<<c8x8cHuH <<c88cxHU8!|N |@&|BA<_!@|vx;BАK<_9b@<_=?b}z[x??;@xxwx8`W:KE/A<|.88uH99`9@	|t/Ax<_x~x|	P/*@<|]8.|t/A0}=0.	|9kI|Bt/@H|9k9J}	Cx|P|t/@8|}.|xK	;A(<_.B/A88`KY/A(@$<<8c4888H
@Ke8!a|}p N =`Px}N =`P|}N =`P}N __dyld_make_delayed_module_initializer_calls__dyld_image_count__dyld_get_image_name__dyld_get_image_header__dyld_NSLookupSymbolInImage__dyld_NSAddressOfSymbollibobjc__objcInit__dyld_mod_term_funcs-This program takes block map data and generates a graphical map of the
sequences.

Usage: %s [infiles] [options]
Example: %s blocks.mapdata -v2 -o blocks.maps -m80

Arguments to options should be '-o[argument]' or '-o [argument]'.
Use '-' to stand for standard input/output.
Default output is to the screen.

Available options:
 Option          Effect
 -[cfm] number   Use scale mode [constant/full/maximum]
                 Constant: Each character is  amino acids.
                 Full: Each sequence is  characters long.
                 Maximum: The longest sequence in each family is 
                 characters long, the rest are to scale.
                 The default is -c10 (each character is 10 amino acids).
 -h              Get this help screen.
 -i filename     Add an input file(s) (this is not needed if input files
                 are placed before the options). Seperate multiple filenames
                 with spaces.
 -o filename     Set the output filename. The input filename is substituted
                 for '*' within , so '*.vis' is '.vis'.
                 You must use single quotes around  if it contains
                 '*'.
 -v number       Set verbosity level, 0-5. 0 = no messages, 1 = errors only,
                 2 = quiet, 3 = normal (default), 4 = verbose, 5 = debug.
 -a BLxxxxx      Do only a single block family.
Debug messages on.
Output is in bare format.
Warning: unrecognized option '-%c'.
Scale type is %c, scale value is %i.
Input file %i is '%s'.
Output file is '%s'.
Verbosity level is %i.
Warning: option '-%c' not used.
Warning: option '-%c' has an attached argument (ignored).
Warning: option '-%c' has too many arguments (ignored).
Reading line: %s
# %s
Reading one family...
End of input file reached.
blocks_map#MAP#>%s %d %d %d %s%s %s %d %d %d %sdescriptionError: premature end of input file.
sequence_map%s %d %dblock_pos%c %d %dmarker//Error: bad data read.
%-20s (%4d)  [---- %d aa]%s: %s
%d distinct blocks in %d sequences
%20s---- %d amino acids

Opening '%s' for read.
rbError: cannot open input file '%s'.
Opening '%s' for write.
wbError: cannot open output file '%s'.
Error: Family '%s' not found in file '%s'
.Error: no usable data in file '%s'.
Processing file '%s'.
Warning: no input files.
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Example: %s blocks.mapdata blimps-3.9/bin/OSX/blocks_search000075500001460000012000000576441062461240100171330ustar00jorjastaff00000400000027
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=`P}N =`P}N =`P}N __dyld_make_delayed_module_initializer_calls__dyld_image_count__dyld_get_image_name__dyld_get_image_header__dyld_NSLookupSymbolInImage__dyld_NSAddressOfSymbollibobjc__objcInit__dyld_mod_term_funcsSCRIPT_NAMEBLOCKS_EMAIL%sblocks@fhcrc.orgrdate '+%y%m'date "+%y%m%d"%s/blimps.%s/blksort%s/blkprob/usr/bin/mailx%s/blocks.dat../data-blocks%s/prints.dat../data-prints../data-blplus../data-blplus-minus%s/default.qij../docs%s/default.amino.frq%s/%d.seq../tmp%s/%d.cs%s/%d.csh%s/%s../log%s/%d.mail%s/%d.out%s/%d.blk%s/%d.htmlNoauto-allCONTENT_LENGTHQUERY_STRING-sum-gffsequencetitleaddressdatabaseprintsminusprodomdomopfambiastystgehiexouoldrawsumgffwERror_level          2
DBase                %s
SQuence              %s
OUtput_file          %s
TYpe                 %s
STrands_to_search    %s
FRequency            %s
GEnetic_code         %s
HIstogram            %s
REpeats_allowed      yes
SV                   yes
NUmber_to_report     0
COnversion_method    3
OP alts: 5.0 %s :alts
chmod -f 660 %s#!/bin/csh
unalias mv
%s %s >& /dev/null
%s Block Search ResultsBlock Search Results%s/htmlize-blimps.pl %s >& %s
%s %s -mast -E %s %s >& %s
%s/htmlize-blkprob.pl %s >& %s
%s %s >& %s
%s/htmlize-blksort.pl %s >& %s
%s -r %s -s "%s" %s < %s
exit(0)
chmod a+x %s
Search Error
You need to enter a sequence to search with.
Your sequence has more than 5000 characters.
Please break it into smaller pieces for searching.
>%s
>Unknown
date%s %s > /dev/null 2>&1
Blimps Error
%s %s -mast -E %s %s > %s 2>&1
Blkprob Error
%s %s > %s 2>&1
Blksort Error
An error occured during the search:
%s
%s/htmlize-blimps.pl %s%s/htmlize-blkprob.pl %s%s/htmlize-blksort.pl %sError opening pipeblocks_search: Error opening %s
Content-type: text/html


Blocks Search Results
REQUEST_METHODPOSTCONTENT_TYPEapplication/x-www-form-urlencodedumask 006You can check this URL within 4 hours for your results.

Your results will also be emailed to %s

Queuing %d...%s/add_queue_entry.pl BLOCKS_queue %s&;`'"|*?~<>^()[]{}$\|B}h=k|(}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N  	

&%0$LQQQeQQ`YS````[_]``````a`UWQTc$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$P $<3 D$$$L%0$QBPOP$]P `kP41QvP(P<PP9QP8P@P,P0AQOQc&P@fQnS}UWY[QpQtQx9Q|]_a9P84LQfQQQQQQQ@ce;P4@<`AF>O;H1`X?>`G`Q`\``9f;x`*T`>@``'fQA(]>l6hc?l``&=	2h4l=h] wZ-`4@Gq
<!)Mxp&(68=Y09Qkt|#b4			
h
ggYc^]_pba`eynogzhmql}v~idwkxs|r{jutf\Z5[= SA@?!'&R9KEHJ(BG4gYc^]_pba`eynozhmql}v~idwkxs|r{ju_NXArgc_NXArgv___progname__dyld_func_lookup__start_environdyld_stub_binding_helperstart___darwin_gcc3_preregister_frame_info___keymgr_dwarf2_register_sections__cthread_init_routine__mh_execute_header_atexit_catch_exception_raise_catch_exception_raise_state_catch_exception_raise_state_identity_clock_alarm_reply_do_mach_notify_dead_name_do_mach_notify_no_senders_do_mach_notify_port_deleted_do_mach_notify_send_once_do_seqnos_mach_notify_dead_name_do_seqnos_mach_notify_no_senders_do_seqnos_mach_notify_port_deleted_do_seqnos_mach_notify_send_once_errno_exit_mach_init_routine_main_receive_samples___keymgr_global__dyld_register_func_for_add_image__dyld_register_func_for_remove_image__init_keymgr__keymgr_get_and_lock_processwide_ptr__keymgr_set_and_unlock_processwide_ptr_abort_calloc_free_Blimps_Flag_Blkprob_Flag_Blksort_Flag_Domo_Flag_Mail_Flag_Minus_Flag_Pfam_Flag_Post_Prints_Flag_Prodom_Flag_display_html_display_output_parse_and_cs_setup_read_startup_info_run_search_write_csh_write_sequence_Address_Ptr_Expect_Output_Sequence_Ptr_Title_Ptr___sF_atoi_blimps_blimps_output_blkprob_blksort_blksort_output_buf_cs_file_csh_file_database_email_addr_entries_fclose_feof_fgets_fmakeword_fopen_fprintf_fputc_fputs_frq_fwrite_getenv_getpid_html_output_log_dir_log_file_mail_file_mailprog_makeword_memcmp_minusbase_pclose_pid_plusbase_plustospace_popen_printf_printsbase_puts_qij_remove_trailing_whitespace_seq_file_sprintf_strcpy_strlen_strncpy_system_tmp_dir_unescape_url_escape_shell_cmd_getline_getword_ind_rind_send_fd_x2c_fgetc_malloc_realloc_blank_line_eat_whitespace_get_token_Buffer_strtok_pointer_to__darwin_gcc3_preregister_frame_info_darwin_unwind_dyld_add_image_hook_darwin_unwind_dyld_remove_image_hook %s
%s/htmlize-blksort.pl %s >& %s
%s -r %s -s "%s" %s < %s
exit(0)
chmod a+x %sblimps-3.9/bin/OSX/blosum000075500001460000012000001175741062461240100156310ustar00jorjastaff00000400000027
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KJAD<~x84~exHH,|[.;!@<b8|yH|dx8a H<_:A $`~Ox}kxH$+AA8a@~xH1;~xHP||tT`1@Tb:|B4TH8H0C|/A\L8B\L;8a@H@AH|[.bH|[.|ex8a@H/@p~CxH|}x8a@H+AP~Dx~cxH<8~cxH|[.~cx|"H<8 ~cxH}~Cx~dxHp/@l<8a@888H/@P<8aI8DH=/A8<8`8HH%|dyA |t/ @88|=HA|[.bH|[.|ex8a@H/@t<}{x8}{xH/@<}{x8H/A8Px~cxH~cxHi+K@KA<~x8L~exHe}kxH|[.<8Tb|yH/AA|[.~x|"H%|[.~xHP||tT`1@Tb:|B4TH8H0C|/A\L8B\L;8a@H@AxHQ/@D8a@8xH/A,|[.bHe|[.|ex8a@H/@xH/@l8a@8xH/AT|[.bH|[.|ex8a@H/A,|[.bH|[.|ex8a@H/@lA0/A~xHY@ZbHZ|ex8a@HU/@\<8a@8 H<88a@H~cx8xH/A$~dx8a@HH8a@8xHxH/@Aa48!a|}a N |B!#t|#x/A<999@X/@<#x88H%/#xA$x8a@H<8l8a@H;@|}yA@;a;/	A|{x;Z;~H<8`8lH]|}y@~xH-/x|vx@:x~x~ųx}{xHi8<}{x8lH}kx|}yADx:@}sx:!@<x8AH||y@8axxH	|XB;@~x~7x~ux~xxHu/A(|t/Ax8aHQ/@~x~x~x~ųxH8;;;`H4|X|t/|@/@;Hb~ܳx;xH@Ax8yH1#xH8;A8<8`8lH|}y@ԃ9t/@8`(8! |N 9(|~x88@|`T>T@.|Jx|`}K4}GSx}iFpT@.8I+T>|Hx}CxA8	UB>T@.|x|4|4|IFp8	+A8	U>T@.|x|4}`Fp|BFp|bP@9(Al8`N px!Aaځڡ!AaہۡN px!Aaʁʡ!Aaˁˡ|N =`}N =`}N =`}N __dyld_make_delayed_module_initializer_calls__dyld_image_count__dyld_get_image_name__dyld_get_image_header__dyld_NSLookupSymbolInImage__dyld_NSAddressOfSymbollibobjc__objcInit__dyld_mod_term_funcsBLOSUM: (C) Copyright 1992, Fred Hutchinson Cancer Research CenterEnter name of blocks database:rCannot open %s
Reading %s
Enter minimum block strength [%d]: Enter maximum block strength [%d]: Minimum block strength=%d, Maximum block strength=%d
Enter n for no clustering   or a number between 0 and 100 for percent identity clustering   or e for existing (implied) clusters   or w for existing sequence weights   or pn for position-based weights, PB weight = 1/nEnter clustering identity percentage or n/e/w/pn [e]: Existing clustering will be usedNo clustering will be usedSequence weights will be usedPosition-based weights will be used with parameter = %.2f
Re-clustering percentage = %d
Enter scale n for 1/n bits [%d]: Scale based on relative entropyRequested scale = 1/%d bits

%d blocks processed, %ld blocks contributed pairs to matrix
 %f clumps contributed pairs to matrix (%f)
 %ld segments contributed pairs to matrix (%f)
%f total pairs, %f total weight
 %ld total sequences, %ld total columns, %ld total AAs

Frequencies = fij pairs (off-diagonals = 2*fij):    %1s  %9.2f    %1s  blosum%d.qijblosump%d.qijblosumw.qijblosumn.qijblosume.qijwt
Target Probabilities=qij in %s
#  BLOSUM Clustered Target Frequencies=qij
#  Blocks Database = %s
#  Cluster Percentage: >= %d
#  Position-based Clustering Parameter: <= %.4f
#  Explicit Sequence Weights Used
#  No Sequence Clustering Used
#  Existing Clusters Used
   %1s   %.4f sumqij = %f

Marginal Probabilities by AA = p(i,*):%.3f 
sumpi=%.3f
AA Frequencies = ai:%8ld 
AA Probabilities = fi:

totpairs=%.3f, FTotWeight=%.3f
 totdiag=%.3f, totoffd=%.3f totaas=%ld, TotAas=%ld

Entropy=%.4f bits, expected=%.4f bits
blosum%d.sijblosump%d.sijblosumw.sijblosumn.sijblosume.sij
Scoring matrix in bit units=sij in %s
#  BLOSUM Clustered Scoring Matrix in Bit Units=sij
#  Entropy = % 8.4f, Expected = % 8.4f
   %1s     B   Z   X
% 8.4f blosum%d.iijblosump%d.iijblosumw.iijblosumn.iijblosume.iij
Integer scoring matrix in 1/%d bit units in %s
#  BLOSUM Clustered Scoring Matrix in 1/%d Bit Units
 %1s  %3d 
Maximum=%d, minimum=%d, sum=%d

Positive matrix (+%d):
B   Z   X
10 times log base 10 matrix:AC   BL   strength==
	
// 
	
cluster_seqs: Unable to allocate pair structure!ARNDCQEGHILKMFPSTWYVX.*rtprotomat.stpSCORE ,	
Could not open %s, using default BLOSUM scoring matrix
HIGH
Using scoring matrix from %s
+-0123456789
Using BLOSUM62 scoring matrix.GENBANKLOCUSDEFINITIONACCESSIONORIGINPROCLASSPIRENTRYTITLESEQUENCE///EMBLIDDEACSQUNI>VMSPCF_ACPCF_DEPCS_ID

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directory 	
FRAGMENTBLOCKLSTPS=LENGTH=
Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.  
	
fragment
%d. Entry %s found....dna.proCreating %sw+t
Cannot open %s

%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P>%sDR   PIR;.

>%s
ARNDCQEGHILKMFPSTWYVBZXactg-_|B}h=k|	}N |B}h=k|	}N |B}h=k|	}N |B}h=k|	}N |B}h=k|	h}N |B}h=k|	L}N |B}h=k|	0}N |B}h=k|	}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|p}N |B}h=k|T}N |B}h=k|8}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|p}N |B}h=k|T}N |B}h=k|8}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|t}N |B}h=k|X}N |B}h=k|<}N |B}h=k| }N >.&֕C0?C0?@$4@| 
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8(ƺ|E}&bI9 |`|tT:|T>@,^|HH||C @9)PA9xA;{Jx~xAP|#xN Tc>|+B}H|A   	=input file of blocks to weight	=output file of weighted blocks	=P (position-based) | V (Voronoi) | 
		A (Vingron & Argos) | Cn (n percent clumping)	=M (max=100) | N (sum=#seqs) | # (sum=#)
Enter name of blocks database: r
Cannot open file %s

Enter name of new weighted blocks database: w
Enter weighting scheme (P=position-based, V=Voronoi, 
 A=Vingron & Argos, Cn = n-percent cluster [P]: blweight: Calculating position-based weightsblweight: Calculating Voronoi weightsblweight: Calculating %d percent cluster weights
blweight: Calculating Vingron & Argos weights
Enter scale (M=>max=100, N=>sum=#seq, ###=>sum=###) [M]: blweight: Integer weights, maximum weight = 100blweight: Decimal weights, sum = number of sequencesblweight: Integer weights, sum = %d
ERROR: Block %s is too wide (%d), truncated to %d
Residue not counted: %d
ERROR: Block %s is too deep (%d), truncated to %d sequences
ERROR: Block %s is too deep (%d), truncated to %d rows
ERROR: Block %s is too deep (%d), truncated to %d nseq
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %7.3f
 %3d
//
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motif%swidth=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
 %f
idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.Reclaim space function is not defined.  No memory will be reclaimed.
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Enter name of configuration file: r
Cannot open file %s
Configuration file errors>%s %s
BLIMPS_DIR 	
 	
;TYBL
Cannot open BL file %s
OUw
Cannot open OU file %s
Consensus written to %s
ML
Cannot open ML file %s
Most like consensus written to %s
LL
Cannot open LL file %s
Least like consensus written to %s
SQ
Cannot open SQ file %s
DB
Cannot open DB file %s
FR
Cannot open FR file %s
PCSU
Cannot open SU file %s
MA
Cannot open MA file %s
PFPSIPFSBLIQM
Cannot open QM file %s
TR%s/docs/default.iij%s/docs/default.amino.frq%s/docs/default.qij.prfProfile written to %s
Missing SU input file nameFR and QM required with Type 3FR and QM required with Type 4Invalid consensus type: %d
Missing BL input file nameMissing OU output file nameCannot specify both DB and SQFR and QM required with SQFR and QM required with MADB required with MLDB required with LLType 1: Consensus based on percentage: %d
Type 2: Consensus based on substitution matrix with counts (no pseudo-counts)Type 3: Consensus based on substitution matrix with counts + pseudo-countsType 4: Consensus based on PSSMUnknown residue: %d
%s %s	is first sequence most like consensus (%d %d)
%s %s	is first sequence least like consensus (%d %d)
%s: %s not found
COBBLER; MATRIX%s %s from %d to %d with embedded PSSMwidth=%d seqs=%d>%s %s from %d to %d with embedded consensus blocks
#COBBLER Profile for %s %s from %d to %d
#
        %c  %c    %4d (Peptide) Length: %d
COBBLER Profile for %s %s from %d to %d
Cons  Gap Len ..
 100 100
*    |(, ,
+-0123456789Query sequence %s is shorter than minimum path width
WARNING: Aligned blocks overlap!!!  block=%s, pos=%d, last pos = %d
 block=%s, pos=%d
Sequence %s not found
%s %sBLOCK; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
.+-0123456789convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
pb_weights:%d ignored for %s
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
dirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 ID   AC   DE   BL   MATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
//
idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
No width field for matrix %sError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
%fresize_matrix() not finished.  Exiting.
  |% 4d    --+----%c |% 6.4fMA   %s
 %c   *   -
%3d %3d
% 6.4f % 6.4f
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
% 9.4f % 9.4f
GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.load_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
default.amino.frqdefault.qijaInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
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H<ـh<8!`|8c9XaH<|B||x|#x<87ܔ!cxx8dH stdin/stdout
          The order of the arguments is not important but the
          first name is for the input file and the second for the output.
pssm_type = 2 odds ratios normalized to 100
	3 pseudos, log odds, nats
	5 pseudos, log odds, half bits
	6 pseudos, log odds, third bits
	10 pseudos, odds ratios, nats
	20 just counts+pseudo counts
	30 average score
Genetic code type = 0 Standard
	1 Vertebrate Mitochondrial
	2 Yeast Mitochondrial
	3 Mold Mitochondrial and Mycoplasma
	4 Invertebrate Mitochondrial
	5 Ciliate Nuclear
	6 Echinoderm Mitochondrial
	7 Euplotid Nuclear
	8 Bacterial and Plant Plastid
	9 Alternative Yeast Nuclear
	10 Ascidian Mitochondrial
	11 Flatworm Mitochondrial
	12 Blepharisma Macronuclear
	13 Chlorophycean Mitochondrial
	14 Trematode Mitochondrial
	15 Scenedesmus obliquus mitochondrial
	16 Thraustochytrium mitochondrial
Degeneracy parameters=0.0 all nucleotides that actually appear are counted
	1.0 only nucleotide with highest value counted
	Between 0 and 1 nucleotides with high values counted,
	 if value/highest-value >= degeneracy parameter
Clamp temperature     Target melting temperature for clamp in degC 
Concentration         Probe concentration in nM
Rose restrictions     If set, uses Tim Rose's restrictions on boundaries
                      of core degenerate region.
Most common codons    If set, uses most common codons in clamp.
Begin oligo           If set, oligo must start on a conserved column,
                       otherwise core strictness is applied.
Apoly-x       Maxiumum number of consecutive nucleotides of same type.

 %d  2 3 5 6 10 20 30 Warning: Unspecified pssm type (%d) requested.
Using default pssm type (%d).
"%s help" for help.

Warning: Unspecified gcode type (%d) requested.
Using default gcode type (%d).
"%s help" for help.

Warning: Core strictness parameter requested (%3.2f) is out of range (%3.2f to %3.2f)
Using default value (%3.2f).
Warning: Clamp strictness parameter requested (%3.2f) is out of range (%3.2f to %3.2f)
Using default value (%3.2f).
Warning: Clamp strictness parameter requested (%3.2f) is less than core strictness parameter (%3.2f)
Using default values (%3.2f, %3.2f).
Warning: Clamp temperature requested (%3.2f) is negative
Using default value (%3.2f).
Warning: Concentration requested (%3.2f) is negative
Using default value (%3.2f).
rCannot open input file %s
wCannot open output file %s
%s/docs/%sdefault.amino.frqidentity.frq%s%s/docs/default.iijdefault.qijCannot open codon usage file %s
...trying %s ...

Parameters:
 Amino acids PSSM calculated with %s
 and back-translated with %s genetic code
 and codon usage table "%s"
 Maximum core degeneracy %3.0f    Core strictness %3.2f
 Clamp strictness %3.2f   Target clamp temperature %3.2f C
 DNA Concentration %3.2f nM   Salt Concentration %3.2f mM
 Codon boundary %d   Most common codon %d
 Verbose %d   Output %d
 Begin %d   PolyX %d
Suggested CODEHOPS: The degenerate region (core) is printed in lower case,
the non-degenerate region (clamp) is printed in upper case.
No correctly formatted blocks found to processWarning: Unrecognized parameter - "%s".

Processing Block %s

Processing Complement of Block %s
end:   pos=%d, len=%d, core_score=%.1f
oligo start: pos=%d, len=%d, core_score=%.1f,
 last pos=%d, core score=%.2f %s
No suggested primers found.Block is too narrow Complement -3'   -5'  Core: degen=%.0f len=%d  Clamp: score=%d, len=%d temp=% .1f *** CLAMP NEEDS EXTENSION%c  
%s Complement
  |% 4d    %4d--+----%c |%s
% 4d                    %4d        ------------BLOCK; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
 ,
.+-0123456789convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
pb_weights:%d ignored for %s
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
dirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 ID   AC   DE   BL   MATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motifwidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
//
idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
No width field for matrix %sError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
%fresize_matrix() not finished.  Exiting.
% 6.4fMA   %s
 %c   *   -
%3d %3d
% 6.4f % 6.4f
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
% 9.4f % 9.4f
load_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
%s/docs/default.amino.frq%s/docs/default.qijaInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
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Cannot open file %s

Enter name of output file: w%d sequences read
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleUnable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
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untranslate_sequence(): Not an amino acid sequence, not untranslating.aInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
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?4ƺ|E}&bI9 |`|tT:|T>@,^|HH||C @9)PA9xA;{Jx~xAP|#xN Tc>|+B}H|AErrorNo sequences specified.
Warning
Sequence names box is used and the alignment is in FASTA format.
Sequence names will be taken from the alignment
(first word in the sequence header lines -
'>seq_name 123 aa example protein').
Judging by the first sequence length (%d) the alignment is too long. The maximal length is %d.

Judging by the first sequence length (%d) the alignment is too short. The minimal length is %d.

The alignment width you gave (%s) is different than the first sequence length (%d).

Sequence %d not found.

Error reading sequence %d. %d more residues in the sequence than the expected %d.

Sequence (%d) is too short (%d). The minimal length is %d.

Error reading sequence %d. It is shorter (%d) than the apparent alignment length. Padding the end of the sequence with gaps.

Error reading sequence %d.

%s%dunknownNo name found for sequence %d.

Number of sequence names (%d) is different than number of sequences (%d).

No start position found for sequence %d.

Number of sequence start positions (%d) is different than number of sequences (%d).

The number of sequences you gave (%s) is different from the number found (%d).

None; BLOCK%s; distance from previous block = (%d%s,%d)Method unspecified%s; width=%d; seqs=%d;w%s %s %s %s %s > /dev/nullAn error occured weighting the block.Please try again at a later time.If it fails again contact the maintainer of these pagesand describe what caused the problem with an example.
Block Formatter output
Block Formatter output
Sequences weighted by position-based weights Voronoi weights Vingron & Argos weights %% clustering. The weights were scaled to 1-100, 100 having most weight.
[block logo (GIF image)] [block PSSM (what is a PSSM)][block logo [block PSSM (what is a PSSM)]
Content-type: text/html

REQUEST_METHODPOSTThis script should be referenced with a METHOD of POST.If you don't understand this, see this forms overview.%c
What could have happened is that you just reloaded this page rather than redoing the search.
If you use NETSCAPE it has a tendency to try to reload a page when you go back to it.  This may be why you have this error.CONTENT_TYPEapplication/x-www-form-urlencodedThis script can only be used to decode form results. umask 006aInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
&;`'"|*?~<>^()[]{}$\ID   AC   DE   BL   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motifwidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
//
idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.Reclaim space function is not defined.  No memory will be reclaimed.
|B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|p}N |B}h=k|T}N |B}h=k|8}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|t}N |B}h=k|X}N |B}h=k|<}N |B}h=k| }N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|x}N |B}h=k|\}N |B}h=k|@}N |B}h=k|$}N |B}h=k|}N |B}h=k|}N |B}h=k|X}N |B}h=k|}N |B}h=k|}N |B}h=k|x}N |B}h=k|\}N |B}h=k|@}N |B}h=k|$}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k||}N |B}h=k|`}N |B}h=k|D}N |B}h=k|(}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N  	

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g\[DT3&'HhP2b._-`_NXArgc_NXArgv___progname__dyld_func_lookup__start_environdyld_stub_binding_helperstart___darwin_gcc3_preregister_frame_info___keymgr_dwarf2_register_sections__cthread_init_routine__mh_execute_header_atexit_catch_exception_raise_catch_exception_raise_state_catch_exception_raise_state_identity_clock_alarm_reply_do_mach_notify_dead_name_do_mach_notify_no_senders_do_mach_notify_port_deleted_do_mach_notify_send_once_do_seqnos_mach_notify_dead_name_do_seqnos_mach_notify_no_senders_do_seqnos_mach_notify_port_deleted_do_seqnos_mach_notify_send_once_errno_exit_mach_init_routine_main_receive_samples___keymgr_global__dyld_register_func_for_add_image__dyld_register_func_for_remove_image__init_keymgr__keymgr_get_and_lock_processwide_ptr__keymgr_set_and_unlock_processwide_ptr_abort_calloc_free_AC_Ptr_DE_Ptr_ID_Ptr_MAX_DIST_Ptr_MA_METH_Ptr_MA_SEQS_Ptr_MA_WIDTH_Ptr_MIN_DIST_Ptr_SEQS_Ptr_SEQ_NAMES_Ptr_SEQ_POS_Ptr_aa_adegen_aa_atob_aa_btoa_aafq_clean_temp_files_display_output_gcodes_make_block_nt_adegen_nt_arevcomp_nt_atob_nt_bdegen_nt_brevcomp_nt_btoa_ntfq_parse_read_startup_info_weight_block_Block_file_Block_fileNW_Blweight_ErrorBuffer_ErrorReport_Weight_scale_Weight_type__DefaultRuneLocale___maskrune___sF_atoi_btest_flag_buf_entries_error_file_extblock_stdout_fclose_feof_fgets_fmakeword_fopen_free_block_getenv_getpid_home_dir_log_dir_log_file_makeword_malloc_memcmp_no_seq_names_no_seq_pos_output_block_pclose_pid_plustospace_popen_printf_puts_read_a_block_read_sequence_realloc_reclaim_space_remove_trailing_whitespace_sprintf_strcat_strchr_strcpy_strlen_strncpy_strstr_system_tmp_dir_unescape_url_ABRT_signal_handler_set_error_file_name_ErrorLevelReport_fprintf_escape_shell_cmd_getline_getword_ind_rind_send_fd_x2c_fgetc_fputc_block_comparison_new_block_next_cluster_output_block_s_print_block_read_a_block_faster_read_block_body_read_block_header_read_to_block_resize_block_clusters_resize_block_sequences_Buffer_atof_blank_line_eat_whitespace_fflush_fseek_ftell_fwrite_get_token_memcpy_putchar_sscanf_strcmp_strncat_strncmp_DbInfo_free_sequence_output_sequence_print_sequence_read_a_sequence_resize_sequence_seq_type_dbs_sequence_comparison_sequence_type_translate_sequence_type_dbs_untranslate_sequence___toupper_aa2codon_codon2aa_rewind_init_reclaim_space_strtok_init_gcode_pointer_to__darwin_gcc3_preregister_frame_info_darwin_unwind_dyld_add_image_hook_darwin_unwind_dyld_remove_image_hook_resize_block_sequences_ErrorFile_BlockBuffer_BlockBufLength_lbuff.0_first_time.1_read_sequence_header_process_sequence_db_line_RecFunc_gctrans.0HDPPPL
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USAGE:  getblock AC blocks cobb maps trees proweb blinks blk2pdb cyrca [prosite_dir]		AC = block accession (eg BL00094 or IPB001525)		blocks = name of blocks database file		cobb = name of cobbler database file		maps = name of map structure database file		trees = name of tree structure database file		proweb = name of Proweb database file		blinks = name of file of links to ProDom		blk2pdb = name of PDB cross-reference file		cyrca = name of CYRCA cross-reference file		prosite_dir = name of directory containing prosite.dat and prosite.doc files
Enter Block accession number: Chrom/howard/btest/bin/blocks.dat
Enter name of Blocks database file [%s]:
r
Cannot open blocks database %s

%d blocks processed
cobbler.pros
COBBLER sequence:end cobblermaps.datend maptrees.datend treeproweb.datend prowebblinks.datend blinksblk2pdb.datend pdbcyrca.datend cyrca/prosite.dat
Cannot open prosite.dat file %s
.doc
Cannot open prosite.doc file %s
AC   ; 

	%ssparkySteven!

DO   {%s}{END}ARNDCQEGHILKMFPSTWYVX.*rtprotomat.stpSCORE ,	
Could not open %s, using default BLOSUM scoring matrix
HIGH
Using scoring matrix from %s
+-0123456789
Using BLOSUM62 scoring matrix.GENBANK//LOCUSDEFINITIONACCESSIONORIGINPROCLASSPIRENTRYTITLESEQUENCE///EMBLIDDEACSQUNI>VMSPCF_ACPCF_DEPCS_IDmkdir %s
Created directory %s

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Protein files will be placed in current directory 	
FRAGMENTBLOCKLSTPS=LENGTH=
Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.  
	
fragment
%d. Entry %s found....dna.proCreating %sw+t
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Cannot open prosite.dat file %s
.doc
Cannot blimps-3.9/bin/OSX/getseq000075500001460000012000000561341062461240200156130ustar00jorjastaff00000400000027
 8__PAGEZERO__TEXT@@__text__TEXTD'D__symbol_stub__TEXTD4__picsymbol_stub__TEXTD4$__symbol_stub1__TEXTD04__cstring__TEXTD@4@__picsymbolstub1__TEXTJ: __const__TEXTO?__DATAP@__data__DATAP@__nl_symbol_ptr__DATASC*__la_symbol_ptr__DATASC1__dyld__DATATTDT__common__DATAT`8__LINKEDIT`P\/usr/lib/dyld4FZX/usr/lib/libSystem.B.dylibP_VP*0/U0ZTt/(D|:x8!T!48!z8;cW{:|H	|<@!= |#x|yx|+x!bPP<@P$/}"Kx@8= 9)D@H<|i|lxN!HX//A8BH9"}"Kx|t/@<@fx"PH8/@<@;FBSB/A|I|LxN!<@BSB/A|I|LxN!H&<@BP/A|I|LxN!<`8<8cDDHI<|	|xN!<`8@8cDtH)<`888cDH<`8H8cDH	<`8L8cDH<`8P8cDHA@/A,8/A H/AL/AP/A|I|Lx?;;DN!|~xHԀ8x|	|xN!H//A8BH8b|bx|t/@=`9 9kD|t/A |	9k|t@`9)K؀Hx|	|xN!/A<Lx8|	|xN!/AP|	|xN!,@;@A,<`8D8cEHaD/AH$<@8xexBSFx#xHH$=aD}N =a#P}N =aD0}N =a}N =aD }N =TT}=9N =`kTX}iN |!|>x~x|8`8(H+|`x8^8x^8|^88(8`-H*|`x^88`-8H+E!|N |B}=|9+$}N |B}=|9*}N |B}=|9+}N |!|>x~x|888`-H*E|`x@8@xBH(<_B188/A^8T>+A<_8b`H(5<_8bHH(I!|N |B}=|9((}N |B}=|9'}N |B}=|9((}N |@&.|BAA!|}x|#xAL<8c!H)<8c!H(<8c"H(<8c",H(<8c"\H(<8c"H(/@;xH(H<;8c"H(xH(IH|zxHŐztxH(Q@8a@H(AH<8c"H(q8a@H(	<8a@8#H'|{y@<8@Hp/8@;xH'H<;8c#$H(xH'|t/AH<x8#DH'i|~y@<x8c#H'8`H|<x8c#HH'H<_B0H;X?80D;0xH	axxFxxex9 8`H|}xcxH&/8`A8`H&8c|+B}H|AAd8/;pHI/AP<x8;pHm|dxxHxH|ao|t//A<x8Hp|t/Ax8a@H9xH;@|C8;a<8xcxHxH|}y@HcxHQ/@<x8cHH$<x8cH<8c8Hٛp8!xa|N |8`|!H89`9 9@xcJ#lCpccc=LhdTX\P`tX8!P|N |@&|АAB!|yx|#x;::: H @|t/A/>A8a@8/Hi|}y@K%<|{x88a@;H/(||x@;(8{8@xH/|\@;cx8@xHa9 8@@<9`||t/|@/@9 H}{x8BA<t88a@H~x/AP<8a@8H/A\<8a@8H/AT<8a@8H|cyA<;J88xH<Kx88Hu/@P<8a@8H9|cyAT;<8xH]||y@8xx~xH%8A@|B~xHѐ{LHxt.AxdxH/At[xztA~x#xH	/@8a@8%xH/@x8!pax|}p N |@&|AB!pa|+x}Cx|+x|#x:!K=+ T|8@|qx0A4@<8c,HUHLT{:-|[.<8cTH5@<8ctH%<8cH8a@8x9H88H|[.bH-|[.|ex8a@H/@@P<8a@8:aHY<88a@H)~cx8xHy/A8a@~dxHH:a8@~cxH1|[.<b8|sH|dxaH}||yA(;<X8L8a@H:/@<8a@8H/AP;/@0P/@ <8|J88H/@;.A<~x8cxH0A4/8BA4A;xHAx~cxH5x~dxH/@<8H<8 xH<x8c(H1<x8
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8;;;`H4|X|t/|@/@;Hb~ܳx;xH@Ax8yH	m#xH8;A8<8`8H)|}y@ԃ9t/@8`(8! |N 9(|~x88@|`T>T@.|Jx|`}K4}GSx}iFpT@.8I+T>|Hx}CxA8	UB>T@.|x|4|4|IFp8	+A8	U>T@.|x|4}`Fp|BFp|bP@9(Al8`N =`S}N =`S}N =`S}N __dyld_make_delayed_module_initializer_calls__dyld_image_count__dyld_get_image_name__dyld_get_image_header__dyld_NSLookupSymbolInImage__dyld_NSAddressOfSymbollibobjc__objcInit__dyld_mod_term_funcs
GETSEQ: (C) Copyright 1996 by Fred Hutchinson Cancer Research CenterUSAGE: getseq          = name of sequence to extract         = sequence database        = output file name
Enter name of sequence to extract: 
Enter name of database file to extract sequence from: r
Cannot open file %s

Enter name of output file: w+t
Extracting sequence to %sARNDCQEGHILKMFPSTWYVX.*rtprotomat.stpSCORE ,	
Could not open %s, using default BLOSUM scoring matrix
HIGH
Using scoring matrix from %s
+-0123456789
Using BLOSUM62 scoring matrix.GENBANK//LOCUSDEFINITIONACCESSIONORIGINPROCLASSPIRENTRYTITLESEQUENCE///EMBLIDDEACSQUNI>VMSPCF_ACPCF_DEPCS_ID

/mkdir %s
Created directory %s

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8ƺ|E}&bI9 |`|tT:|T>@,^|HH||C @9)PA9xA;{Jx~xAP|#xN Tc>|+B}H|AUniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.Reclaim space function is not defined.  No memory will be reclaimed.
|B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|h}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|p}N |B}h=k|T}N |B}h=k|8}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|t}N |B}h=k|X}N |B}h=k|<}N |B}h=k| }N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N | 
	 	

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m#xH8;A8<8`80H	|}y@ԃ9t/@8`(8! |N 9(|~x88@|`T>T@.|Jx|`}K4}GSx}iFpT@.8I+T>|Hx}CxA8	UB>T@.|x|4|4|IFp8	+A8	U>T@.|x|4}`Fp|BFp|bP@9(Al8`N =`S}N =`S}N =`S}N __dyld_make_delayed_module_initializer_calls__dyld_image_count__dyld_get_image_name__dyld_get_image_header__dyld_NSLookupSymbolInImage__dyld_NSAddressOfSymbollibobjc__objcInit__dyld_mod_term_funcs
LISLIS: (C) Copyright 1995-2007 by Fred Hutchinson Cancer Research Center
Enter name of file containing first list of sequences: r
Cannot open file %s
Reading %s ... 
Enter name of file containing second list of sequences: %d sequences read
Sequences in first list but not in second list:%d/%d sequences (%.2f) in first list but not in second list:
Sequences in second list but not in first list:%d/%d sequences (%.2f) in second list but not in first list:
|_ARNDCQEGHILKMFPSTWYVX.*rtprotomat.stpSCORE ,	
Could not open %s, using default BLOSUM scoring matrix
HIGH
Using scoring matrix from %s
+-0123456789
Using BLOSUM62 scoring matrix.GENBANK//LOCUSDEFINITIONACCESSIONORIGINPROCLASSPIRENTRYTITLESEQUENCE///EMBLIDDEACSQUNI>VMSPCF_ACPCF_DEPCS_ID

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directory 	
FRAGMENTBLOCKLSTPS=LENGTH=
Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.  
	
fragment
%d. Entry %s found....dna.proCreating %sw+t
Cannot open %s

%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P>%sDR   PIR;.

>%s
ARNDCQEGHILKMFPSTWYVBZXactg-|B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|x}N |B}h=k|\}N |B}h=k|@}N |B}h=k|$}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k||}N |B}h=k|`}N |B}h=k|D}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k||}N |B}h=k|`}N |B}h=k|D}N |B}h=k|(}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N C0@Y| 
		
	
					
			

			
	

	
			
							
	
			


		
		
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LISLIS: (C) Copyright 1995-2007 by Fred Hutchinson Cancer Research Center
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Sequences in first list blimps-3.9/bin/OSX/mablock000075500001460000012000002147141062461240200157330ustar00jorjastaff00000400000027
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Enter name of blocks database: r
Cannot open file %s
%s; BLOCK
Enter name of output file: .blksw.seqsB
Enter type of output file [B=blocks|F=fasta]: WARNING: Sequences appear to be DNA but will be treated as proteinWARNING: Maximum number of sequences = %d


%d blocks found with minimum width %d and maximum with %d
Output written to %s.blks and %s.seqs
no blocks found with minimum width %d
WARNING: sequence segments are of different lengths
%s %d : %s %d
CLUSTALSTOCKHOLMClustalStockholmTrying CLUSTAL/STOCKHOLM format.
%s.%d 	 	
>%s
%s
ERROR reading Clustal file
%s\rm %sTrying  MSF format.
//mablock.%d
ERROR reading MSF file
%sUNK motif; width=%d; seqs=%d;JOUXZ%s; distance from previous block=(%d,%d)>%20s          from blocks
%5d P1;Non-unique sequence name: %s
%s%dModified name to %s
GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleUnable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, AA) 	NA) 	??) 	>--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.AC   BL   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, --- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
//
idacde ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
BLOCKInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
 ,
.+-0123456789convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
pb_weights:%d ignored for %s
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
dirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 aInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
No width field for matrix %sError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
%fresize_matrix() not finished.  Exiting.
  |% 4d    --+----%c |% 6.4fMA   %s
 %c   *   -
%3d %3d
% 6.4f % 6.4f
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
% 9.4f % 9.4f
|B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|p}N |B}h=k|T}N |B}h=k|8}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|t}N |B}h=k|X}N |B}h=k|<}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|t}N |B}h=k|X}N |B}h=k|<}N |B}h=k| }N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|x}N |B}h=k|\}N |B}h=k|@}N |B}h=k|$}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N MATRIX 	

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           The order of the arguments is not important but the
           first name is for the input file and the second for the output.
          block_family_name = "" : all block families in input

((input now expected from screen; CTRL-C to quit))

rCannot open input file %s
wCannot open output file %s
Input file "%s" processed by program "%s"
Note: The sequence lengths shown are the 'right-most' sequence positions found in the blocks.
Unable to allocate idsError ! Input file %s does not contain any blocks.
Couldn't make a block map for block family %s.
Couldn't make a block map for block family %s.


Couldn't find or process block family %s !

%d block family(ies) processed into maps.
%d block family(ies) could not be processed.
Output in file %s.
Warning ! The name of the first block in family %s
does not end with an "A".
Error ! Block %s is not the block expected to follow (by name)
block %s.
Note - Not all sequences in family %s contain all the blocks.
%sError ! Couldn't find all %d sequences.
Error ! Last block (%c, %d-%d) in sequence %s of family %s
is out of bounds.
Note - Sequence %s in family %s does not contain block %c.
Note, first block (%c %d-%d) in sequence %s of family %s
begins BEFORE the first aa of the sequence !
Note - Block %c PRECEDES block %c in sequence %s of family %s.
Note - Blocks %c (%d-%d) and %c (%d-%d) in sequence %s
of family %s overlap.
>%s %d %d %d %s
%s
%s %d %d
%c %d %d
//
Warning unrecognized parameter - "%s".
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motifwidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
X.rtprotomat.stpSCORE ,	
Could not open %s, using default BLOSUM scoring matrix
HIGH
Using scoring matrix from %s
+-0123456789
Using BLOSUM62 scoring matrix.

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directory 	
FRAGMENTBLOCKLSTPS=LENGTH=aInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.Reclaim space function is not defined.  No memory will be reclaimed.
|B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k||}N |B}h=k|`}N |B}h=k|D}N |B}h=k|(}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|$}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N | 
	 	

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Subject:%19s...SubjectLine%s.lis%s.seqlen%s.pros%s.warnw>%s;%s;%s;;$
%s
Only %d sequence found, need at least 3
%s_%d%s	LENGTH=%d
%s	%d
Unknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Trying with Fasta format.
Sequences appear to be DNA: Block Maker is designed for protein.Unable to read sequence file: %s to determine the type of database
P1;%s family%s... familyNon-unique sequence name: %s
First 20 characters of sequence name must be unique.
%s%dModified name to %s
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleUnable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUNKNOWN%s Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, AA) 	NA) 	??) 	>--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.%s:%u: failed assertion `%s'
sl.cp->key != NULLInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
get_file_list(): Unknown file group %d.insert_file(): Bad file list, not entering filename "%s"               into a file list
Already have a frequency file: %sThe file %s will be ignored.
get_file(): Bad file list, unable to open a file
Unable to open block file: %s
Unable to read sequence file: %s
Unable to read pattern file: %s
get_file(): Unknown file group            Unable to open a file
Assuming there is no title and just sequence.
Unable to open matrix file: %s
Unable to open database file: %s
Unable to open frequency file: %s
Unable to read sequence file: %sUnable to read pattern file: %srewind_file(): Bad file group, unable to rewind file list
get_current_file_name(): Bad file group, unable to return a file name
get_current_file_name(): No files in the file group                         Unable to return a file name
get_file_name(): Bad file group, unable to return a file name
get_file_name(): No files in the file groupget_file_name(): Requested file out of the range of the files                 in the file group                 Unable to return a file name
number_of_files(): Bad file group, unable to report number of files
close_file() : Bad file group, unable to rewind file list
Reclaim space function is not defined.  No memory will be reclaimed.
AC   BL   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, --- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
//
idacde ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
score_and_enter(): Tried to score a sequence that is not an                   amino acid sequence.  Not scoring the                   sequence %s
Invalid matrix-sequence scoring method specified, %d.Setting the method to the default value and using thedefault scoring method.
No pattern for matrix %s, Scoring the entire matrix
%-11.11s %-50.50s      %4d   %4d %2d %6d %s
%-20.20s %-62.62s %4d %2d %5d %6d %s
%-8s vs %-7s   %-20s... & %-20s... %4d %4d %2d %6d %6d %s
%-8s %4u %-45s      %4d   %4d %2d %6d %s
-------------------------------------------------------- score ---	Score: %d
	Position: %d
	Frame: %d
	Mat Num: %s
	Seq Num: %s
	Mat Desc: %s
	Seq Desc: %s
	Consensus: %s
S:% 6d	P:% 6d	F:% 6d
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
No width field for matrix %sError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
%fresize_matrix() not finished.  Exiting.
  |% 4d    --+----%c |% 6.4fMA   %s
 %c   *   -
%3d %3d
% 6.4f % 6.4f
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
% 9.4f % 9.4f
Unable to find pattern for PSSM %s
pattern.cpat_file != NULLNumInSL(residue_list) == 0%d: (null);(%d, [%s]) default_scoring_method(): matrix %s has length <= 0default_scoring_method(): sequence %s has length (amino acids) <= 0default_scoring_method(): Not scoring the sequence.
enter_score(): Error placing matrix score into list
Histogram:
   %5d - %-5d : %d
   %5d -       : %d
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/cm {cmfactor mul} bind def %% defines centimeters

%% user defined parameters
/lowest %ld def
/highest %ld def
/bar %ld def
/xcorner %*.*f cm def
/ycorner %*.*f cm def
/rotation %*.*f def %% degrees
/charwidth %*.*f cm def
/barheight %*.*f cm def
/barwidth %*.*f cm def
/barbits %*.*f def %% bits
/Ibeamfraction %*.*f def
/barends  def
/showingbox /outline /caps /stacksperline %ld def
/linesperpage %ld def
/linemove %*.*f def
/numbering /shrinking /shrink %*.*f def
/HalfWhiteIbeam  def

/knirhs 1 shrink sub 2 div def
/charwidth4 charwidth 4 div def
/charwidth2 charwidth 2 div def

%% Since outlining goes around the inner edge of the character
%% make the thickness of the character bigger to compensate.
/setthelinewidth {2 setlinewidth} def
/setthelinewidth {1 setlinewidth} def
setthelinewidth %% set to normal linewidth

%% Set up the font size for the graphics
/fontsize charwidth def

(*[[ This special comment allows deletion of the repeated
%% procedures when several logos are concatenated together
%% See the censor program.

/charparams { %% char charparams => uy ux ly lx
%% takes a single character and returns the coordinates that
%% defines the outer bounds of where the ink goes
  gsave
    newpath
    0 0 moveto
    %% take the character off the stack and use it here:
    true charpath 
    flattenpath 
    pathbbox %% compute bounding box of 1 pt. char => lx ly ux uy
    %% the path is here, but toss it away ...
  grestore
  /uy exch def
  /ux exch def
  /ly exch def
  /lx exch def
} bind def

/dashbox { %% xsize ysize dashbox -
%% draw a dashed box of xsize by ysize (in points)
  /ysize exch def %% the y size of the box
  /xsize exch def %% the x size of the box
  1 setlinewidth
    %% Define the width of the dashed lines for boxes:
    xsize 0 lineto
    xsize ysize lineto
    0 ysize lineto
    0 0 lineto
    [3] 0 setdash
    stroke
  setthelinewidth
/boxshow { %% xsize ysize char boxshow
%% show the character with a box around it, sizes in points
gsave
  /tc exch def %% define the character
  /ysize exch def %% the y size of the character
  /xsize exch def %% the x size of the character
  /xmulfactor 1 def /ymulfactor 1 def

  %% if ysize is negative, make everything upside down!
  ysize 0 lt {
    %% put ysize normal in this orientation
    /ysize ysize abs def
    xsize ysize translate
    180 rotate
  } if

  %% Don't show the box if it is a vertical bar, otherwise do.
  showingbox {tc (|) ne {xsize ysize dashbox} if} if

  shrinking {tc (|) ne {
    xsize knirhs mul ysize knirhs mul translate
    shrink shrink scale
  } if} if

  2 {
    gsave
    xmulfactor ymulfactor scale
    tc charparams
    grestore

    ysize %% desired size of character in points
    uy ly sub %% height of character in points
    dup 0.0 ne {
      div %% factor by which to scale up the character
      /ymulfactor exch def
    } %% end if
    {pop pop}
    ifelse

    xsize %% desired size of character in points
    ux lx sub %% width of character in points
      /xmulfactor exch def
    ifelse
  } repeat

  %% Adjust horizontal position if the symbol is an I
  tc (I) eq {charwidth 2 div %% half of requested character width
             ux lx sub 2 div %% half of the actual character
                sub      0 translate} if
  %% Avoid x scaling for I
  tc (I) eq {/xmulfactor 1 def} if

  /xmove xmulfactor lx mul neg def
  /ymove ymulfactor ly mul neg def

  newpath
  xmove ymove moveto
  xmulfactor ymulfactor scale

  %% Outline characters:
  tc true charpath
  gsave 1 setgray fill grestore
  clip stroke

WARNING: Outlined characters will not display at all under NeWSbut will print fine on an Apple LaserWriter IIntx
  tc show
grestore
} def

/numchar{ %% charheight character numchar
%% Make a character of given height in cm,
%% then move vertically by that amount
    /char exch def
    /charheight exch cm def
%c%lg%lg%lg%*[^
]    char (%c) eq {%ld%*.*f setrgbcolor} if
    charwidth charheight char boxshow
  charheight abs 1 gt {0 charheight abs translate} if
/Ibar{
%% make a horizontal bar
    charwidth4 neg 0 moveto
    charwidth4 0 lineto
  stroke
/Ibeam{ %% height Ibeam
%% Make an Ibeam of twice the given height, in cm
  /height exch cm def
  /heightDRAW height Ibeamfraction mul def
     HalfWhiteIbeam outline not and
     {0.75 setgray} %% grey on bottom
     {0 setgray} %% black on bottom
  ifelse
    charwidth2 height neg translate
    Ibar
      0 0 moveto
      0 heightDRAW rlineto
    0 setgray %% black on top
      0 height moveto
      0 height rmoveto
      currentpoint translate
      0 heightDRAW neg rlineto
/makenumber { %% number makenumber
%% make the number
  shift %% shift to the other side of the stack
  90 rotate %% rotate so the number fits
  dup stringwidth pop %% find the length of the number
  neg %% prepare for move
  charwidth (0) charparams uy ly sub %% height of numbers
  sub 2 div %%
  moveto %% move back to provide space
  show
/shift{ %% move to the next horizontal position
charwidth 0 translate
/makebar { %% make a vertical bar and shift
   barwidth barheight (|) boxshow
   barwidth 0 translate
%% definitions for maketic
/str 10 string def %% string to hold number
%% points of movement between tic marks:
%% (abs protects against barbits being negative)
/ticmovement barheight barbits abs div def

/maketic { %% make tic marks and numbers
  %% initial increment limit proc for
  0 1 barbits abs cvi
  {/loopnumber exch def

    %% convert the number coming from the loop to a string
    %% and find its width
    loopnumber 10 str cvrs
    /stringnumber exch def %% string representing the number

    stringnumber stringwidth pop
    /numberwidth exch def %% width of number to show

    /halfnumberheight
      stringnumber charparams %% capture sizes
      uy ly sub 2 div
    def

    numberwidth 2 mul %% move back two digits
    neg loopnumber ticmovement mul %% shift on y axis
    halfnumberheight sub %% down half the digit

    moveto %% move back the width of the string

    stringnumber show

    %% now show the tic mark
    0 halfnumberheight rmoveto %% shift up again
    numberwidth 0 rlineto
  } for
    /labelstring (bits) def
    numberwidth neg 2.5 mul
    barheight
    labelstring stringwidth pop
    sub 2 div
    translate
    90 rotate
    labelstring show
} def

/degpercycle 360 def
 
/cosine {%%    amplitude  phase  wavelength  base
%%             xmin ymin xmax ymax step dash thickness
%%             cosine -
%% draws a cosine wave with the given parameters:
%% amplitude (points): height of the wave
%% phase (points): starting point of the wave
%% wavelength (points): length from crest to crest
%% base (points): lowest point of the curve
%% xmin ymin xmax ymax (points): region in which to draw
%% step steps for drawing a cosine wave
%% dash if greater than zero, size of dashes of the wave (points)
%% thickness if greater than zero, thickness of wave (points)

  /thickness exch def
  /dash exch def
  /step exch def
  /ymax exch def
  /xmax exch def
  /ymin exch def
  /xmin exch def
  /base exch def
  /wavelength exch def
  /phase exch def
  /amplitude exch def
  %% fun := amplitude*cos( ((-y-phase)/wavelength)*360) + base
  /fun {phase sub wavelength div degpercycle mul cos
           amplitude mul base add} def

    /originallinewidth currentlinewidth def
    thickness 0 gt {thickness setlinewidth} if
    /c currentlinewidth def
%%   Make the curve fit into the region specified
    xmin ymin c sub moveto
    xmax ymin c sub lineto
    xmax ymax c add lineto
    xmin ymax c add lineto
    closepath
    clip

    xmin dup fun moveto
    xmin step xmax { %% loop from xmin by step to xmax
      dup fun lineto } for
    dash 0 gt {[dash cvi] 0 setdash} if %% turn dash on
    stroke

    originallinewidth setlinewidth
/circle { %% x y radius circle - (path)
newpath 0 360 arc closepath} bind def

%% The following special comment allows deletion of the repeated
%% See the censor program.
%%]]%%*)

/startpage { %% start a page
  %% set the font used in the title strings
  /Times-Bold findfont fontsize scalefont setfont
  erasepage %% REMOVE FOR PACKAGING INTO ANOTHER FIGURE
  xcorner ycorner translate
  rotation rotate
  %% create the user defined strings
    %% string number %ld
    %% center the string
    /stringscale %*.*f def
    
    stringwidth pop stringscale mul neg stacksperline

WARNING: if you don't see centered string number %ld:
    ""it may be off the page because stacksperline is large (%ld) relative to the
FROM-TO range (%ld to %ld) and centering is based on stacks-per-line.  To
solve this, reduce parameter stacksperline to FROM-TO+1 = %ld

    charwidth mul add 2 div
    %*.*f cm moveto
    %*.*f cm %*.*f cm moveto
    stringscale stringscale scale
 show
    %%
  %% now move up to the top of the top line:
  0 linesperpage linemove barheight mul mul translate

  %% set the font used in the logos
  /Helvetica-Bold findfont fontsize scalefont setfont
%%(*[[ This special comment allows deletion of the repeated
/endpage { %% end a page
  showpage %% REMOVE FOR PACKAGING INTO ANOTHER FIGURE
/startline{ %% start a line
%% move down to the bottom of the line:
  0 linemove barheight mul neg translate
  maketic
  makebar
/endline{ %% end a line
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% End of procedures %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%ld%ld%*[^
]missing all parameters%ld%*[^
]missing bar coordinate parameter%lg%lg%*[^
]missing corner coordinate parametersmissing rotation parameter
WARNING: rotations that are not multiples ofof 90 degrees are likely to be scaledincorrectly, due to a PostScript limitation.See the description of the pathbbox functionin the Red book.
missing charwidth parametercharwidth parameter must be > 0 cmmissing barheight and barwidth parametersbarheight parameter must be > 0 cmbarwidth parameter must be > 0 cmmissing barbits parameter
WARNING: are you SURE you don't want to show the variation due to a smallnumber of samples (i.e. the I-beam error bars)?
Reminder: the I-beam error bars show thevariation of the entire stack not just the highestsymbol, even though it may look like that.barbits parameter must not be zerobarends parameter is missingshowingbox parameter is missingoutline parameter is missingcaps parameter is missingstacksperline parameter is missingstacksperline parameter must be positivelinesperpage parameter is missinglinesperpage parameter must be positivelinemove parameter is missinglinemove parameter must be positivenumbering parameters are missingshrink parameter is missingShrink parameter must be less than or equal to 1.This way, you won't create a misleading logowhich has an apparent height larger than it should.Shrinking can only be done when showing the dashed box.which has an apparent height smaller than it should.number of user defined strings must be givenmissing a user defined string coordinate%lg%lg%lg%*[^
]missing a user defined string******************************************************************************
* NOTE: since the data come from the sites program, the error bar is not     *
* printed on the sequence logo.                                              *
%*.*f () numchar
%*.*f Ibeam
%c Rs total is %*.*f +/- %*.*f bits bits (sample error not known) in the range from %ld to %ld
(%ld ) makenumber
%% amplitude  phase  wavelength  base:
 %*.*f cm %*.*f cm %*.*f cm %*.*f cm
%% xmin ymin xmax ymax step:
 %*.*f cm %*.*f cm %*.*f cm %*.*f cm %ld
%% dash thickness:
 %*.*f cm %*.*f cm cosine
mark symbol in file marks must be one of: "of"mark scale must be positive %*.*f cm %*.*f cm %*.*f cm circle
 fill
 stroke
 %*.*f cm 0 translate
makelogo %4.2f
Half-White Ibeams are used because the symbols are solid black.w%%!PS-Adobe-
%%%%Title: makelogo %4.2f
%% %ld symbols.
Alphabet Logo%% Alphabet Logo
startpage startline
makebar
%% find out how high the bar is in centimeters:
/barincm barheight cmfactor div def
  gsave barincm (%c) numchar grestore shift
endline endpage
%ld%ld%lg%lg%*[^
]%c%ld%*[^
]This is a Chilogo! - Upside down letterswill be produced
THE SYMVEC FILE IS BAD!At position %ld the sum of symbols found is %ld
But the noted number is %ld
%%%%Page:? ?

startpage
writing page %ld
startline %% line number %ld
%% before coordinate %ld: make the bar
%% at coordinate %ld
WARNING: negative Rs variation found in symvec,but the data are not from the sites programpossible program or data error.shift
%% bar at end of logo: make the bar before position %ld
endline
endpage

WARNING: symvec does not contain data for position %ld
It seems that you don't have a zero coordinate."... the invention, probably by the Hindus, of the digit zero has beendescribed as one of the greatest importance in the history of mathematics."--- Encyclopaedia Britannica (1:1175, 1982)Please use a zero!
WARNING: Highest position requested was not found in symvec
colorsmakelogopsymveclogowavemarks.: Pascal system I/O error %d (illegal I/O request) (bad file name) (file not found) (file not open) (bad input format) (not open for reading) (not open for writing) (not open for direct access) (string subscript out of range) (end-of-file) (file write error)Pascal system error %d (out of memory) (reference to NIL pointer) (integer overflow) (divide by zero) (real math overflow) (value range error) (CASE value range error) (bus error) (stopped by user)%s
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Cƺ|E}&bI9 |`|tT:|T>@,^|HH||C @9)PA9xA;{Jx~xAP|#xN Tc>|+B}H|A /dev/nulllogo.%sNo block with name %s found in file %s !
MATRIX_LOGOB: Copyright 1995-8 Fred Hutchinson Cancer Research CenterUSAGE: matrix_logob blocks|pssms AC|- suffix   pssms must be in blimps format and consist of values betwen 0 and 100
    which sum to 100 in each column.These files must be in the current directory:   makelogob, colors, default.amino.frq
Enter name of BLOCK or MATRIX file: r
Cannot open file "%s"

Enter AC in %s or - to make logos for all: 
Enter file name suffix: Logos will be written to logo.%s
* position, samples, information, variance
%d number of symbols
col   %c   info.  sum     residues   #_of_specified_residues/#_of_seqs   e   var%*ld %*.0lf %*.*f % .1E
%c %4d
%2d| %3d  %6.3f  %3.0f       %2d/%d %6.3f %6.3f
small sample correction (e) : %6.3f, variance (avarhnb) : %6.3f
(these are are actually the values for the last column and will be different for the other columns if they contain a different number of unspecified residues - gaps, Xs, etc.)
1 %d
1
1 20
0
0.365
5.48 0.1
-4
bars on
-
no outline
capitals
55
1.5
numbers
1.0
0.0 -1.5 %.2f
pageview-left
The created sequence-logo file (%s) is a PostScript file.
  (V to view logo with program %s (%s %s %s))
     after viewing you can also choose to print,   P to print logo (%s %s).)
%s %s %s%s %s
File %s sent to printer.
BLOCKInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
 ,
.+-0123456789convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
pb_weights:%d ignored for %s
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
dirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 ID   AC   DE   BL   MATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
//
idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
No width field for matrix %sError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
%fresize_matrix() not finished.  Exiting.
  |% 4d    --+----%c |% 6.4fMA   %s
 %c   *   -
%3d %3d
% 6.4f % 6.4f
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
% 9.4f % 9.4f
load_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
%s/docs/default.amino.frq%s/docs/default.qijdefault.qijaInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.|B}h=k|8}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|t}N |B}h=k|X}N |B}h=k|<}N |B}h=k| }N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|x}N |B}h=k|\}N |B}h=k|@}N |B}h=k|$}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k||}N |B}h=k|`}N |B}h=k|D}N |B}h=k|(}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k||}N |B}h=k|`}N |B}h=k|D}N |B}h=k|(}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N MATRIX 	

@@4C0@3???@?R@Ç3333Ç3333@X@Y@@?333333+*)$	

	

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MOTIFJ Version %s
Please cite Hamilton O. Smith, et al, PNAS 87 (1990), pp. 826-830.
CANNOT ALLOCATE SMatrix
Using RunType=%d

Enter input file name: rCannot open file %s not found

Reading batch file %s
Reading sequence file %s
%spros/.lst
filepath=%s
.lis
NumSeqs=%d batch=%d Title=%s

Too few sequences to process(need at least 2).Sequence #%d:	%s		Length of sequence #%d =  %d
MOTIFJ=[[,]
Enter significance level [2-%d; %d]: Enter number of allowable internal duplicates [0-%d; 0]: Enter search width [1-24; 17]: Enter drop score [0-18540; %d]: Allocating and initializing arrays...Couldn't allocate AA3_OBS pointer.Couldn't allocate AA3_OBS array.Couldn't allocate MOTIF.
RunType = %d, Normalized drop score = %d
Motif parameters = [%d, %d, %d] with shuffled sequences.

CPU time to find and sort motifs: %ld seconds.
Found %d motifs. Enter number to save or -1 to redo [1-%d; %d]: 
Previous significance level was %d. Enter new level [2-%d; %d]: Previous number of internal duplications was %d. Enter new number [0-;%d]:  Using previous distance  %d
Enter 'g' to print first motif in each group: Enter 'l' for long form:  
_________________________________Group #%d_________________________________


___________________________________________________________________________
Printed %d motifs out of %d total.
Mean score: %ld 
Enter number of motif groups to map (maximum %d) or 0 to assemble blocks: 
Starting motifj...3
Starting motomat...motomat1
Motif:  in %d proteins (%d duplicates), Merged %d, Score %d
  + *   Score (Position) for best two fits.--.   %3ld (%3d)  %3ld (%3d)  %s (Motif at %d)  Most common amino acids
:
cutting %d %d %d: last score = %d, groups = %d
Couldn't allocate GROUPS.                    Protein %s:
%d %d

 
	
.pro***%s not found
 	
Couldn't allocate Seq[%d]
ERROR reading %s, sequence longer than %d, truncated
Use shuffled sequences [y/n; n]?    %5d %5.3f Total amino acids in %d proteins: %d

.motmotifj.motw+b
Unable to open file %s.motifj.prosmotifj.pros>%s %d MINIMUM
 MAXIMUM
%1sARNDCQEGHILKMFPSTWYVX.*rtprotomat.stpSCORE ,	
Could not open %s, using default BLOSUM scoring matrix
HIGH
Using scoring matrix from %s
+-0123456789
Using BLOSUM62 scoring matrix.GENBANK//LOCUSDEFINITIONACCESSIONORIGINPROCLASSPIRENTRYTITLESEQUENCE///EMBLIDDEACSQUNI>VMSPCF_ACPCF_DEPCS_ID

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directoryFRAGMENTBLOCKLSTPS=LENGTH=
Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments. fragment
%d. Entry %s found....dnaCreating %sw+t
Cannot open %s

%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P>%sDR   PIR;.

>%s
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MOTOMAT %s: (C) Copyright 1991 by Fred Hutchinson Cancer Research Center
Please cite: S.Henikoff & J.Henikoff, NAR 19:6565-6572 (1991).
CANNOT ALLOCATE SMatrixls -al *.mot
Enter name of file containing motifs: .motrb
Cannot open file %s


Input file was created using wrong motifj version!
Assuming input from Gibbs
%s

%d blocks read using parameters [%d, %d, %d]. %d sequences.none;asis
Processing blocks in %s using a cut-off score of %d 
   and a clustering threshold of %d percent.
Quitting becasuse no motifs to work on.motomat.erra

Merging raw blocks...
Recalculating block column scores
Extending blocks...%s.blksw+t
Cannot open %s
Saving blocks to %s

Block %d: %.1s%.1s%.1s has been merged.
Enter minimum block extension column score or 1 for best block [100-2500 or 1; %d]: Enter clustering identity threshold [1-100; %d]: 
Processing block %d in %s using a cut-off score of %d 
Extended width was %d, re-extending with cutoff score of %d.
Block %d has been dropped for low width:

Type S[ENTER] to save this block, or N[ENTER] to skip to next block,
or anything else[ENTER] to re-extend this block...

Merging extended blocks....

Removing duplicate blocks....
Enter drop standard deviations [-30 to 30; %d]: 
Using a drop score of %d standard deviations or %d.
Mean score=%.2f, standard deviation=%.2f
Dropping blocks with score below %ld...
 unless they have more than one merged motif
Block %d has been dropped for low score:
Block %d:
Surviving blocks=%d, max dups=%d
Reducing block overlaps ..., reduced significance=%d

Looking for best path..., npath=%d, nseqs=%d

No surviving blocks%s %d %d %d %d %d %d %d %d %d %d %d %d %ld %d %d %d

NumSeqs=%d, Total_Motifs=%d
Sequence #%d: %20s %d %.5s

MOTIF %d: %d(%d)%d(%d)%d  domain=%d, score=%d, freq=%d, dups=%d, mots=%d
%20s (% 5d) %.1s
                   
merged_motif: Unable to allocate merged_motif structure!
Merging motif %d into motif %d
Blocks %d and %d have been dividedBlock %d has been trimmed by %d to eliminate overlap with Block %d.

Score              %1s
 %.1s%.1s%.1s (extended width=%d, score=%d  motifs=%d, motif width=%d, conserved=%d)
Saving block %.1s%.1s%.1sID   %s; BLOCK
AC   %s; distance from previous block=(%d,%d)
DE   %s
BL   %.1s%.1s%.1s gibbs=[%d,%d,%d] motomat=[%d,%d,%d]BL   %.1s%.1s%.1s motif=[%d,%d,%d] motomat=[%d,%d,%d] width=%d seqs=%d


//

cluster_seqs: Unable to allocate pair structure! % 3d%20s (% 5d) 
>>>MOTOMAT out of memory!  Restarting with DropScore = %d
%s
 prune_blocks: Unable to allocate temp structure!

Revised TopScore=%ld order_blocks: Unable to allocate temp structure!

seq=%d: %d,%d 
row %.3d:  %.3d   x makematrix: Unable to allocate matrix structure!
 makepath: Unable to allocate path structure!
 ***MOTOMAT STOPPING BECAUSE >1500 PATHS***
find_paths: single %d find_paths: Unable to allocate temp structure!


find_paths: more----------- follow_arcs: Unable to allocate temp structure!


follow:  row=%d, ntemp=%d
 curpath blocks=%d 
 curpath_seqs:%d=%d 
 row=%d temp[i].index=%d nseq=%d
End of follow_arcs for %d makebllist: Unable to allocate block_list structure!

best_path: paths->nblocks=%d
 New path: nblocks=%d, tots=%d B%d %.1s%.1s%.1s
 (%d, %d) B%d %.1s%.1s%.1s
   thisb: 
    allb: 
   saveb, allb: %d=%d,%d 
 Best sub-path:%d blocks, %d AAs, total score=%ld,
 total motifs=%d, total idents=%d, total sequences=%d, prop=%d
 >>>NEW BESTPATH check_seqs: Unable to allocate temp structure!

Best path has %d sequences out of %d:
%d blocks, %d AAs, total score=%ld, total motifs=%d, total conserved=%d
 total sequences=%d out of %d
Sequences in the best path:%.3d:%20s 
Sequences not in the best path:
Path: %d%d  %d
ARNDCQEGHILKMFPSTWYVX.*rtprotomat.stpSCORE ,	
Could not open %s, using default BLOSUM scoring matrix
HIGH
Using scoring matrix from %s
+-0123456789
Using BLOSUM62 scoring matrix.GENBANK//LOCUSDEFINITIONACCESSIONORIGINPROCLASSPIRENTRYTITLESEQUENCE///EMBLIDDEACSQUNI>VMSPCF_ACPCF_DEPCS_ID

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directory 	
FRAGMENTBLOCKLSTPS=LENGTH=
Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.  
	
fragment
%d. Entry %s found....dna.proCreating %s
%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P>%sDR   PIR.

>%s
ARNDCQEGHILKMFPSTWYVBZXactg-_|B}h=k|
}N |B}h=k|
}N |B}h=k|
}N |B}h=k|
|}N |B}h=k|
`}N |B}h=k|
D}N |B}h=k|
(}N |B}h=k|
}N |B}h=k|	}N |B}h=k|	}N |B}h=k|	}N |B}h=k|	}N |B}h=k|	}N |B}h=k|	d}N |B}h=k|	H}N |B}h=k|	,}N |B}h=k|	}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|p}N ?zG{C0@$?A@Y?C0| 
	 6/ 6/00.1_	
	
					
			

			
	

	
			
							
	
			


		
		
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 8__PAGEZERO__TEXT	__text__TEXT"c$__symbol_stub__TEXTv__picsymbol_stub__TEXTv$__symbol_stub1__TEXT0v__cstring__TEXT@xv@__picsymbolstub1__TEXT __literal8__TEXT8__literal4__TEXT__const__TEXT__DATA__data__DATA__nl_symbol_ptr__DATAT1__la_symbol_ptr__DATAF__dyld__DATA__common__DATA8__LINKEDIT /usr/lib/dyld4FZX/usr/lib/libSystem.B.dyliblPU[5v5("|:x8!T!48!z8;cW{:|H	|<@!= |#x|yx|+x!b<@$/}"Kx@8= 9)@H<|i|lxN!HX//A8BH9"}"Kx|t/@<@fx"H8/@<@;FBB/A|I|LxN!<@BB/A|I|LxN!Hb<@B/A|I|LxN!<`8<8cDHI<|	|xN!<`8@8ctH)<`888cH<`8H8cH	<`8L8cH<`8P8cHA@/A,8/A H/AL/AP/A|I|Lx?;;N!|~xHԀ8x|	|xN!H//A8BH8b|bx|t/@=`9 9k|t/A |	9k|t@`9)K؀Hx|	|xN!/A<Lx8|	|xN!/AP|	|xN!,@;@A,<`8D8cHaD/AH`A<@8xexBFx#xHH_=a}N =a)}N =a0}N =a&}N =a }N =}=9N =`k}iN |!|>x~x|8`8(Hs|`x8^8x^8|^88(8`-Hs5|`x^88`-8Hs}!|N |B}=|9s\}N |B}=|9r}N |B}=|9s<}N |!|>x~x|888`-Hr}|`x@8@xBHq	<_Bz88/A^8T>+A<_8b`Hpm<_8bHHp!|N |B}=|9p`}N |B}=|9p }N |B}=|9p`}N |B|@&|{x<A8c] !p|#x.Ht5<8c]XHt	<<8c]h8vHtAL<8c]tHs<8c]Hs<8c]Hs<8c^Hs<8c^XHs<8c^Hs<<8c^8^Hsu>/Py?8
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#xH=%$x|ex|wH;<#x87|*8H:#xH<$x|ex|rH;PE<#x87;Z|W|;	|t|tH:#xH<$x|ex|nH;qW:|B<a87#xH:U#xH8|d@T<@C0l=jAl`k:DАAAd8/;pH(/AP<x8;pH&E|dxxH'xH&|ao|t//A<x8 H#p|t/Ax8a@H&xH%;@|C8;a<8 xcxH#xH'y|}y@HcxH'I/@<x8c H&H$<x8c!H&<8c!(H&p8!xa|N |8`|!H%89`9 9@xcJ#lCpccc=LhdTX\P`tX8!P|N |@&|АAB!|yx|#x;::: H @|t/A/>A8a@8/H&|}y@K%<|{x88a@;H%/(||x@;(8{8@xH"/|\@;cx8@xH"9 8@@<9`||t/|@/@9 H}{x8BA<t88a@H"~x/AP<8a@8H"/A\<8a@8H"}/AT<8a@8H"a|cyA<;J88xH"<Kx88H!M/@P<8a@8H"|cyAT;<8xH$u||y@8xx~xH!8A@|B~xH#i{LHxt.AxdxH!/At[xztA~x#xH!/@8a@8%xH!/@x8!pax|}p N |@&|AB!pa|+x}Cx|+x|#x:!K=+ T|8@|qx0A4@<8cH#
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|[.|ex8a@H/@p~CxH|}x8a@H+AP~Dx~cxH<8h~cxH|[.~cx|"H<8L~cxH~Cx~dxHp/@l<8a@8|8H/@P<8aI8Hq/A8<8`8HY|dyA |t/ @88|=H|[.bH	|[.|ex8a@H/@t<}{x8}{xH/@<}{x8H/A8Px~cxH~cxH+K@KA<~x8~exH}kxH|[.<8b|yH/AA|[.~x|"H|[.~xHP||tT`1@Tb:|B4TH8H=0C|/A\L8B\L;8a@H@AxH%/@D8a@8xH/A,|[.bH|[.|ex8a@HE/@xH/@l8a@8xH/AT|[.bHI|[.|ex8a@H/A,|[.bH!|[.|ex8a@H/@lA0/A~xH@ZbH݀Z|ex8a@H/@\<8a@8LH<8h8a@H~cx8xH/A$~dx8a@H}H8a@8xHxH/@Aa48!a|}a N |B!#t|#x/A<999@X/@<#x88H/#xA$x8a@H<88a@H;@|}yA@;a;/	A|{x;Z;~H<8`8H|}y@~xHa/x|vx@:x~x~ųx}{xH8<}{x8ԘHE}kx|}yADx:@}sx:!@<x8̚AH||y@8axxH|XB;@~x~7x~ux~xxH)/A(|t/Ax8aH/@~x~x~x~ųxHI8;;;`H4|X|t/|@/@;Hb~ܳx;xH@Ax8yH#xH8;A8<8`8H|}y@ԃ9t/@8`(8! |N 9(|~x88@|`T>T@.|Jx|`}K4}GSx}iFpT@.8I+T>|Hx}CxA8	UB>T@.|x|4|4|IFp8	+A8	U>T@.|x|4}`Fp|BFp|bP@9(Al8`N =`}N =`}N =`}N __dyld_make_delayed_module_initializer_calls__dyld_image_count__dyld_get_image_name__dyld_get_image_header__dyld_NSLookupSymbolInImage__dyld_NSAddressOfSymbollibobjc__objcInit__dyld_mod_term_funcsMULTIMAT: (C) Copyright 1991 by Fred Hutchinson Cancer Research CenterVersion %s
USAGE:   multimat                  = Maximum # of hits to report             = File containing blocks for comparison               = File containing list of TP sequences             = Blimps search result files,  blocks vs sequence dbmultimat.data
Enter maximum number of hits to report [%d]: 
Enter name of blocks database:r
Cannot open file %s;
search results will not be compared with blocks database.
Search results will be compared with %s
Enter name of file containing list of true positives:
Cannot open file %s;
search results will not be compared with true positive list.
Search results will be compared with %s;
only hits not in this list will be reported%d IDs in %s
multimat.miswmultimat.fnd
Enter name of BLIMPS results file: 
No results files specified.

NOT ENOUGH MEMORY!
Cannot open file %s

Reading %s....
%d scores read from %s

WARNING: AC family name truncated to 9 characters. AC family name = %s
	BLOCK	FRAGMENTVersion 3.2.3Version 3.2.2Version 3.2.1Version 3.2.4Version 3.2.5Records Searched::	
Scores Done:

Top %d sequences sorted by maximum normalized score:
(the normalized score is the Score divided by the99.5 score in the block if available, or by thesmallest Score in the search results file for the block)

Block     Rank Frame Score      Location(bp) Sequence

Block     Rank Frame Score      Location(aa) Sequence
%d.----------------------------------------------------------------------------------
%8s  %4d  %2d    %4d  %7ld-%7ld %s %s%s %d %d %d %d %d %d %d %d %d %d %d %f
blksrch.stp
===============================================================================
Search results from the BLOCKS e-mail searcher.
Please report problems to jorja@sparky.fhcrc.org, include your query
and this output. To obtain help, send the word HELP on a single
line to blocks@howard.fhcrc.org
Copyright (c) 1992 by the Fred Hutchinson Cancer Research Center
If you use BLOCKS in your research, please cite:
Steven Henikoff and Jorja G. Henikoff, Automated assembly of protein
blocks for database searching, NAR 19:23 (1991), 6565-6572.
Each numbered result consists of one or more blocks from a PROSITE group
found in the query sequence. One set of the highest-scoring blocks that
are in the correct order and separated by distances comparable to the BLOCKS
database is selected for analysis. If this set includes multiple blocks
the probability that the lower scoring blocks support the highest scoring
block is reported. Maps of the database blocks and query sequence are shown:
  < indicates the sequence has been truncated to fit the page
  : indicates the minimum distance between blocks in the database
  . indicates the maximum distance
The maps are aligned on the highest scoring block. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database
is shown. Upper case in the query sequence indicates at least one
occurrence of the residue in that column of the block.%sAC   
OUT OF MEMORY
(,)BL   99.5%==

strength=// 	
 

P<%6.2g for 
                %sin support of %s

No P-value computed for single block hits.

ERROR: Anchor block not found in blocks database.%s %s %d %d %d %d %d %d %6.2g %s

                         |-----%5d residues----|
%-20s %-20s %s

%s
%s
%-20s%c<->%c%6d(%d,%d):%d
No blocks for family %s found in database.ARNDCQEGHILKMFPSTWYVX*rtprotomat.stpSCORE ,	
Could not open %s, using default BLOSUM scoring matrix
HIGH
Using scoring matrix from %s
+-0123456789
Using BLOSUM62 scoring matrix.GENBANKLOCUSDEFINITIONACCESSIONORIGINPROCLASSPIRENTRYTITLESEQUENCE///EMBLIDDEACSQUNI>VMSPCF_ACPCF_DEPCS_ID/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directoryFRAGMENTBLOCKLSTPS=LENGTH=
Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments. 
	
fragment
%d. Entry %s found....dna.proCreating %sw+t
Cannot open %s

%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P>%sDR   PIR;.

>%s
ARNDCQEGHILKMFPSTWYVBZXactg-_|B}h=k|
D}N |B}h=k|
(}N |B}h=k|
}N |B}h=k|	}N |B}h=k|	}N |B}h=k|	}N |B}h=k|	}N |B}h=k|	}N |B}h=k|	d}N |B}h=k|	H}N |B}h=k|	,}N |B}h=k|	}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|x}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|p}N |B}h=k|T}N C0??PbM?@N@9Dz| 
	) 6/11/00.1cB4@	
	
					
			

			
	

	
			
							
	
			


		
		
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Enter type of input file (Block|Frequencies|Weights): 
Enter name of input file: r
Cannot open file %s
ERROR:No block found in file %s
Please verify input format typeALPHABET  
	

Problem finding ALPHABET in %s
log-oddsfrequencyalength=alength= %d w=%d
ALPHABET length (%d) not alength (%d)

Problem finding width in %s
Not sure about the format of %s, assuming first line contains alphabetWEIGHTSwidth=%d; 	

Problem finding value for pos=%d aa=%c
ERROR: Negative frequencies readERROR: All values read as zeroCould not find alphabet or width in %s
FREQSseqs=%d; width=%d;%s.mastw%s.blimpsUnable to recover enough memory to continue.  Aborting.
ALPHABET= ARNDCQEGHILKMFPSTWYVBZX
log-odds matrix: alength= 23 w= %d
% 6.3f aInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
load_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
%lgUnable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqdefault.qijID   AC   DE   BL   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motif%swidth=No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
//
idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
No width field for matrix %sError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
%fresize_matrix() not finished.  Exiting.
  |% 4d    --+----%c |% 6.4fMA   %s
 %c   *   -
%3d %3d
% 6.4f % 6.4f
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
% 9.4f % 9.4f
Reclaim space function is not defined.  No memory will be reclaimed.
BLOCKInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
 ,
.+-0123456789convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
pb_weights:%d ignored for %s
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
dirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.|B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|t}N |B}h=k|X}N |B}h=k|<}N |B}h=k| }N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|x}N |B}h=k|\}N |B}h=k|@}N |B}h=k|$}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k||}N |B}h=k|`}N |B}h=k|D}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k||}N |B}h=k|`}N |B}h=k|D}N |B}h=k|(}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N MATRIX 	

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Estimated melting temperatures of non-degenerate clamp region (C=%.2fnM):

-----------------------------------------------------------Length=%d, clamp=%d

---Using Breslauer's entropy=-%.1f & enthalpy=-%.1f
AT/GC=%.1f, NAR=%.1f, PRIMER3=%.1f
---Using SantaLucia's entropy=-%.1f & enthalpy=-%.1f
References:Entropy/Enthalpy: Table 2 from Breslauer, et al, (1986) PNAS 83:3746-3750Entropy/Enthalpy: Table 2 from SantaLucia, (1998) PNAS 95:1460-1465AT/GC: Suggs, et al, (1981) ICN-UCLA Symp.Dev.Biol. 23:683-693NAR: Eqn [2] from Freier, et al, (1986) PNAS 83:9373-9377PRIMER3: Eqn (ii) from Rychlik, et al, (1990) NAR 18:6409-6412
Oligo in reverse order:GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleUnable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, AA) 	NA) 	??) 	>--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.aInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
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A8|^x|xX8!P|N |B}H|<88H|B<_+l!/AX8!P}|N <<c*L8H8`KQX8!P8`|N |~y|B!@ <<c)84H}8`KX<_8!P*|N px!Aaځڡ!AaہۡN px!Aaʁʡ!Aaˁˡ|N =`}N =`}N =`}N __dyld_make_delayed_module_initializer_calls__dyld_image_count__dyld_get_image_name__dyld_get_image_header__dyld_NSLookupSymbolInImage__dyld_NSAddressOfSymbollibobjc__objcInit__dyld_mod_term_funcs-ARNDCQEGHILKMFPSTWYVDNEQARNDCQEGHILKMFPSTWYV*AGCTACGTATCGCGTAGTACTACGACGTStandardFFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000Vertebrate MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000Yeast MitochondrialFFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000Invertebrate MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000Ciliate NuclearFFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Echinoderm MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000Euplotid NuclearFFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGBacterial and Plant Plastid0001000000000000000100000000000011110000000000000001000000000000Alternative Yeast NuclearFFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000Ascidian MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFlatworm MitochondrialFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGBlepharisma MacronuclearFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGChlorophycean MitochondrialFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGTrematode MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Enter name of matrix database: r
Cannot open file %s

Enter name of observed frequencies database: 
Cannot open file %s, TP distribution not computed.

Enter name of frequency file: 
Enter number of sequences in a typical search [%.0f]: 
Enter number of amino acids in a typical database [%.0f]: Assuming %.0f sequences, %.0f amino acids in a search
and 100 true positive alignmentspssmdist%s.data
Cannot open file ctemp%s.cum
======>%s
>%s
 ;%s %d %d  %d %.4lf %d %d

True positive distribution
Random distributionminscore without ends=%d
minvalue=%d maxvalue=%d minscore=%d maxscore=%d
maxscore is too big, increase MAXSCORE from %d
%d %6.2g
Sum of probabilities = %8.4f
Score range  log(Possible ways)  Probability  Expected scores%4d %4d  %8.4f      %11.8f      %8.2f
%4d %4d       0.0000       0.000000

CumScrs  Score   ExpectedScrs%8.4f %4d %8.4f
Median TP score = %d, TPabove = %lf
99.5 TN score = %d, 80.0 = %d
Read a frequency of value of %f for: %c
Read a frequency of value of %f for: not a residue
The non-amino acid codes J and O weights are differentThe non-amino acid codes O and U weights are differentThe non-amino acid codes U and J weights are differentThe value for the non-amino acid will be the last weight seen.Currently the program ignores non-residue characters so thisfield has no effect.
%lgInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
%fresize_matrix() not finished.  Exiting.
  |% 4d    --+----%c |% 6.4fID   %s
AC   %s
DE   %s
MA   %s
 %c   *   -
%3d %3d
% 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
% 9.4f % 9.4f
Reclaim space function is not defined.  No memory will be reclaimed.
|B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|p}N |B}h=k|T}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|p}N |B}h=k|T}N |B}h=k|8}N |B}h=k|}N  	

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Error in matrix file format.  No ID line.
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Error in matrix file format.blimps-3.9/bin/OSX/rank_matrix000075500001460000012000001212241062461240300166340ustar00jorjastaff00000400000027
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3ƺ|E}&bI9 |`|tT:|T>@,^|HH||C @9)PA9xA;{Jx~xAP|#xN Tc>|+B}H|A  [[-n] -f]           = file of blocks           => extract AC or all blocks          -n       => output to stdout, otherwise each block                      will be written to AC?.blk		-f	=> floating point output
Enter name of blocks database: r
Cannot open file %s

Enter AC of blocks to extract, or all [%s]: all-n-f.blkwUnable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
//
idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Warning: %s
Serious: %s
Program Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
GenBankLOCUSDEFINITIONORIGINPIRENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..UnknownUNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.Reclaim space function is not defined.  No memory will be reclaimed.
|B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|t}N |B}h=k|X}N |B}h=k|<}N |B}h=k| }N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|8}N |B}h=k|X}N |B}h=k|<}N |B}h=k| }N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|x}N |B}h=k|\}N |B}h=k|@}N |B}h=k|$}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k||}N |B}h=k|`}N |B}h=k|D}N |B}h=k|(}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N  	

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read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
>--- sequence --->%s 	( %d:%d, >--- -------- --->%s  %s
untranslate_sequence(): Not an amino acid sequence, not untranslating.Reclaim space function is not defined.  No memory will be reclaimed.
|B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|p}N |B}h=k|T}N |B}h=k|8}N |B}h=k|}N  	

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UEXTRACT %s: (C) Copyright 1991-2000 by
 Fred Hutchinson Cancer Research CenterUSAGE: uextract   [-f -o -n]        = file listing sequence names to extract                   in PROTOMAT format         = sequence database       -f          to extract FRAGMENTs       -o to have all sequences put in        -n          to NOT execute motifj or create .lst file       -l          to NOT execute motifj but create .lst file       -k          to NOT execute motifj but create .lst file                    with fewer sequences than -l
Enter name of file containing list of entries to extract: r
Cannot open file %s

Enter name of database file to extract entries from: w+t
Extracting all sequences to %sMOTIFJ=[
%s/
%d sequences requested for extract from %s
  and deposit into directory %s
  and deposit into file %s
%d sequences extracted
The following sequences were not found:.lst%s

%d entries written to %s
[,]174%s MOTIFJ=[%s,%s,%s,%s];$

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%d entries re-written to %s
uextract.data%s %d %d %s %s %s
motifjP$_%-20s  PS=%s  LENGTH=%-6d  FRAGMENT  LST PIR=%sARNDCQEGHILKMFSTWYVX.*rtprotomat.stpSCORE ,	
Could not open %s, using default BLOSUM scoring matrix
HIGH
Using scoring matrix from %s
+-0123456789
Using BLOSUM62 scoring matrix.GENBANK//LOCUSDEFINITIONACCESSIONORIGINPROCLASSPIRENTRYTITLESEQUENCE///EMBLIDDEACSQUNI>VMSPCF_ACPCF_DEPCS_ID

mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directory 	
FRAGMENTBLOCKLSTPS=LENGTH=
Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.  
	
fragment
%d. Entry %s found....dna.proCreating %s
Cannot open %s

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>%s
ARNDCQEGHILKMFPSTWYVBZXactg-_|B}h=k|	|}N |B}h=k|	`}N |B}h=k|	D}N |B}h=k|	(}N |B}h=k|	}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|d}N |B}h=k|H}N |B}h=k|,}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|h}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|L}N |B}h=k|0}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|l}N |B}h=k|P}N |B}h=k|4}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N | 
	# 2/21/00.1	
	
					
			

			
	

	
			
							
	
			


		
		
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%d entries written to %s
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motifjP$_%-20sblimps-3.9/bin/Sun_sparc/000075500001460000012000000000001062460464300156605ustar00jorjastaff00000400000027blimps-3.9/bin/Sun_sparc/README000064400001460000012000000001241062460521200165260ustar00jorjastaff00000400000027SunOS 5.9 Generic_122300-02 sun4u sparc SUNW,Sun-Fire-V240
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%sLAMA version %s.
LAMA version %s.
Cannot determine type of input file

Note - the two input files have different types of data.

Minimal length of reported alignments %3d
Score cutoff is %.1f Z score units (in the top %.1e percentile of chance scores)
%s
%s

                                            alignment     Z-score  expected number for
block 1     from:to       block 2     from:to   length                 searching %d blocks
%s%sBLIMPS_DIR%s/docs/%sTrying %s...

Comparisons skipped !
Block matrix %s shorter (%d) than narrowest width allowed (%d)

Comparison skipped !
Block matrix %s shorter (%d) than narrowest width allowed (%d)


%s
%s

%s


%s
%.1e-%-10s  %3d : %3d and %-10s  %3d : %3d (%2d) score %3.0f (%4.1f  %s)%s
%s
No hits found above score cutoff %.1f.%s
%s
Output written in file %s.
,Error in reading first file name from first argument !
Error in reading second file name from first argument !

Enter name of a file with blocks or block matrices: 
The blocks/matrices in this file will be intercompared.
If you wish to compare them against blocks/matrices in
another file enter that file name (else just hit ).
r
Cannot open file "%s"

Enter name of output file: w
Cannot open file "%s"

Minimal alignment width can not be negative !
The value given (%d) is out of range.

Minimal alignment width can not be less 
than narrowest allowed blocks (%d).

Cutoff score should be specified as a Z score (mean+Z*std).
The Z score must be positive (corresponding to the 50 percentile or higher).
A negative cutoff score (%f) was specified, default value (%.2f) used.
Column scores for %s and %s -
%6.3f 

S matrix for %s and %s -
%6.3f 


Column scores for optimal alignment of %s and %s -

Column scores for optimal alignment of %s and %s -
%3d,%2d %3d,%2d 

%6.3f %6.3f 

%-10s %3d %3d %-10s %3d %3d %2d Prpo %6.2f (%4.1f)
Error ! Extrapolated mean of shuffled PSSMs requested for 
a block too narrow (%d).
Error ! Extrapolated variance of shuffled PSSMs requested for 
a block too narrow (%d).
BL   MA   Error. variable db_type (%c) is of unknown type !
Unable to recover enough memory to continue.  Aborting.
Error ! Problem in format of ProDom entry description -line
%s%s;%s%s%s; ProDom_mulError ! Problem in format of ProDom entry description-line
Error ! Problem in ProDom entry %s
second word in description line doesn't begin with a (
Error ! Problem in ProDom entry %s
second word in description line doesn't end with a )
Error ! Problem in format of ProDom entry %s
A non-digit in the number-of-sequences field "%s"
Error ! Number of sequences in ProDom entry %s (%d) is less than 2
Unable to recover enough memory to continue.  Aborting.
Error ! Problem in format of ProDom entry %s sequence-line %d
Error ! Problem in format of ProDom entry %s sequence-line %d
Error ! Problem in format of ProDom entry %s sequence-line %d
A non-digit in the sequence start position %s
Error ! Problem in format of ProDom entry %s sequence-line %d
Error ! Problem in format of ProDom entry %s sequence-line %d
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Error ! Problem in format of ProDom entry sequence-line %d
Sequence %s has length of %d instead of expected %d
Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
read_a_prodom_entry(): Error reading sequence %s in block %s,Undocumented return value, %d, from read_sequence().
Error ! Not enough sequences (%d) in ProDom entry %s
Error ! Actual number of sequences in ProDom entry %s
different than what the entry reports
 distance from previous block=(%d,%d)adapted from ProDom entry; width=%d; seqs=%d;
  |% 4d    
  |% 4d    
  |%4d
--+----
%c |% 4d
%c |% 4d
rload_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
%lg%lgUnable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqdefault.qijrBLOCKBLOCKMATRIX; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
A ,
.+-0123456789 ,
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
pb_weights:%d ignored for %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
rdirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 	

 Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

&00<0H0T0`0l0x00000000000000 0,080D0P0\0h0t0000000000Pc

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G(G0G4G8G<G@GLGPGTGXG\GpGtGxG|-ARNDCQEGHILKMFPSTWYVDNEQARNDCQEGHILKMFPSTWYV*ACGTAGCTACGTATCGCGTAGTACTACGACGT-StandardFFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000Vertebrate MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000Yeast MitochondrialFFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000Invertebrate MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000Ciliate NuclearFFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Echinoderm MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000Euplotid NuclearFFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Bacterial and Plant PlastidFFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000Alternative Yeast NuclearFFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000Ascidian MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Flatworm MitochondrialFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Blepharisma MacronuclearFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Chlorophycean MitochondrialFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Trematode MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000Scenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Thraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Usage: 
LAMA inp_file1[,inp_file2] out_file [min_algn_wdth] [dbg_lvl] [scrn] [cutoff] [expected target]

The program must have the names of one or two files with entry(ies) to compare
and an output file name. These can be specified on the command line or
interactively. On the command line the first argument is the entry(ies) file
name(s), if two files are specified they should be separated by a comma
with no spaces. Each file can be of either block, matrix, ProDom 
multiple alignment entry(ies). The second argument is the output file name,
it will be overwritten if it already exists. Optional arguments are 3rd -
minimal alignment width (0 for default), 4th - the debug level, 5th -
screen output (0 to forbid, anything else to allow), 6th - score
cutoff (in Z units [std's from mean], >=0, 0 for default), and 7th - for
how many searched blocks to calculate the number a score is expected to appear
(0 for default).
default.amino.frqdefault.amino.frqGenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQ//GCGGCG-GenBankLOCUSDEFINITIONORIGINLOCUSGCG-PIRENTRYTITLESEQUENCEENTRYGCG-EMBLIDDESQIDFasta>>>Universa>>*Flat-file, no title|	

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4x 	LAMAcrti.scrt1.s__get_exit_frame_monitor_ptr__do_exit_code_ptr__crt_scratchvalues-Xa.cBbss.bssDdata.dataDrodata.rodataLAMA.c___const_seg_900000205___const_seg_900000408___const_seg_900000601___const_seg_900000801___const_seg_900000901___const_seg_900001001___const_seg_900001101___const_seg_900001401___const_seg_900001501___const_seg_900001603___const_seg_900001701frequency.c___const_seg_900000106___const_seg_900000301___const_seg_900000403convert.ccompute_BZXpositive_matrixmake_altsbasic_matrix_construction___const_seg_900000501___const_seg_900000803___const_seg_900001004___const_seg_900001202___const_seg_900001301___const_seg_900001601___const_seg_900001801___const_seg_900001901___const_seg_900002004___const_seg_900002201___const_seg_900002401___const_seg_900002701blocks.cBlockBufferBlockBufLength___const_seg_900001201errors.cErrorFilematrix.cread_matrix_header___const_seg_900000802___const_seg_900000902memory.cRecFuncsequences.cread_sequence_header___const_seg_900000502___const_seg_900001102strutil.cgcode.c___const_seg_900000303crtn.s_END__START_untranslate_sequencegribskov_conversion_methodoutput_matrixread_a_prodom_entryBlockToMatrixConversionMethodfree_work_pssmstrncpystatsgcodesoutput_matrix_s__iobtouppersscanflgammaalignments_doneexpfprint_matrixresize_block_clusters_environread_block_headerErrorReport__cg92_usedread_a_blockset_error_file_namegetargslogfrequencyalloctd_zVsPrcntlNumberToReportextrpltd_meancallocaa_btoant_btoainit_gcodeCodon_Usageload_ZvsPrcntl1GeneticCodeInitializerSIFT_conversion_methodmake_gribsstrncmpstrspn_exitseq_type_dbsatexit_PROCEDURE_LINKAGE_TABLE_cols_scoremin_algnmnt_width_GLOBAL_OFFSET_TABLE_strcatload_qij_edatafflushnormalizestrcmpblank_lineZtoPrcntlstrlennew_matrixfind_max_aa_col_finioutput_block_sremove_trailing_whitespaceQij_startinit_reclaim_spaceprint_blockget_tokenload_frequenciesnt_adegenABRT_signal_handlerfgetsErrorLevelReport_get_exit_frame_monitor___Argvmallocaa_atobatof_etext__ctypeatoint_atobErrorBufferSW_matricesstrtokextrpltd_varresize_block_sequencesgetenvread_to_blockZ_cutoffread_sequencefind_max_aa_pssmscreen_out__xargvoutput_sequenceSiteSpecificScoringMatrixTypematrix_comparisonsprintf_DYNAMICfrq_qijrewindstrstrfcloseload_dirinext_clustersequence_comparisonpb_weightscodon2aaaa2codon_lib_version__environ_lockstrcpyfseekload_codonsblock_to_matrixSequenceMatrixScoringMethodnt_arevcompnt_bdegenpre_weighted_conversion_methoddata_readpseudo_diriSIFT_pssmmaincounts_nogapsfopenoutput_blockoriginal_conversion_methodWWW_FLAGread_a_block_fasteroriginal_conversion_method_cleaned_upadd_logsnt_brevcomp__1cG__CrunMdo_exit_code6F_v_output_matrix_stresize_sequenceread_a_sequencefree_sequencesequence_typeread_block_bodyload_stats3__fsr_init_value__xargcfree_blockSearchTypedbg_lvleat_whitespaceRTotaltschul_data_dependent_conversion_methodaa_adegenDBtypestrncatDbInforead_a_matrixaafqfprintfsimilarity_dependent_scaleftellfree_matrixStrandsToSearchblock_comparisonalloctd_algnmnts_endset_defaultsprint_sequencefreerealloc_initntfqnew_block<J4*
<O4<M4
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<O4<M4	<K4cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)ieeefp.h	2.8 99/10/29@(#)unistd.h	1.60	01/07/29 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)unistd.h	1.39	01/07/29 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 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SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 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SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12ld: Software Generation Utilities - Solaris Link Editors: 5.9-1.393.interp.hash.dynsym.dynstr.SUNW_version.rela.data.rela.bss.rela.plt.text.init.fini.rodata.rodata1.got.dynamic.data1.symtab.strtab.stab.index.comment.shstrtab.stab.indexstrLAMA.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  LAMA.cmainfrequency.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  frequency.cconvert.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  convert.cblocks.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  blocks.cerrors.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  errors.cmatrix.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  matrix.cmemory.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  memory.csequences.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  sequences.cstrutil.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  strutil.cgcode.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  gcode.c	P"o||P-B8BBBL(RX^f6
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	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Cblimps-3.9/bin/Sun_sparc/LAMA_search000075500001460000012000002163441054326165300176570ustar00jorjastaff00000400000027ELF44 (44L/usr/lib/ld.so.1 #%&')*+012456789:;=@DEFHJKLNOPSTUVWXYZ[^_`bcefhiklpqtuvx~	

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Search Error

You need to enter a block to search with by writing or pasting a block in the query block window.

%s/%d.LAMA_Qblock_errorsw%s
//
rr
Search Error

There seems to be an error in the format of query block number %d:
Search Error

No blocks were read from the query.

Search Error

Sorry, you can not compare more than %d query blocks in each run.
w%s
//
rr
Search Error

There seems to be an error in the format of target block number %d:
Search Error

No blocks were read from the target data.

Search Error

Sorry, you can not compare more than %d target blocks in each run.
dater/usr/bin/nice -5 %s %s,%s %s 0 %d 0 %f > /dev/null 2>&1
Search Error

An error occured during the search.
Please try your search again at a later time.
If it fails again contact the maintainer of these pages
and describe what caused the problem with an example.

daterrError opening LAMA output file.
%s/htmlize-blimps.pl %s | %s/htmlize-LAMA %s %s - -rError opening pipe


LAMA Search Results

LAMA Search Results (%s)

dater%s %s "/usr/bin/nice -10 %s %s,%s %s 0 %d 0 %f > /dev/null 2>&1"%s %s '(cat %s) | /usr/bin/mailx -s "LAMA Results" -r "blocks@fhcrc.org" %s'%s %s 'rm -f %s/%d.*'LAMA Search Submitted

LAMA Search Submitted

Your search has been submitted.
You will receive the results via email to the address you gave ("%s").
%dC.html%s/%s%s %s %s %sCYRCA results
Content-type: text/html


REQUEST_METHODPOSTThis script should be referenced with a METHOD of POST.
If you don't understand this, see this forms overview.%c
What could have happened is that you just reloaded this page rather than redoing the search.

If you use NETSCAPE it has a tendency to try to reload a page when you go back to it.  This may be why you have this error.
CONTENT_TYPEapplication/x-www-form-urlencodedThis script can only be used to decode form results. 
umask 006Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

00<0H0T0`0l0x00000000000000 0,080D0P0\0h0t0000000000000~

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SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: 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 ***`!*`!*!8*!4*`!*!8*!*`!*!d*!*`!*!d*!T*`!*!d*!*`!*!H*!*`!*!H*!*`!*!8*!*`!*!d*!*`!P*! *!d*`!P*!8*!*`!*!H*!*`!P*!*!P*`!P*!d*!*`!*!8*!\*`!L*!8*!*`!*!8*!P*`!*!*!P*`!*!d*!*`!P*!8*!H*`!*!d*!L*`!*!H*!8*`!8*!8*!P*`!H*!H*!8*`!8*!8*㿠㿠ADDSEQS Version %s
ADDSEQS: Copyright 1999 by the Fred Hutchinson Cancer Research Center
Adds sequences to blocks.
USAGE:  addseqs   
                 = input blocks
		           = fasta format sequences
                      = output file
                = processing option
                   blks = add sequences to blocks & output blocks
                   seqs = add sequences to blocks & output sequences
                   simi = add sequences to blocks & do similarity analysis

Enter name of file containing blocks: r
Cannot open file %s

Enter name of sequence file: r
Cannot open file %s

Enter name of output seqs file: w
Cannot open file %s
seqssimiBLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijrNo blocks found in %s .
FRAGMENT%s already in block
 out of order %d, previous end %d
 pad1=%d bestpos=%d endpos=%d seqlen=%d
 pad2=%d bestpos=%d endpos=%d seqlen=%d
 bad bestpos=%d endpos=%d seqlen=%d
No sequences found in %s .

Query added to %s
%d sequences added
addseqs.data%s %d %d %d %d
%s %s calibrated best score = %5d at %d
(,)Median TP score = %d, TPabove = %d
99.5 TN score = %d
%s; distance from previous block=(%d,%d)Cannot write %s of length %d from %d to %d
>%s %s from %d to %d
%c

WARNING: sequence segments are of different lengths
%s %d : %s %d
Mean dissimilarity distance = %.2f
%s %.0f %.0f %.2f 

|||__|rload_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
%lg%lgUnable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqdefault.qijrBLOCKBLOCKMATRIX; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
A ,
.+-0123456789 ,
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
pb_weights:%d ignored for %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
rdirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 	

 Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 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Error

You need to enter a block by writing or pasting a block in the window.

%s/%d.block_errorsw%s
//
rr
Error

There seems to be an error in the format of block number %d:
Error

No blocks were read.

Error

Sorry, you can not check more than %d blocks each time.
%s %s %f %f %d > %s 2>&1
Program Error

An error occured during the execution.
Please try again at a later time.
If it fails again contact the maintainer of these pages
and describe what caused the problem with an example.

Biassed Blocks Results

Biassed Blocks Results



rError opening program output file.


Content-type: text/html


REQUEST_METHODPOSTThis script should be referenced with a METHOD of POST.
If you don't understand this, see this forms overview.%c
What could have happened is that you just reloaded this page rather than redoing the search.

If you use NETSCAPE it has a tendency to try to reload a page when you go back to it.  This may be why you have this error.
CONTENT_TYPEapplication/x-www-form-urlencodedThis script can only be used to decode form results. 
umask 006Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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 ***`!*`!*!8*!4*`!*!8*!*`!*!d*!*`!*!d*!T*`!*!d*!*`!*!H*!*`!*!H*!*`!*!8*!*`!*!d*!*`!P*! *!d*`!P*!8*!*`!*!H*!*`!P*!*!P*`!P*!d*!*`!*!8*!\*`!L*!8*!*`!*!8*!P*`!*!*!P*`!*!d*!*`!P*!8*!H*`!*!d*!L*`!*!H*!8*`!8*!8*!P*`!H*!H*!8*`!8*!8*㿠㿠BLALIGN Version %s
Copyright 1999-2003 Fred Hutchinson Cancer Research Center
Prints blocks as a multiple alignment.
USAGE:  blalign  [-p|s|f|m|h|q|g] [width]
          p=Posfai style, s=short style, f=fasta style,
          m=MSF style, h=STOCKHOLM style, q=ungapped STOCKHOLM,
          g=giant block
          defaults are short style, width = 66

Enter name of file of blocks: r
Cannot open file %s
>%s %s
ERROR in block %s: %d sequences found but  %d expected
%d sequences are included in %d blocks

posfai_seqs: OUT OF MEMORY .%5d 
%20s %c


short_seqs: OUT OF MEMORY
            %s
%20s %s
, width = %d (%4d) %5d  
            %s
%20s %s

fasta_seqs: OUT OF MEMORY>%s|%d              from %10.10s blocks
%c

msf_seqs: OUT OF MEMORY//
-.%-s/%d
%-28s 
%-28s %c


giant: OUT OF MEMORY
stockholm_seqs: OUT OF MEMORY# STOCKHOLM 1.0
-.
%-28s %c
//
BLOCKBLOCKMATRIX; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
A ,
.+-0123456789 ,
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
pb_weights:%d ignored for %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
rdirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 	

 Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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USAGE: bldist   
    = file of fasta multiple alignments (blocks)
    = substitution matrix
      = output distance matrix
     = output matrix type:
			S=similarity
			D=dissimilarity
			P=dissimilarity in protdist format
			C=correlation

Enter name of file of fasta multiple alignments: rCannot open file %s
WARNING: Sequences appear to be DNA but will be treated as protein
BLIMPS_DIR
Enter name of file containing substitution matrix: rCannot open file %s
%s/docs/%srCannot open file %s
%s/docs/default.iijrCannot open file %s
Using %s

Enter name of output file: wCannot open file %s

Enter type (S=similarity, D=dissimilarity, C=correlation): Writing similarity dissimilarity correlation protdist matrix to %s
WARNING: sequence segments are of different lengths
%s %d : %s %d
Mean dissimilarity distance = %.2f
%d
%s %.0f %.0f %.2f %.5f 

BLOCKBLOCKMATRIX; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
A ,
.+-0123456789 ,
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
pb_weights:%d ignored for %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
rdirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 	

 aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

00<0H0T0`0l0x00000000000000 0,080D0P0\0h0t00000

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 @& &&`&` --- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
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untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

%s   Version %s (%s)  %s%s
%s   Version %s  %s%s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover memory.
Decreasing the NumberToReport from saving all (%d currently) to %d.Ran out of memory (1), fewer scores will be reported.
Decreasing the number of saved nodes in the list.The saved nodes level of the list has been reduced to %d.The list saved nodes cannot be reduced any more.
The saved nodes level of the list has been reduced to %d.
Decreasing the number of saved nodes in the list.The saved nodes level of the list has been reduced to %d.The list saved nodes cannot be reduced any more.
The saved nodes level of the list has been reduced to %d.
Decreasing the NumberToReport from %d to %d.Ran out of memory (2), fewer scores will be reported.
blimps_reclaim_space(): NumInSL(Scores) is greater than NumberToReport.                 NumInSL(Scores) is supposed to be maintained                 less than or equal to the NumberToReport.                 NumberToReport = %d, NumInSL(Scores) = %d.                 Ran out of memory, removing the excess scores                 in the Scores list.
Unknown configuration file key: %s
MA field already used.  Cannot have both the BL and the MAfields.  Ignoring the BL line.
Using the PAttern switch causes the REpeats switch to be ignored.Alignments reported will include repeats.
%d%d%dTRUEYESTY0BL field already used.  Cannot have both the MA and the BLfields.  Ignoring the MA line.
%dTRUEYESTY0%dOld style configuration file.New style does not use the SE field.
MATRIXBLOCKUnknown search type: %s
%dTRUEYESTY0DNAAA.err.errrConfiguration file "%s" not found.  Exiting
Old style configuration file.New style uses the ST field instead of P4.
Old style configuration file.New style uses the RE field instead of P5.
Old style configuration file.New style uses the NU field instead of P9.
No block file (BL) or sequence file (SQ) given, aborting.
No sequence file (SQ) or block file (BL) given, aborting.
Configuration file has SQ, BL, and DB entries.Unable to determine the type of search.Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
Missing either the BL or SQ field, aborting.
Configuration file has SQ and BL entries.Unable to determine the type of search.Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
No sequence files given for the sequence database, aborting.
No DB field given, assuming data is in the SQ field.
No block file given (BL field), aborting.
No block files given for the block database, aborting.
No DB field given, assuming data is in the BL field.
No sequence file given (SQ field), aborting.
Unknown search type given, assuming SQ vs BL search.
read_config_file_end(): SearchType variable corrupted.                        Should never have reached this part of the program.                        Possible memory problems.                        The rest of the run may be invalid.                        Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
rUnknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Assuming there is no title and just sequence.
Unable to read sequence file: %s to determine the type of database
score_and_enter(): Tried to score a sequence that is not an                   amino acid sequence.  Not scoring the                   sequence %s
Invalid matrix-sequence scoring method specified, %d.Setting the method to the default value and using thedefault scoring method.
No pattern for matrix %s, Scoring the entire matrix
%-11.11s %-50.50s      %4d   %4d %2d %6d %s
%-20.20s %-62.62s %4d %2d %5d %6d %s
%-8s vs %-7s   %-20s... & %-20s... %4d %4d %2d %6d %6d %s
%-8s %4u %-45s      %4d   %4d %2d %6d %s
--- score ---
	Score: %d
	Position: %d
	Frame: %d
	Mat Num: %s
	Seq Num: %s
	Mat Desc: %s
	Seq Desc: %s
	Consensus: %s
--- ----- ---
S:% 6d	P:% 6d	F:% 6d
default_scoring_method(): matrix %s has length <= 0default_scoring_method(): Not scoring the sequence.
default_scoring_method(): sequence %s has length (amino acids) <= 0default_scoring_method(): Not scoring the sequence.
enter_score(): Error placing matrix score into list
Unable to recover enough memory to continue.  Aborting.
Histogram:
   %5d - %-5d : %d
   %5d -       : %d

Unable to recover enough memory to continue.  Aborting.
Unable to find pattern for PSSM %s
pat_file != NULLpattern.cUnable to recover enough memory to continue.  Aborting.
NumInSL(residue_list) == 0pattern.c0pattern.cNumInSL(residue_list) == 0pattern.cUnable to recover enough memory to continue.  Aborting.
NumInSL(residue_list) == 0pattern.cUnable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
0pattern.c%d: (null)
%d: ;
(%d, [%s]) Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
p->key != NULLsl.cl00<0H0T0`0l0x00000000000000 0,080D0P0\0h0t0000000000000~0{0x(0u40r@0oL0lX0iK^ǐ
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SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)ieeefp.h	2.8 99/10/29@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)ieeefp.h	2.8 99/10/29@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)assert.h	1.9	92/07/14 SMI@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)assert.h	1.9	92/07/14 SMI@(#)time.h	1.39	99/08/10 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12ld: Software Generation Utilities - Solaris Link Editors: 5.9-1.393.interp.hash.dynsym.dynstr.SUNW_version.rela.data.rela.bss.rela.plt.text.init.fini.rodata.rodata1.got.dynamic.data1.symtab.strtab.stab.index.comment.shstrtab.stab.indexstrblimps.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  blimps.cmainfiles.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  files.cfrequency.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  frequency.cconvert.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  convert.cblocks.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  blocks.cerrors.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  errors.cgcode.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  gcode.cmatrix.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  matrix.cmemory.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  memory.csequences.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  sequences.cstrutil.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  strutil.cversion.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  version.coptions.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  options.cblimps-mem.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all 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 ***`!*`!*!8*!4*`!*!8*!*`!*!d*!*`!*!d*!T*`!*!d*!*`!*!H*!*`!*!H*!*`!*!8*!*`!*!d*!*`!P*! *!d*`!P*!8*!*`!*!H*!*`!P*!*!P*`!P*!d*!*`!*!8*!\*`!L*!8*!*`!*!8*!P*`!*!*!P*`!*!d*!*`!P*!8*!H*`!*!d*!L*`!*!H*!8*`!8*!8*!P*`!H*!H*!8*`!8*!8*㿠㿠
Enter name of blocks database: r
Cannot open file %s
.lsbw
Cannot open file %s
>%s
pros/
%s	BLOCK
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12ld: Software Generation Utilities - Solaris Link Editors: 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 ***`!*`!*!8*!4*`!*!8*!*`!*!d*!*`!*!d*!T*`!*!d*!*`!*!H*!*`!*!H*!*`!*!8*!*`!*!d*!*`!P*! *!d*`!P*!8*!*`!*!H*!*`!P*!*!P*`!P*!d*!*`!*!8*!\*`!L*!8*!*`!*!8*!P*`!*!*!P*`!*!d*!*`!P*!8*!H*`!*!d*!L*`!*!H*!8*`!8*!8*!P*`!H*!H*!8*`!8*!8*㿠㿠BLK2MOT: Copyright 1995 by Fred Hutchinson Cancer Research Center
USAGE:  blk2mot   
         = input file of protein sequences
         = input file of blocks from sequences
         = output file for motomat

Enter name of file containing sequences: r
Cannot open file %s

No sequences found in file %s

Enter name of blocks file: r
Cannot open file %s
BL   
No blocks found in file %s

Enter name of new motomat file: wb
Cannot open file %s
 	
Couldn't allocate Seq[%d]
MOTIFJ=[[,,,]motif=[[,,]gibbsfreq== 	
dups== 	
mots== 	
score== 	
d1== 	
d2== 	
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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lX	S|	$H,3;Q<XYblk2motcrti.scrt1.s__get_exit_frame_monitor_ptr__do_exit_code_ptr__crt_scratchvalues-Xa.cBbss.bssDdata.dataDrodata.rodatablk2mot.c___const_seg_900000204___const_seg_900000402blocks.cBlockBufferBlockBufLength___const_seg_900001101___const_seg_900001201errors.cErrorFilememory.cRecFuncsequences.cread_sequence_header___const_seg_900000502___const_seg_900001102strutil.cgcode.c___const_seg_900000303crtn.s_END__START_strncmpatexitfreestrcatgetblks__ctype_environ_finint_bdegenatoffgetsuntranslate_sequencesequence_typeatoimainwrite_motifsoutput_sequence_DYNAMIC___Argvfree_sequence_lib_versionread_a_block_edatacodon2aa_endset_error_file_nameget_tokengcodes__environ_locksprintfDbInfont_btoaaa_adegeninit_reclaim_spaceread_a_sequenceparse_BLread_a_block_fasterfree_blockfprintfntfq__cg92_usedinit_gcodeprint_sequencesequence_comparison_init__xargc__iobfseektoupperrealloc_get_exit_frame_monitorErrorLevelReportaa2codonresize_block_sequencesgetseqs_exitresize_sequenceseq_type_dbsblank_lineftellread_block_headerstrcmpresize_block_clusters_startstrncatfopen__1cG__CrunMdo_exit_code6F_v_nt_adegen_PROCEDURE_LINKAGE_TABLE_read_sequencecallocstrlenstrstrmallocread_to_blockErrorReportstrncpysscanfaafqaa_atobfcloseErrorBufferread_block_bodyblock_comparisonLenremove_trailing_whitespaceSeqnameeat_whitespaceoutput_block_sprint_blocknt_arevcompnew_block__fsr_init_valuenext_clusteroutput_block_etextrewindSeqfwriteaa_btoastrcpyABRT_signal_handlernt_atobfflush__xargv_GLOBAL_OFFSET_TABLE_strtoknt_brevcomp<M4*
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<O4<M4	<K4cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)ieeefp.h	2.8 99/10/29@(#)unistd.h	1.60	01/07/29 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)unistd.h	1.39	01/07/29 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun 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Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 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 ***`!*`!*!8*!4*`!*!8*!*`!*!d*!*`!*!d*!T*`!*!d*!*`!*!H*!*`!*!H*!*`!*!8*!*`!*!d*!*`!P*! *!d*`!P*!8*!*`!*!H*!*`!P*!*!P*`!P*!d*!*`!*!8*!\*`!L*!8*!*`!*!8*!P*`!*!*!P*`!*!d*!*`!P*!8*!H*`!*!d*!L*`!*!H*!8*`!8*!8*!P*`!H*!H*!8*`!8*!8*㿠㿠BLK2PSSM: Copyright 1996-2003 Fred Hutchinson Cancer Research Center
USAGE:  blk2pssm    []
         = B BLIMPS|M MAST|G Gribskov|P Psi-Blast
         = 3,6,20,21

Enter name of BLOCKS input file: r
Cannot open file %s

Enter name of PSSM output file: w
Cannot open file %s

Enter PSSM format type (B=blimps, M=mast, G=Gribskov, P=Psi-Blast) [B]:  Using type %d
%s Invalid type %d, using type %d
ALPHABET= ARNDCQEGHILKMFPSTWYVBZX
log-odds matrix: alength= 23 w= %d
% 6.3f 
(Peptide) Length: %d
COBBLER Profile for %s %s
Cons      %c
dmin=%f
%c    %6d 
rload_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
%lg%lgUnable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqdefault.qijrBLOCKBLOCKMATRIX; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
A ,
.+-0123456789 ,
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
pb_weights:%d ignored for %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
rdirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 	

 Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)assert.h	1.9	92/07/14 SMI@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)ieeefp.h	2.8 99/10/29@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun 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 ***`!*`!*!8*!4*`!*!8*!*`!*!d*!*`!*!d*!T*`!*!d*!*`!*!H*!*`!*!H*!*`!*!8*!*`!*!d*!*`!P*! *!d*`!P*!8*!*`!*!H*!*`!P*!*!P*`!P*!d*!*`!*!8*!\*`!L*!8*!*`!*!8*!P*`!*!*!P*`!*!d*!*`!P*!8*!H*`!*!d*!L*`!*!H*!8*`!8*!8*!P*`!H*!H*!8*`!8*!8*㿠㿠
Enter name of blocks database: r
Cannot open file %s

Enter name of new slx database: w
Cannot open file %s
%-20s %c
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler 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SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12ld: Software Generation Utilities - Solaris Link Editors: 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BLKPROB Version %s
COPYRIGHT 1992-8 Fred Hutchinson Cancer Research Center
USAGE: blkprob    [-H n -E n -C n -mast|-rank -sum|-gff -stats]
           = number of hits to report, use 0 for default
     = blimps search output file
     = blocks database searched by blimps
OR:    blkprob 
     = name of blimps configuration file
Other options
    -H n            maximum number of hits to report
    -E n            cutoff expected value for anchor blocks
    -C n            min cutoff raw score for anchor blocks
    -mast           order results by MAST-type e-values
    -rank           order results by RANK-statistic e-values
    -sum            output summary only (one line per hit)
    -gff		  Sanger Center's GFF output
    -stats          produces .dat statistics file
    -S filename     header file (default=blkprob.stp)

Enter number of hits to report or blimps configuration file name [%d]: 0r
BLKPROB: Cannot open configuration file %s

Enter name of file containing blocks search results: 
Enter name of blocks database searched: -mast-rank-stats-sum-gff-E-H-C-Sr
BLKPROB: Cannot open file blimps file %s

Query=%s
Size=%ld Amino Acids
Base Pairs
Blocks Searched=%d
Blocks searched is negative, cannot use for statistics.
Alignments Done=%16.0f
Alignments done is negative, cannot use for statistics.
Cutoff combined expected value for hits=%3.0f
Cutoff block expected value for repeats/other=%3.0f

Results: OUT OF MEMORY


hits: OUT OF MEMORY

No hits found

%d possible hits reported
 	
 	
;OUDB//r%sblkprob.stpblkprob.stprblkprob.stpr
===============================================================================
Here are your search results from the BLOCKS searcher.
===============================================================================
%sVersion 3.2.5Version 3.2.4Version 3.2.3Probe Sequence:Probe Sequence:Size:Base Pair: 

Size:Base Pair  

Target:  

Records:  

Alignments:  

AC#r
BLKPROB: Cannot open blocks file %sDatabase=%s
blksort.stnr%sblksort.stnr%d %frepeats.datr%srepeats.datr%s %dblksort.biasr%sblksort.biasr%s %dassemble_hits(): OUT OF MEMORY

assemble_hits(): OUT OF MEMORY

blksort.data==============================================================================
                                                             Combined
Family                                       Strand  Blocks   E-value
                                                           Rank
Family                                       Strand  Blocks   P-value
%-10s %s  % 2d  %2d of %-2d %8.2g
 %8.2g

%d %s %s %d %d %g %g %g %g

==============================================================================
>%s %d/%d blocks Combined E-value=%8.2g: %s
Block    Frame    Location (bp)      Block E-value
 (aa)      Block E-value
%-10s % 1d     %6ld-%-6ld        %8.2g       **biased**

%s	BLOCKS	similarity	%ld	%ld	%8.2g -	%d	+	%d	%s  **biased** (hit) %s	"%d"
Up to %d repeats expected:
%-10s % 1d     %6ld-%-6ld        %8.2g
%s BLOCKS similarity %ld %ld %8.2g - %d + %d %s  **biased** (repeat) %s
Other reported alignments:
%-10s % 1d     %6ld-%-6ld        %8.2g
%s BLOCKS similarity %ld %ld %8.2g - %d + %d %s (other) %s

------------------------------------------------------------------------------

                         |---%5d amino acids---|
%20s %s
%20s  %s
%20s  %s
%20s  %s
          
%s
%s
%s
%s
<->%ld%ld(%d,%d):%d
%s
%s
%s
%s
%d%s

%s
%s
%s
%s

pvalue_rank(): OUT OF MEMORY


closest_seq: Unable to allocate pair structure!
maxscore is too big, increase MAXSCORE from %d
rload_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
%lg%lgUnable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqdefault.qijrBLOCKBLOCKMATRIX; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
A ,
.+-0123456789 ,
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
pb_weights:%d ignored for %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
rdirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 	

 Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

ARNDCQEGHILKMFPSTWYV..* protomat.stprtdefSCORE ,	
 ,	
rtCould not open %s, using default BLOSUM scoring matrix
defHIGH ,	
 ,	

Using scoring matrix from %s
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Using BLOSUM62 scoring matrix.
/

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directory
/\: 	
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<O4<M4<N4	<K4cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)ieeefp.h	2.8 99/10/29@(#)unistd.h	1.60	01/07/29 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)unistd.h	1.39	01/07/29 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)assert.h	1.9	92/07/14 SMI@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)ieeefp.h	2.8 99/10/29@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun 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5.9-1.393.interp.hash.dynsym.dynstr.SUNW_version.rela.data.rela.bss.rela.plt.text.init.fini.rodata.rodata1.got.dynamic.data1.symtab.strtab.stab.index.comment.shstrtab.stab.indexstrblkprob.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  blkprob.cmainfrequency.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  frequency.cconvert.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include 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-xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  memory.csequences.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  sequences.cstrutil.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  strutil.cprotomat.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  protomat.cgcode.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  gcode.c	8	 	 P"ppo$$P-B$$8B$$BB$$L''HRPPX\\^hhfll7{o>>G>>DtA0A02AAQ}TLTL
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BLKSORT Version %s
COPYRIGHT 1992-8 Fred Hutchinson Cancer Research Center
USAGE: blksort    [-stats]
           = number of hits to report, use 0 for default
     = blimps search output file
     = blocks database searched by blimps
    -stats          produces blksort.dat statistics file
OR:    blksort 
     = name of blimps configuration file

Enter number of hits to report or blimps configuration file name [%d]: 0r
BLKSORT: Cannot open configuration file %s

Enter name of file containing blocks search results: 
Enter name of blocks database searched: -stats
Query=%s, 
 Size=%ld Amino AcidsBase Pairs
Blocks Searched=%d

%d possible hits reported
 	
 	
;OUDB//blksort.stpr%sblksort.stpr
===============================================================================
Here are your search results from the BLOCKS searcher.
Please report problems to webmaster@blocks.fhcrc.org, include your query
and this output. To obtain help, send the word HELP on a single line to
blocks@blocks.fhcrc.org
===============================================================================
Copyright (c) 1992-6 by the Fred Hutchinson Cancer Research Center
If you use BLOCKS in your research, please cite:
Steven Henikoff and Jorja G. Henikoff, Protein Family Classification Based
on Searching a Database of Blocks, Genomics 19:97-107 (1994).
===============================================================================
Each numbered result consists of one or more blocks from a PROSITE or PRINTS
group found in the query sequence. One set of the highest-scoring blocks that
are in the correct order and separated by distances comparable to the BLOCKS
database is selected for analysis. If this set includes multiple blocks
the probability that the lower scoring blocks support the highest scoring
block is reported. Maps of the database blocks and query sequence are shown:
  < indicates the sequence has been truncated to fit the page
  : indicates the minimum distance between blocks in the database
  . indicates the maximum distance between blocks in the database
The maps are aligned on the highest scoring block. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database
is shown. Upper case in the query sequence indicates at least one
occurrence of the residue in that column of the block.
===============================================================================
%sr
BLKSORT: Cannot open file blimps file %s
Version 3.2.5Version 3.2.4Version 3.2.3Probe Sequence:Probe Sequence:Size:Base Pair: 

Size:Base Pair  

Target:  

Records:  

AC#r
BLKSORT: Cannot open blocks file %sDatabase=%s
blksort.stnr%sblksort.stnr%d %frepeats.datr%srepeats.datr%s %dblksort.biasr%sblksort.biasr%s %d
OUT OF MEMORY

blksort.datablksort.repa
%d.------------------------------------------------------------------------
Block     Rank Frame Score Strength   Location (bp) Description

Block     Rank Frame Score Strength   Location (aa) Description
%-8s %5d  % 2d   %4d  %4d     %7ld-%7ld %s

AC   AC   
OUT OF MEMORY

; 

	(,)BL   strength==

//()

 

	
OUT OF MEMORY

 (biased)  
%d=%.2fth percentile of anchor block scores for shuffled queries
P<%6.2g for %s
              %sin support of %s
P not calculated for single block %s (biased)%s %s %s 1 %d %d %6.2g %.16f %d %d %d %d %d %ld %.2f

Maximum number of repeats (from Prosite MAX-REPEAT) = %d
OUT OF MEMORY


OUT OF MEMORY


%d non-overlapping repeats in support of %s%s %s %s 2 %d %d %6.2g %.16f

%d non-overlapping repeats in support of %s%s %s %s 2 %d %d %6.2g %.16f

                         |---%5d amino acids---|
%20s %s
%20s  %s
%20s  %s
%20s  %s
        
%s
%s
%s
%s
<->%d%d(%d,%d):%d
%s
%s
%s
%s
%d%s

%s
%s
%s
%s

cluster_seqs: Unable to allocate pair structure!
ARNDCQEGHILKMFPSTWYV..* protomat.stprtdefSCORE ,	
 ,	
rtCould not open %s, using default BLOSUM scoring matrix
defHIGH ,	
 ,	

Using scoring matrix from %s
A ,	
+-0123456789 ,	

Using BLOSUM62 scoring matrix.
/

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directory
/\: 	
FRAGMENTBLOCKLSTPS=PLENGTH= 	

Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.

  
	
FRAGMENTfragmentP
%d. Entry %s found....dna.proCreating %sw+t
Cannot open %s

%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P>%s  

DR   PIR;.

FRAGMENTfragment>%s
ARNDCQEGHILKMFPSTWYVBZXactg

 -| 
	| 
	| 
	_| 
	00<0H0T0`0l0x00000000000000 0,080D0P0\0h0t000000000

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	ARNDCQEGHILKMFPSTWYVX.*GENBANKLOCUSDEFINITIONACCESSIONORIGIN//PIRENTRYTITLESEQUENCE///EMBLIDDEACSQ//UNI>>*VMS>*PROCLASSPCF_ACPCF_DEPCS_ID//
$$0	

x4XW/T]	4GUaXjxuaXju8@	B	J	Oh	aXjugX	i<	"kX	9y	PeO	pfT	y|N\	M	4gt0	xPTxe,	t<e	$L	
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@	.x>/	X>#L	*"	3i	AOVK8	dpkqSx 	dt	gT	XyX	h<	dD	`	Xd	4(#PH	Tu	p0(.[ 	;/P`	!CJ	L
Rp	7![,	i"&0(	qft	m\ 	f8	@B	/T'X	Id	01 	blksortcrti.scrt1.s__get_exit_frame_monitor_ptr__do_exit_code_ptr__crt_scratchvalues-Xa.cBbss.bssDdata.dataDrodata.rodatablksort.c___const_seg_900001501___const_seg_900001601___const_seg_900001702___const_seg_900002101motmisc.c___const_seg_900000102___const_seg_900000202___const_seg_900000301___const_seg_900001201crtn.s_END__START_map_blocksstempcmpstrncpydistanceprev_diststrtokstrcpyinsert_flist__environ_lockQfilenamefprintfbl62_matrixframecmp__xargcfreemallocmincmpread_repeatsNtilesfill_blocksprintfstrcatSeqType_environrewindkr_atoi_exitstrandcmpstrlen_lib_versionopendirDatDirVersionstrspnNRepeatcompute_locextract_seqskr_itoa_DYNAMICfclosefseek__fsr_init_valuedir_unixsplit_namesbl62_highpassstrncmpget_idsBlimpsVerQLenclosest_seqmain___Argvinit_dbs_PROCEDURE_LINKAGE_TABLE_getscore_etextConfig_Flag__cg92_usedStatsTilesftellprint_blurbstrpbrksscanf__1cG__CrunMdo_exit_code6F_v_systempr_num_to_aaadd_queryqsortMaxRepeatstrcspnRepeatscheck_datNBiasread_tilesopen_dbsaachar_to_numbl60_highpassatexitdistance_okaystrcmpfputs_edata_startconsensusmake_flistMaxHitmakedbidnum_to_aacharread_config__ctypefopencheck_entryQueryclose_dbsstrstrNBlocktype_dbs__xargv_GLOBAL_OFFSET_TABLE_strcasecmp_finialign_blocksHomNamehypergeo_initstrnjcmpprint_results_get_exit_frame_monitorbl60_matrixread_biasstrncasecmppr_num_to_aa_spacestempcmp2fgetscheck_repeats_endread_homget_infoatolread_block<M4*<M4cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)types.h	1.75	04/01/06 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)dirent.h	1.31	01/07/29 SMI@(#)dirent.h	1.33	03/09/17 SMI@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12ld: Software Generation Utilities - Solaris Link Editors: 5.9-1.393.interp.hash.dynsym.dynstr.SUNW_version.rela.data.rela.bss.rela.plt.text.init.fini.rodata.rodata1.got.dynamic.data1.symtab.strtab.stab.index.comment.shstrtab.stab.indexstrblksort.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/protomat; /opt/SUNWspro/prod/bin/cc -O -c  blksort.cmainmotmisc.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/protomat; /opt/SUNWspro/prod/bin/cc -O -c  motmisc.c	 "
$
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Unable to create directory %s
Protein files will be placed in current directory
/\: 	
FRAGMENTBLOCKLSTPS=PLENGTH= 	

Cannot determine type of input file
Processing input fiblimps-3.9/bin/Sun_sparc/block_vis000075500001460000012000000510741054326165400175710ustar00jorjastaff00000400000027ELFl4N,4 (449~9~99}::/usr/lib/ld.so.1OL	

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㿠㿠This program takes block map data and generates a graphical map of the
sequences.

Usage: %s [infiles] [options]
Example: %s blocks.mapdata -v2 -o blocks.maps -m80

Arguments to options should be '-o[argument]' or '-o [argument]'.
Use '-' to stand for standard input/output.
Default output is to the screen.

Available options:
 Option          Effect
 -[cfm] number   Use scale mode [constant/full/maximum]
                 Constant: Each character is  amino acids.
                 Full: Each sequence is  characters long.
                 Maximum: The longest sequence in each family is 
                 characters long, the rest are to scale.
                 The default is -c10 (each character is 10 amino acids).
 -h              Get this help screen.
 -i filename     Add an input file(s) (this is not needed if input files
                 are placed before the options). Seperate multiple filenames
                 with spaces.
 -o filename     Set the output filename. The input filename is substituted
                 for '*' within , so '*.vis' is '.vis'.
                 You must use single quotes around  if it contains
                 '*'.
 -v number       Set verbosity level, 0-5. 0 = no messages, 1 = errors only,
                 2 = quiet, 3 = normal (default), 4 = verbose, 5 = debug.
 -a BLxxxxx      Do only a single block family.
Debug messages on.
Output is in bare format.
Warning: unrecognized option '-%c'.
Scale type is %c, scale value is %i.
Input file %i is '%s'.
Output file is '%s'.
Verbosity level is %i.
Warning: option '-%c' not used.
Warning: option '-%c' has an attached argument (ignored).
Warning: option '-%c' has too many arguments (ignored).
Warning: option '-%c' not used.
Reading line: %s
# %s
Reading one family...
End of input file reached.
# %s
End of input file reached.
>#MAP#>>%s %d %d %d %s%s %s %d %d %d %sError: premature end of input file.
%s %d %dError: premature end of input file.
%c %d %dError: premature end of input file.
//Error: bad data read.
%-20s (%4d)  [---- %d aa]
%s: %s
%d distinct blocks in %d sequences
%20s---- %d amino acids

Opening '%s' for read.
rbError: cannot open input file '%s'.
Opening '%s' for write.
wbError: cannot open output file '%s'.
Error: Family '%s' not found in file '%s'
.Error: no usable data in file '%s'.
Processing file '%s'.
Warning: no input files.
:00<0H0T0`0l0x0000000000000/|
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<O4*cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)ieeefp.h	2.8 99/10/29@(#)unistd.h	1.60	01/07/29 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)unistd.h	1.39	01/07/29 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12ld: Software Generation Utilities - Solaris Link Editors: 5.9-1.393.interp.hash.dynsym.dynstr.SUNW_version.rela.data.rela.bss.rela.plt.text.init.fini.rodata.rodata1.got.dynamic.data1.symtab.strtab.stab.index.comment.shstrtab.stab.indexstrblock_vis.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  block_vis.cmain	t\\"#o@@0-Bpp8B||BBLll#R/|/|X//^//f//	o99G99t::2;h;hT};;A=<<L<p, CpG0GL LHM
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DBase                %s
DBase                %s
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OUtput_file          %s
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STrands_to_search    %s
FRequency            %s
GEnetic_code         %s
HIstogram            %s
REpeats_allowed      yes
SV                   yes
NUmber_to_report     0
COnversion_method    3
OP alts: 5.0 %s :alts
chmod -f 660 %sw#!/bin/csh
unalias mv
%s %s >& /dev/null
%s Block Search ResultsBlock Search Results%s/htmlize-blimps.pl %s >& %s
%s -r %s -s "%s" %s < %s
%s %s -mast -E %s %s >& %s
%s/htmlize-blkprob.pl %s >& %s
%s -r %s -s "%s" %s < %s
%s %s >& %s
%s/htmlize-blksort.pl %s >& %s
%s -r %s -s "%s" %s < %s
exit(0)
chmod a+x %s
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REQUEST_METHODPOSTCONTENT_TYPEapplication/x-www-form-urlencodedumask 006You can check this URL within 4 hours for 
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 㿠㿠BLOSUM: (C) Copyright 1992, Fred Hutchinson Cancer Research Center
Enter name of blocks database:
rCannot open %s
Reading %s
Enter minimum block strength [%d]: Enter maximum block strength [%d]: Minimum block strength=%d, Maximum block strength=%d
Enter n for no clustering
   or a number between 0 and 100 for percent identity clustering
   or e for existing (implied) clusters
   or w for existing sequence weights
   or pn for position-based weights, PB weight = 1/n
Enter clustering identity percentage or n/e/w/pn [e]: Existing clustering will be used
No clustering will be used
Sequence weights will be used
Position-based weights will be used with parameter = %.2f
Re-clustering percentage = %d
Enter scale n for 1/n bits [%d]: Scale based on relative entropy
Requested scale = 1/%d bits

%d blocks processed, %ld blocks contributed pairs to matrix
 %f clumps contributed pairs to matrix (%f)
 %ld segments contributed pairs to matrix (%f)
%f total pairs, %f total weight
 %ld total sequences, %ld total columns, %ld total AAs

Frequencies = fij pairs (off-diagonals = 2*fij):
    %1s  
%9.2f %9.2f 
   %1s  
blosum%d.qijblosump%d.qijblosumw.qijblosumn.qijblosume.qijwt
Target Probabilities=qij in %s
#  BLOSUM Clustered Target Frequencies=qij
#  Blocks Database = %s
#  Cluster Percentage: >= %d
#  Position-based Clustering Parameter: <= %.4f
#  Explicit Sequence Weights Used
#  No Sequence Clustering Used
#  Existing Clusters Used
   %1s   
%.4f 
sumqij = %f

Marginal Probabilities by AA = p(i,*):
   %1s  
%.3f 
sumpi=%.3f
AA Frequencies = ai:
%8ld 
AA Probabilities = fi:
   %1s  
%.3f 
sumpi=%.3f

totpairs=%.3f, FTotWeight=%.3f
 totdiag=%.3f, totoffd=%.3f totaas=%ld, TotAas=%ld

Entropy=%.4f bits, expected=%.4f bits
blosum%d.sijblosump%d.sijblosumw.sijblosumn.sijblosume.sijwt
Scoring matrix in bit units=sij in %s
#  BLOSUM Clustered Scoring Matrix in Bit Units=sij
#  Blocks Database = %s
#  Cluster Percentage: >= %d
#  Position-based Clustering Parameter: <= %.4f
#  Explicit Sequence Weights Used
#  No Sequence Clustering Used
#  Existing Clusters Used
#  Entropy = % 8.4f, Expected = % 8.4f
   %1s     B   Z   X

% 8.4f 
blosum%d.iijblosump%d.iijblosumw.iijblosumn.iijblosume.iijwt
Integer scoring matrix in 1/%d bit units in %s
#  BLOSUM Clustered Scoring Matrix in 1/%d Bit Units
#  Blocks Database = %s
#  Cluster Percentage: >= %d
#  Position-based Clustering Parameter: <= %.4f
#  Explicit Sequence Weights Used
#  No Sequence Clustering Used
#  Existing Clusters Used
#  Entropy = % 8.4f, Expected = % 8.4f
 %1s  B   Z   X
%3d 

Maximum=%d, minimum=%d, sum=%d

Positive matrix (+%d):
 %1s  B   Z   X
%3d 
 %1s  B   Z   X

10 times log base 10 matrix:
 %1s  
%3d 
 %1s  
AC   BL   strength==
	
// 
	 
	
cluster_seqs: Unable to allocate pair structure!
ARNDCQEGHILKMFPSTWYV..* protomat.stprtdefSCORE ,	
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/

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Created directory %s

Unable to create directory %s
Protein files will be placed in current directory
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FRAGMENTBLOCKLSTPS=PLENGTH= 	

Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
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<L4*<M4cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)ieeefp.h	2.8 99/10/29acomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)types.h	1.75	04/01/06 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)dirent.h	1.31	01/07/29 SMI@(#)dirent.h	1.33	03/09/17 SMI@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12ld: Software Generation Utilities - Solaris Link Editors: 5.9-1.393.interp.hash.dynsym.dynstr.SUNW_version.rela.data.rela.bss.rela.plt.text.init.fini.rodata.rodata1.got.dynamic.data1.symtab.strtab.stab.index.comment.shstrtab.stab.indexstrblosum.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/protomat; /opt/SUNWspro/prod/bin/cc -O -c  blosum.cmainmotmisc.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/protomat; /opt/SUNWspro/prod/bin/cc -O -c  motmisc.c	4`"
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 %1s  
%3d 
 %1s  
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// 
	 
	
cluster_seqs: Unable to allocate pair structure!
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 ***`!*`!*!8*!4*`!*!8*!*`!*!d*!*`!*!d*!T*`!*!d*!*`!*!H*!*`!*!H*!*`!*!8*!*`!*!d*!*`!P*! *!d*`!P*!8*!*`!*!H*!*`!P*!*!P*`!P*!d*!*`!*!8*!\*`!L*!8*!*`!*!8*!P*`!*!*!P*`!*!d*!*`!P*!8*!H*`!*!d*!L*`!*!H*!8*`!8*!8*!P*`!H*!H*!8*`!8*!8*㿠㿠BLWEIGHT: Copyright 1994-2000 by the Fred Hutchinson Cancer Research Center, 
	Seattle, WA, USA
Add sequence weights to blocks.
USAGE: blweight    
	=input file of blocks to weight
	=output file of weighted blocks
	=P (position-based) | V (Voronoi) | 
		A (Vingron & Argos) | Cn (n percent clumping)
	=M (max=100) | N (sum=#seqs) | # (sum=#)

Enter name of blocks database: r
Cannot open file %s

Enter name of new weighted blocks database: w
Cannot open file %s

Enter weighting scheme (P=position-based, V=Voronoi, 
 A=Vingron & Argos, Cn = n-percent cluster [P]: blweight: Calculating position-based weights
blweight: Calculating Voronoi weights
blweight: Calculating %d percent cluster weights
blweight: Calculating Vingron & Argos weights

Enter scale (M=>max=100, N=>sum=#seq, ###=>sum=###) [M]: blweight: Integer weights, maximum weight = 100
blweight: Decimal weights, sum = number of sequences
blweight: Integer weights, sum = %d
ERROR: Block %s is too wide (%d), truncated to %d
Residue not counted: %d
ERROR: Block %s is too wide (%d), truncated to %d
ERROR: Block %s is too deep (%d), truncated to %d sequences
ERROR: Block %s is too deep (%d), truncated to %d sequences
ERROR: Block %s is too wide (%d), truncated to %d
ERROR: Block %s is too deep (%d), truncated to %d sequences
ERROR: Block %s is too wide (%d), truncated to %d
ERROR: Block %s is too deep (%d), truncated to %d rows
ERROR: Block %s is too wide (%d), truncated to %d
ERROR: Block %s is too deep (%d), truncated to %d rows
ERROR: Block %s is too deep (%d), truncated to %d nseq
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %7.3f
 %3d
//
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

00<0H0T0`0l0x00000000000000 0,080D0P0\0h0t000000000

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SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler 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 ***`!*`!*!8*!4*`!*!8*!*`!*!d*!*`!*!d*!T*`!*!d*!*`!*!H*!*`!*!H*!*`!*!8*!*`!*!d*!*`!P*! *!d*`!P*!8*!*`!*!H*!*`!P*!*!P*`!P*!d*!*`!*!8*!\*`!L*!8*!*`!*!8*!P*`!*!*!P*`!*!d*!*`!P*!8*!H*`!*!d*!L*`!*!H*!8*`!8*!8*!P*`!H*!H*!8*`!8*!8*㿠㿠COBBLER Version %s
COPYRIGHT 1999 Fred Hutchinson Cancer Research Center
Make a consensus sequence and PSSM from a family of blocks
USAGE:  cobbler 

Enter name of configuration file: r
Cannot open file %s
Configuration file errors
>%s %s
BLIMPS_DIR 	
 	
;TYBLr
Cannot open BL file %s
OUw
Cannot open OU file %s
Consensus written to %s
MLw
Cannot open ML file %s
Most like consensus written to %s
LLw
Cannot open LL file %s
Least like consensus written to %s
SQr
Cannot open SQ file %s
DBr
Cannot open DB file %s
FR
Cannot open FR file %s
PCSUr
Cannot open SU file %s
MAr
Cannot open MA file %s
PFPSIPFSBLIQMr
Cannot open QM file %s
TR%s/docs/default.iijr%s/docs/default.amino.frq%s/docs/default.qijr.prfw
Cannot open OU file %s
Profile written to %s
Missing SU input file name
Missing SU input file name
FR and QM required with Type 3
FR and QM required with Type 4
Invalid consensus type: %d
Missing BL input file name
Missing OU output file name
Cannot specify both DB and SQ
FR and QM required with SQ
FR and QM required with MA
DB required with ML
DB required with LL
Type 1: Consensus based on percentage: %d
Type 2: Consensus based on substitution matrix with counts (no pseudo-counts)
Type 3: Consensus based on substitution matrix with counts + pseudo-counts
Type 4: Consensus based on PSSM
Unknown residue: %d
%s %s	is first sequence most like consensus (%d %d)
%s %s	is first sequence least like consensus (%d %d)
%s: %s not found
COBBLER; MATRIX%s %s from %d to %d with embedded PSSMwidth=%d seqs=%d>%s %s from %d to %d with embedded consensus blocks
%c

#COBBLER Profile for %s %s from %d to %d
#
        %c  
%c    %4d 
(Peptide) Length: %d
COBBLER Profile for %s %s from %d to %d
Cons    %c  Gap Len ..
%c    %4d  100 100
*    %4d 
||X

%cx

X

%cx
(,A ,
+-0123456789 ,
Query sequence %s is shorter than minimum path width
WARNING: Aligned blocks overlap!!!  block=%s, pos=%d, last pos = %d
 block=%s, pos=%d
Sequence %s not found
%s %srload_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
%lg%lgUnable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqdefault.qijrBLOCKBLOCKMATRIX; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
A ,
.+-0123456789 ,
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
pb_weights:%d ignored for %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
rdirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 	

 Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

<00<0H0T0`0l0x00000000000000 0,080D0P0\0h0t0000000000000~0{0x(0u40rn

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8	0@!d	;p-x5d@	AX	0@IPag mxh	xK	x(s	X	d44	write_cobblercrti.scrt1.s__get_exit_frame_monitor_ptr__do_exit_code_ptr__crt_scratchvalues-Xa.cBbss.bssDdata.dataDrodata.rodatacobbler.c___const_seg_900000305___const_seg_900000602___const_seg_900000802___const_seg_900001001___const_seg_900001101___const_seg_900001201___const_seg_900001301___const_seg_900001602___const_seg_900001901___const_seg_900002001___const_seg_900002801frequency.c___const_seg_900000106___const_seg_900000301___const_seg_900000403convert.ccompute_BZXpositive_matrixmake_altsbasic_matrix_construction___const_seg_900000501___const_seg_900000803___const_seg_900000901___const_seg_900001004___const_seg_900001202___const_seg_900001401___const_seg_900001501___const_seg_900001601___const_seg_900001701___const_seg_900001801___const_seg_900002004___const_seg_900002201___const_seg_900002401___const_seg_900002701blocks.cBlockBufferBlockBufLengtherrors.cErrorFilematrix.cread_matrix_header___const_seg_900000902memory.cRecFuncsequences.cread_sequence_header___const_seg_900000502___const_seg_900001102strutil.cgcode.c___const_seg_900000303crtn.s_END__START_counts_nogapsseq_type_dbscons_diff_DYNAMICstrcmpstrtokblank_linent_brevcompstrncmpoutput_sequenceprint_consensusuntranslate_sequencelgammastrcatftellErrorBufferaafqinit_reclaim_spaceatexitfree_blockfree_work_pssmntfqfprintfeat_whitespacepercent_consensus_GLOBAL_OFFSET_TABLE_read_cf_lib_versionSeqTypeexpread_to_blockread_a_matrixProfile_environScoresmatrix_comparisonQijcodon2aaaa_btoasequence_comparisonstrstrfgetsresize_block_sequencesShortTrim_start__cg92_usedDbInfoatofsprintfstrncasecmpatoiinit_gcode_etexttolowerfind_max_aa_pssmgetenvread_block_header_exitShortFllfree_sequencePrfOutTypefree_matrixSIFT_pssmread_a_blockfwriteprint_blocksrandommainstrcpyran0load_dirinew_blockprint_matrixmake_randomFml_edata__environ_lockRTotaltschul_data_dependent_conversion_methodnt_adegenlogcallocresize_block_clustersread_sequencesortcmppseudo_diriblock_to_matrixaa_adegensscanfaa2codonread_a_sequenceoutput_blockread_block_bodyload_qijload_sijread_a_block_fasterFblread_seqqsortclosestscore_pseudosnext_clusteroutput_block_smake_consensus__ctypeoutput_matrixmake_blistget_tokenpssm_consensusremove_trailing_whitespacefree_blistoutput_matrix_snew_matrixnt_btoafind_max_aa_coloriginal_conversion_method_cleaned_uprewindFounormalizeFdboutput_matrix_stsequence_type__1cG__CrunMdo_exit_code6F_v_nt_bdegenaa_atobpb_weightsfflushFprfrq_qijblock_comparisonmalloc__xargv_endCPropprint_sequenceinsert_blistgettimeofdaygcodes_get_exit_frame_monitorPrfInTyperesize_sequence_PROCEDURE_LINKAGE_TABLE_order_seqload_frequenciesfreestrncatErrorLevelReportadd_logsscore_consensusfrequencytoupper_initCodon_Usageoriginal_conversion_methodfopenABRT_signal_handlerpre_weighted_conversion_methodquery_consensusrealloc___Argvgribskov_conversion_methodstrspnload_codonsstrncpyFsqSIFT_conversion_methodbest_pos__iobset_error_file_name__xargcErrorReportget_seqfclose__fsr_init_value_finifseekmake_gribsnt_arevcompprocess_familystrlennt_atobVersionembed_consensussimilarity_dependent_scale<M4*
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@ &N` /‚c@O:㿠㿠stdinstdoutdefault.codon.use,@,D,H,h,,,,,,,,,,,,------,-0-4-8-<-@-D-H-L-PBLIMPS_DIRCODEHOP Version %s
COPYRIGHT 1997-2004, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
%s 
 ? help HELP usage USAGE Usage: %s [blocks-input_file_name [output_file_name]]
 [-Ffamily_name]
 [-Ppssm_type]
 [-Ccodon_usage_file]
 [-Ggenetic_code_type]
 [-Dcore_degeneracy_parameter]
 [-Score_strictness_parameter]
 [-Lclamp_strictness_parameter]
 [-Tclamp_temperature]
 [-Nconcentration]
 [-Rose_restrictions]
 [-Most_common_codon]
 [-Verbose]
 [-Output]
 [-Begin]
 [-ApolyX_parameter]

Defaults: in-"%s" out-"%s"
 family-"%s"
 pssm_type-"%d"
 codon_usage-"%s"
 genetic_code_type-"%d"
 core_degeneracy-"%3.1f"
 core_strictness-"%3.1f"
 clamp_strictness-"%3.1f"
 clamp-temperature-"%3.1f"
 concentration-"%3.1f"pM
 Rose-FALSE
 most_common_codon-FALSE
 verbose-FALSE
 begin_oligo-TRUE
 polyX-"%d"

Comments: "-" instead of a input/output file name => stdin/stdout
          The order of the arguments is not important but the
          first name is for the input file and the second for the output.
pssm_type = 2 odds ratios normalized to 100
	3 pseudos, log odds, nats
	5 pseudos, log odds, half bits
	6 pseudos, log odds, third bits
	10 pseudos, odds ratios, nats
	20 just counts+pseudo counts
	30 average score
Genetic code type = 0 Standard
	1 Vertebrate Mitochondrial
	2 Yeast Mitochondrial
	3 Mold Mitochondrial and Mycoplasma
	4 Invertebrate Mitochondrial
	5 Ciliate Nuclear
	6 Echinoderm Mitochondrial
	7 Euplotid Nuclear
	8 Bacterial and Plant Plastid
	9 Alternative Yeast Nuclear
	10 Ascidian Mitochondrial
	11 Flatworm Mitochondrial
	12 Blepharisma Macronuclear
	13 Chlorophycean Mitochondrial
	14 Trematode Mitochondrial
	15 Scenedesmus obliquus mitochondrial
	16 Thraustochytrium mitochondrial
Degeneracy parameters=0.0 all nucleotides that actually appear are counted
	1.0 only nucleotide with highest value counted
	Between 0 and 1 nucleotides with high values counted,
	 if value/highest-value >= degeneracy parameter
Clamp temperature     Target melting temperature for clamp in degC 
Concentration         Probe concentration in nM
Rose restrictions     If set, uses Tim Rose's restrictions on boundaries
                      of core degenerate region.
Most common codons    If set, uses most common codons in clamp.
Begin oligo           If set, oligo must start on a conserved column,
                       otherwise core strictness is applied.
Apoly-x       Maxiumum number of consecutive nucleotides of same type.

 %d  2 3 5 6 10 20 30 Warning: Unspecified pssm type (%d) requested.
Using default pssm type (%d).
"%s help" for help.

Warning: Unspecified gcode type (%d) requested.
Using default gcode type (%d).
"%s help" for help.

Warning: Core strictness parameter requested (%3.2f) is out of range (%3.2f to %3.2f)
Using default value (%3.2f).
Warning: Clamp strictness parameter requested (%3.2f) is out of range (%3.2f to %3.2f)
Using default value (%3.2f).
Warning: Clamp strictness parameter requested (%3.2f) is less than core strictness parameter (%3.2f)
Using default values (%3.2f, %3.2f).
Warning: Clamp temperature requested (%3.2f) is negative
Using default value (%3.2f).
Warning: Concentration requested (%3.2f) is negative
Using default value (%3.2f).
stdinrCannot open input file %s
stdoutwCannot open output file %s
%s/docs/%s%s/docs/%s%s%s%s/docs/default.iijdefault.qijrrCannot open codon usage file %s
%s/docs/%s...trying %s ...
rCannot open codon usage file %s
default.codon.use...trying %s ...
rCannot open codon usage file %s
%s/docs/%s...trying %s ...
rCannot open codon usage file %s
default.codon.use...trying %s ...
rCannot open codon usage file %s

Parameters:
 Amino acids PSSM calculated with %s
 and back-translated with %s genetic code
 and codon usage table "%s"
 Maximum core degeneracy %3.0f    Core strictness %3.2f
 Clamp strictness %3.2f   Target clamp temperature %3.2f C
 DNA Concentration %3.2f nM   Salt Concentration %3.2f mM
 Codon boundary %d   Most common codon %d
 Verbose %d   Output %d
 Begin %d   PolyX %d
Suggested CODEHOPS: The degenerate region (core) is printed in lower case,
the non-degenerate region (clamp) is printed in upper case.

No correctly formatted blocks found to process
%s
Warning: Unrecognized parameter - "%s".
Warning: Unrecognized parameter - "%s".

Processing Block %s

Processing Complement of Block %s
end:   pos=%d, len=%d, core_score=%.1f
oligo start: pos=%d, len=%d, core_score=%.1f,
 last pos=%d, core score=%.2f %s
No suggested primers found.
Block is too narrow
%s Complement

 %c%c %c%c -3'   -5'  Core: degen=%.0f len=%d  Clamp: score=%d, len=%d temp=% .1f *** CLAMP NEEDS EXTENSION

%c  

%s Complement

  |% 4d    
  |% 4d    
  |%4d
--+----
%c |% 4d

%s
  |% 4d    
  |% 4d                    
  |%4d        
--+------------
%c |% 4d        
rload_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
%lg%lgUnable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqdefault.qijrBLOCKBLOCKMATRIX; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
A ,
.+-0123456789 ,
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
pb_weights:%d ignored for %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
rdirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 	

 Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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...........////-ARNDCQEGHILKMFPSTWYVDNEQARNDCQEGHILKMFPSTWYV*ACGTAGCTACGTATCGCGTAGTACTACGACGT-StandardFFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000Vertebrate MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000Yeast MitochondrialFFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000Invertebrate MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000Ciliate NuclearFFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Echinoderm MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000Euplotid NuclearFFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Bacterial and Plant PlastidFFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000Alternative Yeast NuclearFFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000Ascidian MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Flatworm MitochondrialFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Blepharisma MacronuclearFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Chlorophycean MitochondrialFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Trematode MitochondrialFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000Scenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000Thraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000odds ratios normalized to 100pseudos, log odds, natspseudos, log odds, half bitspseudos, log odds, third bitspseudos, odds ratios, natsjust counts+pseudo countsaverage scorefirst_in_inputdefault.amino.frqidentity.frqdefault.amino.frqidentity.frqGenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQ//GCGGCG-GenBankLOCUSDEFINITIONORIGINLOCUSGCG-PIRENTRYTITLESEQUENCEENTRYGCG-EMBLIDDESQIDFasta>>>Universa>>*Flat-file, no title||LXp 	а
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2003/03/12cg: Sun Compiler Common 7.1 2003/03/12ld: Software Generation Utilities - Solaris Link Editors: 5.9-1.393.interp.hash.dynsym.dynstr.SUNW_version.rela.data.rela.bss.rela.plt.text.init.fini.rodata.rodata1.got.dynamic.data1.symtab.strtab.stab.index.comment.shstrtab.stab.indexstrcodehop.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  codehop.cmainfrequency.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  frequency.cconvert.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  convert.cblocks.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  blocks.cerrors.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  errors.cgcode.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  gcode.cmatrix.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  matrix.cmemory.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  memory.csequences.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  sequences.cstrutil.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  strutil.c	||
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Enter name of CUTG spsum file: r
Cannot open file %s
Enter organism name (leave blank for first organism in file): Looking for organism %s in %s
Taking first organism in %s
Enter name of Blimps codon usage output file: w
Cannot open file %s
---------------------------------------------
%s
Codon usage for %s from %s: %.0f codons
 	
 	
%8.6f	-- [%2d] %s
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fastaseqs: Converts a file of sequences to FASTA format
USAGE: fastaseqs  
     = input file of seqences in a common format
    = output file of sequences in FASTA format

Enter name of input sequence file: r
Cannot open file %s

Enter name of output file: w
Cannot open file %s
%d sequences read
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
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 ***`!*`!*!8*!4*`!*!8*!*`!*!d*!*`!*!d*!T*`!*!d*!*`!*!H*!*`!*!H*!*`!*!8*!*`!*!d*!*`!P*! *!d*`!P*!8*!*`!*!H*!*`!P*!*!P*`!P*!d*!*`!*!8*!\*`!L*!8*!*`!*!8*!P*`!*!*!P*`!*!d*!*`!P*!8*!H*`!*!d*!L*`!*!H*!8*`!8*!8*!P*`!H*!H*!8*`!8*!8*㿠㿠
%s blocks_db [column score cutoff [bias fraction cutoff [min biased cols [debug level]]]]
%s.biassed_blocksw
Cannot open output file file "%s"
%%%s.
Normalized Sum-of-Products column score
Column score cutoff %.3f. Bias-fraction cutoff %2d percent (minimum %d columns).
%s
%s
BLIMPS_DIR%s/docs/%sTrying %s...
               Pairs                 Columns         Clumps
Block    Width Total Biassed Percent Biassed Percent Biassed Percent
%-10s (%2d columns)
 %2d %2d  %.3f
 %2d %2d  %.3f
%-10s %2d   %4d  %4d   %3d      %4d   %3d      %4d   %3d%s
%s
%-10s %2d   %4d  %4d   %3d      %4d   %3d      %4d   %3d
%d biassed blocks found in the %d blocks.%d biassed blocks found in the %d blocks from file %s.
%s
%s
Output written in file %s.

Enter name of a file with blocks or block matrices: r
Cannot open file "%s"

Column score cutoff has to be between -1 and 1 !
The value given (%f) is out of range.

Bias fraction cutoff has to be between 0 and 1 !
The value given (%f) is out of range.

BL   
MA   First entry in input file has both block and matrix lines !
First entry in input file has neither block nor matrix lines !
Input file doesn't have any entries !
Error. variable db_type (%c) is of unknown type !
Unable to recover enough memory to continue.  Aborting.
Error ! Problem in format of ProDom entry description -line
%s%s;%s%s%s; ProDom_mulError ! Problem in format of ProDom entry description-line
Error ! Problem in ProDom entry %s
second word in description line doesn't begin with a (
Error ! Problem in ProDom entry %s
second word in description line doesn't end with a )
Error ! Problem in format of ProDom entry %s
A non-digit in the number-of-sequences field "%s"
Error ! Number of sequences in ProDom entry %s (%d) is less than 2
Unable to recover enough memory to continue.  Aborting.
Error ! Problem in format of ProDom entry %s sequence-line %d
Error ! Problem in format of ProDom entry %s sequence-line %d
Error ! Problem in format of ProDom entry %s sequence-line %d
A non-digit in the sequence start position %s
Error ! Problem in format of ProDom entry %s sequence-line %d
Error ! Problem in format of ProDom entry %s sequence-line %d
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Error ! Problem in format of ProDom entry sequence-line %d
Sequence %s has length of %d instead of expected %d
Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
read_a_prodom_entry(): Error reading sequence %s in block %s,Undocumented return value, %d, from read_sequence().
Error ! Not enough sequences (%d) in ProDom entry %s
Error ! Actual number of sequences in ProDom entry %s
different than what the entry reports
 distance from previous block=(%d,%d)adapted from ProDom entry; width=%d; seqs=%d;
  |% 4d    
  |% 4d    
  |%4d
--+----
%c |% 4d
%c |% 4d
rload_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
%lg%lgUnable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqdefault.qijrBLOCKBLOCKMATRIX; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
A ,
.+-0123456789 ,
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
pb_weights:%d ignored for %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
rdirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 	

 Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

00<0H0T0`0l0x00000000000000 0,080D0P0\0h0t00000000000d
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BL	&find_biassed_blockscrti.scrt1.s__get_exit_frame_monitor_ptr__do_exit_code_ptr__crt_scratchvalues-Xa.cBbss.bssDdata.dataDrodata.rodatafind_biassed_blocks.c___const_seg_900000205___const_seg_900000306___const_seg_900000501___const_seg_900000601___const_seg_900000902___const_seg_900001001___const_seg_900001101frequency.c___const_seg_900000106___const_seg_900000301___const_seg_900000403convert.ccompute_BZXpositive_matrixmake_altsbasic_matrix_construction___const_seg_900000803___const_seg_900000901___const_seg_900001004___const_seg_900001202___const_seg_900001301___const_seg_900001401___const_seg_900001501___const_seg_900001601___const_seg_900001701___const_seg_900001801___const_seg_900001901___const_seg_900002004___const_seg_900002201___const_seg_900002401___const_seg_900002701BlockBufferBlockBufLength___const_seg_900001201errors.cErrorFilematrix.cread_matrix_header___const_seg_900000802memory.cRecFuncsequences.cread_sequence_header___const_seg_900000502___const_seg_900001102strutil.cgcode.c___const_seg_900000303crtn.s_END__START_find_max_aa_colload_qijmake_gribscols_scorematrix_comparisongcodes_PROCEDURE_LINKAGE_TABLE_next_clusterresize_block_clustersnt_bdegen__environ_lockinit_reclaim_spaceoutput_sequenceatof_finiatointfqstrtokload_frequencies_environ_initread_block_bodystrcpyresize_block_sequencesstrstrnt_arevcompblock_to_matrixfprint_matrixQijexp__xargcfree_work_pssm_etextBlockToMatrixConversionMethodErrorLevelReportseq_type_dbsload_codonssprintf_startaafqfgetsSequenceMatrixScoringMethod_exitSiteSpecificScoringMatrixTypeftell__filbufnt_brevcompnew_matrixeat_whitespaceget_tokenoriginal_conversion_method_cleaned_upSIFT_conversion_method__1cG__CrunMdo_exit_code6F_v__GLOBAL_OFFSET_TABLE_find_max_aa_pssm__ctypefclosefree_sequencesequence_typeblank_lineCodon_Usageprint_blockgetenvpseudo_diriatexit_DYNAMICread_block_headerstrlenuntranslate_sequenceSearchTypeWWW_FLAG__ioblgammapre_weighted_conversion_methodoutput_matrix_stalloctd_algnmnts_endNumberToReport__cg92_usedgetargscallocload_diridata_read_get_exit_frame_monitororiginal_conversion_methoddbg_lvlfopenfprintfalignments_done__fsr_init_valuefree_matrixABRT_signal_handlerread_a_prodom_entryaa_adegenstrncataa_btoamainfreegribskov_conversion_methodprint_sequencecodon2aant_btoanormalizecols_scoreNPrdfrequencyset_error_file_nameremove_trailing_whitespaceoutput_blockDBtyperewindaltschul_data_dependent_conversion_methodaa2codonlogstrncpyfree_blocktoupperSIFT_pssmfflushread_a_blockRTotpb_weightsDbInforead_a_block_fasterreallocErrorBufferGeneticCodeInitializerstrcatread_sequenceread_a_sequencenew_blockstrspncounts_nogapsread_a_matrix___Argvmallocset_defaultsoutput_block_sstrcmpadd_logsinit_gcodeoutput_matrix_s_lib_versionread_to_blockStrandsToSearchsequence_comparisonblock_comparisonfrq_qijstrncmpaa_atobnt_adegenoutput_matrixErrorReportfseeksimilarity_dependent_scalesscanf__xargvnt_atobresize_sequence_edata4<Y4/*
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<O4<M4	<K4cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)ieeefp.h	2.8 99/10/29@(#)unistd.h	1.60	01/07/29 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)unistd.h	1.39	01/07/29 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)assert.h	1.9	92/07/14 SMI@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)ieeefp.h	2.8 99/10/29@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12ld: Software Generation Utilities - Solaris Link Editors: 5.9-1.393.interp.hash.dynsym.dynstr.SUNW_version.rela.data.rela.bss.rela.plt.text.init.fini.rodata.rodata1.got.dynamic.data1.symtab.strtab.stab.index.comment.shstrtab.stab.indexstrfind_biassed_blocks.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  find_biassed_blocks.cmainfrequency.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  frequency.cconvert.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  convert.cblocks.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  blocks.cerrors.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  errors.cmatrix.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  matrix.cmemory.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  memory.csequences.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  sequences.cstrutil.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  strutil.cgcode.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  gcode.c	lTT
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 ***`!*`!*!8*!4*`!*!8*!*`!*!d*!*`!*!d*!T*`!*!d*!*`!*!H*!*`!*!H*!*`!*!8*!*`!*!d*!*`!P*! *!d*`!P*!8*!*`!*!H*!*`!P*!*!P*`!P*!d*!*`!*!8*!\*`!L*!8*!*`!*!8*!P*`!*!*!P*`!*!d*!*`!P*!8*!H*`!*!d*!L*`!*!H*!8*`!8*!8*!P*`!H*!H*!8*`!8*!8*㿠㿠SCRIPT_NAMEBLOCKS_HOME%sbtest%sblocks%sdate '+%y%m'rdate "+%y%m%d"r%s%s/extblock_stdout%s%s/blweight%s%s/%d.blk.NW.temp%s%s/%d.blkPM%s%s/%s%s%sQUERY_STRINGCONTENT_LENGTHIDACMIN_DISTMAX_DISTDEMA_METHMA_WIDTHMA_SEQSSEQ_NAMESSEQ_POSSEQSrm -f %s%s/%d*tempAllocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.

Error

No sequences specified.

Unable to recover enough memory to continue.  Aborting.

Error

No sequences specified.


Warning

Sequence names box is used and the alignment is in FASTA format.

Sequence names will be taken from the alignment

(first word in the sequence header lines -

'>seq_name 123 aa example protein').


Error

Judging by the first sequence length (%d) the alignment is too long. The maximal length is %d.


Error

Judging by the first sequence length (%d) the alignment is too short. The minimal length is %d.


Warning

The alignment width you gave (%s) is different than the first sequence length (%d).

Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
%s%d
Error

Sequence %d not found.


Error

Sequence %d not found.


Warning

Error reading sequence %d. %d more residues in the sequence than the expected %d.


Error

Sequence (%d) is too short (%d). The minimal length is %d.


Warning

Error reading sequence %d. It is shorter (%d) than the apparent alignment length. Padding the end of the sequence with gaps.


Error

Error reading sequence %d.

%s%d
Error

No name found for sequence %d.


Error


Warning

Number of sequence names (%d) is different than number of sequences (%d).


Error

No start position found for sequence %d.


Error


Warning

Number of sequence start positions (%d) is different than number of sequences (%d).


Warning

The number of sequences you gave (%s) is different from the number found (%d).

None; BLOCK%s; distance from previous block = (%d%s,%d)NoneMethod unspecified%s; width=%d; seqs=%d;w%s %s %s %s %s > /dev/null
Error

An error occured weighting the block.
Please try again at a later time.
If it fails again contact the maintainer of these pages
and describe what caused the problem with an example.

Block Formatter output

Block Formatter output

Sequences weighted by position-based weights Voronoi weights Vingron & Argos weights %% clustering. The weights were scaled to 1-100, 100 having most weight.

[block logo (GIF image)] [block PSSM (what is a PSSM)][block logo (GIF image)] [block PSSM (what is a PSSM)]

r
Content-type: text/html


REQUEST_METHODPOSTThis script should be referenced with a METHOD of POST.
If you don't understand this, see this forms overview.%c
What could have happened is that you just reloaded this page rather than redoing the search.

If you use NETSCAPE it has a tendency to try to reload a page when you go back to it.  This may be why you have this error.
CONTENT_TYPEapplication/x-www-form-urlencodedThis script can only be used to decode form results. 
umask 006Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

p00<0H0T0`0l0x00000000000000 0,080D0P0\0h0t000000000000}W
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Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12ld: Software Generation Utilities - Solaris Link Editors: 5.9-1.393.interp.hash.dynsym.dynstr.SUNW_version.rela.data.rela.bss.rela.plt.text.init.fini.rodata.rodata1.got.dynamic.data1.symtab.strtab.stab.index.comment.shstrtab.stab.indexstrformat_block.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  format_block.cmainblocks.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  blocks.cerrors.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  errors.cmemory.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  memory.csequences.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  sequences.cstrutil.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  strutil.cutil.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  util.cgcode.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  gcode.c	 
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Version %s
USAGE:  getblock AC blocks cobb maps trees proweb blinks blk2pdb cyrca [prosite_dir]
		AC = block accession (eg BL00094 or IPB001525)
		blocks = name of blocks database file
		cobb = name of cobbler database file
		maps = name of map structure database file
		trees = name of tree structure database file
		proweb = name of Proweb database file
		blinks = name of file of links to ProDom
		blk2pdb = name of PDB cross-reference file
		cyrca = name of CYRCA cross-reference file
		prosite_dir = name of directory containing prosite.dat and prosite.doc files

Enter Block accession number: Chrom/howard/btest/bin/blocks.dat
Enter name of Blocks database file [%s]:
r
Cannot open blocks database %s

%d blocks processed
cobbler.prosr
COBBLER sequence:
end cobbler
maps.datrend map
trees.datrend tree
proweb.datrend proweb
blinks.datrend blinks
blk2pdb.datrend pdb
cyrca.datrend cyrca
/prosite.datr
Cannot open prosite.dat file %s
.docr
Cannot open prosite.doc file %s


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Created directory %s

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Protein files will be placed in current directory
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Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
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USAGE: interpro interpro.xml 

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Cannot open file %s

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interpro.motifjw> 	
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%s:   not found
Too many dbxref entries for %s
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%s %d %d %d
 %s %d %d
repeats.datr%s %daInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
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Created directory %s

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LISBLK: (C) Copyright 1995-2000, Fred Hutchinson Cancer Research Center
Enter name of file containing list of sequences: r
Cannot open file %s
Enter name of block file: rA.blkr
Enter name of block file: r
Cannot open file %s

Reading %s.../
  %d sequences in %s
Reading %s... %d sequences from %s
  were found in %s
No block found in %s
.lsbw+t
Cannot open file %s
%s%s%d sequences written to %s

%-12s  PS=%s  LENGTH=%-6d  FRAGMENT  BLOCK  LST
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

ARNDCQEGHILKMFPSTWYV..* protomat.stprtdefSCORE ,	
 ,	
rtCould not open %s, using default BLOSUM scoring matrix
defHIGH ,	
 ,	

Using scoring matrix from %s
A ,	
+-0123456789 ,	

Using BLOSUM62 scoring matrix.
/

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directory
/\: 	
FRAGMENTBLOCKLSTPS=PLENGTH= 	
-| 
	| 
	| 
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x	^k0F	l	V8	k	y(	!#p+2e	Ala	Ilisblkcrti.scrt1.s__get_exit_frame_monitor_ptr__do_exit_code_ptr__crt_scratchvalues-Xa.cBbss.bssDdata.dataDrodata.rodatalisblk.cblocks.cBlockBufferBlockBufLength___const_seg_900001101___const_seg_900001201errors.cErrorFilememory.cRecFuncsequences.cread_sequence_header___const_seg_900000502___const_seg_900001102strutil.cprotomat.c___const_seg_900000102___const_seg_900000202___const_seg_900000301___const_seg_900000401gcode.c___const_seg_900000303crtn.s_END__START__GLOBAL_OFFSET_TABLE_bl62_highpassnew_blockread_sequence_PROCEDURE_LINKAGE_TABLE_strncat_exitTitle_finiErrorBufferuntranslate_sequenceaafq__environ_lockbl62_matrixfreeread_a_blockreallocinit_reclaim_spacecodon2aaoutput_block_s__cg92_usedstrncpyrewind__iobstrcpymainoutput_blockaa2codon_get_exit_frame_monitor__fsr_init_valuesscanf_environnt_btoantfqsplit_namesErrorReport_startgetscoresystemget_tokenread_block_headerfclosecheck_entryinit_gcode_etextstrcspnErrorLevelReportmallocnt_atobsprintfget_idsfree_blockstrcat__xargvprint_blockpr_num_to_aa_spacebl60_highpasskr_atoiseq_type_dbsstrncmpnt_bdegenwrite_lisresize_block_clusters_DYNAMICstrstrftellaachar_to_numpr_num_to_aa_lib_versionflag_idsread_a_sequenceaa_adegenfprintfatof___Argvkr_itoaoutput_sequenceeat_whitespacefgets_end_initblock_comparisonread_a_block_fasternt_adegenstrlendir_unixfflushProsDbInforesize_sequenceread_block_bodyaa_btoaresize_block_sequencesstrtokmakedbid__xargcgcodesstrcmpfopenread_to_blockatexitfseek__1cG__CrunMdo_exit_code6F_v_remove_trailing_whitespacefree_sequence__ctypeaa_atobnt_arevcompABRT_signal_handlersequence_comparisonbl60_matrixnext_cluster_edataset_error_file_namenum_to_aacharsequence_typeblank_linent_brevcomptouppercallocprint_sequenceopendirstrspn
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SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)types.h	1.75	04/01/06 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)dirent.h	1.31	01/07/29 SMI@(#)dirent.h	1.33	03/09/17 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12ld: Software Generation Utilities - Solaris Link Editors: 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SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)dirent.h	1.31	01/07/29 SMI@(#)dirent.h	1.33	03/09/17 SMI@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12ld: Software Generation Utilities - Solaris Link Editors: 5.9-1.393.interp.hash.dynsym.dynstr.SUNW_version.rela.data.rela.bss.rela.plt.text.init.fini.rodata.rodata1.got.dynamic.data1.symtab.strtab.stab.index.stab.comment.shstrtab.stab.indexstr.stabstrlislis.c/d0/local/blimps-3.9/protomat/lislis.cV=10.0;DBG_GEN=4.14.14;cd;backend;Xa;g;R=Sun C 5.5 2003/03/12;G=$XAIRyaMCM00F2VM./d0/local/blimps-3.9/protomat; /opt/SUNWspro/prod/bin/cc -g motmisc.o -c  lislis.c -W0,-xp\$XAIRyaMCM00F2VM.mainmainmake_listcompare_listscompare_namesPros/d0/local/blimps-3.9/protomatlislis.omotmisc.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/protomat; /opt/SUNWspro/prod/bin/cc -O -c  motmisc.clislis.c/d0/local/blimps-3.9/protomat/lislis.cV=10.0;DBG_GEN=4.14.14;cd;backend;Xa;g;R=Sun C 5.5 2003/03/12;G=$XAIRyaMCM00F2VM.lislis.cchar:t(0,1)=bsc1;0;8short:t(0,2)=bs2;0;16int:t(0,3)=bs4;0;32long:t(0,4)=bs4;0;32long long:t(0,5)=bs8;0;64signed char:t(0,6)=bsc1;0;8signed short:t(0,7)=bs2;0;16signed int:t(0,8)=bs4;0;32signed long:t(0,9)=bs4;0;32signed long long:t(0,10)=bs8;0;64unsigned char:t(0,11)=buc1;0;8unsigned short:t(0,12)=bu2;0;16unsigned int:t(0,13)=bu4;0;32unsigned:t(0,14)=bu4;0;32unsigned long:t(0,15)=bu4;0;32unsigned long long:t(0,16)=bu8;0;64_Bool:t(0,17)=bu1;0;8float:t(0,18)=R1;4double:t(0,19)=R2;8long double:t(0,20)=R6;16void:t(0,21)=bs0;0;0float imaginary:t(0,22)=R10;4double imaginary:t(0,23)=R11;8long double imaginary:t(0,24)=R12;16float complex:t(0,25)=R3;8double complex:t(0,26)=R4;16long double complex:t(0,27)=R5;32motifj.h/usr/include/stdlib.h/usr/include/iso/stdlib_iso.h/usr/include/sys/feature_tests.h/usr/include/sys/isa_defs.h:T(3,1)=s8quot:(0,3),0,32;rem:(0,3),32,32;div_t:t(3,2)=(3,1):T(3,3)=s8quot:(0,4),0,32;rem:(0,4),32,32;ldiv_t:t(3,4)=(3,3)size_t:t(3,5)=(0,14)wchar_t:t(3,6)=bsc4;0;32:T(2,1)=s16quot:(0,5),0,64;rem:(0,5),64,64;lldiv_t:t(2,2)=(2,1)uid_t:t(2,3)=(0,4)ssize_t:t(2,4)=(0,3)/usr/include/stdio.h/usr/include/iso/stdio_iso.h/usr/include/sys/va_list.h__va_list:t(8,1)=*(0,21)/usr/include/stdio_tag.h__FILE:t(9,1)=xs__FILE:/usr/include/stdio_impl.h__FILE:T(10,1)=s16_cnt:(2,4),0,32;_ptr:(10,2)=*(0,11),32,32;_base:(10,2),64,32;_flag:(0,11),96,8;_file:(0,11),104,8;__orientation:(0,14),112,2;__ionolock:(0,14),114,1;__seekable:(0,14),115,1;__filler:(0,14),116,4;__longlong_t:t(7,1)=(0,5)FILE:t(7,2)=(10,1)fpos_t:t(7,3)=(0,4)off_t:t(6,1)=(0,4)off64_t:t(6,2)=(0,5)fpos64_t:t(6,3)=(0,5)/usr/include/string.h/usr/include/iso/string_iso.h/usr/include/ctype.h/usr/include/iso/ctype_iso.haa_type:t(1,1)=ar(0,4);0;19;(1,2)=ar(0,4);0;19;(1,3)=ar(0,4);0;23;(10,2)motif_struct:T(1,4)=s8252aa1:(0,11),0,8;aa2:(0,11),8,8;aa3:(0,11),16,8;distance1:(0,11),24,8;distance2:(0,11),32,8;freq:(0,3),64,32;dups:(0,3),96,32;seq_no:(1,5)=ar(0,4);0;999;(0,3),128,32000;pos:(1,6)=ar(0,4);0;999;(0,3),32128,32000;score:(0,3),64128,32;scores:(1,7)=ar(0,4);0;54;(0,3),64160,1760;domain:(0,3),65920,32;mots:(0,3),65952,32;group:(0,1),65984,8;sub_group:(0,1),65992,8;group_struct:T(1,8)=s12group_no:(0,3),0,32;sub_no:(0,3),32,32;position:(0,3),64,32;merged_motif:T(1,9)=s12284dropped:(0,3),0,32;aa:(1,10)=ar(0,4);0;2;(0,1),32,24;nmotif:(0,3),64,32;nident:(0,3),96,32;max_score:(0,3),128,32;domain:(0,3),160,32;distance:(0,3),192,32;dups:(0,3),224,32;loffset:(0,3),256,32;leftpos:(1,11)=ar(0,4);0;999;(0,3),288,32000;cluster:(1,12)=ar(0,4);0;999;(0,3),32288,32000;scores:(1,13)=ar(0,4);0;54;(0,3),64288,1760;t_loffset:(0,3),66048,32;t_domain:(0,3),66080,32;t_score:(0,3),66112,32;position:(1,14)=ar(0,4);0;999;(0,3),66144,32000;maxpos:(0,3),98144,32;minpos:(0,3),98176,32;in_degree:(0,3),98208,32;out_degree:(0,3),98240,32;sequences:T(1,15)=s24num:(0,3),0,32;totlen:(0,3),32,32;len:(1,16)=*(0,3),64,32;offlen:(1,16),96,32;name:(1,17)=*(0,1),128,32;seq:(1,17),160,32;aux_seq:T(1,18)=s200block:(1,19)=ar(0,4);0;49;(0,3),0,1600;temp:T(1,20)=s12value:(0,3),0,32;index:(0,3),32,32;flag:(0,3),64,32;pair:T(1,21)=s8score:(0,3),0,32;cluster:(0,3),32,32;block_list:T(1,22)=s24b:(0,3),0,32;minprev:(0,3),32,32;maxprev:(0,3),64,32;next_block:(1,23)=*(1,22),96,32;next_best:(1,23),128,32;prev_best:(1,23),160,32;path:T(1,24)=s4040nblocks:(0,3),0,32;nbest:(0,3),32,32;naas:(0,3),64,32;totscore:(0,15),96,32;totmotif:(0,3),128,32;totident:(0,3),160,32;nseqs:(0,3),192,32;seqs:(1,25)=ar(0,4);0;999;(0,3),224,32000;first_block:(1,23),32224,32;first_best:(1,23),32256,32;next_path:(1,26)=*(1,24),32288,32;matrix:T(1,27)=s12npos:(0,3),0,32;maxdiff:(0,3),32,32;mark:(0,3),64,32;follow_data:T(1,28)=s10004path:(1,26),0,32;mark:(1,29)=ar(0,4);0;49;(1,30)=ar(0,4);0;49;(0,3),32,80000;score:T(1,31)=s448scores:(1,32)=ar(0,4);0;20;(1,33)=ar(0,4);0;20;(0,1),0,3528;highpass:(0,3),3552,32;db_info:T(1,34)=s32type:(1,17),0,32;start:(1,17),32,32;desc:(1,17),64,32;acc:(1,17),96,32;seq:(1,17),128,32;end:(1,17),160,32;title_offset:(0,3),192,32;seq_offset:(0,3),224,32;split_name:T(1,35)=s12dir_len:(0,3),0,32;file_len:(0,3),32,32;name_len:(0,3),64,32;db_id:T(1,36)=s128entry:(1,37)=ar(0,4);0;20;(0,1),0,168;full_entry:(1,38)=ar(0,4);0;39;(0,1),168,320;pir:(1,39)=ar(0,4);0;12;(0,1),488,104;ps:(1,40)=ar(0,4);0;1;(0,1),592,16;len:(0,3),608,32;frag:(0,3),640,32;lst:(0,3),672,32;found:(0,3),704,32;block:(0,3),736,32;search:(0,3),768,32;rank:(0,3),800,32;score:(0,3),832,32;pvalue:(0,19),896,64;next:(1,41)=*(1,36),960,32;prior:(1,41),992,32;pb_counts:T(1,42)=s176diffaas:(0,19),0,64;naas:(1,43)=ar(0,4);0;20;(0,19),64,1344;/usr/include/sys/types.h/usr/include/sys/machtypes.h_label_t:T(16,1)=s8val:(16,2)=ar(0,4);0;1;(0,4),0,64;label_t:t(16,3)=(16,1)lock_t:t(16,4)=(0,11)/usr/include/sys/int_types.hint8_t:t(17,1)=(0,1)int16_t:t(17,2)=(0,2)int32_t:t(17,3)=(0,3)int64_t:t(17,4)=(0,5)uint8_t:t(17,5)=(0,11)uint16_t:t(17,6)=(0,12)uint32_t:t(17,7)=(0,14)uint64_t:t(17,8)=(0,16)intmax_t:t(17,9)=(0,5)uintmax_t:t(17,10)=(0,16)intptr_t:t(17,11)=(0,3)uintptr_t:t(17,12)=(0,14)int_least8_t:t(17,13)=(0,1)int_least16_t:t(17,14)=(0,2)int_least32_t:t(17,15)=(0,3)int_least64_t:t(17,16)=(0,5)uint_least8_t:t(17,17)=(0,11)uint_least16_t:t(17,18)=(0,12)uint_least32_t:t(17,19)=(0,14)uint_least64_t:t(17,20)=(0,16)longlong_t:t(15,1)=(0,5)u_longlong_t:t(15,2)=(0,16)t_scalar_t:t(15,3)=(0,4)t_uscalar_t:t(15,4)=(0,15)uchar_t:t(15,5)=(0,11)ushort_t:t(15,6)=(0,12)uint_t:t(15,7)=(0,14)ulong_t:t(15,8)=(0,15)caddr_t:t(15,9)=(1,17)daddr_t:t(15,10)=(0,4)cnt_t:t(15,11)=(0,2)ptrdiff_t:t(15,12)=(0,3)pfn_t:t(15,13)=(0,15)pgcnt_t:t(15,14)=(0,15)spgcnt_t:t(15,15)=(0,4)use_t:t(15,16)=(0,11)sysid_t:t(15,17)=(0,2)index_t:t(15,18)=(0,2)timeout_id_t:t(15,19)=*(0,21)bufcall_id_t:t(15,20)=*(0,21)ino_t:t(15,21)=(0,15)blkcnt_t:t(15,22)=(0,4)fsblkcnt_t:t(15,23)=(0,15)fsfilcnt_t:t(15,24)=(0,15)ino64_t:t(15,25)=(0,16)blkcnt64_t:t(15,26)=(0,5)fsblkcnt64_t:t(15,27)=(0,16)fsfilcnt64_t:t(15,28)=(0,16)blksize_t:t(15,29)=(0,4):T(15,30)=eB_FALSE:0,B_TRUE:1,;boolean_t:t(15,31)=(15,30)pad64_t:t(15,32)=(0,5)upad64_t:t(15,33)=(0,16):T(15,34)=u16_q:(0,20),0,128;_l:(15,35)=ar(0,4);0;3;(17,3),0,128;pad128_t:t(15,36)=(15,34):T(15,37)=u16_q:(0,20),0,128;_l:(15,38)=ar(0,4);0;3;(17,7),0,128;upad128_t:t(15,39)=(15,37)offset_t:t(15,40)=(0,5)u_offset_t:t(15,41)=(0,16)len_t:t(15,42)=(0,16)diskaddr_t:t(15,43)=(0,16):T(15,44)=s8_u:(17,3),0,32;_l:(17,3),32,32;:T(15,45)=u8_f:(15,40),0,64;_p:(15,44),0,64;lloff_t:t(15,46)=(15,45):T(15,47)=s8_u:(17,3),0,32;_l:(17,3),32,32;:T(15,48)=u8_f:(15,1),0,64;_p:(15,47),0,64;lldaddr_t:t(15,49)=(15,48)k_fltset_t:t(15,50)=(0,14)id_t:t(15,51)=(0,4)useconds_t:t(15,52)=(0,14)suseconds_t:t(15,53)=(0,4)major_t:t(15,54)=(0,15)minor_t:t(15,55)=(0,15)pri_t:t(15,56)=(0,2)o_mode_t:t(15,57)=(0,12)o_dev_t:t(15,58)=(0,2)o_uid_t:t(15,59)=(0,12)o_gid_t:t(15,60)=(0,12)o_nlink_t:t(15,61)=(0,2)o_pid_t:t(15,62)=(0,2)o_ino_t:t(15,63)=(0,12)key_t:t(15,64)=(0,3)mode_t:t(15,65)=(0,15)gid_t:t(15,66)=(0,4)taskid_t:t(15,67)=(0,4)projid_t:t(15,68)=(0,4)pthread_t:t(15,69)=(0,14)pthread_key_t:t(15,70)=(0,14):T(15,71)=s8__pthread_mutex_flag1:(17,6),0,16;__pthread_mutex_flag2:(17,5),16,8;__pthread_mutex_ceiling:(17,5),24,8;__pthread_mutex_type:(17,6),32,16;__pthread_mutex_magic:(17,6),48,16;:T(15,72)=s8__pthread_mutex_pad:(15,73)=ar(0,4);0;7;(17,5),0,64;:T(15,74)=s8__pthread_ownerpid:(17,7),0,32;__pthread_lockword:(17,7),32,32;:T(15,75)=u8__pthread_mutex_lock64:(15,72),0,64;__pthread_mutex_lock32:(15,74),0,64;__pthread_mutex_owner64:(15,33),0,64;_pthread_mutex:T(15,76)=s24__pthread_mutex_flags:(15,71),0,64;__pthread_mutex_lock:(15,75),64,64;__pthread_mutex_data:(15,33),128,64;pthread_mutex_t:t(15,77)=(15,76):T(15,78)=s8__pthread_cond_flag:(15,79)=ar(0,4);0;3;(17,5),0,32;__pthread_cond_type:(17,6),32,16;__pthread_cond_magic:(17,6),48,16;_pthread_cond:T(15,80)=s16__pthread_cond_flags:(15,78),0,64;__pthread_cond_data:(15,33),64,64;pthread_cond_t:t(15,81)=(15,80)_pthread_rwlock:T(15,82)=s64__pthread_rwlock_readers:(17,3),0,32;__pthread_rwlock_type:(17,6),32,16;__pthread_rwlock_magic:(17,6),48,16;__pthread_rwlock_mutex:(15,77),64,192;__pthread_rwlock_readercv:(15,81),256,128;__pthread_rwlock_writercv:(15,81),384,128;pthread_rwlock_t:t(15,83)=(15,82)_pthread_attr:T(15,84)=s4__pthread_attrp:(15,85)=*(0,21),0,32;pthread_attr_t:t(15,86)=(15,84)_pthread_mutexattr:T(15,87)=s4__pthread_mutexattrp:(15,85),0,32;pthread_mutexattr_t:t(15,88)=(15,87)_pthread_condattr:T(15,89)=s4__pthread_condattrp:(15,85),0,32;pthread_condattr_t:t(15,90)=(15,89)_once:T(15,91)=s32__pthread_once_pad:(15,92)=ar(0,4);0;3;(15,33),0,256;pthread_once_t:t(15,93)=(15,91)_pthread_rwlockattr:T(15,94)=s4__pthread_rwlockattrp:(15,85),0,32;pthread_rwlockattr_t:t(15,95)=(15,94)dev_t:t(15,96)=(0,15)nlink_t:t(15,97)=(0,15)pid_t:t(15,98)=(0,4)time_t:t(15,99)=(0,4)clock_t:t(15,100)=(0,4)clockid_t:t(15,101)=(0,3)timer_t:t(15,102)=(0,3)unchar:t(15,103)=(0,11)ushort:t(15,104)=(0,12)uint:t(15,105)=(0,14)ulong:t(15,106)=(0,15)u_char:t(15,107)=(0,11)u_short:t(15,108)=(0,12)u_int:t(15,109)=(0,14)u_long:t(15,110)=(0,15)_quad:T(15,111)=s8val:(15,112)=ar(0,4);0;1;(0,3),0,64;quad_t:t(15,113)=(15,111)quad:t(15,114)=(15,111)/usr/include/sys/select.h/usr/include/sys/time.htimeval:T(19,1)=s8tv_sec:(15,99),0,32;tv_usec:(15,53),32,32;timezone:T(19,2)=s8tz_minuteswest:(0,3),0,32;tz_dsttime:(0,3),32,32;/usr/include/sys/types.hitimerval:T(19,3)=s16it_interval:(19,1),0,64;it_value:(19,1),64,64;hrtime_t:t(19,4)=(0,5)/usr/include/time.h/usr/include/iso/time_iso.htm:T(22,1)=s36tm_sec:(0,3),0,32;tm_min:(0,3),32,32;tm_hour:(0,3),64,32;tm_mday:(0,3),96,32;tm_mon:(0,3),128,32;tm_year:(0,3),160,32;tm_wday:(0,3),192,32;tm_yday:(0,3),224,32;tm_isdst:(0,3),256,32;/usr/include/sys/time_impl.htimespec:T(23,1)=s8tv_sec:(15,99),0,32;tv_nsec:(0,4),32,32;timespec_t:t(23,2)=(23,1)timestruc_t:t(23,3)=(23,1)itimerspec:T(23,4)=s16it_interval:(23,1),0,64;it_value:(23,1),64,64;itimerspec_t:t(23,5)=(23,4)sigval:T(21,1)=u4sival_int:(0,3),0,32;sival_ptr:(15,85),0,32;sigevent:T(21,2)=s24sigev_notify:(0,3),0,32;sigev_signo:(0,3),32,32;sigev_value:(21,1),64,32;sigev_notify_function:(21,3)=*(21,4)=f(0,21),96,32;sigev_notify_attributes:(21,5)=*(15,86),128,32;__sigev_pad2:(0,3),160,32;/usr/include/sys/select.hfd_mask:t(18,1)=(0,4)fds_mask:t(18,2)=(0,4)fd_set:T(18,3)=s128fds_bits:(18,4)=ar(0,4);0;31;(0,4),0,1024;fd_set:t(18,5)=(18,3)main:F(0,21);(0,3);(0,28)=*(1,17)mainargc:p(0,3)argv:p(0,28)lisfile:(0,29)=ar(0,4);0;79;(0,1)lis2file:(0,30)=ar(0,4);0;79;(0,1)ids:(1,41)ids2:(1,41)flis:(0,31)=*(7,2)flis2:(0,31)$XBIRyaMCM00F2VM.main.__func__:V(0,32)=ar(0,4);0;4;(0,33)=k(0,1)make_list:F(1,41);(0,34)=*(10,1)flis:p(0,31)title:(0,35)=ar(0,4);0;479;(0,1)stemp:(0,36)=ar(0,4);0;479;(0,1)ptr:(1,17)nids:(0,3)ids:(1,41)$XBIRyaMCM00F2VM.make_list.__func__:V(0,37)=ar(0,4);0;9;(0,38)=k(0,1)compare_lists:F(0,21);(1,41);(1,41)ids1:p(1,41)ids2:p(1,41)id1:(1,41)id2:(1,41)tot1:(0,3)tot2:(0,3)n1:(0,3)n2:(0,3)per1:(0,19)per2:(0,19)$XBIRyaMCM00F2VM.compare_lists.__func__:V(0,39)=ar(0,4);0;13;(0,40)=k(0,1)compare_names:F(0,3);(1,17);(1,17)name1:p(1,17)name2:p(1,17)match:(0,3)n2:(0,3)i:(0,3)ptr1:(1,17)ptr2:(1,17)parts:(0,41)=ar(0,4);0;9;(0,42)=ar(0,4);0;11;(0,1)ctemp1:(0,43)=ar(0,4);0;119;(0,1)ctemp2:(0,44)=ar(0,4);0;119;(0,1)$XBIRyaMCM00F2VM.compare_names.__func__:V(0,45)=ar(0,4);0;13;(0,46)=k(0,1)Pros:G(0,47)=ar(0,4);0;79;(0,1)makedbid:P(1,41)get_ids:P(0,3)strtok:P(1,17);(1,17);(0,48)=*(0,49)=k(0,1)strncmp:P(0,3);(0,50)=*(0,51)=k(0,1);(0,52)=*(0,53)=k(0,1);(0,14)strlen:P(3,5);(0,54)=*(0,55)=k(0,1)strcspn:P(3,5);(0,56)=*(0,57)=k(0,1);(0,58)=*(0,59)=k(0,1)strcpy:P(1,17);(1,17);(0,60)=*(0,61)=k(0,1)strcmp:P(0,3);(0,62)=*(0,63)=k(0,1);(0,64)=*(0,65)=k(0,1)gets:P(1,17);(1,17)printf:P(0,3);(0,66)=*(0,67)=k(0,1);0fopen:P(0,31);(0,68)=*(0,69)=k(0,1);(0,70)=*(0,71)=k(0,1)fclose:P(0,3);(0,34)exit:P(0,21);(0,3)	hh"XXro0-B8BBBPL
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h*$R77X77^77;f77[o>@>@G>D>Dt??2@@}D8D8=EXEXdEX05 MHQRgx mnp/1,16),96,32;name:(1,17)=*(0,1),128,32;seq:(1,17),160,32;aux_seq:T(1,18)=s200block:(1,19)=ar(0,4);0;49;(0,3),0,1600;temp:T(1,20)=s12value:(0,3),0,32;index:(0,3),32,32;flag:(0,3),64,32;pair:T(1,21)=s8score:(0,3),0,32;cluster:(0,3),32,32;block_list:T(1,22)=s24b:(0,3),0,32;minprev:(0,3),32,32;maxprev:(0,3),blimps-3.9/bin/Sun_sparc/mablock000075500001460000012000003630041054326156300172240ustar00jorjastaff00000400000027ELF44 (44uuuu*x x /usr/lib/ld.so.1	
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 ***`!*`!*!8*!4*`!*!8*!*`!*!d*!*`!*!d*!T*`!*!d*!*`!*!H*!*`!*!H*!*`!*!8*!*`!*!d*!*`!P*! *!d*`!P*!8*!*`!*!H*!*`!P*!*!P*`!P*!d*!*`!*!8*!\*`!L*!8*!*`!*!8*!P*`!*!*!P*`!*!d*!*`!P*!8*!H*`!*!d*!L*`!*!H*!8*`!8*!8*!P*`!H*!H*!8*`!8*!8*㿠㿠MABLOCK: Copyright 2001 Fred Hutchinson Cancer Research Center
USAGE: mablock     
    = file of fasta or clustal multiple alignments
             Clustal format must have CLUSTAL on first non-blank line
      = output file of blocks
             Puts blocks in out.blks & sequences in out.seqs
      = output type, B=blocks, F=fasta
    = minimum ungapped width to define a block
    = maximum block width

Enter name of blocks database: r
Cannot open file %s
%s; BLOCK
Enter name of output file: .blksw
Cannot open file %s
.seqsw
Cannot open file %s
B
Enter type of output file [B=blocks|F=fasta]: WARNING: Sequences appear to be DNA but will be treated as protein
WARNING: Maximum number of sequences = %d


%d blocks found with minimum width %d and maximum with %d
Output written to %s.blks and %s.seqs
no blocks found with minimum width %d
WARNING: sequence segments are of different lengths
%s %d : %s %d
CLUSTALSTOCKHOLMCLUSTALClustalSTOCKHOLMStockholmTrying CLUSTAL/STOCKHOLM format.
%s.%dw 	 	
>%s
%s
ERROR reading Clustal file
%srWARNING: Sequences appear to be DNA but will be treated as protein
w\rm %sTrying  MSF format.
//mablock.%dw 	
>%s
%s
ERROR reading MSF file
%srWARNING: Sequences appear to be DNA but will be treated as protein
w\rm %sUNKUNK motif; width=%d; seqs=%d;ABCDEFGHIJKLMNOPQRSTUVWXYZ*%s; distance from previous block=(%d,%d)>%20s          from blocks
%5d %c
P1;Non-unique sequence name: %s
%s%dModified name to %s
>%s
%c
BLOCKBLOCKMATRIX; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
A ,
.+-0123456789 ,
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
pb_weights:%d ignored for %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
rdirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 	

 Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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t	wv%|	-5*\	Emablockcrti.scrt1.s__get_exit_frame_monitor_ptr__do_exit_code_ptr__crt_scratchvalues-Xa.cBbss.bssDdata.dataDrodata.rodatamablock.c___const_seg_900000207___const_seg_900000401___const_seg_900000703___const_seg_900001301convert.ccompute_BZXpositive_matrixmake_altsbasic_matrix_construction___const_seg_900000106___const_seg_900000501___const_seg_900000803___const_seg_900000901___const_seg_900001004___const_seg_900001101___const_seg_900001202___const_seg_900001401___const_seg_900001501___const_seg_900001601___const_seg_900001701___const_seg_900001801___const_seg_900001901___const_seg_900002004___const_seg_900002201___const_seg_900002401___const_seg_900002701blocks.cBlockBufferBlockBufLength___const_seg_900001201errors.cErrorFilematrix.cread_matrix_header___const_seg_900000802___const_seg_900000902memory.cRecFuncsequences.cread_sequence_header___const_seg_900000502___const_seg_900001102strutil.cgcode.c___const_seg_900000303crtn.s_END__START_find_max_aa_colload_qij_PROCEDURE_LINKAGE_TABLE_make_gribssystemgcodesmatrix_comparisonresize_block_clustersnt_bdegen__environ_lockfix_namesinit_reclaim_spacenext_clusteroutput_sequencegetpidatof_finiatointfqoutput_fasta_environstrtok_initread_block_bodyfree_blistresize_block_sequencesstrcpyMaxWidthnt_arevcompstrstrblock_to_matrixQijexp_etext__xargcfree_work_pssmtry_msfErrorLevelReportseq_type_dbssprintfaafq_startfgetstry_clustalinsert_blist_exitftellnt_brevcompnew_matrixMinWidtheat_whitespaceget_tokenoriginal_conversion_method_cleaned_upSIFT_conversion_method__1cG__CrunMdo_exit_code6F_v__GLOBAL_OFFSET_TABLE_find_max_aa_pssmfclose__ctypesequence_typefree_sequenceblank_lineprint_blockgetenvpseudo_diriatexit_DYNAMICread_block_headeruntranslate_sequencestrlenBlock_DEBlock_ACmake_blist__ioboutput_matrix_stlgammapre_weighted_conversion_method__cg92_used_endcallocload_dirioriginal_conversion_method_get_exit_frame_monitorfopenfprintf__fsr_init_valuefree_matrixABRT_signal_handlerstrncataa_adegenaa_btoamake_blockmainfreestrrchrgribskov_conversion_methodprint_sequencefind_blockscodon2aant_btoanormalizefrequencyset_error_file_nameremove_trailing_whitespaceoutput_blockaltschul_data_dependent_conversion_methodaa2codonrewindlogstrncpyBlock_IDfree_blockorder_seqSIFT_pssmtoupperRTotread_a_blockfflushpb_weightsDbInfooutput_blocksfasta_seqsread_a_block_fasterreallocErrorBufferstrcatread_sequenceread_a_sequencenew_blockstrspncounts_nogapsread_a_matrix___Argvmallocoutput_block_sstrcmpadd_logsprint_matrixinit_gcodeOutNameoutput_matrix_sread_to_block_lib_versionblock_comparisonsequence_comparisonstrncmpnt_adegenaa_atobErrorReportoutput_matrixfseeksimilarity_dependent_scalesscanflog10__xargvnt_atobresize_sequence_edata<M4*<M4
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<O4<M4	<K4cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)ieeefp.h	2.8 99/10/29@(#)unistd.h	1.60	01/07/29 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)unistd.h	1.39	01/07/29 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)assert.h	1.9	92/07/14 SMI@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)ieeefp.h	2.8 99/10/29@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 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Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler 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 ***`!*`!*!8*!4*`!*!8*!*`!*!d*!*`!*!d*!T*`!*!d*!*`!*!H*!*`!*!H*!*`!*!8*!*`!*!d*!*`!P*! *!d*`!P*!8*!*`!*!H*!*`!P*!*!P*`!P*!d*!*`!*!8*!\*`!L*!8*!*`!*!8*!P*`!*!*!P*`!*!d*!*`!P*!8*!H*`!*!d*!L*`!*!H*!8*`!8*!8*!P*`!H*!H*!8*`!8*!8*㿠㿠stdinstdoutA program to create block map description(s) from block family(ies) data:
%s blocks-input_file_name [output_file_name] [-Fblock_family_name] [-Lsequence_length_file]
Defaults: in-"%s" out-"%s" block_family_name-"%s"

Comments: "-" instead of an input/output file name => stdin/stdout
           The order of the arguments is not important but the
           first name is for the input file and the second for the output.
          block_family_name = "" : all block families in input

((input now expected from screen; CTRL-C to quit))

stdinrCannot open input file %s
rCannot open input file %s
stdoutwCannot open output file %s
Input file "%s" processed by program "%s"
Note: The sequence lengths shown are the 'right-most' sequence positions found in the blocks.
Unable to allocate ids
Error ! Input file %s does not contain any blocks.
Couldn't make a block map for block family %s.
Couldn't make a block map for block family %s.


Couldn't find or process block family %s !

%d block family(ies) processed into maps.
%d block family(ies) could not be processed.
Output in file %s.
Warning ! The name of the first block in family %s
does not end with an "A".
Error ! Block %s is not the block expected to follow (by name)
block %s.
Note - Not all sequences in family %s contain all the blocks.
%sError ! Couldn't find all %d sequences.
Note - Sequence %s in family %s does not contain block %c.
Note, first block (%c %d-%d) in sequence %s of family %s
begins BEFORE the first aa of the sequence !
Error ! Last block (%c, %d-%d) in sequence %s of family %s
is out of bounds.
Note - Block %c PRECEDES block %c in sequence %s of family %s.
Note - Blocks %c (%d-%d) and %c (%d-%d) in sequence %s
of family %s overlap.
>%s %d %d %d %s
%s
%s %d %d
%c %d %d
//
Warning unrecognized parameter - "%s".
Warning unrecognized parameter - "%s".
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

ARNDCQEGHILKMFPSTWYV..* protomat.stprtdefSCORE ,	
 ,	
rtCould not open %s, using default BLOSUM scoring matrix
defHIGH ,	
 ,	

Using scoring matrix from %s
A ,	
+-0123456789 ,	

Using BLOSUM62 scoring matrix.
/

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directory
/\: 	
FRAGMENTBLOCKLSTPS=PLENGTH= 	
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<O4<M4<N4	<K4cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)ieeefp.h	2.8 99/10/29@(#)unistd.h	1.60	01/07/29 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)unistd.h	1.39	01/07/29 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)types.h	1.75	04/01/06 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)dirent.h	1.31	01/07/29 SMI@(#)dirent.h	1.33	03/09/17 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 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Only %d sequence found, need at least 3
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rUnknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Trying with Fasta format.
Sequences appear to be DNA: Block Maker is designed for protein.Unable to read sequence file: %s to determine the type of database
P1;  %s family%s... familyNon-unique sequence name: %s
First 20 characters of sequence name must be unique.
%s%dModified name to %s
get_file_list(): Unknown file group %d.insert_file(): Bad file list, not entering filename "%s"               into a file list
Unable to recover enough memory to continue.  Aborting.
Already have a frequency file: %sThe file %s will be ignored.
Unable to recover enough memory to continue.  Aborting.
get_file(): Bad file list, unable to open a file
rUnable to open block file: %s
Unable to open matrix file: %s
Unable to open database file: %s
Unable to open frequency file: %s
Unable to read sequence file: %s
Unable to read pattern file: %s
get_file(): Unknown file group            Unable to open a file
rUnknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Assuming there is no title and just sequence.
Unable to read sequence file: %s to determine the type of database
Unable to open block file: %s
Unable to open matrix file: %s
Unable to open database file: %s
Unable to open frequency file: %s
Unable to read sequence file: %sUnable to read pattern file: %sget_file(): Unknown file group            Unable to open a file
rewind_file(): Bad file group, unable to rewind file list
get_current_file_name(): Bad file group, unable to return a file name
get_current_file_name(): No files in the file group                         Unable to return a file name
get_file_name(): Bad file group, unable to return a file name
get_file_name(): No files in the file group                 Unable to return a file name
get_file_name(): Requested file out of the range of the files                 in the file group                 Unable to return a file name
number_of_files(): Bad file group, unable to report number of files
close_file() : Bad file group, unable to rewind file list
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
p->key != NULLsl.cscore_and_enter(): Tried to score a sequence that is not an                   amino acid sequence.  Not scoring the                   sequence %s
Invalid matrix-sequence scoring method specified, %d.Setting the method to the default value and using thedefault scoring method.
No pattern for matrix %s, Scoring the entire matrix
%-11.11s %-50.50s      %4d   %4d %2d %6d %s
%-20.20s %-62.62s %4d %2d %5d %6d %s
%-8s vs %-7s   %-20s... & %-20s... %4d %4d %2d %6d %6d %s
%-8s %4u %-45s      %4d   %4d %2d %6d %s
--- score ---
	Score: %d
	Position: %d
	Frame: %d
	Mat Num: %s
	Seq Num: %s
	Mat Desc: %s
	Seq Desc: %s
	Consensus: %s
--- ----- ---
S:% 6d	P:% 6d	F:% 6d
default_scoring_method(): matrix %s has length <= 0default_scoring_method(): Not scoring the sequence.
default_scoring_method(): sequence %s has length (amino acids) <= 0default_scoring_method(): Not scoring the sequence.
enter_score(): Error placing matrix score into list
Unable to recover enough memory to continue.  Aborting.
Histogram:
   %5d - %-5d : %d
   %5d -       : %d

Unable to recover enough memory to continue.  Aborting.
Unable to find pattern for PSSM %s
pat_file != NULLpattern.cUnable to recover enough memory to continue.  Aborting.
NumInSL(residue_list) == 0pattern.c0pattern.cNumInSL(residue_list) == 0pattern.cUnable to recover enough memory to continue.  Aborting.
NumInSL(residue_list) == 0pattern.cUnable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
0pattern.c%d: (null)
%d: ;
(%d, [%s]) Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
\00<0H0T0`0l0x00000000000000 0,080D0P0\0h0t0000000000000~0{	W		1

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SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)assert.h	1.9	92/07/14 SMI@(#)time.h	1.39	99/08/10 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)ieeefp.h	2.8 99/10/29@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)ieeefp.h	2.8 99/10/29@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)assert.h	1.9	92/07/14 SMI@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 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5.9-1.393.interp.hash.dynsym.dynstr.SUNW_version.rela.data.rela.bss.rela.plt.text.init.fini.rodata.rodata1.got.dynamic.data1.symtab.strtab.stab.index.comment.shstrtab.stab.indexstrmakelis.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  makelis.cmainfiles.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  files.cerrors.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  errors.cmemory.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  memory.csequences.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  sequences.cstrutil.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  strutil.csl.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  sl.clists.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  lists.cscores.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  scores.cscoring.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  scoring.cpattern.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  pattern.cblocks.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  blocks.cgcode.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  gcode.cmatrix.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all 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%*[^
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]%lg%*[^
]%lg%*[^
]%lg%*[^
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]%lg%*[^
]truefalse%%
%% logo from %ld to %ld
%%%%EndComments

/cmfactor 72 2.54 div def %% defines points -> cm conversion
/cm {cmfactor mul} bind def %% defines centimeters

%% user defined parameters
/lowest %ld def
/highest %ld def
/bar %ld def
/xcorner %*.*f cm def
/ycorner %*.*f cm def
/rotation %*.*f def %% degrees
/charwidth %*.*f cm def
/barheight %*.*f cm def
/barwidth %*.*f cm def
/barbits %*.*f def %% bits
/Ibeamfraction %*.*f def
/barends  def
/showingbox  def
/outline  def
/caps  def
/stacksperline %ld def
/linesperpage %ld def
/linemove %*.*f def
/numbering  def
/shrinking  def
/shrink %*.*f def
/HalfWhiteIbeam  def

/knirhs 1 shrink sub 2 div def
/charwidth4 charwidth 4 div def
/charwidth2 charwidth 2 div def

%% Since outlining goes around the inner edge of the character
%% make the thickness of the character bigger to compensate.
/setthelinewidth {2 setlinewidth} def
/setthelinewidth {1 setlinewidth} def
setthelinewidth %% set to normal linewidth

%% Set up the font size for the graphics
/fontsize charwidth def

(*[[ This special comment allows deletion of the repeated
%% procedures when several logos are concatenated together
%% See the censor program.

/charparams { %% char charparams => uy ux ly lx
%% takes a single character and returns the coordinates that
%% defines the outer bounds of where the ink goes
  gsave
    newpath
    0 0 moveto
    %% take the character off the stack and use it here:
    true charpath 
    flattenpath 
    pathbbox %% compute bounding box of 1 pt. char => lx ly ux uy
    %% the path is here, but toss it away ...
  grestore
  /uy exch def
  /ux exch def
  /ly exch def
  /lx exch def
} bind def

/dashbox { %% xsize ysize dashbox -
%% draw a dashed box of xsize by ysize (in points)
  /ysize exch def %% the y size of the box
  /xsize exch def %% the x size of the box
  1 setlinewidth
  gsave
    %% Define the width of the dashed lines for boxes:
    newpath
    0 0 moveto
    xsize 0 lineto
    xsize ysize lineto
    0 ysize lineto
    0 0 lineto
    [3] 0 setdash
    stroke
  grestore
  setthelinewidth
} bind def

/boxshow { %% xsize ysize char boxshow
%% show the character with a box around it, sizes in points
gsave
  /tc exch def %% define the character
  /ysize exch def %% the y size of the character
  /xsize exch def %% the x size of the character
  /xmulfactor 1 def /ymulfactor 1 def

  %% if ysize is negative, make everything upside down!
  ysize 0 lt {
    %% put ysize normal in this orientation
    /ysize ysize abs def
    xsize ysize translate
    180 rotate
  } if

  %% Don't show the box if it is a vertical bar, otherwise do.
  showingbox {tc (|) ne {xsize ysize dashbox} if} if

  shrinking {tc (|) ne {
    xsize knirhs mul ysize knirhs mul translate
    shrink shrink scale
  } if} if

  2 {
    gsave
    xmulfactor ymulfactor scale
    tc charparams
    grestore

    ysize %% desired size of character in points
    uy ly sub %% height of character in points
    dup 0.0 ne {
      div %% factor by which to scale up the character
      /ymulfactor exch def
    } %% end if
    {pop pop}
    ifelse

    xsize %% desired size of character in points
    ux lx sub %% width of character in points
    dup 0.0 ne {
      div %% factor by which to scale up the character
      /xmulfactor exch def
    } %% end if
    {pop pop}
    ifelse
  } repeat

  %% Adjust horizontal position if the symbol is an I
  tc (I) eq {charwidth 2 div %% half of requested character width
             ux lx sub 2 div %% half of the actual character
                sub      0 translate} if
  %% Avoid x scaling for I
  tc (I) eq {/xmulfactor 1 def} if

  /xmove xmulfactor lx mul neg def
  /ymove ymulfactor ly mul neg def

  newpath
  xmove ymove moveto
  xmulfactor ymulfactor scale

  %% Outline characters:
  tc true charpath
  gsave 1 setgray fill grestore
  clip stroke

WARNING: Outlined characters will not display at all under NeWS
but will print fine on an Apple LaserWriter IIntx

  tc show
grestore
} def

/numchar{ %% charheight character numchar
%% Make a character of given height in cm,
%% then move vertically by that amount
  gsave
    /char exch def
    /charheight exch cm def
rr%*[^
]%c%lg%lg%lg%*[^
]    char (%c) eq {%ld%*.*f%ld%*.*f%ld%*.*f setrgbcolor} if
    charwidth charheight char boxshow
  grestore
  0 charheight abs translate
  charheight abs 1 gt {0 charheight abs translate} if
} bind def

/Ibar{
%% make a horizontal bar
gsave
  newpath
    charwidth4 neg 0 moveto
    charwidth4 0 lineto
  stroke
grestore
} bind def

/Ibeam{ %% height Ibeam
%% Make an Ibeam of twice the given height, in cm
  /height exch cm def
  /heightDRAW height Ibeamfraction mul def
  1 setlinewidth
     HalfWhiteIbeam outline not and
     {0.75 setgray} %% grey on bottom
     {0 setgray} %% black on bottom
  ifelse
  gsave
    charwidth2 height neg translate
    Ibar
    newpath
      0 0 moveto
      0 heightDRAW rlineto
    stroke
    0 setgray %% black on top
    newpath
      0 height moveto
      0 height rmoveto
      currentpoint translate
    Ibar
    newpath
      0 0 moveto
      0 heightDRAW neg rlineto
      currentpoint translate
    stroke
  grestore
  setthelinewidth
} bind def

/makenumber { %% number makenumber
%% make the number
gsave
  shift %% shift to the other side of the stack
  90 rotate %% rotate so the number fits
  dup stringwidth pop %% find the length of the number
  neg %% prepare for move
  charwidth (0) charparams uy ly sub %% height of numbers
  sub 2 div %%
  moveto %% move back to provide space
  show
grestore
} bind def

/shift{ %% move to the next horizontal position
charwidth 0 translate
} bind def

/makebar { %% make a vertical bar and shift
   barwidth barheight (|) boxshow
   barwidth 0 translate
} def

%% definitions for maketic
/str 10 string def %% string to hold number
%% points of movement between tic marks:
%% (abs protects against barbits being negative)
/ticmovement barheight barbits abs div def

/maketic { %% make tic marks and numbers
gsave
  %% initial increment limit proc for
  0 1 barbits abs cvi
  {/loopnumber exch def

    %% convert the number coming from the loop to a string
    %% and find its width
    loopnumber 10 str cvrs
    /stringnumber exch def %% string representing the number

    stringnumber stringwidth pop
    /numberwidth exch def %% width of number to show

    /halfnumberheight
      stringnumber charparams %% capture sizes
      uy ly sub 2 div
    def

    numberwidth 2 mul %% move back two digits
    neg loopnumber ticmovement mul %% shift on y axis
    halfnumberheight sub %% down half the digit

    moveto %% move back the width of the string

    stringnumber show

    %% now show the tic mark
    0 halfnumberheight rmoveto %% shift up again
    numberwidth 0 rlineto
    stroke
  } for
  grestore
  gsave
    /labelstring (bits) def
    numberwidth neg 2.5 mul
    barheight
    labelstring stringwidth pop
    sub 2 div
    translate
    90 rotate
    0 0 moveto
    labelstring show
  grestore
} def

/degpercycle 360 def
 
/cosine {%%    amplitude  phase  wavelength  base
%%             xmin ymin xmax ymax step dash thickness
%%             cosine -
%% draws a cosine wave with the given parameters:
%% amplitude (points): height of the wave
%% phase (points): starting point of the wave
%% wavelength (points): length from crest to crest
%% base (points): lowest point of the curve
%% xmin ymin xmax ymax (points): region in which to draw
%% step steps for drawing a cosine wave
%% dash if greater than zero, size of dashes of the wave (points)
%% thickness if greater than zero, thickness of wave (points)

  /thickness exch def
  /dash exch def
  /step exch def
  /ymax exch def
  /xmax exch def
  /ymin exch def
  /xmin exch def
  /base exch def
  /wavelength exch def
  /phase exch def
  /amplitude exch def
  %% fun := amplitude*cos( ((-y-phase)/wavelength)*360) + base
  /fun {phase sub wavelength div degpercycle mul cos
           amplitude mul base add} def

  gsave
    /originallinewidth currentlinewidth def
    thickness 0 gt {thickness setlinewidth} if
    /c currentlinewidth def
%%   Make the curve fit into the region specified
    newpath
    xmin ymin c sub moveto
    xmax ymin c sub lineto
    xmax ymax c add lineto
    xmin ymax c add lineto
    closepath
    clip

    newpath
    xmin dup fun moveto
    xmin step xmax { %% loop from xmin by step to xmax
      dup fun lineto } for
    dash 0 gt {[dash cvi] 0 setdash} if %% turn dash on
    stroke

    originallinewidth setlinewidth
  grestore
} bind def

/circle { %% x y radius circle - (path)
newpath 0 360 arc closepath} bind def

%% The following special comment allows deletion of the repeated
%% procedures when several logos are concatenated together
%% See the censor program.
%%]]%%*)

/startpage { %% start a page
  %% set the font used in the title strings
  /Times-Bold findfont fontsize scalefont setfont
  gsave
  erasepage %% REMOVE FOR PACKAGING INTO ANOTHER FIGURE
  xcorner ycorner translate
  rotation rotate
  %% create the user defined strings
  gsave
    %% string number %ld
    %% center the string
    /stringscale %*.*f def
    
    stringwidth pop stringscale mul neg stacksperline

WARNING: if you don't see centered string number %ld:
    ""
it may be off the page because stacksperline is large (%ld) relative to the
FROM-TO range (%ld to %ld) and centering is based on stacks-per-line.  To
solve this, reduce parameter stacksperline to FROM-TO+1 = %ld

    charwidth mul add 2 div
    %*.*f cm moveto
    /stringscale %*.*f def
    %*.*f cm %*.*f cm moveto
    stringscale stringscale scale
     show
    %%
  grestore
  %% now move up to the top of the top line:
  0 linesperpage linemove barheight mul mul translate

  %% set the font used in the logos
  /Helvetica-Bold findfont fontsize scalefont setfont
} def

%%(*[[ This special comment allows deletion of the repeated
%% procedures when several logos are concatenated together
%% See the censor program.

/endpage { %% end a page
  grestore
  showpage %% REMOVE FOR PACKAGING INTO ANOTHER FIGURE
} def

/startline{ %% start a line
%% move down to the bottom of the line:
  0 linemove barheight mul neg translate
  gsave
  maketic
  makebar
} def

/endline{ %% end a line
  grestore
} def

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% End of procedures %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% The following special comment allows deletion of the repeated
%% procedures when several logos are concatenated together
%% See the censor program.
%%]]%%*)

rr%ld%ld%*[^
]missing all parameters
%ld%*[^
]missing bar coordinate parameter
%lg%lg%*[^
]missing corner coordinate parameters
%lg%*[^
]missing rotation parameter

WARNING: rotations that are not multiples of
of 90 degrees are likely to be scaled
incorrectly, due to a PostScript limitation.
See the description of the pathbbox function
in the Red book.

%lg%*[^
]missing charwidth parameter
charwidth parameter must be > 0 cm
%lg%lg%*[^
]missing barheight and barwidth parameters
barheight parameter must be > 0 cm
barwidth parameter must be > 0 cm
%lg%*[^
]missing barbits parameter

WARNING: are you SURE you don't want to show the variation due to a small
number of samples (i.e. the I-beam error bars)?

Reminder: the I-beam error bars show the
variation of the entire stack not just the highest
symbol, even though it may look like that.
barbits parameter must not be zero
%lg%*[^
]%*[^
]barends parameter is missing
%*[^
]showingbox parameter is missing
%*[^
]outline parameter is missing
%*[^
]caps parameter is missing
%ld%*[^
]stacksperline parameter is missing
stacksperline parameter must be positive
%ld%*[^
]linesperpage parameter is missing
linesperpage parameter must be positive
%lg%*[^
]linemove parameter is missing
linemove parameter must be positive
%*[^
]numbering parameters are missing
%lg%*[^
]shrink parameter is missing
Shrink parameter must be less than or equal to 1.
This way, you won't create a misleading logo
which has an apparent height larger than it should.
Shrinking can only be done when showing the dashed box.
This way, you won't create a misleading logo
which has an apparent height smaller than it should.
%ld%*[^
]number of user defined strings must be given
missing a user defined string coordinate
%lg%lg%lg%*[^
]missing a user defined string
rr%*[^
]******************************************************************************
* NOTE: since the data come from the sites program, the error bar is not     *
* printed on the sequence logo.                                              *
******************************************************************************
%*.*f () numchar
%*.*f Ibeam
%c Rs total is %*.*f +/- %*.*f bits bits (sample error not known) in the range from %ld to %ld
(%ld ) makenumber
%% amplitude  phase  wavelength  base:
 %*.*f cm %*.*f cm %*.*f cm %*.*f cm
%% xmin ymin xmax ymax step:
 %*.*f cm %*.*f cm %*.*f cm %*.*f cm %ld
%% dash thickness:
 %*.*f cm %*.*f cm cosine
%c%lg%lg%lg%*[^
]mark symbol in file marks must be one of: "of"
mark scale must be positive
 %*.*f cm %*.*f cm %*.*f cm circle
 fill
 stroke
gsave
 %*.*f cm 0 translate
grestore
makelogo %4.2f
rrrrHalf-White Ibeams are used because the symbols are solid black.
rrww%%!PS-Adobe-
%%%%Title: makelogo %4.2f
%% %ld%*[^
]%ld symbols.
Alphabet Logo
%% Alphabet Logo
startpage startline
makebar
%% find out how high the bar is in centimeters:
/barincm barheight cmfactor div def
makebar
  gsave barincm (%c) numchar grestore shift
makebar
endline endpage
%ld%ld%lg%lg%*[^
]%c%ld%*[^
]This is a Chilogo! - Upside down letterswill be produced

THE SYMVEC FILE IS BAD!
At position %ld the sum of symbols found is %ld
But the noted number is %ld
%%%%Page:? ?

startpage
writing page %ld
startline %% line number %ld
%% before coordinate %ld: make the bar
makebar
%% at coordinate %ld
%% WARNING: negative Rs variation found in symvec,
but the data are not from the sites program
possible program or data error.
gsave
grestore
gsave
grestore
shift
%% bar at end of logo: make the bar before position %ld
makebar
endline
endpage
endline

WARNING: symvec does not contain data for position %ld
It seems that you don't have a zero coordinate.
"... the invention, probably by the Hindus, of the digit zero has been
described as one of the greatest importance in the history of mathematics."
--- Encyclopaedia Britannica (1:1175, 1982)
Please use a zero!
ww
WARNING: Highest position requested was not found in symvec

endline
endpage
logowavemarkscolorsmakelogopsymvec....: Pascal system I/O error %d (illegal I/O request) (bad file name) (file not found) (file not open) (bad input format) (not open for reading) (not open for writing) (not open for direct access) (string subscript out of range) (end-of-file) (file write error)Pascal system error %d (out of memory) (reference to NIL pointer) (integer overflow) (divide by zero) (real math overflow) (value range error) (CASE value range error) (bus error) (stopped by user)%s
L00<0H0T0`0l0x00000000000000 0,080D0P0\0h0t0000


onoot\8	oo<	8D\	

Lt@6DI4Wclw$	`	tP	<	@	 @	$X	*x4	9	A	FP	LX	O`p	b	f`	k(p	clw0!'.8?*`	VOH	mfx	j(	clHwP		dd	0	!
l	xT	(D<	1@	< 	x(	E0	PLY	`<h@	r	w(\	P		y0	8,	x|		dd	8x	8&<	20!9 	E
KS\@]@!bmsl	~x	<"			<	(Tt	l		
@	 \	)$	3 	$: X@^l8	x4	0	P	X\	|P|	p	t	 	d,		4	\	$p,l	7HD	R
YL`g	oyH	t	l	makelogobcrti.scrt1.s__get_exit_frame_monitor_ptr__do_exit_code_ptr__crt_scratchvalues-Xa.cBbss.bssDdata.dataDrodata.rodatamakelogob.chaltlessthanswap_quicksortcopyalinereadwaveparametersp1p2p3p4p5p6readparameterswarnifsitesuseddocosinewavethemain_JL1maplogomarkscolorsmakelogopsymvec___const_seg_900000801___const_seg_900001322___const_seg_900001601___const_seg_900001702p2clib.c___const_seg_900005001crtn.s_END__START_strncmpP_readlnpaocP_maxposatexitstrcat_environ__ctypeTimeStamp_finiP_setunionstrltrimP_sun_argvP_expset_CaseCheck_DYNAMICstrpad___Argv_NilCheckipow_lib_versionstrrptmemavailfscanfP_setdiff_edata_endmy_memcpy__environ_locksprintfmy_toupperP_setcpystrrtrimlongjmpfprintfP_setxorP_remset__flsbuf__cg92_used_ShowEscapeP_argcPASCAL_MAIN_init__xargc__top_jb__iobP_ioresultfseekP_readpaocungetcP_trimname_get_exit_frame_monitorP_escapecodeP_setint_EscIOmy_labsP_addsetctime__filbufstrdeletemaxavailP_argvstrpos2_exitftellP_getcmdlineP_subsetP_packset_start__1cG__CrunMdo_exit_code6F_v_fopen_PROCEDURE_LINKAGE_TABLE_freopenEXCP_LINEstrlenstrinsertmy_memsetsetjmpstrsubmallocP_setequalfputcVAXdateP_peekVAXtime_OutMemmy_tolowerfclosestrcicmpP_addsetr__MallocTemp__P_eoftmpfilemy_memmove__fsr_init_valuemy_memcmp_etextrewindstrcpy_EscapelocaltimeP_insetP_eoln__xargv_GLOBAL_OFFSET_TABLE_strmove 
<O4*
<L4cg: Sun Compiler Common 7.1 2003/03/12@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)ieeefp.h	2.8 99/10/29@(#)setjmp.h	1.36	99/08/10 SMI@(#)setjmp_iso.h	1.1	99/08/09 SMI@(#)assert.h	1.9	92/07/14 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)math.h	2.11	00/09/07 SMI@(#)math_iso.h	1.3	03/04/08 SMI@(#)floatingpoint.h	2.5	99/06/22 SMI@(#)ieeefp.h	2.8 99/10/29@(#)setjmp.h	1.36	99/08/10 SMI@(#)setjmp_iso.h	1.1	99/08/09 SMI@(#)assert.h	1.9	92/07/14 SMI@(#)time.h	1.39	99/08/10 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12ld: Software Generation Utilities - Solaris Link Editors: 5.9-1.393.interp.hash.dynsym.dynstr.SUNW_version.rela.data.rela.bss.rela.plt.text.init.fini.rodata.rodata1.got.dynamic.data1.symtab.strtab.stab.index.comment.shstrtab.stab.indexstrmakelogob.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  makelogob.cmainp2clib.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  p2clib.c	0"o0-B888BDDBB\\tLRX^fAoGtLL2\}tt=|L \T` W5bar before position %ld
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WARNING: symvec does not contain data for position %ld
It seems that you don't have a zero coordinate.
"... the invention, probably by the Hindus, of the digit zero has been
described as one of the greatest importance in the history of mathematics."
--- Encyclopaedia Britannica (1:1175, 1982)
Please use a zero!
wwblimps-3.9/bin/Sun_sparc/matrix_logob000075500001460000012000003666141054326164200203120ustar00jorjastaff00000400000027ELF4|4 (44wFwFwHwH+xyTyT/usr/lib/ld.so.1
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makelogop.w
Cannot open file %s
PSSM of %s (%s) %d sequences.
%s/makelogob '%s' > /dev/nulllogo.%sNo block with name %s found in file %s !
MATRIX_LOGOB: Copyright 1995-8 Fred Hutchinson Cancer Research Center
USAGE: matrix_logob blocks|pssms AC|- suffix
   pssms must be in blimps format and consist of values betwen 0 and 100
    which sum to 100 in each column.
These files must be in the current directory:
   makelogob, colors, default.amino.frq

Enter name of BLOCK or MATRIX file: r
Cannot open file "%s"

Enter AC in %s or - to make logos for all: 
Enter file name suffix: Logos will be written to logo.%s
* position, samples, information, variance
%d number of symbols
col   %c   info.  sum     residues   #_of_specified_residues/#_of_seqs   e   var
%*ld %*.0lf %*.*f % .1E
%c %4d
%2d| %3d  %6.3f  %3.0f     %c  %2d/%d %6.3f %6.3f

small sample correction (e) : %6.3f, variance (avarhnb) : %6.3f
(these are are actually the values for the last column and will be different for the other columns if they contain a different number of unspecified residues - gaps, Xs, etc.)
1 %d
1
1 20
0
0.365
5.48 0.1
-4
1
bars on
-
no outline
capitals
55
1
1.5
numbers
1.0
1
0.0 -1.5 %.2f
pageview-leftlpr
The created sequence-logo file (%s) is a PostScript file.
  (V to view logo with program %s (%s %s %s))
     after viewing you can also choose to print,
   P to print logo (%s %s).)
%s %s %s%s %s
File %s sent to printer.
rload_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
%lg%lgUnable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqdefault.qijrBLOCKBLOCKMATRIX; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
A ,
.+-0123456789 ,
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
pb_weights:%d ignored for %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
rdirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 	

 Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 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MOTIFJ Version %s
Please cite Hamilton O. Smith, et al, PNAS 87 (1990), pp. 826-830.

CANNOT ALLOCATE SMatrix

Using RunType=%d

Enter input file name: rCannot open file %s not found

Reading batch file %s
Reading sequence file %s
%spros/.lst
filepath=%s
r.lisr
filepath=%s

NumSeqs=%d batch=%d Title=%s

Too few sequences to process(need at least 2).

Sequence #%d:	%s		Length of sequence #%d =  %d

MOTIFJ=[[,,,]
Enter significance level [2-%d; %d]: Enter number of allowable internal duplicates [0-%d; 0]: Enter search width [1-24; 17]: Enter drop score [0-18540; %d]: Allocating and initializing arrays...
Couldn't allocate AA3_OBS pointer.
Couldn't allocate AA3_OBS array.
Couldn't allocate MOTIF.

RunType = %d, Normalized drop score = %d
Motif parameters = [%d, %d, %d] with shuffled sequences.

.,


CPU time to find and sort motifs: %ld seconds.
Found %d motifs. Enter number to save or -1 to redo [1-%d; %d]: 
Previous significance level was %d. Enter new level [2-%d; %d]: Previous number of internal duplications was %d. Enter new number [0-;%d]:  Using previous distance  %d
Enter 'g' to print first motif in each group: Enter 'l' for long form:  
_________________________________Group #%d_________________________________



___________________________________________________________________________

Printed %d motifs out of %d total.
Mean score: %ld 
Enter number of motif groups to map (maximum %d) or 0 to assemble blocks: 
Starting motifj...
-
Starting motomat...
motomatmotomat

Motif:  in %d proteins (%d duplicates), Merged %d, Score %d

  + *   Score (Position) for best two fits.
--
.   %3ld (%3d)  %3ld (%3d)  %s (Motif at %d)

  Most common amino acids

:
cutting %d %d %d %d: last score = %d, groups = %d
Couldn't allocate GROUPS.
                    Protein %s:
.%d.%c. %d

/: 
	
 
	
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Couldn't allocate Seq[%d]
ERROR reading %s, sequence longer than %d, truncated

Use shuffled sequences [y/n; n]? yn     
%5d 
%5.3f 
Total amino acids in %d proteins: %d

.motmotifj.motw+b
Unable to open file %s.motifj.prosmotifj.prosw+b
Unable to open file %s>%s %d MINIMUM
 MAXIMUM

%1s

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/

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Created directory %s

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/\: 	
FRAGMENTBLOCKLSTPS=PLENGTH= 	

Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
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MOTOMAT %s: (C) Copyright 1991 by Fred Hutchinson Cancer Research Center
Please cite: S.Henikoff & J.Henikoff, NAR 19:6565-6572 (1991).
CANNOT ALLOCATE SMatrix

ls -al *.mot
Enter name of file containing motifs: .motrb
Cannot open file %s


Input file was created using wrong motifj version!

Assuming input from Gibbs

%s

%d blocks read using parameters [%d, %d, %d]. %d sequences.nonenone;;;asis
Processing blocks in %s using a cut-off score of %d 
   and a clustering threshold of %d percent.
Quitting becasuse no motifs to work on.
motomat.erra

Merging raw blocks...
Recalculating block column scores.
Extending blocks...%s.blksw+t
Cannot open %s
Saving blocks to %s

Block %d: %.1s%.1s%.1s has been merged.
Enter minimum block extension column score or 1 for best block [100-2500 or 1; %d]: Enter clustering identity threshold [1-100; %d]: 
Processing block %d in %s using a cut-off score of %d 
   and a clustering threshold of %d percent.
Extended width was %d, re-extending with cutoff score of %d.
Block %d has been dropped for low width:

Type S[ENTER] to save this block, or N[ENTER] to skip to next block,
or anything else[ENTER] to re-extend this block...

Merging extended blocks....

Removing duplicate blocks....
Enter drop standard deviations [-30 to 30; %d]: 
Using a drop score of %d standard deviations or %d.
Mean score=%.2f, standard deviation=%.2f
Dropping blocks with score below %ld...
 unless they have more than one merged motif
Block %d has been dropped for low score:
Block %d:
Surviving blocks=%d, max dups=%d
Reducing block overlaps ...
, reduced significance=%d

Looking for best path..., npath=%d, nseqs=%d

No surviving blocks
%s %d %d %d %d %d %d %d %d %d %d %d %d %ld %d %d %d

NumSeqs=%d, Total_Motifs=%d
Sequence #%d: %20s %d %.5s

MOTIF %d: %d(%d)%d(%d)%d  domain=%d, score=%d, freq=%d, dups=%d, mots=%d
%20s (% 5d) %.1s.
                   [|]_
merged_motif: Unable to allocate merged_motif structure!

Merging motif %d into motif %d
Blocks %d and %d have been dividedBlock %d has been trimmed by %d to eliminate overlap with Block %d.

Score              *%1s
 %.1s%.1s%.1s (extended width=%d, score=%d  motifs=%d, motif width=%d, conserved=%d)
Saving block %.1s%.1s%.1sID   %s; BLOCK
AC   %s; distance from previous block=(%d,%d)
DE   %s
BL   %.1s%.1s%.1s gibbs=[%d,%d,%d] motomat=[%d,%d,%d]BL   %.1s%.1s%.1s motif=[%d,%d,%d] motomat=[%d,%d,%d] width=%d seqs=%d




//

cluster_seqs: Unable to allocate pair structure!

%20s (% 5d) %.1s. % 3d%20s (% 5d) %.1sX
>>>MOTOMAT out of memory!  Restarting with DropScore = %d
%s
 prune_blocks: Unable to allocate temp structure!

Revised TopScore=%ld%s
 order_blocks: Unable to allocate temp structure!

seq=%d: %d,%d 
row %.3d:  %.3d   x%s
 makematrix: Unable to allocate matrix structure!
%s
 makepath: Unable to allocate path structure!
%s
 ***MOTOMAT STOPPING BECAUSE >1500 PATHS***
find_paths: single %d%s
 find_paths: Unable to allocate temp structure!


find_paths: more-----------%s
 follow_arcs: Unable to allocate temp structure!


follow:  row=%d, ntemp=%d
 curpath blocks=%d 
 curpath_seqs:%d=%d 
 row=%d temp[i].index=%d nseq=%d
End of follow_arcs for %d%s
 makebllist: Unable to allocate block_list structure!

best_path: paths->nblocks=%d
 New path: nblocks=%d, tots=%d B%d %.1s%.1s%.1s
 (%d, %d) B%d %.1s%.1s%.1s
   thisb: %d=%d 
    allb: %d=%d 
   saveb, allb: %d=%d,%d 
 Best sub-path:%d blocks, %d AAs, total score=%ld,
 total motifs=%d, total idents=%d, total sequences=%d, prop=%d
 >>>NEW BESTPATH%s
 check_seqs: Unable to allocate temp structure!

Best path has %d sequences out of %d:
 (%d, %d) B%d %.1s%.1s%.1s
%d blocks, %d AAs, total score=%ld, total motifs=%d, total conserved=%d
 total sequences=%d out of %d
Sequences in the best path:
%.3d:%20s 
Sequences not in the best path:
%.3d:%20s 
Path: %d%d  %d
%d  %d
ARNDCQEGHILKMFPSTWYV..* protomat.stprtdefSCORE ,	
 ,	
rtCould not open %s, using default BLOSUM scoring matrix
defHIGH ,	
 ,	

Using scoring matrix from %s
A ,	
+-0123456789 ,	

Using BLOSUM62 scoring matrix.
/

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directory
/\: 	
FRAGMENTBLOCKLSTPS=PLENGTH= 	

Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.

  
	
FRAGMENTfragmentP
%d. Entry %s found....dna.proCreating %sw+t
Cannot open %s

%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P>%s  

DR   PIR;.

FRAGMENTfragment>%s
ARNDCQEGHILKMFPSTWYVBZXactg

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 㿠㿠MULTIMAT: (C) Copyright 1991 by Fred Hutchinson Cancer Research Center
Version %s
USAGE:   multimat    
              = Maximum # of hits to report
             = File containing blocks for comparison
               = File containing list of TP sequences
             = Blimps search result files,  blocks vs sequence db
multimat.data
Enter maximum number of hits to report [%d]: 
Enter name of blocks database:
r
Cannot open file %s;
search results will not be compared with blocks database.
Search results will be compared with %s
Enter name of file containing list of true positives:
r
Cannot open file %s;
search results will not be compared with true positive list.

Search results will be compared with %s;
only hits not in this list will be reported
%d IDs in %s
multimat.miswmultimat.fndw
Enter name of BLIMPS results file: 
No results files specified.


NOT ENOUGH MEMORY!
r
Cannot open file %s

Reading %s.....
%d scores read from %s

WARNING: AC family name truncated to 9 characters. AC family name = %s
%s	BLOCK	FRAGMENT
%s	BLOCK	FRAGMENT

Version 3.2.3Version 3.2.2Version 3.2.1Version 3.2.4Version 3.2.5Records Searched::	
Scores Done::	


Top %d sequences sorted by maximum normalized score:
(the normalized score is the Score divided by the
99.5 score in the block if available, or by the
smallest Score in the search results file for the block)

Block     Rank Frame Score      Location(bp) Sequence

Block     Rank Frame Score      Location(aa) Sequence
%d.----------------------------------------------------------------------------------
%8s  %4d  %2d    %4d  %7ld-%7ld %s %s
Blocks not found in database

%d.----------------------------------------------------------------------------------
%8s  %4d  %2d    %4d  %7ld-%7ld %s %s%s %d %d %d %d %d %d %d %d %d %d %d %f
blksrch.stpr
===============================================================================
Search results from the BLOCKS e-mail searcher.
Please report problems to jorja@sparky.fhcrc.org, include your query
and this output. To obtain help, send the word HELP on a single
line to blocks@howard.fhcrc.org
===============================================================================
Copyright (c) 1992 by the Fred Hutchinson Cancer Research Center
If you use BLOCKS in your research, please cite:
Steven Henikoff and Jorja G. Henikoff, Automated assembly of protein
blocks for database searching, NAR 19:23 (1991), 6565-6572.
===============================================================================
Each numbered result consists of one or more blocks from a PROSITE group
found in the query sequence. One set of the highest-scoring blocks that
are in the correct order and separated by distances comparable to the BLOCKS
database is selected for analysis. If this set includes multiple blocks
the probability that the lower scoring blocks support the highest scoring
block is reported. Maps of the database blocks and query sequence are shown:
  < indicates the sequence has been truncated to fit the page
  : indicates the minimum distance between blocks in the database
  . indicates the maximum distance between blocks in the database
The maps are aligned on the highest scoring block. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database
is shown. Upper case in the query sequence indicates at least one
occurrence of the residue in that column of the block.
===============================================================================
%s
AC   AC   
OUT OF MEMORY

(,)BL   99.5%==

strength==

//()

 	

OUT OF MEMORY

 

P<%6.2g for %s
                %sin support of %s

No P-value computed for single block hits.

ERROR: Anchor block not found in blocks database.%s %s %d %d %d %d %d %d %6.2g %s

                         |-----%5d residues----|
%-20s %s
%-20s  %s
%-20s %s

 
%s
%s
%s
%s
%-20s%-20s%-20s%c<->%c%6d%6d(%d,%d):%d
%s
%s
%s
%s

No blocks for family %s found in database.ARNDCQEGHILKMFPSTWYV..* protomat.stprtdefSCORE ,	
 ,	
rtCould not open %s, using default BLOSUM scoring matrix
defHIGH ,	
 ,	

Using scoring matrix from %s
A ,	
+-0123456789 ,	

Using BLOSUM62 scoring matrix.
/

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directory
/\: 	
FRAGMENTBLOCKLSTPS=PLENGTH= 	

Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.

  
	
FRAGMENTfragmentP
%d. Entry %s found....dna.proCreating %sw+t
Cannot open %s

%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P>%s  

DR   PIR;.

FRAGMENTfragment>%s
ARNDCQEGHILKMFPSTWYVBZXactg

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	| 
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|tmultimatcrti.scrt1.s__get_exit_frame_monitor_ptr__do_exit_code_ptr__crt_scratchvalues-Xa.cBbss.bssDdata.dataDrodata.rodatamultimat.c___const_seg_900000203___const_seg_900000401___const_seg_900001301___const_seg_900001403___const_seg_900001801___const_seg_900002401___const_seg_900002501motmisc.c___const_seg_900000102___const_seg_900000202___const_seg_900000301___const_seg_900001201crtn.s_END__START_strncmpbl62_matrixfreeatexitstrcataachar_to_num_fini__ctype_environFoutatofnum_to_aacharfgetsclosest_seqrank_cmpkr_atoihypergeomainstrpbrk_DYNAMICmap_blocksstrspnbl60_highpass___Argvpr_num_to_aa_lib_versionget_blocksalign_blockssystem_edataid_cmp_endsprintf__environ_lockre_normalizecompute_locstrncasecmpSeqTypecheck_tpFragSeqinit_dbsfprintfconsensus__cg92_usedDBType_init__xargcget_idsstrcspnFdatNRankAskcheck_datsplit_namesMaxHit_get_exit_frame_monitorstrnjcmpshow_hom_exitftellFmistype_dbsread_blockprint_blurbLisSeqstrcmp_startfopenpr_num_to_aa_space__1cG__CrunMdo_exit_code6F_v_BlkSeqextract_seqs_PROCEDURE_LINKAGE_TABLE_DBLenqsortNSeqfill_blockstrlenidnorm_cmpstrrchrbl62_highpassmakedbidstrstrNBlockmallocdistance_okaystrncpyread_homdistanceACACLenVersiondir_unixbl60_matrixfcloseNScoregetscorekr_itoafputsadd_querytempcmpopendir__fsr_init_valueprev_distcheck_entryFfnd_etextrewindQuerystrcpy__xargv_GLOBAL_OFFSET_TABLE_strtok<N4*<M4cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)types.h	1.75	04/01/06 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMI@(#)dirent.h	1.31	01/07/29 SMI@(#)dirent.h	1.33	03/09/17 SMI@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12ld: Software Generation Utilities - Solaris Link Editors: 5.9-1.393.interp.hash.dynsym.dynstr.SUNW_version.rela.data.rela.bss.rela.plt.text.init.fini.rodata.rodata1.got.dynamic.data1.symtab.strtab.stab.index.comment.shstrtab.stab.indexstrmultimat.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/protomat; /opt/SUNWspro/prod/bin/cc -O -c  multimat.cmainmotmisc.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/protomat; /opt/SUNWspro/prod/bin/cc -O -c  motmisc.c	"``Eo0-B8BBBLeRxxXxx^xxfxxgoGt2}TT=xxt : XT k5HIGH ,	
 ,	

Using scoring matrix from %s
A ,	
+-0123456789 ,	

Using BLOSUM62 scoring matrix.
/

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directory
/\: 	
FRAGMENTBLOCKLSTPS=PLENGTH= 	

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USAGE:  narrow  
		file_type = B|F|W	B=block, F=frequencies, W=weights
					F or W in MAST format
Writes a positive PSSM to stdout in BLIMPS format

Enter type of input file (Block|Frequencies|Weights): 
Enter name of input file: r
Cannot open file %s
ERROR:No block found in file %s
Please verify input format type
ALPHABETALPHABET  
	

Problem finding ALPHABET in %s
log-oddsfrequencyalength=alength= %d w=%d
ALPHABET length (%d) not alength (%d)

Problem finding width in %s
Not sure about the format of %s, assuming first line contains alphabet
 
	
WEIGHTSWEIGHTSwidth=%d; 	
 	

Problem finding value for pos=%d aa=%c
ERROR: Negative frequencies read
Please verify input format type
ERROR: All values read as zero
Please verify input format type
Could not find alphabet or width in %s
FREQSFREQSseqs=%d; width=%d;%s.mastw
Cannot open file %s
%s.blimpsw
Cannot open file %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ALPHABET= ARNDCQEGHILKMFPSTWYVBZX
log-odds matrix: alength= 23 w= %d
% 6.3f 
rload_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
%lg%lgUnable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqdefault.qijrBLOCKBLOCKMATRIX; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
A ,
.+-0123456789 ,
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
pb_weights:%d ignored for %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
rdirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 	

 Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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9"7W@C\  @㿠@;b9W@C  ;'` 㿠㿠OLIGO_MELT %s
COPYRIGHT 1997, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

USAGE:  oligo_melt  [DNA conc in nM]
Enter name of file containing oligos: rCannot open %s

Estimated melting temperatures of non-degenerate clamp region (C=%.2fnM):

-----------------------------------------------------------
Length=%d, clamp=%d

---Using Breslauer's entropy=-%.1f & enthalpy=-%.1f
AT/GC=%.1f, NAR=%.1f, PRIMER3=%.1f
---Using SantaLucia's entropy=-%.1f & enthalpy=-%.1f
AT/GC=%.1f, NAR=%.1f, PRIMER3=%.1f

-----------------------------------------------------------
References:
Entropy/Enthalpy: Table 2 from Breslauer, et al, (1986) PNAS 83:3746-3750
Entropy/Enthalpy: Table 2 from SantaLucia, (1998) PNAS 95:1460-1465
AT/GC: Suggs, et al, (1981) ICN-UCLA Symp.Dev.Biol. 23:683-693
NAR: Eqn [2] from Freier, et al, (1986) PNAS 83:9373-9377
PRIMER3: Eqn (ii) from Rychlik, et al, (1990) NAR 18:6409-6412

Oligo in reverse order:
%c

aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
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Configuration file errors
Using PATMAT algorithm...
Using Gribskov algorithm...
Using Altschul's pseudo-counts...
Using Claverie pseudo-counts...
Using Dirichlet pseudo-counts
Using background pseudo-counts (like Gibbs)
Using Gribskov algorithm with qij...
Using Steve's method...
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FRr
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GRr
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GQr
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DIr
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CLr
Cannot open CL file %s
LOBRHYNNFPHCGIPA 	
w
Cannot open PA file %s

No valid PSSM type specified

Missing BL (input block) file

Missing EX (output PSSM) file
r
Cannot open file %s

OUT OF MEMORY
Mixture=Alpha==	

 	

 Read a frequency of value of %f for: %c
Read a frequency of value of %f for: not a residue
The non-amino acid codes J and O weights are differentThe non-amino acid codes O and U weights are differentThe non-amino acid codes U and J weights are differentThe value for the non-amino acid will be the last weight seen.Currently the program ignores non-residue characters so thisfield has no effect.
%lg%lgA ,	
+-0123456789 ,	
BLOCKMATRIXseqs=

%s seqs=%dUncounted character for %s: %d
make_pssm: OUT OF MEMORY
make_col:  OUT OF MEMORY

float_qij: OUT OF MEMORY
A ,
.+-0123456789 ,
dataw
bruno_rind(): Cannot open file data
%10s %c

Executing rind ....
rind
bruno_rind(): Execution of rind failed
countsr
bruno_rind(): Cannot open file counts
position 	- 	 	
clump_seqs: Unable to allocate pair structure!
;; PATMATID   %s
AC   %s
DE   %s
PA   %s
xxx[]x%s
//
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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Enter name of input file (Prints protein motifs database): r
Cannot open input file %s
%s.datw
Cannot open output file %s
%s.infow
Cannot open output file %s
Block family PRINTS entry name    # of   Cross references to -
                                  blocks PROSITE    BLOCKS     PRINTS
------------ -------------------- ------ ---------- ---------- ----------

%d entries with %d motifs read from Prints database %s
and written as blocks in file %s.
Information about the processed entries written in file %s.
%sfc;Extra motif: %s
gc;gc;Error ! Problem in format of Prints entry gc line,
can't find the general code
gx;gx;Error ! Accession line (gx; ...) not found in Prints entry %s.
Error ! Problem in format of Prints entry %s gx line.
Can't find the accession code.
Note - the accesion code of Prints %s ("%s")
is shorter than 7 characters.
gn;gn;Error ! Type line (gn; ...) not found in Prints entry %s.
SIMPLECOMPOUND)Error ! Problem in format of gn line in Prints entry %s -
%scan't find closing )
(Error ! Problem in format of gn line, can't find (
in Prints entry %s.
Error ! Type line (gn; ...) is neither SIMPLE or COMPOUND
in Prints entry %s.
Unable to recover enough memory to continue.  Aborting.
%s%c%s%s;%s; BLOCKgt;gt;Error ! title line (gt; ...) not found in Prints entry %s.
gp;PROSITEBLOCKSPRINTS fm;fm;Error ! Final motifs line (fm; ...) not found in Prints entry %s.
%-12s %-20s %5d  %-10s %-10s %s
fc;fc;Error ! final motif code line (fc; ...) not found in
motif %d of Prints entry %s.
Error ! Problem in motif %d of Prints entry %s.
  The motif's code line (fc; ...) does not contain the entry name = %s
%sfl;fl;Error ! final motif length line (fl; ...) not found in
motif %d of Prints entry %s.
Error ! Problem in format of final motif length line (fl; ...) in
motif %d of Prints entry %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
fd;Error ! Problem in format of sequence line %d in
motif %d of Prints entry %s.
Sequence not found in line.
Error ! Sequence %d in motif %d of Prints entry %s.
is %d chars long, instead of the %d expected
Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
read_a_prodom_entry(): Error reading sequence %s in block %s,Undocumented return value, %d, from read_sequence().
Error ! Problem in format of sequence line %d in
motif %d of Prints entry %s.
Sequence name not found in line.
Error ! Problem in format of sequence line %d (%s) in
motif %d of Prints entry %s.
Error reading sequence start position.
Error ! Problem in format of sequence line %d (%s) in
motif %d of Prints entry %s.
Error reading sequence distance from last motif.
bb;bb;Error ! End of file reached while readingmotif %d of Prints entry %s.
 distance from previous block=(%d,%d)adapted from PRINTS entry; width=%d; seqs=%d;Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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Enter name of blocks database: r
Cannot open file %s

Enter name of output file: w
Cannot open file %s
%-20s	%s	%d	%d	%f
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun 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Enter name of pssmdist.dat file: r
Cannot open file %s

Enter name of blocks database: r
Cannot open file %s

Enter name of new blocks database: a
Cannot open file %s
 	
 	
 	
 	
; 	
%s; width=%d; seqs=%d; 99.5%%=%d; strength=%d;Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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Enter name of matrix database: r
Cannot open file %s

Enter name of observed frequencies database: r
Cannot open file %s, TP distribution not computed.

Enter name of frequency file: r
Cannot open file %s

Enter number of sequences in a typical search [%.0f]: 
Enter number of amino acids in a typical database [%.0f]: Assuming %.0f sequences, %.0f amino acids in a search
and 100 true positive alignments
pssmdist%s.data
Cannot open file ctemp
%s.cuma
Cannot open file ctemp

======>%s
>%s
 ;%s %d %d  %d %.4lf %d %d

True positive distribution

Random distribution
minscore without ends=%d
minvalue=%d maxvalue=%d minscore=%d maxscore=%d
maxscore is too big, increase MAXSCORE from %d
%d %6.2g
Sum of probabilities = %8.4f
Score range  log(Possible ways)  Probability  Expected scores
%4d %4d  %8.4f      %11.8f      %8.2f
%4d %4d       0.0000       0.000000

CumScrs  Score   ExpectedScrs
%8.4f %4d %8.4f
Median TP score = %d, TPabove = %lf
%8.4f %4d %8.4f
99.5 TN score = %d, 80.0 = %d
Read a frequency of value of %f for: %c
Read a frequency of value of %f for: not a residue
The non-amino acid codes J and O weights are differentThe non-amino acid codes O and U weights are differentThe non-amino acid codes U and J weights are differentThe value for the non-amino acid will be the last weight seen.Currently the program ignores non-residue characters so thisfield has no effect.
%lg%lg/\:aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
 	

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Enter name of scoring matrix: r
Cannot open file %s
# Rank matrix constructed from scoring matrix %s
# Each aa row contains the rank of the score for the all aas
   %c 
%c %2d 
BLIMPS_DIR%s/docs/default.sijdefault.sijrconstruct_rank_matrix(): Cannot open %s
BLOCKBLOCKMATRIX; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
A ,
.+-0123456789 ,
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
pb_weights:%d ignored for %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
rdirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 	

 aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
motif%swidth=width=%d;No width field for matrix %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
Unable to recover enough memory to continue.  Aborting.
%f%f%fUnable to recover enough memory to continue.  Aborting.
width=%d;Unable to recover enough memory to continue.  Aborting.
resize_matrix() not finished.  Exiting.

  |% 4d    
  |% 4d    
  |% 4d
--+----
%c |% 6.4f
%c |% 6.4f
%c |% 6.4f
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
%3d %3d %3d
//
ID   %s
AC   %s
DE   %s
MA   %s
  %c   *   -
% 6.4f % 6.4f % 6.4f
//
Unknown output type: %d, using integer output
Unknown output style: %d, using integer output
Unknown sequence type: %d, using amino acid
ID   %s
AC   %s
DE   %s
MA   %s
    %c       %c     *         -
  *   -
    A         C         G         T
  A   C   G   T
%3d %3d %3d
%3d 
% 9.4f % 9.4f % 9.4f
% 9.4f 
//
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
 	

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 ***`!*`!*!8*!4*`!*!8*!*`!*!d*!*`!*!d*!T*`!*!d*!*`!*!H*!*`!*!H*!*`!*!8*!*`!*!d*!*`!P*! *!d*`!P*!8*!*`!*!H*!*`!P*!*!P*`!P*!d*!*`!*!8*!\*`!L*!8*!*`!*!8*!P*`!*!*!P*`!*!d*!*`!P*!8*!H*`!*!d*!L*`!*!H*!8*`!8*!8*!P*`!H*!H*!8*`!8*!8*㿠㿠RETBLOCK: Copyright 1997 Fred Hutchinson Cancer Research Center
Extract blocks from a Blocks Database
USAGE:  retblock   [[-n] -f]
           = file of blocks
           => extract AC or all blocks
          -n       => output to stdout, otherwise each block
                      will be written to AC?.blk
		-f	=> floating point output

Enter name of blocks database: r
Cannot open file %s
all
Enter AC of blocks to extract, or all [%s]: all-n-f-n-f.blkw
Cannot open file %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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r
Cannot open file %s

Third argument should be the start position of the aligned region in block 1
r
Cannot open file %s

Sixth argument should be the start position of the aligned region in block 2

Seventh argument should be the alignment length

Block %s not found in file %s

Block %s not found in file %s
Something seems wrong in the alignment coordinates !!!

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 %-20.20s (%5d) %s%c

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%s
 %-20.20s (%5d) %s%c
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
aInformation: %s
Information: %s
Warning: %s
Warning: %s
Serious: %s
Serious: %s
Program Error: %s
Program Error: %s
Fatal Error: %s
Fatal Error: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
Reclaim space function is not defined.  No memory will be reclaimed.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
 	

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SMI@(#)limits.h	1.53	03/08/07 SMI@(#)limits_iso.h	1.1	99/08/09 SMI@(#)int_limits.h	1.6	99/08/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/12cg: Sun 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 Fred Hutchinson Cancer Research Center
USAGE: uextract   [-f -o -n]
        = file listing sequence names to extract
                   in PROTOMAT format
         = sequence database
       -f          to extract FRAGMENTs
       -o to have all sequences put in 
       -n          to NOT execute motifj or create .lst file
       -l          to NOT execute motifj but create .lst file
       -k          to NOT execute motifj but create .lst file                    with fewer sequences than -l

Enter name of file containing list of entries to extract: r
Cannot open file %s

Enter name of database file to extract entries from: r
Cannot open file %s
w+t
Cannot open file %s

Extracting all sequences to %sMOTIFJ=[
%s//
%d sequences requested for extract from %s
  and deposit into directory %s
  and deposit into file %s
%d sequences extracted
The following sequences were not found:
%s
.lstw+t
Cannot open file %s
%s%s

%d entries written to %s
MOTIFJ=[[,,,]40174%s MOTIFJ=[%s,%s,%s,%s];$
w+t
Cannot open file %s for update
%s%s

%d entries re-written to %s
uextract.data%s %d %d %s %s %s
-motifjmotifjPP$_PP$_%-20s  PS=%s  LENGTH=%-6d
PP%-20s  PS=%s  LENGTH=%-6d
%-20s  PS=%s  LENGTH=%-6d  FRAGMENT  LST PIR=%s
ARNDCQEGHILKMFPSTWYV..* protomat.stprtdefSCORE ,	
 ,	
rtCould not open %s, using default BLOSUM scoring matrix
defHIGH ,	
 ,	

Using scoring matrix from %s
A ,	
+-0123456789 ,	

Using BLOSUM62 scoring matrix.
/

/mkdir %s
Created directory %s

Unable to create directory %s
Protein files will be placed in current directory
/ 	
FRAGMENTBLOCKLSTPS=PLENGTH= 	

Cannot determine type of input file
Processing input file as %s
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.

  
	
FRAGMENTfragmentP
%d. Entry %s found....dna.proCreating %sw+t
Cannot open %s

%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P>%s  

DR   PIR;.

FRAGMENTfragment>%s
ARNDCQEGHILKMFPSTWYVBZXactg

 -| 
	| 
	| 
	_| 
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Cannot open file %s
w+t
Cannot open file %s

Extracting all sequences to %sMOTIFJ=[
%s//
%d sequences requested for extract from %s
  and deposit into directory %s
  and deposit into file %s
%d sequences extracted
The following sequences were not found:
%s
.lstw+t
Cannot open file %s
%s%s

%d entries written to %s
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$=Al]M9}GE9~Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Error in reading first file name from first argument !
Enter name of a file with blocks or block matrices: 
The blocks/matrices in this file will be intercompared.If you wish to compare them against blocks/matrices inanother file enter that file name (else just hit ).
Cutoff score should be specified as a Z score (mean+Z*std).The Z score must be positive (corresponding to the 50 percentile or higher).A negative cutoff score (%f) was specified, default value (%.2f) used.

Minimal alignment width can not be less than narrowest allowed blocks (%d).
Error in reading second file name from first argument !
Minimal alignment width can not be negative !The value given (%d) is out of range.
Error ! Extrapolated variance of shuffled PSSMs requested for 
a block too narrow (%d).
Error ! Extrapolated mean of shuffled PSSMs requested for 
a block too narrow (%d).
%-10s %3d %3d %-10s %3d %3d %2d Prpo %6.2f (%4.1f)
Column scores for %s and %s -

Column scores for optimal alignment of %s and %s -
Unable to recover enough memory to continue.  Aborting.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.read_a_prodom_entry(): Error reading sequence %s in block %s,Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.
Error ! Problem in ProDom entry %s
second word in description line doesn't begin with a (second word in description line doesn't end with a )Error ! Problem in format of ProDom entry %s
A non-digit in the number-of-sequences field "%s"
 distance from previous block=(%d,%d)adapted from ProDom entry; width=%d; seqs=%d;Error ! Problem in format of ProDom entry %s sequence-line %d
A non-digit in the sequence start position %s
Error ! Problem in format of ProDom entry sequence-line %d
Sequence %s has length of %d instead of expected %d
Error ! Actual number of sequences in ProDom entry %s
different than what the entry reportsError ! Problem in format of ProDom entry description-lineError ! Problem in format of ProDom entry description -lineError ! Number of sequences in ProDom entry %s (%d) is less than 2
Error ! Not enough sequences (%d) in ProDom entry %s
Error. variable db_type (%c) is of unknown type !
Cannot determine type of input fileUsage: 
LAMA inp_file1[,inp_file2] out_file [min_algn_wdth] [dbg_lvl] [scrn] [cutoff] [expected target]

The program must have the names of one or two files with entry(ies) to compare
and an output file name. These can be specified on the command line or
interactively. On the command line the first argument is the entry(ies) file
name(s), if two files are specified they should be separated by a comma
with no spaces. Each file can be of either block, matrix, ProDom 
multiple alignment entry(ies). The second argument is the output file name,
it will be overwritten if it already exists. Optional arguments are 3rd -
minimal alignment width (0 for default), 4th - the debug level, 5th -
screen output (0 to forbid, anything else to allow), 6th - score
cutoff (in Z units [std's from mean], >=0, 0 for default), and 7th - for
how many searched blocks to calculate the number a score is expected to appear
(0 for default).

Note - the two input files have different types of data.
Minimal length of reported alignments %3d
Score cutoff is %.1f Z score units (in the top %.1e percentile of chance scores)

                                            alignment     Z-score  expected number for
block 1     from:to       block 2     from:to   length                 searching %d blocks
Block matrix %s shorter (%d) than narrowest width allowed (%d)
%-10s  %3d : %3d and %-10s  %3d : %3d (%2d) score %3.0f (%4.1f  %s)No hits found above score cutoff %.1f.load_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.@@?AB@@BBABzD???[|
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"] x2(LAMAfsr.s__get_exit_frame_monitor_ptr__do_exit_code_ptrtrap_tablecrti.svalues-Xa.ccrtstuff.c__CTOR_LIST____DTOR_LIST____EH_FRAME_BEGIN____JCR_LIST__p.0completed.1__do_global_dtors_auxobject.2frame_dummyLAMA.cfrequency.cread_freqconvert.cbasic_matrix_constructionmake_colpre_weighted_sequencesmake_work_pssmcountscount_residuespseudo_altscompute_BZXblocks.cBlockBufLengthBlockBuffererrors.cErrorFilematrix.cmemory.cRecFuncsequences.clbuff.0first_time.1strutil.cgcode.cgctrans.0__CTOR_END____DTOR_END____FRAME_END____JCR_END____do_global_ctors_auxcrtn.s_END__START__initexpread_a_blocknt_arevcompextrpltd_meanfind_max_aa_pssmremove_trailing_whitespacent_adegengetargsatexitload_diriscreen_outoutput_matrix_scallocaltschul_data_dependent_conversion_methodnew_matrixfprintfset_defaultsaa_adegennt_brevcomp___Argvalloctd_zVsPrcntlsequence_typeoutput_sequenceputcharprint_blockfrequencyload_codonsABRT_signal_handlerfreefputc_exittoupperoutput_block_sSearchTyperead_block_body__longdouble_usedpseudo_diriSequenceMatrixScoringMethodread_a_matrix__fpstartrewindfree_work_pssmblank_linesscanf__iobfputsstrchrblock_to_matrixload_ZvsPrcntl1extrpltd_varpb_weights_environfree_blockaafqreallocfprint_matrixmallocread_to_block_finidata_read__ctypecodon2aa_GLOBAL_OFFSET_TABLE_strspn__register_frame_info_bases_endlgammaZtoPrcntlalloctd_algnmntsmemcpyadd_logscounts_nogaps_PROCEDURE_LINKAGE_TABLE_output_blockCodon_Usagefind_max_aa_colErrorBufferErrorReportinit_gcodenormalizegetenvread_a_sequenceprint_sequencefcloseaa_atob_get_exit_frame_monitoratoffree_sequencent_atobatoieat_whitespacesequence_comparisonfgetscols_scoreload_qijoriginal_conversion_methodfwritentfqmatrix_comparison_lib_version_Jv_RegisterClassesread_a_block_fasterread_a_prodom_entrylogresize_block_sequencesstrtokload_frequenciesresize_block_clustersmin_algnmnt_widthsimilarity_dependent_scaleSIFT_conversion_methodoutput_matrix_st__fsr__dso_handleNumberToReportsprintfblock_comparisonstrncat_startDBtypeget_tokenstrcmpStrandsToSearchstrcatread_sequencestrstrWWW_FLAGresize_sequence__fsr_init_valueread_block_headerSiteSpecificScoringMatrixTypestrncpymake_gribspre_weighted_conversion_methodsqrtfrq_qijZ_cutoffstatsGeneticCodeInitializerSIFT_pssmaa2codonfopendbg_lvl_etextfseekSW_matricesfree_matrixoriginal_conversion_method_cleaned_upgcodesfflushDbInfogribskov_conversion_methodBlockToMatrixConversionMethodalignments_doneaa_btoa__deregister_frame_info_basesnext_clusterErrorLevelReportmainftell_DYNAMICuntranslate_sequenceoutput_matrixQij__1cG__CrunMdo_exit_code6F_v_nt_btoainit_reclaim_space_edataseq_type_dbsnew_blocknt_bdegen_mcountstrcpyload_stats3strncmpset_error_file_nameRTot@(#)SunOS 5.10 Generic January 2005@(#)SunOS 5.10 Generic January 2005@(#)SunOS 5.10 Generic January 2005GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)@(#)SunOS 5.10 Generic January 2005ld: Software Generation Utilities - Solaris Link Editors: 5.10-1.482.interp.hash.dynsym.dynstr.SUNW_version.rel.text.rel.got.rel.data.rel.bss.rel.plt.init.fini.rodata.rodata.str1.1.rodata.str1.4.rodata.cst4.rodata.cst8.dynamic.ctors.dtors.eh_frame.jcr.data.rel.local.symtab.strtab.comment.shstrtab	"	oP-	BTT7	B\\@	BttJ	B||S	BW1!!x\88b88h888p2::	2CC[(pkpkDkk;PlPl(m(mDnn@ @}@}H}H}P}P}T}T}X}X}N`}`} \}@U 7әI blimps-3.9/bin/Sun_intel/LAMA_search000075500001460000012000001462441062462063500176620ustar00jorjastaff00000400000027ELF4|4 (! 44$z/usr/lib/ld.so.1	
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dateError opening pipe?../help/LAMA_help.html%s %s 'rm -f %s/%d.*'%dC.html5.6./cyrcaLama.pl%s %s %s %s/blocks/icons/cyrcashLogo.gifContent-type: text/html

REQUEST_METHODPOSTCONTENT_TYPEumask 006ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
&;`'"|*?~<>^()[]{}$\FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Sorry, you can not compare more than %d target blocks in each run.
There seems to be an error in the format of query block number %d:
There seems to be an error in the format of target block number %d:
You need to enter a block to search with by writing or pasting a block in the query block window.
No blocks were read from the query.No blocks were read from the target data.Sorry, you can not compare more than %d query blocks in each run.
/usr/bin/nice -5 %s %s,%s %s 0 %d 0 %f > /dev/null 2>&1An error occured during the search.Please try your search again at a later time.If it fails again contact the maintainer of these pagesand describe what caused the problem with an example.
%s/htmlize-blimps.pl %s | %s/htmlize-LAMA %s %s - -Error opening LAMA output file.LAMA Search Results
LAMA Search Results (%s)

%s %s "/usr/bin/nice -10 %s %s,%s %s 0 %d 0 %f > /dev/null 2>&1"%s %s '(cat %s) | /usr/bin/mailx -s "LAMA Results" -r "blocks@fhcrc.org" %s'LAMA Search Submitted
LAMA Search Submitted
Your search has been submitted.You will receive the results via email to the address you gave ("%s").
CYRCA results
application/x-www-form-urlencodedThis script can only be used to decode form results. This script should be referenced with a METHOD of POST.If you don't understand this, see this forms overview.%c
What could have happened is that you just reloaded this page rather than redoing the search.
If you use NETSCAPE it has a tendency to try to reload a page when you go back to it.  This may be why you have this error.MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.?333333?&6FVfv&6FVfv&6FVfvO)x
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wf\RA7vH_StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialACGTAGCTACGTATCGCGTAGTACTACGACGT-RNDQEHILKMFPSWYVDNEQARNDCQEGHILKMFPSTWYV*%s %s calibrated best score = %5d at %d
>%s %s from %d to %d
99.5 TN score = %d
(,)%s %d : %s %d
%s %.0f %.2f |_ADDSEQS Version %s
rwBLIMPS_DIR%s/docs/default.amino.frqFRAGMENT%s already in block
No sequences found in %s .
 Research CenterAdds sequences to blocks.seqssimi
Cannot open file %s
No blocks found in %s .
%d sequences added
Query added to %s
aaddseqs.dat%s %d %d %d %d
%lgrfield has no effect.
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqpb_weights:%d ignored for %s
 ,
.+-0123456789BLIMPS_DIR%s/docs/default.sijrMixture=Alpha==	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIXID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
width=%d;%fmotif%swidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for matrix %sSetting width to zero
  |% 4d--+----%c |% 6.4f    ID   %s
AC   %s
DE   %s
MA   %s
  %c     %c       A   C   G   T
%3d   *   -
//
% 9.4f % 9.4f
%3d
    *         -
 %c   *   -
% 6.4f % 6.4f
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000%s; distance from previous block=(%d,%d)Cannot write %s of length %d from %d to %d
Median TP score = %d, TPabove = %d
WARNING: sequence segments are of different lengthsMean dissimilarity distance = %.2f

Enter name of file containing blocks: 
Enter name of output seqs file: 
Enter name of sequence file: ADDSEQS: Copyright 1999 by the Fred Hutchinson CancerUSAGE:  addseqs                    = input blocks		           = fasta format sequences                      = output file                = processing option                   blks = add sequences to blocks & output blocks                   seqs = add sequences to blocks & output sequences                   simi = add sequences to blocks & do similarity analysis bad bestpos=%d endpos=%d seqlen=%d
 out of order %d, previous end %d
 pad1=%d bestpos=%d endpos=%d seqlen=%d
 pad2=%d bestpos=%d endpos=%d seqlen=%d
load_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating..Ap=
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lllllllllwl]lVlLl>l0l)lllkkkkkkkStandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialACGTAGCTACGTATCGCGTAGTACTACGACGT-RNDQEHILKMFPSWYVDNEQARNDCQEGHILKMFPSTWYV*SCRIPT_NAME./blimps-bin%s/find_biassed_blocks../tmp%s/%d.biassed_blocks_out%s/%d.blkQUERY_STRINGCONTENT_LENGTHBLOCKrm -f %s/%d*temp%s/%d.block_errorsw%s
//
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Program Error
Content-type: text/html

REQUEST_METHODPOSTCONTENT_TYPEumask 006ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
&;`'"|*?~<>^()[]{}$\FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000There seems to be an error in the format of block number %d:
You need to enter a block by writing or pasting a block in the window.
Sorry, you can not check more than %d blocks each time.
An error occured during the execution.Please try again at a later time.If it fails again contact the maintainer of these pagesand describe what caused the problem with an example.
Biassed Blocks Results
Biassed Blocks Results
Error opening program output file.application/x-www-form-urlencodedThis script can only be used to decode form results. This script should be referenced with a METHOD of POST.If you don't understand this, see this forms overview.%c
What could have happened is that you just reloaded this page rather than redoing the search.
If you use NETSCAPE it has a tendency to try to reload a page when you go back to it.  This may be why you have this error.MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.?333333?N^n~.>N^n~.>N^n~/	 m
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 ,
.+-0123456789BLIMPS_DIR%s/docs/default.sijrMixture=Alpha==	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIXID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
width=%d;%fmotif%swidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for matrix %sSetting width to zero
  |% 4d--+----%c |% 6.4f    ID   %s
AC   %s
DE   %s
MA   %s
  %c     %c       A   C   G   T
%3d   *   -
//
% 9.4f % 9.4f
%3d
    *         -
 %c   *   -
% 6.4f % 6.4f
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000>%s|%d              from %10.10s blocks

stockholm_seqs: OUT OF MEMORYERROR in block %s: %d sequences found but %d sequences are included in %d blocks
Copyright 1999-2003 Fred Hutchinson Cancer Research Center
Prints blocks as a multiple alignment.USAGE:  blalign  [-p|s|f|m|h|q|g] [width]          p=Posfai style, s=short style, f=fasta style,          m=MSF style, h=STOCKHOLM style, q=ungapped STOCKHOLM,          defaults are short style, width = 66
Enter name of file of blocks: Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.??R?@3333@3333????333333?BABzD???l"2BRbr"2BRbr"2BRbr

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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000WARNING: sequence segments are of different lengthsMean dissimilarity distance = %.2f

Enter name of file containing substitution matrix: 
Enter name of file of fasta multiple alignments: BLDIST: Copyright 1998 Fred Hutchinson Cancer Research Center
USAGE: bldist       = file of fasta multiple alignments (blocks)    = substitution matrix      = output distance matrix     = output matrix type:			P=dissimilarity in protdist formatWARNING: Sequences appear to be DNA but will be treated
Enter type (S=similarity, D=dissimilarity, C=correlation): Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.yyD?BABzD?????R?@3333@3333????333333?BRbr"2BRbr"2BRbr.
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.errb6_<bC~tAStandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialACGTAGCTACGTATCGCGTAGTACTACGACGT-RNDQEHILKMFPSWYVDNEQARNDCQEGHILKMFPSTWYV*Scoring vs sequence %s.
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default.codon.frqProbe Sequence: NO SEQUENCE
Probe Size: UNKNOWN
Block File: %s
Probe Size: %d Base Pairs
Not scoring the block.
Block File (s) :    %s
Matrix File: %s
Not scoring the sequence.
Matrix File (s) :    %s
The file %s will be ignored.
r%lgrfield has no effect.
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqpb_weights:%d ignored for %s
 ,
.+-0123456789BLIMPS_DIR%s/docs/default.sijrMixture=Alpha==	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIXID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
width=%d;%fmotif%swidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for matrix %sSetting width to zero
  |% 4d--+----%c |% 6.4f    ID   %s
AC   %s
DE   %s
MA   %s
  %c     %c       A   C   G   T
%3d   *   -
//
% 9.4f % 9.4f
%3d
    *         -
 %c   *   -
% 6.4f % 6.4f
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
%s   Version %s  %s%s
%s   Version %s (%s)  %s%s
Unable to recover memory.
%dTRUEYESTY0rOld style configuration file.DNAMATRIXAABLOCKUnknown search type: %s
default scoring method.
--------Histogram:
   %5d - %-5d : %d
   %5d -       : %d
pattern.cNumInSL(residue_list) == 0pat_file != NULLsl.cp->key != NULLFFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Scoring sequence %s vs block %s.
Searching matrix %s against the sequence database.
Unable to read matrix for scoring against the sequences.Scoring sequence %s vs matrix %s.
(C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center

BLIMPS (BLocks IMProved Searcher)Using pseudo-count parameters %f and %s.
main(): SearchType variable corrupted, possible memory problems.        Should never have reached this part of the program.        The rest of the run may be invalid.        Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
Unable to open output file "%s" for writing.Not outputing the matrix output.
Unable to open output file "%s" for writing, aborting.Unknown genetic code %d.  Setting to Standard code (0).                                         Strength  Score Searching sequence %s against the matrices database.
AC#                    Description                                                Score Searching block %s against the sequence database.
Cannot open 'alts' file "%s".  Exiting...
Unable to read block for scoring against the sequences.Unable to read the sequence for scoring against the matrices.Unable to read the sequence for scoring against the blocks.Query sequence has zero length, not scoring it.
get_file_list(): Unknown file group %d.Unable to recover enough memory to continue.  Aborting.
Already have a frequency file: %sinsert_file(): Bad file list, not entering filename "%s"               into a file list
get_file(): Unknown file group            Unable to open a file
Unable to read sequence file: %s to determine the type of database
Unable to open frequency file: %s
Unable to open database file: %s
Unable to open matrix file: %s
Unable to read pattern file: %sUnable to read sequence file: %sUnable to open block file: %s
Unknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Assuming there is no title and just sequence.
Unable to read pattern file: %s
Unable to read sequence file: %s
get_file(): Bad file list, unable to open a file
rewind_file(): Bad file group, unable to rewind file list
get_current_file_name(): No files in the file group                         Unable to return a file name
get_current_file_name(): Bad file group, unable to return a file name
get_file_name(): Requested file out of the range of the files                 in the file group                 Unable to return a file name
get_file_name(): No files in the file groupget_file_name(): Bad file group, unable to return a file name
number_of_files(): Bad file group, unable to report number of files
close_file() : Bad file group, unable to rewind file list
load_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.Unable to recover enough memory to continue.  Aborting.
Decreasing the NumberToReport from %d to %d.Ran out of memory (2), fewer scores will be reported.
Decreasing the NumberToReport from saving all (%d currently) to %d.Ran out of memory (1), fewer scores will be reported.
blimps_reclaim_space(): NumInSL(Scores) is greater than NumberToReport.                 NumInSL(Scores) is supposed to be maintained                 less than or equal to the NumberToReport.                 NumberToReport = %d, NumInSL(Scores) = %d.                 Ran out of memory, removing the excess scores                 in the Scores list.
Decreasing the number of saved nodes in the list.The saved nodes level of the list has been reduced to %d.
The saved nodes level of the list has been reduced to %d.The list saved nodes cannot be reduced any more.
Unknown configuration file key: %s
read_config_file_end(): SearchType variable corrupted.                        Should never have reached this part of the program.                        Possible memory problems.                        The rest of the run may be invalid.                        Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
Unable to read sequence file: %s to determine the type of database
Unknown search type given, assuming SQ vs BL search.
No sequence files given for the sequence database, aborting.
Unknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Assuming there is no title and just sequence.
No block files given for the block database, aborting.
No block file given (BL field), aborting.
No sequence file given (SQ field), aborting.
No DB field given, assuming data is in the SQ field.
No DB field given, assuming data is in the BL field.
Missing either the BL or SQ field, aborting.
Configuration file has SQ, BL, and DB entries.Unable to determine the type of search.Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
Configuration file has SQ and BL entries.No block file (BL) or sequence file (SQ) given, aborting.
No sequence file (SQ) or block file (BL) given, aborting.
New style uses the ST field instead of P4.
MA field already used.  Cannot have both the BL and the MAfields.  Ignoring the BL line.
Configuration file "%s" not found.  Exiting
Using the PAttern switch causes the REpeats switch to be ignored.Alignments reported will include repeats.
New style does not use the SE field.
New style uses the RE field instead of P5.
BL field already used.  Cannot have both the MA and the BLfields.  Ignoring the MA line.
New style uses the NU field instead of P9.
Invalid matrix-sequence scoring method specified, %d.Setting the method to the default value and using theNo pattern for matrix %s, Scoring the entire matrix
score_and_enter(): Tried to score a sequence that is not an                   amino acid sequence.  Not scoring the                   sequence %s
---------------------------------------------%-8s %4u %-45s      %4d   %4d %2d %6d %s
%-8s vs %-7s   %-20s... & %-20s... %4d %4d %2d %6d %6d %s
%-11.11s %-50.50s      %4d   %4d %2d %6d %s
%-20.20s %-62.62s %4d %2d %5d %6d %s
Unable to recover enough memory to continue.  Aborting.
enter_score(): Error placing matrix score into list
default_scoring_method(): matrix %s has length <= 0default_scoring_method(): Not scoring the sequence.
default_scoring_method(): sequence %s has length (amino acids) <= 0Unable to recover enough memory to continue.  Aborting.
Unable to find pattern for PSSM %s
Unable to recover enough memory to continue.  Aborting.
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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Enter name of file containing sequences: BLK2MOT: Copyright 1995 by Fred Hutchinson CancerUSAGE:  blk2mot            = input file of protein sequences         = input file of blocks from sequences         = output file for motomat
Enter name of new motomat file: 
No sequences found in file %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.??Q@333333?l&6FVfv&6FVfv&6FVfv@m
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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000log-odds matrix: alength= 23 w= %d

Enter name of PSSM output file: 
Enter name of BLOCKS input file: BLK2PSSM: Copyright 1996-2003 Fred Hutchinson Cancer ResearchUSAGE:  blk2pssm    []         = B BLIMPS|M MAST|G Gribskov|P Psi-Blast         = 3,6,20,21
Enter PSSM format type (B=blimps, M=mast, G=Gribskov, P=Psi-Blast) [B]:  ALPHABET= ARNDCQEGHILKMFPSTWYVBZX
%s Invalid type %d, using type %d
load_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.<F<?<BABzD???Y@Q@??R?@3333@3333????333333? .>N^n~.>N^n~.>N^n~m
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ULȃDžH1LDPXQ|X1Iv&H~X|uƄXULDXPheuMLD1ۃ~@uLPELCD9‹}SLD݄ٽVfVxfT٭T۝P٭VPPheuHULH9sLLE9 ujjheYue[^_؋LD݄ٽVfV%x9LDheUniversa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Enter name of new slx database: 
Enter name of blocks database: MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.?333333?y2BRbr"2BRbr"2BRbr`
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hits: OUT OF MEMORY

%d possible hits reported

Results: OUT OF MEMORY
%lgrfield has no effect.
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqpb_weights:%d ignored for %s
 ,
.+-0123456789BLIMPS_DIR%s/docs/default.sijrMixture=Alpha==	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIXID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
width=%d;%fmotif%swidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for matrix %sSetting width to zero
  |% 4d--+----%c |% 6.4f    ID   %s
AC   %s
DE   %s
MA   %s
  %c     %c       A   C   G   T
%3d   *   -
//
% 9.4f % 9.4f
%3d
    *         -
 %c   *   -
% 6.4f % 6.4f
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
*.XVYWTSPFMKLIHGEQCDNRArtprotomat.stpSCOREHIGH ,	
+-0123456789

mkdir %s
Created directory %s
 	
FRAGMENTBLOCKLSTPS=LENGTH=-FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
===============================================================================
Here are your search results from the BLOCKS searcher.
BLKPROB: Cannot open blocks file %smaxscore is too big, increase MAXSCORE from %d

closest_seq: Unable to allocate pair structure!
                         |---%5d amino acids---|==============================================================================                                                           RankFamily                                       Strand  Blocks   P-value
==============================================================================%s	BLOCKS	similarity	%ld	%ld	%8.2g %-10s % 1d     %6ld-%-6ld        %8.2g                                                             CombinedFamily                                       Strand  Blocks   E-value%s BLOCKS similarity %ld %ld %8.2g %-10s % 1d     %6ld-%-6ld        %8.2g

------------------------------------------------------------------------------>%s %d/%d blocks Combined E-value=%8.2g: %s

pvalue_rank(): OUT OF MEMORY
assemble_hits(): OUT OF MEMORY
Cutoff combined expected value for hits=%3.0f
Cutoff block expected value for repeats/other=%3.0f

Enter number of hits to report or blimps configuration file name [%d]: Blocks searched is negative, cannot use for statistics.Alignments done is negative, cannot use for statistics.
Enter name of blocks database searched: 
Enter name of file containing blocks search results: COPYRIGHT 1992-8 Fred Hutchinson Cancer Research CenterUSAGE: blkprob    [-H n -E n -C n -mast|-rank -sum|-gff -stats]           = number of hits to report, use 0 for default     = blimps search output file     = blocks database searched by blimps     = name of blimps configuration file    -H n            maximum number of hits to report    -E n            cutoff expected value for anchor blocks    -C n            min cutoff raw score for anchor blocks    -mast           order results by MAST-type e-values    -rank           order results by RANK-statistic e-values    -sum            output summary only (one line per hit)    -gff		  Sanger Center's GFF output    -stats          produces .dat statistics file    -S filename     header file (default=blkprob.stp)
BLKPROB: Cannot open file blimps file %s

BLKPROB: Cannot open configuration file %s
load_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.
Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directoryA?A BApBA?B?BBABzD??????R?@3333@3333????333333?Dj("(2(B(R(b(r((((((((())")2)B)R)b)r)))))))))**"*2*B*R*b*r*********++"+2+B+R+K^`6
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blkprobfsr.s__get_exit_frame_monitor_ptr__do_exit_code_ptrtrap_tablecrti.svalues-Xa.ccrtstuff.c__CTOR_LIST____DTOR_LIST____EH_FRAME_BEGIN____JCR_LIST__p.0completed.1__do_global_dtors_auxobject.2frame_dummyblkprob.cfrequency.cread_freqconvert.cbasic_matrix_constructionmake_colpre_weighted_sequencesmake_work_pssmcountscount_residuespseudo_altscompute_BZXblocks.cBlockBufLengthBlockBuffererrors.cErrorFilematrix.cmemory.cRecFuncsequences.clbuff.0first_time.1strutil.cprotomat.cgcode.cgctrans.0__CTOR_END____DTOR_END____FRAME_END____JCR_END____do_global_ctors_auxcrtn.s_END__START_putcharfreefree_blockRepeatsassemble_hits_rankstrncpyHomNamehitevalprint_sequence_startCutoffExp__register_frame_info_basesaa_btoaaachar_to_numgroup_resultsuntranslate_sequenceseq_type_dbsaa_adegenmake_binfostrcpyMast__longdouble_usedoutput_matrix_stNRepeatputsNBiasMaxRepeatStatsfputcload_codonsstrtokpvalue_rankstrncasecmpQLendistance_okay__iobCutoffRepeatfwritesequence_typenormalizestrcatstrncmpfree_blistpseudo_diriDatDirmemcpyCutoffScoreset_error_file_nameread_a_matrixbl60_highpasssequence_comparisonfind_max_aa_colmake_blistfrequencyrewind_environgetenvremove_trailing_whitespaceframecmpmatrix_comparisonfprintfstrspnsplit_namesnt_atob___Argvstrandcmpcheck_overlapread_a_blockfopennt_adegenErrorReport__deregister_frame_info_basespr_num_to_aaread_repeatsblank_linefrq_qijpvalues__fpstartoutput_blockget_infoABRT_signal_handlernt_bdegenload_dirigribskov_conversion_methodblock_to_matrixftellgcodescallocfree_sequenceget_token_DYNAMICread_faminit_reclaim_spaceMaxHitinit_binfopb_weightsinsert_flistget_repeatsatofbl62_highpasskr_atoihitprank_etextStrandsnew_blockatoloutput_matrix_mcountalign_blocksCumProbsimilarity_dependent_scaleprint_hits__1cG__CrunMdo_exit_code6F_v_kr_itoadir_unix__ctyperead_block_headerbl60_matrixfflushconsensusnt_btoant_arevcompget_ptile_exiteat_whitespaceinsert_binfostrstrConfig_FlagstrcasecmpSummaryNResultread_a_sequencehitmpvdtempcmpnt_brevcompnext_clusternew_matrixstrchropen_dbsfind_max_aa_pssm__fsrSIFT_pssmErrorBufferfree_matrixRTotread_a_block_fasterbl62_matrix_endcheck_entryVersionoriginal_conversion_method_cleaned_upread_results_get_exit_frame_monitororiginal_conversion_methodread_block_bodyopendir_edatadistanceclose_dbsexpQfilename_finioutput_sequencefseekmainSIFT_conversion_methodmake_flist_PROCEDURE_LINKAGE_TABLE_add_logsMaxHitsmincmpassemble_hitsqfastatexitaa2codonprint_blockmake_gribsQijpvalue_mastfree_work_pssmoutput_matrix_sprev_disthitprob__dso_handleread_biasinit_gcode__fsr_init_valueload_frequencieslogQueryinit_hitsprint_matrixpr_num_to_aa_spacefree_binfoblock_comparisonaltschul_data_dependent_conversion_methodStpFileaafqhitcmpNCumprobTilescumprobfgetsgetscoreaa_atobSeqType_GLOBAL_OFFSET_TABLE_read_sequencestrcspnDbInfontfqstrcmpcodon2aaoutput_block_sclosest_seqNAlignfcloseread_tiles_initmallocNReadcounts_nogapsinsert_blistsystemhypergeoresize_block_sequencesmakedbidsprintflgammamap_blocksCodon_Usagesscanfqsortload_qijreallocget_idshitfamread_configstrncatresize_block_clustersNBlockErrorLevelReportcompute_locpre_weighted_conversion_methodprint_blurbread_to_block_lib_versionNtilesnum_to_aachartoupperBlimpsVerresize_sequencehitrankResults_Jv_RegisterClassesGFF@(#)SunOS 5.10 Generic January 2005@(#)SunOS 5.10 Generic January 2005@(#)SunOS 5.10 Generic January 2005GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)@(#)SunOS 5.10 Generic January 2005ld: Software Generation Utilities - Solaris Link Editors: 5.10-1.482.interp.hash.dynsym.dynstr.SUNW_version.rel.text.rel.got.rel.data.rel.bss.rel.plt.init.fini.rodata.rodata.str1.1.rodata.str1.4.rodata.cst4.rodata.cst8.dynamic.ctors.dtors.eh_frame.jcr.data.rel.local.symtab.strtab.comment.shstrtab	t\	\	"<<o%%P-	B&&7	B$&$&@	B<&<&J	BD&D&S	BT&T&W''`1\+\+\`6`6b66h66p2<9<92DD#hhLiiX;XiXiDjDjD k k }}}}}}}}}}N~~T ~0V 0
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W[SESiTTT-Debug messages on.
Output is in bare format.
Output file is '%s'.
Verbosity level is %i.
Input file %i is '%s'.
# %s
Reading line: %s
blocks_map#MAP#>%s %d %d %d %sdescriptionsequence_map%s %d %dblock_pos%c %d %dReading one family...
%s %s %d %d %d %sEnd of input file reached.
marker//Error: bad data read.
%-20s (%4d)  [---- %d aa]%s: %s
%20s---- %d amino acids

rbOpening '%s' for read.
wbOpening '%s' for write.
Processing file '%s'.
Warning: no input files.
This program takes block map data and generates a graphical map of the
sequences.

Usage: %s [infiles] [options]
Example: %s blocks.mapdata -v2 -o blocks.maps -m80

Arguments to options should be '-o[argument]' or '-o [argument]'.
Use '-' to stand for standard input/output.
Default output is to the screen.

Available options:
 Option          Effect
 -[cfm] number   Use scale mode [constant/full/maximum]
                 Constant: Each character is  amino acids.
                 Full: Each sequence is  characters long.
                 Maximum: The longest sequence in each family is 
                 characters long, the rest are to scale.
                 The default is -c10 (each character is 10 amino acids).
 -h              Get this help screen.
 -i filename     Add an input file(s) (this is not needed if input files
                 are placed before the options). Seperate multiple filenames
                 with spaces.
 -o filename     Set the output filename. The input filename is substituted
                 for '*' within , so '*.vis' is '.vis'.
                 You must use single quotes around  if it contains
                 '*'.
 -v number       Set verbosity level, 0-5. 0 = no messages, 1 = errors only,
                 2 = quiet, 3 = normal (default), 4 = verbose, 5 = debug.
 -a BLxxxxx      Do only a single block family.
Warning: unrecognized option '-%c'.
Scale type is %c, scale value is %i.
Warning: option '-%c' has an attached argument (ignored).
Warning: option '-%c' not used.
Warning: option '-%c' has too many arguments (ignored).
Error: premature end of input file.
%d distinct blocks in %d sequences
Error: cannot open output file '%s'.
Error: Family '%s' not found in file '%s'
.Error: cannot open input file '%s'.
Error: no usable data in file '%s'.
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SCRIPT_NAMEBLOCKS_EMAILrdate '+%y%m'date "+%y%m%d".%s/blimps%s/blksort%s/blkprob/usr/bin/mailx../data-blocks%s/blocks.dat../data-prints%s/prints.dat../data-blplus../data-blplus-minus../docs%s/default.qij%s/default.amino.frq../tmp%s/%d.seq%s/%d.cs%s/%d.csh../log%s/%s%s/%d.mail%s/%d.out%s/%d.blk%s/%d.htmlblocks@fhcrc.orgCONTENT_LENGTHsequencetitleQUERY_STRINGaddresswERror_level          2
DBase                %s
SQuence              %s
OUtput_file          %s
TYpe                 %s
STrands_to_search    %s
FRequency            %s
GEnetic_code         %s
HIstogram            %s
REpeats_allowed      yes
NUmber_to_report     0
COnversion_method    3
OP alts: 5.0 %s :alts
chmod -f 660 %sdatabaseprintsminusbiastystgehiexouoldSV                   yes
prodomdomopfamrawsumgff#!/bin/csh
unalias mv
%s %s >& /dev/null
Block Search Resultsexit(0)
chmod a+x %s%s %s -mast -E %s %s >& %s
%s -r %s -s "%s" %s < %s
%s Block Search Results%s %s >& %s
>%s
>Unknown

Search Error
date%s %s > /dev/null 2>&1%s %s > %s 2>&1
Blksort Error
Blkprob Error
Blimps Error
%s/htmlize-blkprob.pl %s%s/htmlize-blimps.pl %s%s/htmlize-blksort.pl %sError opening pipeContent-type: text/html

REQUEST_METHODPOSTumask 006Queuing %d...CONTENT_TYPE&;`'"|*?~<>^()[]{}$\%s/htmlize-blkprob.pl %s >& %s
%s/htmlize-blimps.pl %s >& %s
%s/htmlize-blksort.pl %s >& %s
You need to enter a sequence to search with.
Your sequence has more than 5000 characters.
Please break it into smaller pieces for searching.
%s %s -mast -E %s %s > %s 2>&1An error occured during the search:
%s
blocks_search: Error opening %s

Blocks Search Results
You can check this URL within 4 hours for your results.

Your results will also be emailed to %s

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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000ERROR: Block %s is too deep (%d), truncated to %d sequences
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ERROR: Block %s is too deep (%d), truncated to %d rows
ERROR: Block %s is too deep (%d), truncated to %d nseq
 width=%d; seqs=%d; 99.5%%=%d; strength=%d 
Enter name of new weighted blocks database: 
Enter name of blocks database: BLWEIGHT: Copyright 1994-2000 by the Fred Hutchinson Cancer Research Center, 
	Seattle, WA, USAAdd sequence weights to blocks.USAGE: blweight    	=input file of blocks to weight	=output file of weighted blocks	=P (position-based) | V (Voronoi) | 
		A (Vingron & Argos) | Cn (n percent clumping)	=M (max=100) | N (sum=#seqs) | # (sum=#)blweight: Calculating position-based weightsblweight: Decimal weights, sum = number of sequencesblweight: Integer weights, maximum weight = 100
Enter scale (M=>max=100, N=>sum=#seq, ###=>sum=###) [M]: 
Enter weighting scheme (P=position-based, V=Voronoi, 
 A=Vingron & Argos, Cn = n-percent cluster [P]: blweight: Calculating Voronoi weightsblweight: Calculating Vingron & Argos weightsblweight: Integer weights, sum = %d
blweight: Calculating %d percent cluster weights
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating..A??333333?BFB88??.>N^n~.>N^n~.>N^n~FY|
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uJD[_ÉUhu8UWVSD$H111ۉ'''"l$D')')')C"l$AT(~F~G~[^_]ÍvUWVS4D$L|$Pw(w#|$TwT$HL$T4[^_]Ékb|$TW@D$$ƍD$TD$ D$TD$L$H,D$,D$$T$L$ D$T$L$T$,D$3D$(‰D$D$L$D$TL$D$T$(L$31҃|$~2L$L$HD$$8u=B9$D$(T$D$(9D$,D$T$,9.	$4[^_]ÐSD$T$L$\$w	$[á¡뫡١떡|kܡ뒡밡e냡&H봡04[UVS[*p@Ћu[^US[×*W8[US[w*7[MATRIXƌˌЌr 	

ukQJ@2$|StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialACGTAGCTACGTATCGCGTAGTACTACGACGT-RNDQEHILKMFPSWYVDNEQARNDCQEGHILKMFPSTWYV*Unknown residue: %d
|width=%d seqs=%d%s: %s not found
  %c  %c    %4d (Peptide) Length: %d
Cons  Gap Len ..
 100 100
*    (, ,
+-0123456789BLIMPS_DIR 	
 	
;TYBLr
Cannot open BL file %s
OUw
Cannot open OU file %s
ML
Cannot open ML file %s
Cannot specify both DB and SQFR and QM required with SQMissing OU output file nameMissing BL input file nameProfile written to %s
%s/docs/default.qij%s/docs/default.amino.frq%s/docs/default.iijFR and QM required with MAConsensus written to %s
LL
Cannot open LL file %s
Invalid consensus type: %d
Missing SU input file nameDB required with LLDB required with MLSQDB
Cannot open DB file %s

Cannot open SQ file %s
FRPCSUMA
Cannot open FR file %s
PFPSIQMPFS
Cannot open QM file %s

Cannot open SU file %s

Cannot open MA file %s
TRBLI block=%s, pos=%d
 with counts + pseudo-counts%s %sSequence %s not found
Configuration file errorsCOBBLER Version %s
USAGE:  cobbler 
Cannot open file %s
>%s %s
%lgrfield has no effect.
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqpb_weights:%d ignored for %s
 ,
.+-0123456789BLIMPS_DIR%s/docs/default.sijrMixture=Alpha==	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIXID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
width=%d;%fmotif%swidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for matrix %sSetting width to zero
  |% 4d--+----%c |% 6.4f    ID   %s
AC   %s
DE   %s
MA   %s
  %c     %c       A   C   G   T
%3d   *   -
//
% 9.4f % 9.4f
%3d
    *         -
 %c   *   -
% 6.4f % 6.4f
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000%s %s	is first sequence most like consensus (%d %d)
%s %s	is first sequence least like consensus (%d %d)
%s %s from %d to %d with embedded PSSM>%s %s from %d to %d with embedded consensus blocks
#COBBLER Profile for %s %s from %d to %d
#
      COBBLER Profile for %s %s from %d to %d
FR and QM required with Type 3FR and QM required with Type 4Most like consensus written to %s
Least like consensus written to %s
WARNING: Aligned blocks overlap!!!  block=%s, pos=%d, last pos = %d
Query sequence %s is shorter than minimum path width
Type 2: Consensus based on substitution matrix with counts (no pseudo-counts)Type 4: Consensus based on PSSMType 1: Consensus based on percentage: %d
Type 3: Consensus based on substitution matrixCOPYRIGHT 1999 Fred Hutchinson Cancer Research CenterMake a consensus sequence and PSSM from a family of blocks
Enter name of configuration file: load_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.G.G.G.$@???R?@3333@3333????333333??B88BBBABzD???  . > N ^ n ~         !!.!>!N!^!n!~!!!!!!!!!"".">"N"^"n"~"""""""""
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t=Ee[^)(((([)y))))('*)	*((stdinstdoutdefault.codon.use	&D_yMATRIX`n|RukZPF5+
ݵ̵xj<S 	

StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialACGTAGCTACGTATCGCGTAGTACTACGACGT-RNDQEHILKMFPSWYVDNEQARNDCQEGHILKMFPSTWYV* -3'  Core: degen=%.0f *** CLAMP NEEDS EXTENSION%s -5'   Complement%c  No suggested primers found.Block is too narrow
Processing Block %s
odds ratios normalized to 100pseudos, log odds, natspseudos, log odds, half bitspseudos, log odds, third bitspseudos, odds ratios, natsjust counts+pseudo countsaverage scoreBLIMPS_DIRCODEHOP Version %s
 Center, Seattle, WA, USA%s  %d  2 3 5 6 10 20 30 default.amino.frq%s/docs/%sidentity.frq%s/docs/r...trying %s ...
 ? help HELP usage USAGE first_in_inputCannot open input file %s
wCannot open output file %s

%s  |%4d--+----%c |% 4d     Complement
%s
%4d        ------------% 4d                    %lgrfield has no effect.
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqpb_weights:%d ignored for %s
 ,
.+-0123456789BLIMPS_DIR%s/docs/default.sijrMixture=Alpha==	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIXID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
width=%d;%fmotif%swidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for matrix %sSetting width to zero
  |% 4d--+----%c |% 6.4f    ID   %s
AC   %s
DE   %s
MA   %s
  %c     %c       A   C   G   T
%3d   *   -
//
% 9.4f % 9.4f
%3d
    *         -
 %c   *   -
% 6.4f % 6.4f
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Warning: Unrecognized parameter - "%s".
 len=%d  Clamp: score=%d, len=%d temp=% .1fend:   pos=%d, len=%d, core_score=%.1f
oligo start: pos=%d, len=%d, core_score=%.1f,
 last pos=%d, core score=%.2f %s

Processing Complement of Block %s
COPYRIGHT 1997-2004, Fred Hutchinson Cancer ResearchWarning: Core strictness parameter requested (%3.2f) is out of range (%3.2f to %3.2f)
Using default value (%3.2f).
Warning: Clamp strictness parameter requested (%3.2f) is out of range (%3.2f to %3.2f)
Using default value (%3.2f).
Cannot open codon usage file %s

Parameters:
 Amino acids PSSM calculated with %s
 and back-translated with %s genetic code
 and codon usage table "%s"
 Maximum core degeneracy %3.0f    Core strictness %3.2f
 Clamp strictness %3.2f   Target clamp temperature %3.2f C
 DNA Concentration %3.2f nM   Salt Concentration %3.2f mM
 Codon boundary %d   Most common codon %d
 Verbose %d   Output %d
 Begin %d   PolyX %d
Suggested CODEHOPS: The degenerate region (core) is printed in lower case,
the non-degenerate region (clamp) is printed in upper case.Usage: %s [blocks-input_file_name [output_file_name]]
 [-Ffamily_name]
 [-Ppssm_type]
 [-Ccodon_usage_file]
 [-Ggenetic_code_type]
 [-Dcore_degeneracy_parameter]
 [-Score_strictness_parameter]
 [-Lclamp_strictness_parameter]
 [-Tclamp_temperature]
 [-Nconcentration]
 [-Rose_restrictions]
 [-Most_common_codon]
 [-Verbose]
 [-Output]
 [-Begin]
 [-ApolyX_parameter]

Defaults: in-"%s" out-"%s"
 family-"%s"
 pssm_type-"%d"
 codon_usage-"%s"
 genetic_code_type-"%d"
 core_degeneracy-"%3.1f"
 core_strictness-"%3.1f"
 clamp_strictness-"%3.1f"
 clamp-temperature-"%3.1f"
 concentration-"%3.1f"pM
 Rose-FALSE
 most_common_codon-FALSE
 verbose-FALSE
 begin_oligo-TRUE
 polyX-"%d"

Comments: "-" instead of a input/output file name => stdin/stdout
          The order of the arguments is not important but the
          first name is for the input file and the second for the output.
pssm_type = 2 odds ratios normalized to 100
	3 pseudos, log odds, nats
	5 pseudos, log odds, half bits
	6 pseudos, log odds, third bits
	10 pseudos, odds ratios, nats
	20 just counts+pseudo counts
	30 average score
Genetic code type = 0 Standard
	1 Vertebrate Mitochondrial
	2 Yeast Mitochondrial
	3 Mold Mitochondrial and Mycoplasma
	4 Invertebrate Mitochondrial
	5 Ciliate Nuclear
	6 Echinoderm Mitochondrial
	7 Euplotid Nuclear
	8 Bacterial and Plant Plastid
	9 Alternative Yeast Nuclear
	10 Ascidian Mitochondrial
	11 Flatworm Mitochondrial
	12 Blepharisma Macronuclear
	13 Chlorophycean Mitochondrial
	14 Trematode Mitochondrial
	15 Scenedesmus obliquus mitochondrial
	16 Thraustochytrium mitochondrial
Degeneracy parameters=0.0 all nucleotides that actually appear are counted
	1.0 only nucleotide with highest value counted
	Between 0 and 1 nucleotides with high values counted,
	 if value/highest-value >= degeneracy parameter
Clamp temperature     Target melting temperature for clamp in degC 
Concentration         Probe concentration in nM
Rose restrictions     If set, uses Tim Rose's restrictions on boundaries
                      of core degenerate region.
Most common codons    If set, uses most common codons in clamp.
Begin oligo           If set, oligo must start on a conserved column,
                       otherwise core strictness is applied.
Apoly-x       Maxiumum number of consecutive nucleotides of same type.

Warning: Unspecified gcode type (%d) requested.
Using default gcode type (%d).
"%s help" for help.

Warning: Clamp temperature requested (%3.2f) is negative
Using default value (%3.2f).
Warning: Concentration requested (%3.2f) is negative
Using default value (%3.2f).
Warning: Clamp strictness parameter requested (%3.2f) is less than core strictness parameter (%3.2f)
Using default values (%3.2f, %3.2f).

No correctly formatted blocks found to processWarning: Unspecified pssm type (%d) requested.
Using default pssm type (%d).
"%s help" for help.

load_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.L4@333333 @Xn?fffffq@0@???R?@3333@3333????333333??B?zD>@@@pBHB??BABzD???t#!!"".">"N"^"n"~"""""""""##.#>#N#^#n#~#########$$.$>$N$^$n$~$$$$$$$$$%%.%>%N%^%		
		

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/[StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialACGTAGCTACGTATCGCGTAGTACTACGACGT-RNDQEHILKMFPSWYVDNEQARNDCQEGHILKMFPSTWYV* 	
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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000 Fred Hutchinson Cancer Research CenterEnter organism name (leave blank for first organism in file): Looking for organism %s in %s

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GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
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Information: %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000COPYRIGHT 1998, Fred Hutchinson Cancer Research Centerfastaseqs: Converts a file of sequences to FASTA formatUSAGE: fastaseqs       = input file of seqences in a common format    = output file of sequences in FASTA format
Enter name of input sequence file: read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
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BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
width=%d;%fmotif%swidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for matrix %sSetting width to zero
  |% 4d--+----%c |% 6.4f    ID   %s
AC   %s
DE   %s
MA   %s
  %c     %c       A   C   G   T
%3d   *   -
//
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 %c   *   -
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GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Column score cutoff has to be between -1 and 1 !The value given (%f) is out of range.

Enter name of a file with blocks or block matrices: 
Bias fraction cutoff has to be between 0 and 1 !Input file doesn't have any entries !First entry in input file has neither block nor matrix lines !First entry in input file has both block and matrix lines !Unable to recover enough memory to continue.  Aborting.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.read_a_prodom_entry(): Error reading sequence %s in block %s,Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.
Error ! Problem in ProDom entry %s
second word in description line doesn't begin with a (second word in description line doesn't end with a )Error ! Problem in format of ProDom entry %s
A non-digit in the number-of-sequences field "%s"
 distance from previous block=(%d,%d)adapted from ProDom entry; width=%d; seqs=%d;Error ! Problem in format of ProDom entry %s sequence-line %d
A non-digit in the sequence start position %s
Error ! Problem in format of ProDom entry sequence-line %d
Sequence %s has length of %d instead of expected %d
Error ! Actual number of sequences in ProDom entry %s
different than what the entry reportsError ! Problem in format of ProDom entry description-lineError ! Problem in format of ProDom entry description -lineError ! Number of sequences in ProDom entry %s (%d) is less than 2
Error ! Not enough sequences (%d) in ProDom entry %s
Error. variable db_type (%c) is of unknown type !

%s blocks_db [column score cutoff [bias fraction cutoff [min biased cols [debug level]]]]

Cannot open output file file "%s"
Normalized Sum-of-Products column score
Column score cutoff %.3f. Bias-fraction cutoff %2d percent (minimum %d columns).
               Pairs                 Columns         ClumpsBlock    Width Total Biassed Percent Biassed Percent Biassed Percent%-10s %2d   %4d  %4d   %3d      %4d   %3d      %4d   %3d%-10s %2d   %4d  %4d   %3d      %4d   %3d      %4d   %3d
%d biassed blocks found in the %d blocks.%d biassed blocks found in the %d blocks from file %s.load_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.@FB?ABBABzD???Y@??R?@3333@3333????333333?.>N^n~.>N^n~.>N^n~]p

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uA9x/Eu@Puuk\UWVSU|[UxhEx^u$ujUvjUxlPEu$ujjExƒE҉u$^ujjUx1U~3El1ɋEF9ujjuue[^_ǂxUWVSU1hu$ujS11uǃǃxǃǃfl=ESu=tP؍e[^_ã5uuj녃SK1UWVSEPhh$wU3t8}PE9tЋEe[^_øǾjEe[^_US]wXkXYYM]]>T$ҋD$ttD$T$vøÉUWVS}hMXZWh[^XGdPhb	Y[PhiXZ,Php^XXPhwtplh |hDEE…E1MDDDPh:UDH&hMD1ۃ~7̵PUCD9˃j
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PUCD9UWVS}v:Puhhh$juue[^_WuhuEdPhuEPhŒuE,1hVY tHVXRFMƁ,1I)SXRVMƄ,Etp|lXhRXQVOVhˌuEDžLuj
#ULȃDžH1LDPXQLX1Iv&H~X|uƄXULDXPhӌu=MLD1ۃ~@u̵P*ELCD9‹}SLD݄ٽVfV<fT٭T۝P٭VPPhuhHULH9sLLE9 ujjhOYuVe[^_؋LD݄ٽVfV%<9LDhErrorNo sequences specified.
Warning
Sequence %d not found.

%s %s %s %s %s > /dev/nullSequences weighted by (GIF image)]
 Vingron & Argos weights %% clustering position-based weights Voronoi weightsContent-type: text/html

REQUEST_METHODPOSTCONTENT_TYPEumask 006ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
&;`'"|*?~<>^()[]{}$\FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
%s; distance from previous block = (%dSequence names box is used and the alignment is in FASTA format.
Sequence names will be taken from the alignment
(first word in the sequence header lines -
'>seq_name 123 aa example protein').
The alignment width you gave (%s) is different than the first sequence length (%d).

Error reading sequence %d. It is shorter (%d) than the apparent alignment length. Padding the end of the sequence with gaps.

Error reading sequence %d.

Error reading sequence %d. %d more residues in the sequence than the expected %d.

Number of sequence start positions (%d) is different than number of sequences (%d).

The number of sequences you gave (%s) is different from the number found (%d).

Number of sequence names (%d) is different than number of sequences (%d).

Sequence (%d) is too short (%d). The minimal length is %d.

Judging by the first sequence length (%d) the alignment is too long. The maximal length is %d.

Judging by the first sequence length (%d) the alignment is too short. The minimal length is %d.

No start position found for sequence %d.

No name found for sequence %d.

An error occured weighting the block.Please try again at a later time.If it fails again contact the maintainer of these pagesand describe what caused the problem with an example.
Block Formatter output
Block Formatter output
. The weights were scaled to 1-100, 100 having most weight.
[block logo [block PSSM (what is a PSSM)][block logo [block PSSM (what is a PSSM)]application/x-www-form-urlencodedThis script can only be used to decode form results. This script should be referenced with a METHOD of POST.If you don't understand this, see this forms overview.%c
What could have happened is that you just reloaded this page rather than redoing the search.
If you use NETSCAPE it has a tendency to try to reload a page when you go back to it.  This may be why you have this error.MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.?333333?.>N^n~.>N^n~.>N^n~ 
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ZdddddddddddddddddydsdmdgdadeeeeeeeeeeeeeeeeeeeNeeUniversa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
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FRAGMENTBLOCKLSTPS=LENGTH=-FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
LISBLK: (C) Copyright 1995-2000, Fred Hutchinson Cancer Research Center %d sequences from %s
  were found in %s

Enter name of file containing list of sequences: MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.
Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directory?333333?@
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e^TF81 StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialACGTAGCTACGTATCGCGTAGTACTACGACGT-RNDQEHILKMFPSWYVDNEQARNDCQEGHILKMFPSTWYV*>%s
CLUSTALSTOCKHOLM%s.%dwr\rm %s 	 	
%s
ClustalStockholmERROR reading Clustal file
%s as proteinTrying  MSF format.
//mablock.%d
ERROR reading MSF file
%sUNK motif; width=%d; seqs=%d;%s %d : %s %d
>%20s          from blocks
%5d P1;Non-unique sequence name: %s
%s%dModified name to %s
%s; BLOCK
Cannot open file %s

Enter name of output file: 

pb_weights:%d ignored for %s
 ,
.+-0123456789BLIMPS_DIR%s/docs/default.sijrMixture=Alpha==	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIXID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
width=%d;%fmotif%swidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for matrix %sSetting width to zero
  |% 4d--+----%c |% 6.4f    ID   %s
AC   %s
DE   %s
MA   %s
  %c     %c       A   C   G   T
%3d   *   -
//
% 9.4f % 9.4f
%3d
    *         -
 %c   *   -
% 6.4f % 6.4f
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Trying CLUSTAL/STOCKHOLM format.
WARNING: Sequences appear to be DNA but will be treated%s; distance from previous block=(%d,%d)WARNING: sequence segments are of different lengths

Enter name of blocks database: MABLOCK: Copyright 2001 Fred Hutchinson Cancer Research Center
USAGE: mablock         = file of fasta or clustal multiple alignments             Clustal format must have CLUSTAL on first non-blank line      = output file of blocks             Puts blocks in out.blks & sequences in out.seqs      = output type, B=blocks, F=fasta    = minimum ungapped width to define a block    = maximum block width%d blocks found with minimum width %d and maximum with %d
Output written to %s.blks and %s.seqs

Enter type of output file [B=blocks|F=fasta]: WARNING: Maximum number of sequences = %d
no blocks found with minimum width %d
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.??R?@3333@3333????333333?BABzD???"2BRbr"2BRbr"2BRbr0
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mablockfsr.s__get_exit_frame_monitor_ptr__do_exit_code_ptrtrap_tablecrti.svalues-Xa.ccrtstuff.c__CTOR_LIST____DTOR_LIST____EH_FRAME_BEGIN____JCR_LIST__p.0completed.1__do_global_dtors_auxobject.2frame_dummymablock.cconvert.cbasic_matrix_constructionmake_colpre_weighted_sequencesmake_work_pssmcountscount_residuespseudo_altscompute_BZXblocks.cBlockBufLengthBlockBuffererrors.cErrorFilematrix.cmemory.cRecFuncsequences.clbuff.0first_time.1strutil.cgcode.cgctrans.0__CTOR_END____DTOR_END____FRAME_END____JCR_END____do_global_ctors_auxcrtn.s_END__START___ctypesequence_typeatofOutNameatoistrrchrmake_blockinit_reclaim_spaceprint_matrixMinWidthsystemaa2codonRTotaafqmatrix_comparisonfrequency__register_frame_info_basesmake_blistfseekstrspnnew_matrixtoupper_GLOBAL_OFFSET_TABLE__edataeat_whitespacestrncatfprintf__iob__deregister_frame_info_basesget_tokenoriginal_conversion_methodrewindread_a_matrixnew_blockputslog10_environpseudo_diri_Jv_RegisterClassesaa_adegenmemcpyDbInfostrncpypre_weighted_conversion_methodSIFT_pssmgetenv_finistrcpy__fpstartremove_trailing_whitespace__fsrblock_to_matrixfopenprint_sequenceuntranslate_sequenceresize_block_sequencesErrorLevelReportABRT_signal_handlerfgetsfree_work_pssm_get_exit_frame_monitorsimilarity_dependent_scalegcodesload_diriputchartry_clustalprint_blockread_block_bodycounts_nogapsBlock_AC_etextread_to_blockstrtokinit_gcodefree_blistreallocnt_btoaBlock_DEgetpidstrncmp_exitnt_bdegennt_arevcompmake_gribsnormalizestrstr_PROCEDURE_LINKAGE_TABLE_block_comparisonread_sequencent_adegen_DYNAMICmallocresize_sequenceset_error_file_namepb_weightsstrchrinsert_blistnt_brevcompaa_btoant_atobblank_lineseq_type_dbsfree_matrixftelloutput_fastafflushfind_max_aa_pssmsequence_comparisonfputcread_block_header_mcountfix_namesfreeoutput_blockfcloseErrorBufferoriginal_conversion_method_cleaned_up__longdouble_used_end__fsr_init_valueaa_atob_init__dso_handleBlock_IDfree_block__1cG__CrunMdo_exit_code6F_v_fasta_seqs_lib_versionload_qijntfqcodon2aaoutput_matrix_stfree_sequence___ArgvErrorReportfind_max_aa_colsscanfadd_logsexpatexitQijlgammaoutput_sequenceoutput_matrixsprintfcallocread_a_blockoutput_block_sresize_block_clustersread_a_sequence_startorder_seqaltschul_data_dependent_conversion_methodstrcatfwriteread_a_block_fastermaingribskov_conversion_methodtry_msffind_blocksnext_clusterlogoutput_matrix_sSIFT_conversion_methodoutput_blocksMaxWidthstrcmp@(#)SunOS 5.10 Generic January 2005@(#)SunOS 5.10 Generic January 2005@(#)SunOS 5.10 Generic January 2005GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath)@(#)SunOS 5.10 Generic January 2005ld: Software Generation Utilities - Solaris Link Editors: 5.10-1.482.interp.hash.dynsym.dynstr.SUNW_version.rel.text.rel.got.rel.data.rel.bss.rel.plt.init.fini.rodata.rodata.str1.1.rodata.str1.4.rodata.cst8.rodata.cst4.dynamic.ctors.dtors.eh_frame.jcr.data.rel.local.symtab.strtab.comment.shstrtab	 "oP-	B7	B@	B44J	B<<S	BLLW01\00bPPhhh8p22hh/P ;D  N @S <-
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sitct]tWtQtKtEt?t9t3t-t't!tttt	ttssstttttttttttttttttttttttttuuuttttttttttttttttt9uFu=v0v#vv	vuuuuuuuuuuzumu`uSu9u| 
	vlbQG-&ׇXoStandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialACGTAGCTACGTATCGCGTAGTACTACGACGT-RNDQEHILKMFPSWYVDNEQARNDCQEGHILKMFPSTWYV*does not end with an "A".
block %s.
>%s %d %d %d %s
%s
%s %d %d
%c %d %d
//
wrCannot open input file %s

Output in file %s.
Unable to allocate idsCannot open output file %s
ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
*.XVYWTSPFMKLIHGEQCDNRArtprotomat.stpSCOREHIGH ,	
+-0123456789

mkdir %s
Created directory %s
 	
FRAGMENTBLOCKLSTPS=LENGTH=-FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Warning ! The name of the first block in family %s
Note - Not all sequences in family %s contain all the blocks.
Error ! Block %s is not the block expected to follow (by name)
Note - Block %c PRECEDES block %c in sequence %s of family %s.
Note - Blocks %c (%d-%d) and %c (%d-%d) in sequence %s
of family %s overlap.
Note - Sequence %s in family %s does not contain block %c.
Note, first block (%c %d-%d) in sequence %s of family %s
begins BEFORE the first aa of the sequence !
Error ! Couldn't find all %d sequences.
Error ! Last block (%c, %d-%d) in sequence %s of family %s
is out of bounds.
Warning unrecognized parameter - "%s".
Input file "%s" processed by program "%s"

Couldn't find or process block family %s !
Couldn't make a block map for block family %s.
A program to create block map description(s) from block family(ies) data:
%s blocks-input_file_name [output_file_name] [-Fblock_family_name] [-Lsequence_length_file]
Defaults: in-"%s" out-"%s" block_family_name-"%s"

Comments: "-" instead of an input/output file name => stdin/stdout
           The order of the arguments is not important but the
           first name is for the input file and the second for the output.
          block_family_name = "" : all block families in input

((input now expected from screen; CTRL-C to quit))


%d block family(ies) processed into maps.
%d block family(ies) could not be processed.Note: The sequence lengths shown are the 'right-most' sequence positions found in the blocks.
Couldn't make a block map for block family %s.

Error ! Input file %s does not contain any blocks.
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.
Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directory?333333?L"2BRbr"2BRbr"2BRbr
$$
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GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
sl.cp->key != NULLdefault scoring method.
--------Histogram:
   %5d - %-5d : %d
   %5d -       : %d
pattern.cNumInSL(residue_list) == 0pat_file != NULLID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
width=%d;%fmotif%swidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for matrix %sSetting width to zero
  |% 4d--+----%c |% 6.4f    ID   %s
AC   %s
DE   %s
MA   %s
  %c     %c       A   C   G   T
%3d   *   -
//
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 %c   *   -
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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000First 20 characters of sequence name must be unique.
Unable to read sequence file: %s to determine the type of database
Unknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Sequences appear to be DNA: Block Maker is designed for protein.Only %d sequence found, need at least 3
get_file_list(): Unknown file group %d.Unable to recover enough memory to continue.  Aborting.
Already have a frequency file: %sinsert_file(): Bad file list, not entering filename "%s"               into a file list
get_file(): Unknown file group            Unable to open a file
Unable to read sequence file: %s to determine the type of database
Unable to open frequency file: %s
Unable to open database file: %s
Unable to open matrix file: %s
Unable to read pattern file: %sUnable to read sequence file: %sUnable to open block file: %s
Unknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Assuming there is no title and just sequence.
Unable to read pattern file: %s
Unable to read sequence file: %s
get_file(): Bad file list, unable to open a file
rewind_file(): Bad file group, unable to rewind file list
get_current_file_name(): No files in the file group                         Unable to return a file name
get_current_file_name(): Bad file group, unable to return a file name
get_file_name(): Requested file out of the range of the files                 in the file group                 Unable to return a file name
get_file_name(): No files in the file groupget_file_name(): Bad file group, unable to return a file name
number_of_files(): Bad file group, unable to report number of files
close_file() : Bad file group, unable to rewind file list
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.Unable to recover enough memory to continue.  Aborting.
Invalid matrix-sequence scoring method specified, %d.Setting the method to the default value and using theNo pattern for matrix %s, Scoring the entire matrix
score_and_enter(): Tried to score a sequence that is not an                   amino acid sequence.  Not scoring the                   sequence %s
---------------------------------------------%-8s %4u %-45s      %4d   %4d %2d %6d %s
%-8s vs %-7s   %-20s... & %-20s... %4d %4d %2d %6d %6d %s
%-11.11s %-50.50s      %4d   %4d %2d %6d %s
%-20.20s %-62.62s %4d %2d %5d %6d %s
Unable to recover enough memory to continue.  Aborting.
enter_score(): Error placing matrix score into list
default_scoring_method(): matrix %s has length <= 0default_scoring_method(): Not scoring the sequence.
default_scoring_method(): sequence %s has length (amino acids) <= 0Unable to recover enough memory to continue.  Aborting.
Unable to find pattern for PSSM %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
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WVSD$+D$1;5L|$X}0Pt9}9BAu9}9 FA;5L|[^_ÐUVS]SuP$XPEQBEA=klQEQEEe[^ÍvUWVS]S}$1ۃ 0PkZC
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0e[^VSt$;5LL$T$sPtvJxCAuJx AJy[^ÉUWVSE]ut8u)t^QVhP%Fw{$vPS1If: D߉уDuVuhPŗE#w$h.SҖe[^_Ãh?hRكh_σhyŃh뻃h뱃h맃hʑ띃h듃h뉃h|h	oh'bh?UhWHhk;h|.h!hUxXEfdut$u)j耔XjBP˔jah5TPEPPhhŔXjUjwÉUjcÉUjOÉUEjT3UVS[&:p@Ћu[^US[9?[US[9Ö[k}a}a}a}a}a}a}a}u}a}a}}}a}}}}}P}7~a}a}a}*~a}a}~a}a}~~a}a}a}a}a}a}a}a}a}}}}a}}a}}a}a}a}a}a}a}a}} program halt.truefalse/Ibar{
%% make a horizontal bar
gsave
  newpath
    charwidth4 neg 0 moveto
    charwidth4 0 lineto
  stroke
grestore
} bind def

/Ibeam{ %% height Ibeam
  /height exch cm def
  1 setlinewidth
  ifelse
  gsave
    Ibar
    newpath
      0 0 moveto
      0 heightDRAW rlineto
    stroke
      0 height moveto
      0 height rmoveto
      currentpoint translate
  grestore
  setthelinewidth
%% make the number
  neg %% prepare for move
  sub 2 div %%
  show
charwidth 0 translate
   barwidth 0 translate
} def

%% definitions for maketic
  0 1 barbits abs cvi
  {/loopnumber exch def

    %% and find its width
    loopnumber 10 str cvrs
    /halfnumberheight
      uy ly sub 2 div
    def

    stringnumber show

    %% now show the tic mark
    numberwidth 0 rlineto
  } for
    /labelstring (bits) def
    numberwidth neg 2.5 mul
    barheight
    sub 2 div
    translate
    90 rotate
    0 0 moveto
    labelstring show
} def

/degpercycle 360 def
 
%%             cosine -
  /thickness exch def
  /dash exch def
  /step exch def
  /ymax exch def
  /xmax exch def
  /ymin exch def
  /xmin exch def
  /base exch def
  /wavelength exch def
  /phase exch def
  /amplitude exch def
    /c currentlinewidth def
    xmin ymin c sub moveto
    xmax ymin c sub lineto
    xmax ymax c add lineto
    xmin ymax c add lineto
    closepath
    clip

    xmin dup fun moveto
      dup fun lineto } for
    stroke

%% See the censor program.
%%]]%%*)

/startpage { %% start a page
  xcorner ycorner translate
  rotation rotate
%% See the censor program.

/endpage { %% end a page
/startline{ %% start a line
/endline{ %% end a line
  maketic
  makebar
%%
%% logo from %ld to %ld
%%%%EndComments

%% user defined parameters
/lowest %ld def
/highest %ld def
/bar %ld def
/xcorner %*.*f cm def
/ycorner %*.*f cm def
/charwidth %*.*f cm def
/barheight %*.*f cm def
/barwidth %*.*f cm def
/barbits %*.*f def %% bits
/Ibeamfraction %*.*f def
/barends  def
/showingbox /outline /caps /stacksperline %ld def
/linesperpage %ld def
/linemove %*.*f def
/numbering /shrinking /shrink %*.*f def
/HalfWhiteIbeam  def

/fontsize charwidth def

    true charpath 
    flattenpath 
  /uy exch def
  /ux exch def
  /ly exch def
  /lx exch def
    xsize 0 lineto
    xsize ysize lineto
    0 ysize lineto
    0 0 lineto
    [3] 0 setdash
  ysize 0 lt {
    /ysize ysize abs def
    xsize ysize translate
    180 rotate
  } if

  shrinking {tc (|) ne {
    shrink shrink scale
  } if} if

  2 {
    gsave
    tc charparams
    grestore

    dup 0.0 ne {
      /ymulfactor exch def
    } %% end if
    {pop pop}
    ifelse

      /xmulfactor exch def
    ifelse
  } repeat

  %% Avoid x scaling for I
  xmove ymove moveto
  %% Outline characters:
  tc true charpath
  clip stroke
    /char exch def
    /charheight exch cm def
r%c%lg%lg%lg%*[^
]    char (%c) eq {%ld setrgbcolor} if
  tc show
%*[^
]%*.*f    %% string number %ld
    %% center the string
    /stringscale %*.*f def
        charwidth mul add 2 div
    %*.*f cm moveto
 show
    %%
    %*.*f cm %*.*f cm moveto
    ""%ld%ld%*[^
]%ld%*[^
]%lg%lg%*[^
]%lg%*[^
]in the Red book.
%lg%lg%lg%*[^
]missing all parametersmissing rotation parametermissing charwidth parameterlinemove parameter is missingshrink parameter is missingbarends parameter is missingmissing barbits parameteroutline parameter is missingcaps parameter is missingmissing a user defined string%c Rs total is %*.*f +/- %*.*f bits(%ld ) makenumber
%% xmin ymin xmax ymax step:
%% dash thickness:
 %*.*f cm %*.*f cm cosine
mark scale must be positive fill
 stroke
 %*.*f cm 0 translate
colorssymvecmakelogo %4.2f
wendline
%%!PS-Adobe-
%%%%Title: makelogo %4.2f
%% %ld symbols.
%ld%ld%lg%lg%*[^
]%c%ld%*[^
]
THE SYMVEC FILE IS BAD!But the noted number is %ld
%% at coordinate %ld
%*.*f () numchar
%*.*f Ibeam
%c%*[^
]shift
endpage
startline %% line number %ld
makebar
%%%%Page:? ?

startpage
Please use a zero!Alphabet Logo%% Alphabet Logo
startpage startline
writing page %ld
endline endpage
Pascal system error %dPascal system I/O error %d (out of memory) (stopped by user) (bus error) (CASE value range error) (value range error) (real math overflow) (divide by zero) (integer overflow) (reference to NIL pointer) (file write error) (end-of-file) (not open for direct access) (not open for writing) (not open for reading) (bad input format) (file not open) (file not found) (bad file name) (illegal I/O request)%s
%% Make an Ibeam of twice the given height, in cm
  /heightDRAW height Ibeamfraction mul def
     HalfWhiteIbeam outline not and
     {0.75 setgray} %% grey on bottom
     {0 setgray} %% black on bottom
    charwidth2 height neg translate
    0 setgray %% black on top
      0 heightDRAW neg rlineto
/makenumber { %% number makenumber
  shift %% shift to the other side of the stack
  90 rotate %% rotate so the number fits
  dup stringwidth pop %% find the length of the number
  charwidth (0) charparams uy ly sub %% height of numbers
  moveto %% move back to provide space
/shift{ %% move to the next horizontal position
/makebar { %% make a vertical bar and shift
   barwidth barheight (|) boxshow
/str 10 string def %% string to hold number
%% points of movement between tic marks:
%% (abs protects against barbits being negative)
/ticmovement barheight barbits abs div def

/maketic { %% make tic marks and numbers
  %% initial increment limit proc for
    %% convert the number coming from the loop to a string
    /stringnumber exch def %% string representing the number

    stringnumber stringwidth pop
    /numberwidth exch def %% width of number to show

      stringnumber charparams %% capture sizes
    numberwidth 2 mul %% move back two digits
    neg loopnumber ticmovement mul %% shift on y axis
    halfnumberheight sub %% down half the digit

    moveto %% move back the width of the string

    0 halfnumberheight rmoveto %% shift up again
    labelstring stringwidth pop
/cosine {%%    amplitude  phase  wavelength  base
%%             xmin ymin xmax ymax step dash thickness
%% draws a cosine wave with the given parameters:
%% amplitude (points): height of the wave
%% phase (points): starting point of the wave
%% wavelength (points): length from crest to crest
%% base (points): lowest point of the curve
%% xmin ymin xmax ymax (points): region in which to draw
%% step steps for drawing a cosine wave
%% dash if greater than zero, size of dashes of the wave (points)
%% thickness if greater than zero, thickness of wave (points)

  %% fun := amplitude*cos( ((-y-phase)/wavelength)*360) + base
  /fun {phase sub wavelength div degpercycle mul cos
           amplitude mul base add} def

    /originallinewidth currentlinewidth def
    thickness 0 gt {thickness setlinewidth} if
%%   Make the curve fit into the region specified
    xmin step xmax { %% loop from xmin by step to xmax
    dash 0 gt {[dash cvi] 0 setdash} if %% turn dash on
    originallinewidth setlinewidth
/circle { %% x y radius circle - (path)
newpath 0 360 arc closepath} bind def

%% The following special comment allows deletion of the repeated
%% procedures when several logos are concatenated together
  %% set the font used in the title strings
  /Times-Bold findfont fontsize scalefont setfont
  erasepage %% REMOVE FOR PACKAGING INTO ANOTHER FIGURE
  %% now move up to the top of the top line:
  0 linesperpage linemove barheight mul mul translate

  %% set the font used in the logos
  /Helvetica-Bold findfont fontsize scalefont setfont
%%(*[[ This special comment allows deletion of the repeated
  showpage %% REMOVE FOR PACKAGING INTO ANOTHER FIGURE
%% move down to the bottom of the line:
  0 linemove barheight mul neg translate
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% End of procedures %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

/cmfactor 72 2.54 div def %% defines points -> cm conversion
/cm {cmfactor mul} bind def %% defines centimeters

/rotation %*.*f def %% degrees
/knirhs 1 shrink sub 2 div def
/charwidth4 charwidth 4 div def
/charwidth2 charwidth 2 div def

%% Since outlining goes around the inner edge of the character
%% make the thickness of the character bigger to compensate.
/setthelinewidth {2 setlinewidth} def
setthelinewidth %% set to normal linewidth

%% Set up the font size for the graphics
(*[[ This special comment allows deletion of the repeated
/charparams { %% char charparams => uy ux ly lx
%% takes a single character and returns the coordinates that
%% defines the outer bounds of where the ink goes
    %% take the character off the stack and use it here:
    pathbbox %% compute bounding box of 1 pt. char => lx ly ux uy
    %% the path is here, but toss it away ...
/dashbox { %% xsize ysize dashbox -
%% draw a dashed box of xsize by ysize (in points)
  /ysize exch def %% the y size of the box
  /xsize exch def %% the x size of the box
    %% Define the width of the dashed lines for boxes:
/boxshow { %% xsize ysize char boxshow
%% show the character with a box around it, sizes in points
  /tc exch def %% define the character
  /ysize exch def %% the y size of the character
  /xsize exch def %% the x size of the character
  /xmulfactor 1 def /ymulfactor 1 def

  %% if ysize is negative, make everything upside down!
    %% put ysize normal in this orientation
  %% Don't show the box if it is a vertical bar, otherwise do.
  showingbox {tc (|) ne {xsize ysize dashbox} if} if

    xsize knirhs mul ysize knirhs mul translate
    xmulfactor ymulfactor scale
    ysize %% desired size of character in points
    uy ly sub %% height of character in points
      div %% factor by which to scale up the character
    xsize %% desired size of character in points
    ux lx sub %% width of character in points
  %% Adjust horizontal position if the symbol is an I
  tc (I) eq {charwidth 2 div %% half of requested character width
             ux lx sub 2 div %% half of the actual character
                sub      0 translate} if
  tc (I) eq {/xmulfactor 1 def} if

  /xmove xmulfactor lx mul neg def
  /ymove ymulfactor ly mul neg def

  xmulfactor ymulfactor scale

  gsave 1 setgray fill grestore

WARNING: Outlined characters will not display at all under NeWSbut will print fine on an Apple LaserWriter IIntx
/numchar{ %% charheight character numchar
%% Make a character of given height in cm,
%% then move vertically by that amount
/setthelinewidth {1 setlinewidth} def
    charwidth charheight char boxshow
  charheight abs 1 gt {0 charheight abs translate} if
  %% create the user defined strings

    stringwidth pop stringscale mul neg stacksperline
    stringscale stringscale scale

WARNING: if you don't see centered string number %ld:
it may be off the page because stacksperline is large (%ld) relative to the
FROM-TO range (%ld to %ld) and centering is based on stacks-per-line.  To
solve this, reduce parameter stacksperline to FROM-TO+1 = %ld


WARNING: rotations that are not multiples ofof 90 degrees are likely to be scaledincorrectly, due to a PostScript limitation.See the description of the pathbbox functioncharwidth parameter must be > 0 cmbarheight parameter must be > 0 cmbarwidth parameter must be > 0 cm
WARNING: are you SURE you don't want to show the variation due to a smallnumber of samples (i.e. the I-beam error bars)?
linemove parameter must be positiveShrink parameter must be less than or equal to 1.This way, you won't create a misleading logowhich has an apparent height larger than it should.Reminder: the I-beam error bars show thevariation of the entire stack not just the highestsymbol, even though it may look like that.missing a user defined string coordinatebarbits parameter must not be zeroShrinking can only be done when showing the dashed box.which has an apparent height smaller than it should.missing bar coordinate parametermissing corner coordinate parametersmissing barheight and barwidth parametersnumbering parameters are missingnumber of user defined strings must be givenshowingbox parameter is missingstacksperline parameter is missinglinesperpage parameter is missing getstring: a line exceeds maximum string size (%ld)
linesperpage parameter must be positivestacksperline parameter must be positive in the range from %ld to %ld
 bits (sample error not known)%% amplitude  phase  wavelength  base:
 %*.*f cm %*.*f cm %*.*f cm %*.*f cm
 %*.*f cm %*.*f cm %*.*f cm %*.*f cm %ld
mark symbol in file marks must be one of: "of" %*.*f cm %*.*f cm %*.*f cm circle
At position %ld the sum of symbols found is %ld
******************************************************************************
* NOTE: since the data come from the sites program, the error bar is not     *
* printed on the sequence logo.                                              *
This is a Chilogo! - Upside down letterswill be produced
WARNING: symvec does not contain data for position %ld
WARNING: negative Rs variation found in symvec,but the data are not from the sites programpossible program or data error.%% before coordinate %ld: make the bar
It seems that you don't have a zero coordinate."... the invention, probably by the Hindus, of the digit zero has beendescribed as one of the greatest importance in the history of mathematics."--- Encyclopaedia Britannica (1:1175, 1982)
WARNING: Highest position requested was not found in symvec
%% find out how high the bar is in centimeters:
/barincm barheight cmfactor div def
  gsave barincm (%c) numchar grestore shift
Half-White Ibeams are used because the symbols are solid black.%% bar at end of logo: make the bar before position %ld
 (string subscript out of range)????PG?h㈵>?&6FVfv&6FVfv&NaP
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Y  barheight parameter must be > 0 cmbarwidth parameter must be > 0 cm
WARNING: are you SURE you don't want to show the variation due to a smallnumber of samples (i.e. the I-beam error bars)?
linemove parameter must be positiveShrink parameter must be less than or equal to 1blimps-3.9/bin/Sun_intel/matrix_logob000075500001460000012000002201301062462103300202650ustar00jorjastaff00000400000027ELF404 (! 44 /usr/lib/ld.so.1

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P$`]M9}GE9~ /dev/nulllogo.%s
Cannot open file %s
cp %s/colors %stouch wavetouch marks   P to print logo (%s %s).)
%s %s %s%s %s
File %s sent to printer.
%lgrfield has no effect.
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqpb_weights:%d ignored for %s
 ,
.+-0123456789BLIMPS_DIR%s/docs/default.sijrMixture=Alpha==	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIXID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
width=%d;%fmotif%swidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for matrix %sSetting width to zero
  |% 4d--+----%c |% 6.4f    ID   %s
AC   %s
DE   %s
MA   %s
  %c     %c       A   C   G   T
%3d   *   -
//
% 9.4f % 9.4f
%3d
    *         -
 %c   *   -
% 6.4f % 6.4f
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Enter AC in %s or - to make logos for all: 
Enter name of BLOCK or MATRIX file: Logos will be written to logo.%s
MATRIX_LOGOB: Copyright 1995-8 Fred Hutchinson Cancer USAGE: matrix_logob blocks|pssms AC|- suffix   pssms must be in blimps format and consist of values betwen 0 and 100
    which sum to 100 in each column.These files must be in the current directory:   makelogob, colors, default.amino.frq* position, samples, information, variance

small sample correction (e) : %6.3f, variance (avarhnb) : %6.3f
(these are are actually the values for the last column and will be different for the other columns if they contain a different number of unspecified residues - gaps, Xs, etc.)
     residues   #_of_specified_residues/#_of_seqs   e   var* PSSM of block %s (%s) from file %s.
PSSM of %s (%s) %d sequences.
No block with name %s found in file %s !

The created sequence-logo file (%s) is a PostScript file.
  (V to view logo with program %s (%s %s %s))
     after viewing you can also choose to print,load_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.A?BABzD?????R?@3333@3333????333333?"2BRbr"2BRbr"2BRbr"5
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H>7-#s\UG0"StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialACGTAGCTACGTATCGCGTAGTACTACGACGT-RNDQEHILKMFPSWYVDNEQARNDCQEGHILKMFPSTWYV*% 6.3f rALPHABETlog-oddsfrequency  
	

Enter name of input file: 					F or W in MAST format%s.mastw%s.blimpswidth=%d; 	
seqs=%d; width=%d;
Cannot open file %s
alength=alength= %d w=%d
Problem finding width in %s
%lgrfield has no effect.
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqpb_weights:%d ignored for %s
 ,
.+-0123456789BLIMPS_DIR%s/docs/default.sijrMixture=Alpha==	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIXID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
width=%d;%fmotif%swidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for matrix %sSetting width to zero
  |% 4d--+----%c |% 6.4f    ID   %s
AC   %s
DE   %s
MA   %s
  %c     %c       A   C   G   T
%3d   *   -
//
% 9.4f % 9.4f
%3d
    *         -
 %c   *   -
% 6.4f % 6.4f
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Unable to recover enough memory to continue.  Aborting.
ALPHABET= ARNDCQEGHILKMFPSTWYVBZX
log-odds matrix: alength= 23 w= %d

Enter type of input file (Block|Frequencies|Weights): COPYRIGHT 2000 Fred Hutchinson Cancer Research CenterUSAGE:  narrow  		file_type = B|F|W	B=block, F=frequencies, W=weightsWrites a positive PSSM to stdout in BLIMPS format
Problem finding value for pos=%d aa=%c
Not sure about the format of %s, assuming first line contains alphabetCould not find alphabet or width in %s
ERROR: Negative frequencies readPlease verify input format type
Problem finding ALPHABET in %s
ERROR:No block found in file %s
ERROR: All values read as zero
ALPHABET length (%d) not alength (%d)
load_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
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translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
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==========}=v=l=^=P=I=8='==	=<<<<<StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialACGTAGCTACGTATCGCGTAGTACTACGACGT-RNDQEHILKMFPSWYVDNEQARNDCQEGHILKMFPSTWYV*rLength=%d, clamp=%d
References:OLIGO_MELT %s
 Center, Seattle, WA, USACannot open %s

Oligo in reverse order:aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Estimated melting temperatures of non-degenerate clamp region (C=%.2fnM):

-----------------------------------------------------------
---Using Breslauer's entropy=-%.1f & enthalpy=-%.1f
AT/GC=%.1f, NAR=%.1f, PRIMER3=%.1f
---Using SantaLucia's entropy=-%.1f & enthalpy=-%.1f
Entropy/Enthalpy: Table 2 from Breslauer, et al, (1986) PNAS 83:3746-3750Entropy/Enthalpy: Table 2 from SantaLucia, (1998) PNAS 95:1460-1465AT/GC: Suggs, et al, (1981) ICN-UCLA Symp.Dev.Biol. 23:683-693NAR: Eqn [2] from Freier, et al, (1986) PNAS 83:9373-9377PRIMER3: Eqn (ii) from Rychlik, et al, (1990) NAR 18:6409-6412COPYRIGHT 1997, Fred Hutchinson Cancer Research
USAGE:  oligo_melt  [DNA conc in nM]Enter name of file containing oligos: Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.Reclaim space function is not defined.  No memory will be reclaimed.
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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Missing BL (input block) file
Missing EX (output PSSM) fileUncounted character for %s: %d

clump_seqs: Unable to allocate pair structure!Read a frequency of value of %f for: %c
Read a frequency of value of %f for: not a residue
The value for the non-amino acid will be the last weight seen.Currently the program ignores non-residue characters so thisThe non-amino acid codes U and J weights are differentThe non-amino acid codes O and U weights are differentThe non-amino acid codes J and O weights are different
bruno_rind(): Cannot open file data
bruno_rind(): Cannot open file counts
bruno_rind(): Execution of rind failed
Enter name of configuration file: WARNING: Parameters are not checked for validity!Using Gribskov algorithm with qij...Using background pseudo-counts (like Gibbs)Using Claverie pseudo-counts...Using Altschul's pseudo-counts...MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.? A@@?HB?B?B?BB?BB???PERT!	@3333@33333333@3333??3333@??33333?33333?@333333?&6FVfv&6FVfv  & 6 F V f v       
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uuuuuuuu}usuYuRuHu:u,u%uuutttttttStandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialACGTAGCTACGTATCGCGTAGTACTACGACGT-RNDQEHILKMFPSWYVDNEQARNDCQEGHILKMFPSTWYV*gc;fc;Extra motif: %s
gx;gn;SIMPLEgt;%s%c%s;%s; BLOCKmotif %d of Prints entry %s.
is shorter than 7 characters.fm;gp;PROSITEfl;bb;fd;BLOCKSPRINTSCOMPOUNDSequence not found in line.%scan't find the general codein Prints entry %s.
can't find closing )r%s.datw%s.info
Cannot open output file %s

Cannot open input file %s
ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Unable to recover enough memory to continue.  Aborting.
Error ! Problem in format of final motif length line (fl; ...) inNote - the accesion code of Prints %s ("%s")
%-12s %-20s %5d  %-10s %-10s %s
 distance from previous block=(%d,%d)adapted from PRINTS entry; width=%d; seqs=%d;Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.read_a_prodom_entry(): Error reading sequence %s in block %s,Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.
Error ! Problem in format of sequence line %d (%s) in
Error reading sequence start position.Error ! Problem in format of sequence line %d in
Sequence name not found in line.Error ! Sequence %d in motif %d of Prints entry %s.
is %d chars long, instead of the %d expected
Error ! Accession line (gx; ...) not found in Prints entry %s.
Error ! Final motifs line (fm; ...) not found in Prints entry %s.
Error reading sequence distance from last motif.Error ! Type line (gn; ...) not found in Prints entry %s.
Error ! title line (gt; ...) not found in Prints entry %s.
Error ! Problem in motif %d of Prints entry %s.
  The motif's code line (fc; ...) does not contain the entry name = %s
Error ! final motif code line (fc; ...) not found inError ! final motif length line (fl; ...) not found inError ! Problem in format of Prints entry gc line,Error ! End of file reached while readingError ! Problem in format of gn line, can't find (Error ! Problem in format of Prints entry %s gx line.
Can't find the accession code.Error ! Problem in format of gn line in Prints entry %s -
Error ! Type line (gn; ...) is neither SIMPLE or COMPOUND
Enter name of input file (Prints protein motifs database): Block family PRINTS entry name    # of   Cross references to -
                                  blocks PROSITE    BLOCKS     PRINTS
------------ -------------------- ------ ---------- ---------- ----------

%d entries with %d motifs read from Prints database %s
and written as blocks in file %s.
Information about the processed entries written in file %s.
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.?333333?4&6FVfv&6FVfv&6FVfv`: v
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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000%s; width=%d; seqs=%d; 99.5%%=%d; strength=%d;
Enter name of blocks database: 
Enter name of pssmdist.dat file: 
Enter name of new blocks database: MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.?333333?L{Rbr"2BRbr"2BRbr b
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Information: %s
width=%d;%fmotif%swidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for matrix %sSetting width to zero
  |% 4d--+----%c |% 6.4f    ID   %s
AC   %s
DE   %s
MA   %s
  %c     %c       A   C   G   T
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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000minvalue=%d maxvalue=%d minscore=%d maxscore=%d
maxscore is too big, increase MAXSCORE from %d
Score range  log(Possible ways)  Probability  Expected scores%4d %4d  %8.4f      %11.8f      %8.2f

CumScrs  Score   ExpectedScrs%4d %4d       0.0000       0.000000
99.5 TN score = %d, 80.0 = %d
Median TP score = %d, TPabove = %lf
Read a frequency of value of %f for: %c
Read a frequency of value of %f for: not a residue
The value for the non-amino acid will be the last weight seen.Currently the program ignores non-residue characters so thisThe non-amino acid codes U and J weights are differentThe non-amino acid codes O and U weights are differentThe non-amino acid codes J and O weights are different
Enter name of observed frequencies database: 
Enter name of matrix database: 
Enter name of frequency file: 
Cannot open file %s, TP distribution not computed.
Assuming %.0f sequences, %.0f amino acids in a search
and 100 true positive alignments
Enter number of amino acids in a typical database [%.0f]: 
Enter number of sequences in a typical search [%.0f]: Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
Reclaim space function is not defined.  No memory will be reclaimed.
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ccbbbbbbbbbbbrbdb]bLb;b$bbbaaaaStandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialACGTAGCTACGTATCGCGTAGTACTACGACGT-RNDQEHILKMFPSWYVDNEQARNDCQEGHILKMFPSTWYV*rallw
Cannot open file %s
-n-fCenter		-f	=> floating point outputID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Enter AC of blocks to extract, or all [%s]: RETBLOCK: Copyright 1997 Fred Hutchinson Cancer Research Extract blocks from a Blocks DatabaseUSAGE:  retblock   [[-n] -f]           = file of blocks           => extract AC or all blocks          -n       => output to stdout, otherwise each block                      will be written to AC?.blk
Enter name of blocks database: MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.?333333?}^n~.>N^n~.>N^n~Pc
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ddddddddd{dadZdPdBd4d-dddcccccccStandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialACGTAGCTACGTATCGCGTAGTACTACGACGT-RNDQEHILKMFPSWYVDNEQARNDCQEGHILKMFPSTWYV*r%s
%-20.20s (%5d) %s
                   aligned:
Cannot open file %s
ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motif%swidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%d%s
No width field for block %sSetting width to zero
%d)%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>Universa*Flat-file, no titleLength:Check:.. %s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Block %s not found in file %s
Something seems wrong in the alignment coordinates !!!


Sixth argument should be the start position of the aligned region in block 2

Seventh argument should be the alignment length
%s  blocks_file  block1_accession  block1_alignment_start  blocks_file  block2_accession  block2_alignment_start  alignment_length

Third argument should be the start position of the aligned region in block 1
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid AC line:Error in block file format.  Invalid ID line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.?333333?*:JZjz
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Reading %s...
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wt
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Cannot open file %s

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*.XVYWTSPFMKLIHGEQCDNRArtprotomat.stpSCOREHIGH ,	
+-0123456789GENBANKLOCUSDEFINITIONORIGIN//ACCESSIONPIRENTRYTITLESEQUENCE///EMBLIDDESQACUNI>VMSPROCLASSPCF_ACPCF_DEPCS_ID

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Created directory %s
 	
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 Creating %sw+t
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 BLOCK:Rank %.3d=%.20s, score=%d, P=%g
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Cannot open file blastdat.dat
BLASTDAT: (C) Copyright 1992-2000, Fred Hutchinson Cancer Research Center
Enter name of file containing list of sequences: # True negative sequences for %s

%d missed sequences written to %s
Enter name of BLASTP results file: 
No list of sequences will be checked.
%d found sequences written to %s
Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directory
%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P
 WARNING: Titles are sometimes truncated in this format;
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blocks@blocks.fhcrc.org Research Center truncated to fit the page column of the block.Version 3.2.5Version 3.2.4Version 3.2.3Probe Sequence:Size:Base Pair: 

Size TargetRecordsAC#Database=%s
blksort.bias%s %d%sblksort.biasrepeats.dat%srepeats.datblksort.stn%d %f%sblksort.stn// 	
 	
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OUT OF MEMORY
%s %s %s 2 %d %d %6.2g %.16f

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-------------ablksort.datblksort.rep
BLKSORT Version %s

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 Size=%ld 
Blocks Searched=%d

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Amino AcidsBase PairsOR:    blksort -stats*.XVYWTSPFMKLIHGEQCDNRArtprotomat.stpSCOREHIGH ,	
+-0123456789GENBANKLOCUSDEFINITIONORIGIN//ACCESSIONPIRENTRYTITLESEQUENCE///EMBLIDDESQACUNI>VMSPROCLASSPCF_ACPCF_DEPCS_ID

mkdir %s
Created directory %s
 	
FRAGMENTBLOCKLSTPS=LENGTH=-_
Processing input file as %s 
	

%d. Entry %s found...ARNDCQEGHILKMFPSTWYVBZXactgDR   PIR;.

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 Creating %sw+t
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>%sfragment
===============================================================================
Here are your search results from the BLOCKS searcher.
Please report problems to webmaster@blocks.fhcrc.org, include your query
and this output. To obtain help, send the word HELP on a single line to
Copyright (c) 1992-6 by the Fred Hutchinson Cancer
If you use BLOCKS in your research, please cite:
Steven Henikoff and Jorja G. Henikoff, Protein Family Classification Based
on Searching a Database of Blocks, Genomics 19:97-107 (1994).
Each numbered result consists of one or more blocks from a PROSITE or PRINTS
group found in the query sequence. One set of the highest-scoring blocks that
are in the correct order and separated by distances comparable to the BLOCKS
database is selected for analysis. If this set includes multiple blocks
the probability that the lower scoring blocks support the highest scoring
block is reported. Maps of the database blocks and query sequence are shown:
  < indicates the sequence has been
  : indicates the minimum distance between blocks in the database
  . indicates the maximum distance
The maps are aligned on the highest scoring block. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database
is shown. Upper case in the query sequence indicates at least one
occurrence of the residue in that
BLKSORT: Cannot open file blimps file %s

BLKSORT: Cannot open blocks file %s
                         |---%5d amino acids---|
Maximum number of repeats (from Prosite MAX-REPEAT) = %d
%d non-overlapping repeats in support of %s
%d=%.2fth percentile of anchor block scores for shuffled queries
P not calculated for single block %s%s %s %s 1 %d %d %6.2g %.16f %d %d %d %d %d %ld %.2f

cluster_seqs: Unable to allocate pair structure!
%d.-----------------------------------------------------------
Block     Rank Frame Score Strength   Location (aa) Description%-8s %5d  % 2d   %4d  %4d     %7ld-%7ld %s

Block     Rank Frame Score Strength   Location (bp) Description
Enter number of hits to report or blimps configuration file name [%d]: COPYRIGHT 1992-8 Fred Hutchinson Cancer Research CenterUSAGE: blksort    [-stats]           = number of hits to report, use 0 for default     = blimps search output file     = blocks database searched by blimps    -stats          produces blksort.dat statistics file     = name of blimps configuration file
BLKSORT: Cannot open configuration file %s

Enter name of blocks database searched: 
Enter name of file containing blocks search results: 
Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directory
%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.
Cannot determine type of input filepBA??.>N^n~.>N^n~.>
&&

34oooPHooH812/23/06.1	


		
		
		
	
					
			

			
	

	
			
							
	
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BLKSORT: Cannot open file blimps file %s

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 Research CenterrCannot open %s
Reading %s
Requested scale = 1/%d bits

%d blocks processed %ld total sequences, %ld total columns, %ld total AAs

    %1s  %9.2f    %1s  blosum%d.qijwt#  Blocks Database = %s
#  Cluster Percentage: >= %d
   %1s   %.4f sumqij = %f
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 totdiag=%.3f, totoffd=%.3f totaas=%ld, TotAas=%ld
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Positive matrix (+%d):
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10 times log base 10 matrix:Enter n for no clustering#  Existing Clusters Used
 with parameter = %.2f
blosump%d.qijblosump%d.sijSequence weights will be usedblosump%d.iijNo clustering will be used*.XVYWTSPFMKLIHGEQCDNRArtprotomat.stpSCOREHIGH ,	
+-0123456789GENBANKLOCUSDEFINITIONORIGIN//ACCESSIONPIRENTRYTITLESEQUENCE///EMBLIDDESQACUNI>VMSPROCLASSPCF_ACPCF_DEPCS_ID

mkdir %s
Created directory %s
 	
FRAGMENTBLOCKLSTPS=LENGTH=-_
Processing input file as %s 
	

%d. Entry %s found...ARNDCQEGHILKMFPSTWYVBZXactgDR   PIR;.

>%s
 Creating %sw+t
Cannot open %s
>%sfragment
cluster_seqs: Unable to allocate pair structure!BLOSUM: (C) Copyright 1992, Fred Hutchinson CancerEnter name of blocks database:Minimum block strength=%d, Maximum block strength=%d
Existing clustering will be used, %ld blocks contributed pairs to matrix
 %f clumps contributed pairs to matrix (%f)
 %ld segments contributed pairs to matrix (%f)
%f total pairs, %f total weight
Frequencies = fij pairs (off-diagonals = 2*fij):
Target Probabilities=qij in %s
#  BLOSUM Clustered Target Frequencies=qij

Marginal Probabilities by AA = p(i,*):

totpairs=%.3f, FTotWeight=%.3f
Entropy=%.4f bits, expected=%.4f bits

Scoring matrix in bit units=sij in %s
#  BLOSUM Clustered Scoring Matrix in Bit Units=sij
#  Entropy = % 8.4f, Expected = % 8.4f

Integer scoring matrix in 1/%d bit units in %s
#  BLOSUM Clustered Scoring Matrix in 1/%d Bit Units

Maximum=%d, minimum=%d, sum=%d
Enter scale n for 1/n bits [%d]: Scale based on relative entropyRe-clustering percentage = %d
   or a number between 0 and 100 for percent identity clustering   or e for existing (implied) clusters   or w for existing sequence weights   or pn for position-based weights, PB weight = 1/nEnter clustering identity percentage or n/e/w/pn [e]: Enter maximum block strength [%d]: Enter minimum block strength [%d]: Position-based weights will be used#  Position-based Clustering Parameter: <= %.4f
#  No Sequence Clustering Used
#  Explicit Sequence Weights Used

Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directory
%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P
 WARNING: Titles are sometimes truncated in this format;
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COBBLER sequence:end cobblerend mapend treeend prowebend blinksend pdbend cyrcablinks.datproweb.datcobbler.pros/howard/btest/bin/blocks.datVersion %s
[prosite_dir]*.XVYWTSPFMKLIHGEQCDNRArtprotomat.stpSCOREHIGH ,	
+-0123456789GENBANKLOCUSDEFINITIONORIGIN//ACCESSIONPIRENTRYTITLESEQUENCE///EMBLIDDESQACUNI>VMSPROCLASSPCF_ACPCF_DEPCS_ID

mkdir %s
Created directory %s
 	
FRAGMENTBLOCKLSTPS=LENGTH=-_
Processing input file as %s 
	

%d. Entry %s found...ARNDCQEGHILKMFPSTWYVBZXactgDR   PIR;.

>%s
 Creating %sw+t
Cannot open %s
>%sfragment
Enter Block accession number: 
Enter name of Blocks database file [%s]:
GETBLOCK: (C) Copyright 1992-1999, Fred Hutchinson Cancer Research CenterUSAGE:  getblock AC blocks cobb maps trees proweb blinks blk2pdb cyrca 		AC = block accession (eg BL00094 or IPB001525)		blocks = name of blocks database file		cobb = name of cobbler database file		maps = name of map structure database file		trees = name of tree structure database file		proweb = name of Proweb database file		blinks = name of file of links to ProDom		blk2pdb = name of PDB cross-reference file		cyrca = name of CYRCA cross-reference file		prosite_dir = name of directory containing prosite.dat and prosite.doc files
Cannot open blocks database %s

Cannot open prosite.dat file %s

Cannot open prosite.doc file %s

Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directory
%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P
 WARNING: Titles are sometimes truncated in this format;
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Created directory %s
 	
FRAGMENTBLOCKLSTPS=LENGTH=-_
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 Creating %sw+t
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Enter name of sequence to extract: 
Enter name of database file to extract sequence from: 
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Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
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Using RunType=%d
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filepath=%s
Sequence #%d:	%s		Length of sequence #%d =  %d
MOTIFJ=[Couldn't allocate MOTIF.
Reading sequence file %s
%s
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 with shuffled sequences.

Found %d motifs.
Starting motomat...1motomat
Starting motifj...3 or 0 to assemble blocks: Enter 'l' for long form:  *.XVYWTSPFMKLIHGEQCDNRArtprotomat.stpSCOREHIGH ,	
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 Creating %sw+t
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 last score = %d, groups = %d
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Motif parameters = [%d, %d, %d]
CPU time to find and sort motifs: %ld seconds.
___________________________________________________________________________
Printed %d motifs out of %d total.
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Using scoring matrix from %s
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Unable to create directory %s
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%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P
 WARNING: Titles are sometimes truncated in this format;
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NumSeqs=%d, Total_Motifs=%d
Sequence #%d: %20s %d %.5s

MOTIF %d: %d(%d)%d(%d)%d
%20s (% 5d) %.1s
                   
Path: %d % 3d
Score              %1s%20s (% 5d) 
Saving block %.1s%.1s%.1sID   %s; BLOCK
AC   %s;DE   %s
 width=%d seqs=%d


//

>>>MOTOMAT out of memory!%s
%d,%d 
seq=%d: 
Revised TopScore=%ld
row %.3d:  %.3d   x
 (%d, %d) B%d %.1s%.1s%.1s
   thisb: %d=%d 
    allb:  B%d %.1s%.1s%.1s
best_path: paths->nblocks=%d
 , total sequences=%d, prop=%d
   saveb, allb: %d=%d,%d 
 >>>NEW BESTPATH

follow:  row=%d, ntemp=%d
 curpath blocks=%d 
 curpath_seqs:
End of follow_arcs for %d
find_paths: single %d

find_paths: more-----------%d  %d
, total conserved=%d
Sequences in the best path:%.3d:%20s 
MOTOMAT %s: ls -al *.motrb
Assuming input from Gibbs
%s

%d blocks read %d sequences.amotomat.err
Extending blocks...%s.blksw+t
Cannot open %s
asis

Merging raw blocks...;
CANNOT ALLOCATE SMatrix
Cannot open file %s
Saving blocks to %s

Block %d: %.1s%.1s%.1s has been merged.
Extended width was %d
Block %d:

Looking for best path..., npath=%d, reduced significance=%d
Reducing block overlaps ...

Merging extended blocks...., nseqs=%d

No surviving blocks*.XVYWTSPFMKLIHGEQCDNRArtprotomat.stpSCOREHIGH ,	
+-0123456789GENBANKLOCUSDEFINITIONORIGIN//ACCESSIONPIRENTRYTITLESEQUENCE///EMBLIDDESQACUNI>VMSPROCLASSPCF_ACPCF_DEPCS_ID

mkdir %s
Created directory %s
 	
FRAGMENTBLOCKLSTPS=LENGTH=-_
Processing input file as %s 
	

%d. Entry %s found...ARNDCQEGHILKMFPSTWYVBZXactgDR   PIR;.

>%s
 Creating %sw+t
Cannot open %s
>%sfragment  domain=%d, score=%d, freq=%d, dups=%d, mots=%d
 %.1s%.1s%.1s (extended width=%d, score=%d  motifs=%d, motif width=%d, conserved=%d)
merged_motif: Unable to allocate merged_motif structure!
Blocks %d and %d have been divided
Merging motif %d into motif %d distance from previous block=(%d,%d)
BL   %.1s%.1s%.1s gibbs=[%d,%d,%d] motomat=[%d,%d,%d]BL   %.1s%.1s%.1s motif=[%d,%d,%d] motomat=[%d,%d,%d]
cluster_seqs: Unable to allocate pair structure!Block %d has been trimmed by %d to eliminate overlap with Block %d.
  Restarting with DropScore = %d
 makepath: Unable to allocate path structure!
 order_blocks: Unable to allocate temp structure!
 prune_blocks: Unable to allocate temp structure!
 check_seqs: Unable to allocate temp structure!
 makematrix: Unable to allocate matrix structure!
 ***MOTOMAT STOPPING BECAUSE >1500 PATHS*** makebllist: Unable to allocate block_list structure!

 New path: nblocks=%d, tots=%dBest sub-path:%d blocks, %d AAs, total score=%ld,
 total motifs=%d, total idents=%d
 row=%d temp[i].index=%d nseq=%d follow_arcs: Unable to allocate temp structure!
 find_paths: Unable to allocate temp structure!

Best path has %d sequences out of %d:
%d blocks, %d AAs, total score=%ld, total motifs=%d
 total sequences=%d out of %d
Sequences not in the best path:(C) Copyright 1991 by Fred Hutchinson Cancer Research Center
Please cite: S.Henikoff & J.Henikoff, NAR 19:6565-6572 (1991).
Enter name of file containing motifs:  using parameters [%d, %d, %d].
Processing blocks in %s using a cut-off score of %d 
   and a clustering threshold of %d percent.
Recalculating block column scores

Input file was created using wrong motifj version!
Enter minimum block extension column score or 1 for best block [100-2500 or 1; %d]: Enter clustering identity threshold [1-100; %d]: 
Processing block %d in %s using a cut-off score of %d 

Type S[ENTER] to save this block, or N[ENTER] to skip to next block,
or anything else[ENTER] to re-extend this block...

Removing duplicate blocks....
Using a drop score of %d standard deviations or %d., re-extending with cutoff score of %d.
Block %d has been dropped for low width:
Quitting becasuse no motifs to work on.
Mean score=%.2f, standard deviation=%.2f
Surviving blocks=%d, max dups=%d%s %d %d %d %d %d %d %d %d %d %d %d %d %ld %d %d %d

Enter drop standard deviations [-30 to 30; %d]: 
Block %d has been dropped for low score:
Dropping blocks with score below %ld...
 unless they have more than one merged motif
Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directory
%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.
Cannot determine type of input file?{Gz?B? A*:JZjz
*:JZjz
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VVVWWWW}WpWcWVWIW%c%6d(%d,%d):%dResearch CenterVersion %s
amultimat.dat%d IDs in %s
wmultimat.mismultimat.fnd.
%d scores read from %s

Reading %s...
Cannot open file %s;
Cannot open file %s blocks vs sequence db
No results files specified.AC family name = %s
	FRAGMENT	BLOCK
Cannot open file %s


NOT ENOUGH MEMORY!*.XVYWTSPFMKLIHGEQCDNRArtprotomat.stpSCOREHIGH ,	
+-0123456789GENBANKLOCUSDEFINITIONORIGIN//ACCESSIONPIRENTRYTITLESEQUENCE///EMBLIDDESQACUNI>VMSPROCLASSPCF_ACPCF_DEPCS_ID

mkdir %s
Created directory %s
 	
FRAGMENTBLOCKLSTPS=LENGTH=-_
Processing input file as %s 
	

%d. Entry %s found...ARNDCQEGHILKMFPSTWYVBZXactgDR   PIR;.

>%s
 Creating %sw+t
Cannot open %s
>%sfragmentzD??pB?A?MbP?
===============================================================================
Search results from the BLOCKS e-mail searcher.
Please report problems to jorja@sparky.fhcrc.org, include your query
and this output. To obtain help, send the word HELP on a single
line to blocks@howard.fhcrc.org
Copyright (c) 1992 by the Fred Hutchinson Cancer Research Center
If you use BLOCKS in your research, please cite:
Steven Henikoff and Jorja G. Henikoff, Automated assembly of protein
blocks for database searching, NAR 19:23 (1991), 6565-6572.
Each numbered result consists of one or more blocks from a PROSITE group
found in the query sequence. One set of the highest-scoring blocks that
are in the correct order and separated by distances comparable to the BLOCKS
database is selected for analysis. If this set includes multiple blocks
the probability that the lower scoring blocks support the highest scoring
block is reported. Maps of the database blocks and query sequence are shown:
  < indicates the sequence has been
  : indicates the minimum distance between blocks in the database
  . indicates the maximum distance
The maps are aligned on the highest scoring block. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database
is shown. Upper case in the query sequence indicates at least one
occurrence of the residue in that
                         |-----%5d residues----|
No blocks for family %s found in database.%s %s %d %d %d %d %d %d %6.2g %s


No P-value computed for single block hits.

ERROR: Anchor block not found in blocks database.

Top %d sequences sorted by maximum normalized score:
(the normalized score is the Score divided by the99.5 score in the block if available, or by thesmallest Score in the search results file for the block)

Block     Rank Frame Score      Location(aa) Sequence
%d.----------------------------------------------------------------------------------
%8s  %4d  %2d    %4d  %7ld-%7ld %s %s

Block     Rank Frame Score      Location(bp) Sequence%s %d %d %d %d %d %d %d %d %d %d %d %f
MULTIMAT: (C) Copyright 1991 by Fred Hutchinson Cancer 
Search results will be compared with %s
Search results will be compared with %s;
only hits not in this list will be reported
Enter name of file containing list of true positives:
search results will not be compared with true positive list.
Enter name of BLIMPS results file: 
Enter name of blocks database:;
search results will not be compared with blocks database.
Enter maximum number of hits to report [%d]: USAGE:   multimat                  = Maximum # of hits to report             = File containing blocks for comparison               = File containing list of TP sequences             = Blimps search result files, 
WARNING: AC family name truncated to 9 characters. 
Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directory
%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.
Cannot determine type of input file
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  and deposit into file %s
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Cannot open file %s
*.XVYWTSPFMKLIHGEQCDNRArtprotomat.stpSCOREHIGH ,	
+-0123456789GENBANKLOCUSDEFINITIONORIGIN//ACCESSIONPIRENTRYTITLESEQUENCE///EMBLIDDESQACUNI>VMSPROCLASSPCF_ACPCF_DEPCS_ID

mkdir %s
Created directory %s
 	
FRAGMENTBLOCKLSTPS=LENGTH=-_
Processing input file as %s 
	

%d. Entry %s found...ARNDCQEGHILKMFPSTWYVBZXactgDR   PIR;.

>%s
 Creating %sw+t
Cannot open %s
>%sfragment
UEXTRACT %s: (C) Copyright 1991-2000 by
 Fred Hutchinson Cancer Research Center
Enter name of database file to extract entries from: 
%d sequences requested for extract from %s
Enter name of file containing list of entries to extract: USAGE: uextract   [-f -o -n]        = file listing sequence names to extract                   in PROTOMAT format         = sequence database       -f          to extract FRAGMENTs       -o to have all sequences put in        -n          to NOT execute motifj or create .lst file       -l          to NOT execute motifj but create .lst file       -k          to NOT execute motifj but create .lst file                    with fewer sequences than -l
Extracting all sequences to %sThe following sequences were not found:
  and deposit into directory %s
Cannot open file %s for update

Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directory
%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.
Cannot determine type of input fileK"2BRbr"2BRbr"2BRbrN(A
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vЋuX[US[@P.Y[StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialAAGACATAGTACTACGACGTHIMFPWDNEQARNDCQEGHILKMFPSTWYV*  |%4d--+----%c |% 4dw
Enter name of output file: 
Cannot open file "%s"
%6.3f %3d,%2d S matrix for %s and %s -
MA   BL   %s%s;%s%s%s; ProDom_mulLAMA version %s.
BLIMPS_DIR%s/docs/%sTrying %s...

Comparisons skipped !%.1e
Comparison skipped !

%sOutput written in file %s.
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Error in reading first file name from first argument !
Enter name of a file with blocks or block matrices: 
The blocks/matrices in this file will be intercompared.If you wish to compare them against blocks/matrices inanother file enter that file name (else just hit ).
Cutoff score should be specified as a Z score (mean+Z*std).The Z score must be positive (corresponding to the 50 percentile or higher).A negative cutoff score (%f) was specified, default value (%.2f) used.

Minimal alignment width can not be less than narrowest allowed blocks (%d).
Error in reading second file name from first argument !
Minimal alignment width can not be negative !The value given (%d) is out of range.
Error ! Extrapolated variance of shuffled PSSMs requested for 
a block too narrow (%d).
Error ! Extrapolated mean of shuffled PSSMs requested for 
a block too narrow (%d).
%-10s %3d %3d %-10s %3d %3d %2d Prpo %6.2f (%4.1f)
Column scores for %s and %s -

Column scores for optimal alignment of %s and %s -
Unable to recover enough memory to continue.  Aborting.
Error ! Problem in ProDom entry %s
second word in description line doesn't begin with a (second word in description line doesn't end with a )Error ! Problem in format of ProDom entry %s sequence-line %d
A non-digit in the sequence start position %s
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.read_a_prodom_entry(): Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.
Error ! Problem in format of ProDom entry %s
A non-digit in the number-of-sequences field "%s"
 distance from previous block=(%d,%d)adapted from ProDom entry; width=%d; seqs=%d;Error ! Problem in format of ProDom entry sequence-line %d
Sequence %s has length of %d instead of expected %d
Error ! Actual number of sequences in ProDom entry %s
different than what the entry reportsError ! Problem in format of ProDom entry description -lineError ! Not enough sequences (%d) in ProDom entry %s
Error ! Number of sequences in ProDom entry %s (%d) is less than 2
Error ! Problem in format of ProDom entry description-lineError. variable db_type (%c) is of unknown type !
Cannot determine type of input fileUsage: 
LAMA inp_file1[,inp_file2] out_file [min_algn_wdth] [dbg_lvl] [scrn] [cutoff] [expected target]

The program must have the names of one or two files with entry(ies) to compare
and an output file name. These can be specified on the command line or
interactively. On the command line the first argument is the entry(ies) file
name(s), if two files are specified they should be separated by a comma
with no spaces. Each file can be of either block, matrix, ProDom 
multiple alignment entry(ies). The second argument is the output file name,
it will be overwritten if it already exists. Optional arguments are 3rd -
minimal alignment width (0 for default), 4th - the debug level, 5th -
screen output (0 to forbid, anything else to allow), 6th - score
cutoff (in Z units [std's from mean], >=0, 0 for default), and 7th - for
how many searched blocks to calculate the number a score is expected to appear
(0 for default).

Note - the two input files have different types of data.
Minimal length of reported alignments %3d
Score cutoff is %.1f Z score units (in the top %.1e percentile of chance scores)

                                            alignment     Z-score  expected number for
block 1     from:to       block 2     from:to   length                 searching %d blocks
Block matrix %s shorter (%d) than narrowest width allowed (%d)
%-10s  %3d : %3d and %-10s  %3d : %3d (%2d) score %3.0f (%4.1f  %s)No hits found above score cutoff %.1f.@@?AB@[|
?+<?;z?Uka9ffffffʡE?Zd;OE??%lgfield has no effect.
%s/docs/default.amino.frq%s/docs/default.qijload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
pb_weights:%d ignored for %s
 ,
.+-0123456789%s/docs/default.sijMixture=Alpha=	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIX?R?@3333@3333ABzDMATRIX
DD-D=D@DEDJDCCODTDCCCCCCCCCYD^DCCCCCCCCcDCCCCCCCCCCID   AC   DE   block=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
Allocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
%fNo width field for matrix %s% 6.4fMA   %s
  %c     %c       A   C   G   T
%3d   *   -
% 9.4f % 9.4f
    *         -
 %c   *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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0call_gmon_startcrtstuff.c__CTOR_LIST____DTOR_LIST____JCR_LIST__p.0completed.1__do_global_dtors_auxframe_dummy__CTOR_END____DTOR_END____FRAME_END____JCR_END____do_global_ctors_auxLAMA.cfrequency.cread_freqconvert.cbasic_matrix_constructionmake_colpre_weighted_sequencesmake_work_pssmcountscount_residuespseudo_altscompute_BZXblocks.cBlockBufLengthBlockBuffererrors.cErrorFilematrix.cmemory.cRecFuncsequences.clbuff.0first_time.1strutil.cgcode.cgctrans.0nt_atobread_block_bodyremove_trailing_whitespaceaa_btoafree_sequenceZtoPrcntlsimilarity_dependent_scale__strtod_internal@@GLIBC_2.0SiteSpecificScoringMatrixTypeABRT_signal_handlerstrncat@@GLIBC_2.0strchr@@GLIBC_2.0DBtypepre_weighted_conversion_methodfeof@@GLIBC_2.0SIFT_conversion_methoddata_readfrequency_DYNAMICmake_gribsCodon_Usagefree_matrixdbg_lvlstrcmp@@GLIBC_2.0original_conversion_method_cleaned_upinit_reclaim_spaceset_error_file_name_fp_hwaa_atobfprintf@@GLIBC_2.0getenv@@GLIBC_2.0screen_outfflush@@GLIBC_2.0__fini_array_endcodon2aaSequenceMatrixScoringMethodload_codonsnt_arevcompaa2codonread_a_matrixgcodesmin_algnmnt_width__dso_handlent_bdegen__libc_csu_finioutput_block_sputchar@@GLIBC_2.0ErrorLevelReportread_a_prodom_entryzVsPrcntlgets@@GLIBC_2.0aafqfrq_qijsequence_typeload_frequenciesrewind@@GLIBC_2.0block_to_matrixftell@@GLIBC_2.0resize_sequencenext_clusterQijputs@@GLIBC_2.0_initaltschul_data_dependent_conversion_methodmalloc@@GLIBC_2.0output_matrix_stcols_scoreStrandsToSearchNumberToReportinit_gcodeSW_matricesseq_type_dbsextrpltd_varstdout@@GLIBC_2.0stderr@@GLIBC_2.0output_blockaa_adegennew_blockfseek@@GLIBC_2.0gribskov_conversion_methodread_block_headerGeneticCodeInitializer_startgetargsprint_blockfgets@@GLIBC_2.0resize_block_sequencesfree_blockErrorBufferfputs@@GLIBC_2.0load_stats3BlockToMatrixConversionMethodstrstr@@GLIBC_2.0ErrorReportalignments_done__strtol_internal@@GLIBC_2.0output_sequenceblock_comparisonntfqlgamma@@GLIBC_2.0load_qijtranslate_sequencestrncmp@@GLIBC_2.0__fini_array_startmatrix_comparisonfputc@@GLIBC_2.0__libc_csu_initread_a_sequence__bss_startalloctd_zVsPrcntlmainWWW_FLAGtype_dbseat_whitespace__libc_start_main@@GLIBC_2.0__init_array_endalloctd_algnmntsread_sequenceprint_sequenceexp@@GLIBC_2.0fprint_matrixsequence_comparisonrealloc@@GLIBC_2.0strcat@@GLIBC_2.0get_tokenDbInfodata_startoutput_matrix_scounts_nogapsprintf@@GLIBC_2.0blank_lineread_to_block_finimemcpy@@GLIBC_2.0sqrt@@GLIBC_2.0fclose@@GLIBC_2.1__ctype_toupper_loc@@GLIBC_2.3SearchType__preinit_array_endadd_logsfree_work_pssmreclaim_spaceBufferfind_max_aa_colload_diristrspn@@GLIBC_2.0exit@@GLIBC_2.0statscalloc@@GLIBC_2.0nt_brevcompsscanf@@GLIBC_2.0_edataset_defaults_GLOBAL_OFFSET_TABLE_free@@GLIBC_2.0_endpseudo_diriload_ZvsPrcntl1find_max_aa_pssmnew_matrixstrncpy@@GLIBC_2.0fopen@@GLIBC_2.1__init_array_start_IO_stdin_useduntranslate_sequencenormalizestrtok@@GLIBC_2.0Z_cutofforiginal_conversion_methodRTotSIFT_pssmread_a_block_fastersprintf@@GLIBC_2.0fwrite@@GLIBC_2.0resize_block_clustersextrpltd_meannt_btoa__data_startoutput_matrix_Jv_RegisterClasses__ctype_b_loc@@GLIBC_2.3nt_adegen__preinit_array_startlog@@GLIBC_2.0print_matrixread_a_blockpb_weights__gmon_start__strcpy@@GLIBC_2.0blimps-3.9/bin/Linux/LAMA_search000075500001460000012000001345531062462470100170170ustar00jorjastaff00000400000027ELF4`4 (444t(((  Qtd/lib/ld-linux.so.2GNU%410!2,.-3#/%&(

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vЋuX[US[k1PY[StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialAGACATAGTACTACGACGTIKMFPWDNEQARNDCQEGHILKMFPSTWYVBLOCKS_EMAILdate '+%y%m'date "+%y%m%d"%s/LAMA%s/add_queue_entry.pl%s/LAMA_queue%s/extblock_stdout../data-blocks%s/blocks.dat../data-prints%s/prints.dat../data-blplus../tmp%s/%d_tmp.dat%s/%d_tmp.blk../log%s/%s%s/%d.mail%s/%d.outblocks@fhcrc.orgQUERY_STRINGCONTENT_LENGTHUser_target_blockUser_query_blockdebug_levelscore_cutoff_leveladdressdatabaseprints-dbblplus-dbno-dbrm -f %s/%d.*%s/%d.LAMA_Qblock_errorsw//

    Search Error
    dateError opening pipe?../help/LAMA_help.html%s %s 'rm -f %s/%d.*'%dC.html5.6./cyrcaLama.pl%s %s %s %s/blocks/icons/cyrcashLogo.gifContent-type: text/html

REQUEST_METHODPOSTCONTENT_TYPEumask 006FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Sorry, you can not compare more than %d target blocks in each run.
There seems to be an error in the format of query block number %d:
    There seems to be an error in the format of target block number %d:
    You need to enter a block to search with by writing or pasting a block in the query block window.
    No blocks were read from the query.No blocks were read from the target data.Sorry, you can not compare more than %d query blocks in each run.
/usr/bin/nice -5 %s %s,%s %s 0 %d 0 %f > /dev/null 2>&1An error occured during the search.Please try your search again at a later time.If it fails again contact the maintainer of these pagesand describe what caused the problem with an example.
    %s/htmlize-blimps.pl %s | %s/htmlize-LAMA %s %s - -Error opening LAMA output file.LAMA Search Results
    LAMA Search Results (%s)
    
%s %s "/usr/bin/nice -10 %s %s,%s %s 0 %d 0 %f > /dev/null 2>&1"%s %s '(cat %s) | /usr/bin/mailx -s "LAMA Results" -r "blocks@fhcrc.org" %s'LAMA Search Submitted
    LAMA Search Submitted
    Your search has been submitted.You will receive the results via email to the address you gave ("%s").
CYRCA results
application/x-www-form-urlencodedThis script can only be used to decode form results. This script should be referenced with a METHOD of POST.If you don't understand this, see this forms overview.%c
    What could have happened is that you just reloaded this page rather than redoing the search.
    If you use NETSCAPE it has a tendency to try to reload a page when you go back to it.  This may be why you have this error.ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d ?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFastaUniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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 	0call_gmon_startcrtstuff.c__CTOR_LIST____DTOR_LIST____JCR_LIST__p.0completed.1__do_global_dtors_auxframe_dummy__CTOR_END____DTOR_END____FRAME_END____JCR_END____do_global_ctors_auxLAMA_search.cblocks.cBlockBufLengthBlockBuffererrors.cErrorFilememory.cRecFuncsequences.clbuff.0first_time.1strutil.cutil.cgcode.cgctrans.0nt_atobread_block_bodyescape_shell_cmdconvert_LAMA_outputremove_trailing_whitespaceaa_btoaTargetblock_Ptrfgetc@@GLIBC_2.0free_sequence__strtod_internal@@GLIBC_2.0queue_to_mailABRT_signal_handlerdatabasestrncat@@GLIBC_2.0strchr@@GLIBC_2.0Title_Ptrblplusdbasefeof@@GLIBC_2.0pidgetpid@@GLIBC_2.0_DYNAMICstrcmp@@GLIBC_2.0error_fileinit_reclaim_spaceset_error_file_name_fp_hwrunCyrcaaa_atobPrints_FlagLAMA_queuefprintf@@GLIBC_2.0mail_filegetenv@@GLIBC_2.0extblock_stdoutfflush@@GLIBC_2.0pclose@@GLIBC_2.1add_queue_entryunescape_url__fini_array_endcodon2aadisplay_outputnt_arevcompaa2codongcodes__dso_handlent_bdegen__libc_csu_finioutput_block_sQblock_filefmakewordputchar@@GLIBC_2.0ErrorLevelReportsend_fdaafqsequence_typerewind@@GLIBC_2.0ftell@@GLIBC_2.0resize_sequencesystem@@GLIBC_2.0next_clusterputs@@GLIBC_2.0_initpopen@@GLIBC_2.1read_startup_infomalloc@@GLIBC_2.0cyrcaOutputFileinit_gcodeindmakewordseq_type_dbsstdout@@GLIBC_2.0stderr@@GLIBC_2.0log_diroutput_blockaa_adegennew_blockfseek@@GLIBC_2.0email_addrread_block_header_startprint_blockfgets@@GLIBC_2.0resize_block_sequencesfree_blockErrorBufferstrstr@@GLIBC_2.0ErrorReport__strtol_internal@@GLIBC_2.0output_sequenceScore_Cutoff_Levelblock_comparisonntfqtranslate_sequencestrncmp@@GLIBC_2.0__fini_array_startfputc@@GLIBC_2.0__libc_csu_initread_a_sequence__bss_startmaintype_dbseat_whitespaceclean_temp_files__libc_start_main@@GLIBC_2.0__init_array_endread_sequenceDebug_Levelprint_sequencesequence_comparisonrealloc@@GLIBC_2.0LAMA_outputstrcat@@GLIBC_2.0get_tokenDbInfodata_startprintf@@GLIBC_2.0blank_lineprintsdbaseread_to_block_finimemcpy@@GLIBC_2.0fclose@@GLIBC_2.1__ctype_toupper_loc@@GLIBC_2.3x2cBlplus_Flag__preinit_array_endMail_Flagbufreclaim_spaceBufferNo_DB_Flagexit@@GLIBC_2.0blocksdbaseparsecalloc@@GLIBC_2.0run_searchnt_brevcompsscanf@@GLIBC_2.0_edata_IO_putc@@GLIBC_2.0_GLOBAL_OFFSET_TABLE_free@@GLIBC_2.0_endstdin@@GLIBC_2.0getwordstrncpy@@GLIBC_2.0fopen@@GLIBC_2.1write_QblockAddress_PtrLAMA__init_array_startgetline_IO_stdin_useduntranslate_sequencestrtok@@GLIBC_2.0read_a_block_fastersprintf@@GLIBC_2.0fwrite@@GLIBC_2.0resize_block_clustersnt_btoa__data_starttargetdbase_IO_getc@@GLIBC_2.0_Jv_RegisterClasses__ctype_b_loc@@GLIBC_2.3entriesnt_adegen__preinit_array_startlog_fileQblock_Ptrrindread_a_blockplustospace__gmon_start__strcpy@@GLIBC_2.0?{Gz?J+? rh?V-?9v?Mb?x&?-(ARNDCblimps-3.9/bin/Linux/README000064400001460000012000000007551062462470100157060ustar00jorjastaff00000400000027Linux 2.6.9-42.0.2.ELsmp #1 SMP Wed Aug 23 00:17:26 CDT 2006 i686 i686 i386 GNU/Linux

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Thread model: posix
gcc version 3.4.5 20051201 (Red Hat 3.4.5-2)
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>%s %s from %d to %d
99.5 TN score = %d
,%s %d : %s %d
%s %.0f %.2f ADDSEQS Version %s
wseqsBLIMPS_DIR%s/docs/FRAGMENT%s already in block
No sequences found in %s .
simi Research CenterAdds sequences to blocks.
Cannot open file %s
No blocks found in %s .
%d sequences added
Query added to %s
addseqs.dat%s %d %d %d %d
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000%s; distance from previous block=(%d,%d)Cannot write %s of length %d from %d to %d
Median TP score = %d, TPabove = %d
WARNING: sequence segments are of different lengthsMean dissimilarity distance = %.2f

Enter name of output seqs file: 
Enter name of sequence file: 
Enter name of file containing blocks: ADDSEQS: Copyright 1999 by the Fred Hutchinson CancerUSAGE:  addseqs                    = input blocks		           = fasta format sequences                      = output file                = processing option                   blks = add sequences to blocks & output blocks                   seqs = add sequences to blocks & output sequences                   simi = add sequences to blocks & do similarity analysis bad bestpos=%d endpos=%d seqlen=%d
 out of order %d, previous end %d
 pad1=%d bestpos=%d endpos=%d seqlen=%d
 pad2=%d bestpos=%d endpos=%d seqlen=%d
.Ap=
@.A?BzD?HBAA BAy%lgfield has no effect.
%s/docs/default.amino.frq%s/docs/default.qijload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
pb_weights:%d ignored for %s
 ,
.+-0123456789%s/docs/default.sijMixture=Alpha=	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIX?R?@3333@3333BMATRIXIYiy|9ID   AC   DE   BL   block=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
Allocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
%fNo width field for matrix %s  |% 4d--+----%c |% 6.4fMA   %s
  %c     %c       A   C   G   T
%3d   *   -
% 9.4f % 9.4f
    *         -
 %c   *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..>--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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    Error
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    Program Error
    Content-type: text/html

REQUEST_METHODPOSTCONTENT_TYPEumask 006FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000There seems to be an error in the format of block number %d:
    You need to enter a block by writing or pasting a block in the window.
    Sorry, you can not check more than %d blocks each time.
An error occured during the execution.Please try again at a later time.If it fails again contact the maintainer of these pagesand describe what caused the problem with an example.
    Biassed Blocks Results
    Biassed Blocks Results
    Error opening program output file.application/x-www-form-urlencodedThis script can only be used to decode form results. This script should be referenced with a METHOD of POST.If you don't understand this, see this forms overview.%c
    What could have happened is that you just reloaded this page rather than redoing the search.
    If you use NETSCAPE it has a tendency to try to reload a page when you go back to it.  This may be why you have this error.ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d ?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFastaUniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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)';MzlHAp`6ZF1$[):LBU3fy8q$p`Բ-1	L&	@.	;	O	 c	z|	`8			4	Q	*	 	0call_gmon_startcrtstuff.c__CTOR_LIST____DTOR_LIST____JCR_LIST__p.0completed.1__do_global_dtors_auxframe_dummy__CTOR_END____DTOR_END____FRAME_END____JCR_END____do_global_ctors_auxbiassed_blocks_finder.cblocks.cBlockBufLengthBlockBuffererrors.cErrorFilememory.cRecFuncsequences.clbuff.0first_time.1strutil.cutil.cgcode.cgctrans.0nt_atobread_block_bodyescape_shell_cmdremove_trailing_whitespaceaa_btoafgetc@@GLIBC_2.0free_sequence__strtod_internal@@GLIBC_2.0ABRT_signal_handlerstrncat@@GLIBC_2.0strchr@@GLIBC_2.0feof@@GLIBC_2.0pidgetpid@@GLIBC_2.0_DYNAMICBLOCK_Ptrstrcmp@@GLIBC_2.0error_fileinit_reclaim_spaceset_error_file_name_fp_hwaa_atobfprintf@@GLIBC_2.0getenv@@GLIBC_2.0fflush@@GLIBC_2.0unescape_url__fini_array_endcodon2aadisplay_outputnt_arevcompaa2codongcodes__dso_handlent_bdegen__libc_csu_finioutput_block_sfmakewordputchar@@GLIBC_2.0ErrorLevelReportsend_fdaafqprogram_outputsequence_typerewind@@GLIBC_2.0ftell@@GLIBC_2.0resize_sequencesystem@@GLIBC_2.0next_clusterputs@@GLIBC_2.0_initread_startup_infomalloc@@GLIBC_2.0init_gcodeindmakewordseq_type_dbsstdout@@GLIBC_2.0stderr@@GLIBC_2.0output_blockaa_adegennew_blockfseek@@GLIBC_2.0read_block_header_startprint_blockfgets@@GLIBC_2.0resize_block_sequencesfree_blockErrorBufferstrstr@@GLIBC_2.0ErrorReport__strtol_internal@@GLIBC_2.0output_sequenceblock_comparisonntfqBlock_filetranslate_sequencestrncmp@@GLIBC_2.0__fini_array_startfputc@@GLIBC_2.0__libc_csu_initread_a_sequence__bss_startmaintype_dbseat_whitespaceclean_temp_files__libc_start_main@@GLIBC_2.0__init_array_endread_sequencetmp_dirprint_sequencewrite_blocksequence_comparisonrealloc@@GLIBC_2.0strcat@@GLIBC_2.0get_tokenDbInfodata_startprintf@@GLIBC_2.0blank_lineread_to_block_finimemcpy@@GLIBC_2.0fclose@@GLIBC_2.1__ctype_toupper_loc@@GLIBC_2.3x2c__preinit_array_endbufreclaim_spaceBufferexit@@GLIBC_2.0parsecalloc@@GLIBC_2.0nt_brevcompsscanf@@GLIBC_2.0_edata_IO_putc@@GLIBC_2.0_GLOBAL_OFFSET_TABLE_free@@GLIBC_2.0_endstdin@@GLIBC_2.0getwordstrncpy@@GLIBC_2.0fopen@@GLIBC_2.1__init_array_startgetline_IO_stdin_useduntranslate_sequencestrtok@@GLIBC_2.0find_biassed_blocksrun_programread_a_block_fastersprintf@@GLIBC_2.0fwrite@@GLIBC_2.0resize_block_clustersnt_btoa__data_start_IO_getc@@GLIBC_2.0_Jv_RegisterClasses__ctype_b_loc@@GLIBC_2.3entriesnt_adegen__preinit_array_startrindread_a_blockplustospace__gmon_start__strcpy@@GLIBC_2.0	
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fasta_seqs: OUT OF MEMORY# STOCKHOLM 1.0
%-28s %-s/%d
msf_seqs: OUT OF MEMORY, width = %d%5d 
            %s
%20s 
short_seqs: OUT OF MEMORY
posfai_seqs: OUT OF MEMORY
giant: OUT OF MEMORY %d expected

Cannot open file %s
BLALIGN Version %s
          g=giant block>%s %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000>%s|%d              from %10.10s blocks

stockholm_seqs: OUT OF MEMORYERROR in block %s: %d sequences found but %d sequences are included in %d blocks
Copyright 1999-2003 Fred Hutchinson Cancer Research Center
Prints blocks as a multiple alignment.USAGE:  blalign  [-p|s|f|m|h|q|g] [width]          p=Posfai style, s=short style, f=fasta style,          m=MSF style, h=STOCKHOLM style, q=ungapped STOCKHOLM,          defaults are short style, width = 66
Enter name of file of blocks: Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
pb_weights:%d ignored for %s
 ,
.+-0123456789BLIMPS_DIR%s/docs/default.sijMixture=Alpha=	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIX??R?@3333@3333BABzDMATRIXIYiy|9ID   AC   DE   BL   block=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d ?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
%fNo width field for matrix %s  |% 4d--+----%c |% 6.4fMA   %s
  %c     %c       A   C   G   T
%3d   *   -
% 9.4f % 9.4f
    *         -
 %c   *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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protdist dissimilarity correlation FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000WARNING: sequence segments are of different lengthsMean dissimilarity distance = %.2f

Enter name of file containing substitution matrix: 
Enter name of file of fasta multiple alignments: BLDIST: Copyright 1998 Fred Hutchinson Cancer Research Center
USAGE: bldist       = file of fasta multiple alignments (blocks)    = substitution matrix      = output distance matrix     = output matrix type:			P=dissimilarity in protdist formatWARNING: Sequences appear to be DNA but will be treated
Enter type (S=similarity, D=dissimilarity, C=correlation): yyD??Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
pb_weights:%d ignored for %s
 ,
.+-0123456789%s/docs/default.sijMixture=Alpha=	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIX?R?@3333@3333BABzDMATRIXYiyIFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
width=%d;%fmotifwidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for matrix %sSetting width to zero
  |% 4d--+----%c |% 6.4fID   %s
AC   %s
DE   %s
MA   %s
  %c     %c       A   C   G   T
%3d   *   -
//
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 %c   *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..>--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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vЋuX[US[MPY[StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialAGACATAGTACTACGACGTHIMFPWDNEQARNDCQEGHILKMFPSTWYV*Scoring vs sequence %s.
Not scoring the matrix.
Records Searched:   %d
Scores Done:        %16.0f
Alignments Done:    %16.0f
2006/043.8Usage: %s config_file
BLIMPS_DIRUsing frequencies from %s.
%s/docs/altsUsing genetic code %d; %s.
wError loading frequencies.
Probe Sequence: %s %s
Probe Size: %d Amino Acids
Probe File: %s
AC#         DescriptionRF    AA#
Sequence File (s) : %s
                   %s
Scoring vs matrix %s.
Target File (s) : %s
RF  AA# Length
Using default.qij
default.codon.frqProbe Sequence: NO SEQUENCE
Probe Size: UNKNOWN
Block File: %s
Probe Size: %d Base Pairs
Not scoring the block.
Block File (s) :    %s
Matrix File: %s
Not scoring the sequence.
Matrix File (s) :    %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Scoring sequence %s vs block %s.
Searching matrix %s against the sequence database.
Unable to read matrix for scoring against the sequences.Scoring sequence %s vs matrix %s.
(C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center

BLIMPS (BLocks IMProved Searcher)Using pseudo-count parameters %f and %s.
main(): SearchType variable corrupted, possible memory problems.Unable to open output file "%s" for writing.Not outputing the matrix output.
Unable to open output file "%s" for writing, aborting.Unknown genetic code %d.  Setting to Standard code (0).                                         Strength  Score Searching sequence %s against the matrices database.
AC#                    Description                                                Score Searching block %s against the sequence database.
Cannot open 'alts' file "%s".  Exiting...
Unable to read block for scoring against the sequences.Unable to read the sequence for scoring against the matrices.Unable to read the sequence for scoring against the blocks.Query sequence has zero length, not scoring it.
zDget_file_list(): Unknown file group %d.Unable to recover enough memory to continue.  Aborting.
Already have a frequency file: %sinsert_file(): Bad file list, not entering filename "%s"               into a file list
get_file(): Unknown file group            Unable to open a file
Unable to read sequence file: %s to determine the type of database
Unable to read pattern file: %s
Unable to read sequence file: %s
Unable to open frequency file: %s
Unable to open database file: %s
Unable to open matrix file: %s
Unable to open block file: %s
Unable to read pattern file: %sUnable to read sequence file: %sUnknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Assuming there is no title and just sequence.
get_file(): Bad file list, unable to open a file
rewind_file(): Bad file group, unable to rewind file list
get_current_file_name(): No files in the file group                         Unable to return a file name
get_current_file_name(): Bad file group, unable to return a file name
get_file_name(): Requested file out of the range of the files                 in the file groupget_file_name(): No files in the file groupget_file_name(): Bad file group, unable to return a file name
number_of_files(): Bad file group, unable to report number of files
close_file() : Bad file group, unable to rewind file list
ȼs\H4 ڻThe file %s will be ignored.
%lgfield has no effect.
%s/docs/default.amino.frq%s/docs/default.qijload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
pb_weights:%d ignored for %s
 ,
.+-0123456789%s/docs/default.sijMixture=Alpha=	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIX??R?@3333@3333BABMATRIX!$).38=BGID   AC   DE   BL   block=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
Allocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d ?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
ukdZP?5+t]O 8Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
%fNo width field for matrix %s  |% 4d--+%c |% 6.4fMA   %s
  %c     %c       A   C   G   T
%3d   *   -
% 9.4f % 9.4f
    *         -
 %c   *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

%s   Version %s  %s%s
%s   Version %s (%s)  %s%s
Decreasing the NumberToReport from %d to %d.Ran out of memory (2), fewer scores will be reported.
Decreasing the NumberToReport from saving all (%d currently) to %d.Ran out of memory (1), fewer scores will be reported.
blimps_reclaim_space(): NumInSL(Scores) is greater than NumberToReport.                 NumInSL(Scores) is supposed to be maintained                 less than or equal to the NumberToReport.                 NumberToReport = %d, NumInSL(Scores) = %d.                 Ran out of memory, removing the excess scores                 in the Scores list.
Decreasing the number of saved nodes in the list.The saved nodes level of the list has been reduced to %d.
The saved nodes level of the list has been reduced to %d.The list saved nodes cannot be reduced any more.
Unable to recover memory.
>Unknown configuration file key: %s
read_config_file_end(): SearchType variable corrupted.                        Should never have reached this part of the program.                        Possible memory problems.                        The rest of the run may be invalid.                        Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
Unknown search type given, assuming SQ vs BL search.
No sequence files given for the sequence database, aborting.
No block files given for the block database, aborting.
No block file given (BL field), aborting.
No sequence file given (SQ field), aborting.
No DB field given, assuming data is in the SQ field.
No DB field given, assuming data is in the BL field.
Missing either the BL or SQ field, aborting.
Configuration file has SQ, BL, and DB entries.Unable to determine the type of search.Configuration file has SQ and BL entries.No block file (BL) or sequence file (SQ) given, aborting.
No sequence file (SQ) or block file (BL) given, aborting.
New style uses the ST field instead of P4.
MA field already used.  Cannot have both the BL and the MAfields.  Ignoring the BL line.
Configuration file "%s" not found.  Exiting
Using the PAttern switch causes the REpeats switch to be ignored.Alignments reported will include repeats.
New style does not use the SE field.
BL field already used.  Cannot have both the MA and the BLfields.  Ignoring the MA line.
New style uses the RE field instead of P5.
New style uses the NU field instead of P9.
TRUEYESOld style configuration file.DNAAAUnknown search type: %s
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Couldn't allocate Seq[%d]
motif=[,]gibbsfreq=dups=mots=score=d1=d2=MOTIFJ=[
Enter name of blocks file: BL   wb
Cannot open file %s
 Research Center
No blocks found in file %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Enter name of file containing sequences: BLK2MOT: Copyright 1995 by Fred Hutchinson CancerUSAGE:  blk2mot            = input file of protein sequences         = input file of blocks from sequences         = output file for motomat
Enter name of new motomat file: 
No sequences found in file %s
?Q@ID   AC   DE   ; MATRIXblock=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000log-odds matrix: alength= 23 w= %d

Enter name of PSSM output file: 
Enter name of BLOCKS input file: BLK2PSSM: Copyright 1996-2003 Fred Hutchinson Cancer ResearchUSAGE:  blk2pssm    []         = B BLIMPS|M MAST|G Gribskov|P Psi-Blast         = 3,6,20,21
Enter PSSM format type (B=blimps, M=mast, G=Gribskov, P=Psi-Blast) [B]:  ALPHABET= ARNDCQEGHILKMFPSTWYVBZX
%s Invalid type %d, using type %d
<F<?Y@Q@%lgfield has no effect.
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
pb_weights:%d ignored for %s
 ,
.+-0123456789%s/docs/default.sijMixture=Alpha=	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIX??R?@3333@3333BABzDMATRIX((((((((((((((((((((((((((((ID   AC   DE   BL   block=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
Allocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
%fNo width field for matrix %s  |% 4d--+----%c |% 6.4fMA   %s
  %c     %c       A   C   G   T
%3d   *   -
% 9.4f % 9.4f
    *         -
 %c   *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Enter name of new slx database: 
Enter name of blocks database: ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d ?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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vЋuX[US[Ã6PBY[StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialAAGACATAGTACTACGACGTIMFPWDNEQARNDCQEGHILKMFPSTWYV 	
 	
;OUDB%sblkprob.stpDatabase=%s
Version 3.2.5Version 3.2.4Version 3.2.3Probe Sequence:SizeBase Pair 

TargetRecordsAlignmentsAC#Size:%s %d%sblksort.bias%srepeats.dat%d %f%sblksort.stn
%20s           %ld
%s
%s
%d %s %s %d %d %g %g %g %g
%-10s %s  % 2d  %2d of %-2d %8.2g
+	%d	%s (hit) %s	"%d"
       **biased**+ %d (repeat) %s
(other) %s
 **biased** -	%d	- %d Block    Frame    Location (aa)      Block E-valueOther reported alignments:Up to %d repeats expected:
 (bp)      Block E-value
BLKPROB Version %s
-rank-mast
Query=%s
Size=%ld Blocks Searched=%d
No hits found-stats-sumAlignments Done=%16.0f
-gff-E-H-C-SAmino AcidsBase PairsOR:    blkprob Other options
%d possible hits reported

Results: OUT OF MEMORY

hits: OUT OF MEMORY
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
========================================
Here are your search results from the BLOCKS searcher.
BLKPROB: Cannot open blocks file %smaxscore is too big, increase MAXSCORE from %d

closest_seq: Unable to allocate pair structure!
                         |---%5d amino acids---|==============================================================================                                                           RankFamily                                       Strand  Blocks   P-value
==============================================================================%s	BLOCKS	similarity	%ld	%ld	%8.2g %-10s % 1d     %6ld-%-6ld        %8.2g                                                             CombinedFamily                                       Strand  Blocks   E-value%s BLOCKS similarity %ld %ld %8.2g %-10s % 1d     %6ld-%-6ld        %8.2g

------------------------------------------------------------------------------>%s %d/%d blocks Combined E-value=%8.2g: %s

pvalue_rank(): OUT OF MEMORY
assemble_hits(): OUT OF MEMORY
Cutoff combined expected value for hits=%3.0f
Cutoff block expected value for repeats/other=%3.0f

Enter number of hits to report or blimps configuration file name [%d]: 
Enter name of file containing blocks search results: 
Enter name of blocks database searched: Blocks searched is negative, cannot use for statistics.Alignments done is negative, cannot use for statistics.COPYRIGHT 1992-8 Fred Hutchinson Cancer Research CenterUSAGE: blkprob    [-H n -E n -C n -mast|-rank -sum|-gff -stats]           = number of hits to report, use 0 for default     = blimps search output file     = blocks database searched by blimps     = name of blimps configuration file    -H n            maximum number of hits to report    -E n            cutoff expected value for anchor blocks    -C n            min cutoff raw score for anchor blocks    -mast           order results by MAST-type e-values    -rank           order results by RANK-statistic e-values    -sum            output summary only (one line per hit)    -gff		  Sanger Center's GFF output    -stats          produces .dat statistics file    -S filename     header file (default=blkprob.stp)
BLKPROB: Cannot open configuration file %s

BLKPROB: Cannot open file blimps file %s
A?A BApBABB?%lgfield has no effect.
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
pb_weights:%d ignored for %s
 ,
.+-0123456789%s/docs/default.sijMixture=Alpha=	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIX??R?@3333@3333zDMATRIX())%)()-)2)((7)<)(((((((((A)F)((((((((K)((((((((((ID   AC   DE   BL   block=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
Allocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
No width field for matrix %s  |% 4d--+----%c |% 6.4fMA   %s
  %c     %c       A   C   G   T
%3d   *   -
% 9.4f % 9.4f
    *         -
 %c   *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFastaUniversaFlat-file, no titleLength:Check:..>--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

rtprotomat.stpSCOREHIGH ,	
mkdir %s
Created directory %s
FRAGMENTLSTPS=LENGTH=,…|ung`YRKD=6LW^
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Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directoryvl[QG6,ޘ͘yk<T=D
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blocks@blocks.fhcrc.org Research Center truncated to fit the page column of the block.Version 3.2.5Version 3.2.4Version 3.2.3Probe Sequence:Size:Base Pair 

SizeTargetRecordsAC#Database=%s
%s %d%sblksort.bias%srepeats.dat%d %f%sblksort.stn 	
 	
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-------------ablksort.datblksort.rep
BLKSORT Version %s

Query=%s, 
 Size=%ld 
Blocks Searched=%d

%d possible hits reported
Amino AcidsBase PairsOR:    blksort -stats
===============================================================================
Here are your search results from the BLOCKS searcher.
Please report problems to webmaster@blocks.fhcrc.org, include your query
and this output. To obtain help, send the word HELP on a single line to
Copyright (c) 1992-6 by the Fred Hutchinson Cancer
If you use BLOCKS in your research, please cite:
Steven Henikoff and Jorja G. Henikoff, Protein Family Classification Based
on Searching a Database of Blocks, Genomics 19:97-107 (1994).
Each numbered result consists of one or more blocks from a PROSITE or PRINTS
group found in the query sequence. One set of the highest-scoring blocks that
are in the correct order and separated by distances comparable to the BLOCKS
database is selected for analysis. If this set includes multiple blocks
the probability that the lower scoring blocks support the highest scoring
block is reported. Maps of the database blocks and query sequence are shown:
  < indicates the sequence has been
  : indicates the minimum distance between blocks in the database
  . indicates the maximum distance
The maps are aligned on the highest scoring block. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database
is shown. Upper case in the query sequence indicates at least one
occurrence of the residue in that
BLKSORT: Cannot open file blimps file %s

BLKSORT: Cannot open blocks file %s
                         |---%5d amino acids---|
Maximum number of repeats (from Prosite MAX-REPEAT) = %d
%d non-overlapping repeats in support of %s
%d=%.2fth percentile of anchor block scores for shuffled queries
P not calculated for single block %s%s %s %s 1 %d %d %6.2g %.16f %d %d %d %d %d %ld %.2f

cluster_seqs: Unable to allocate pair structure!
%d.-----------------------------------------------------------
Block     Rank Frame Score Strength   Location (aa) Description%-8s %5d  % 2d   %4d  %4d     %7ld-%7ld %s

Block     Rank Frame Score Strength   Location (bp) Description
Enter number of hits to report or blimps configuration file name [%d]: COPYRIGHT 1992-8 Fred Hutchinson Cancer Research CenterUSAGE: blksort    [-stats]           = number of hits to report, use 0 for default     = blimps search output file     = blocks database searched by blimps    -stats          produces blksort.dat statistics file     = name of blimps configuration file
BLKSORT: Cannot open configuration file %s

Enter name of file containing blocks search results: 
Enter name of blocks database searched: pBA??*XVWPFMGArtprotomat.stpSCOREHIGH ,	
+-0123456789GENBANKLOCUSDEFINITIONORIGINACCESSIONENTRYTITLESEQUENCE///EMBLSQUNIVMSPROCLASSPCF_ACPCF_DEPCS_IDmkdir %s
Created directory %s
FRAGMENTBLOCKLSTPS=LENGTH=
Processing input file as %s 
	

%d. Entry %s found...ARNDCQEGHILKMFPSTWYVBZXactgDR   PIR.

>%s
fragmentCreating %sw+t
Cannot open %s
>%s2+$hhhhhhhhhhhhhhhhhhhvvo}``h`o#}tkbYPG>5,| 
	
Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directory
%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.
Cannot determine type of input file.P
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+-0123456789GENBANKLOCUSDEFINITIONORIGINACCESSIONENTRYTITLESEQUENCE///EMBLSQUNIVMSPROCLASSPCF_ACPCF_DEPCS_IDmkdir %s
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>%s %d %d %d %sEnd of input file reached.
markerError: bad data read.
%-20s (%4d)  [---- %d aa]%s: %s
%20s---- %d amino acids

rbOpening '%s' for read.
wbOpening '%s' for write.
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Warning: no input files.
This program takes block map data and generates a graphical map of the
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Usage: %s [infiles] [options]
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Arguments to options should be '-o[argument]' or '-o [argument]'.
Use '-' to stand for standard input/output.
Default output is to the screen.

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                 Full: Each sequence is  characters long.
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                 characters long, the rest are to scale.
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 -h              Get this help screen.
 -i filename     Add an input file(s) (this is not needed if input files
                 are placed before the options). Seperate multiple filenames
                 with spaces.
 -o filename     Set the output filename. The input filename is substituted
                 for '*' within , so '*.vis' is '.vis'.
                 You must use single quotes around  if it contains
                 '*'.
 -v number       Set verbosity level, 0-5. 0 = no messages, 1 = errors only,
                 2 = quiet, 3 = normal (default), 4 = verbose, 5 = debug.
 -a BLxxxxx      Do only a single block family.
Warning: unrecognized option '-%c'.
Scale type is %c, scale value is %i.
Warning: option '-%c' has an attached argument (ignored).
Warning: option '-%c' not used.
Warning: option '-%c' has too many arguments (ignored).
Error: premature end of input file.
%d distinct blocks in %d sequences
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vЋuX[US[ëPY[SCRIPT_NAMEBLOCKS_EMAILrdate '+%y%m'date "+%y%m%d"%s/blimps%s/blksort%s/blkprob/usr/bin/mailx../data-blocks%s/blocks.dat../data-prints%s/prints.dat../data-blplus../data-blplus-minus../docs%s/default.qij%s/default.amino.frq../tmp%s/%d.seq%s/%d.cs%s/%d.csh../log%s/%s%s/%d.mail%s/%d.out%s/%d.blk%s/%d.htmlblocks@fhcrc.orgCONTENT_LENGTHsequencetitleQUERY_STRINGaddresswERror_level          2
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prodomdomopfam#!/bin/csh
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    Blksort Error
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REQUEST_METHODPOSTumask 006Queuing %d...CONTENT_TYPE%s/htmlize-blkprob.pl %s >& %s
%s/htmlize-blimps.pl %s >& %s
%s/htmlize-blksort.pl %s >& %s
You need to enter a sequence to search with.
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    %s
blocks_search: Error opening %s

    Blocks Search Results
    You can check this URL within 4 hours for your results.
    
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%s/add_queue_entry.pl BLOCKS_queue %sapplication/x-www-form-urlencoded 	

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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000ERROR: Block %s is too deep (%d), truncated to %d sequences
ERROR: Block %s is too wide (%d), truncated to %d
ERROR: Block %s is too deep (%d), truncated to %d rows
ERROR: Block %s is too deep (%d), truncated to %d nseq
 width=%d; seqs=%d; 99.5%%=%d; strength=%d 
Enter name of new weighted blocks database: 
Enter name of blocks database: BLWEIGHT: Copyright 1994-2000 by the Fred Hutchinson Cancer Research Center, 
	Seattle, WA, USAAdd sequence weights to blocks.USAGE: blweight    	=input file of blocks to weight	=output file of weighted blocks	=P (position-based) | V (Voronoi) | 
		A (Vingron & Argos) | Cn (n percent clumping)	=M (max=100) | N (sum=#seqs) | # (sum=#)blweight: Calculating position-based weightsblweight: Decimal weights, sum = number of sequencesblweight: Integer weights, maximum weight = 100
Enter scale (M=>max=100, N=>sum=#seq, ###=>sum=###) [M]: 
Enter weighting scheme (P=position-based, V=Voronoi, 
 A=Vingron & Argos, Cn = n-percent cluster [P]: blweight: Calculating Voronoi weightsblweight: Calculating Vingron & Argos weightsblweight: Integer weights, sum = %d
blweight: Calculating %d percent cluster weights
.A?BFB0?ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motifwidth=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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Puhh=uhhz=uhhe=xPZe[^_ÉUVSuh|}4@EƍEEEE܋MɈEEEU܋MEȉUԉMċUEE~~‰E̋EċMEMЉE؋UM1҃}~3MME؋EvM8u4B9UEŰE9EEȋU9CE 4[^_ÐUSEUM]w
$@v؆؆؆[á몡١땡{jܡ뒡밡e냡%HԆ봡0T[ÐUWVS[R)2E)19s׉M)F9Ήr[^_ÉUWVS[))pNu.[^_ÐUSR
vЋuX[US[Û(Pb5Y[StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialAGACATAGTACTACGACGTHPWDNEQARNDCQEGHILKMFPSTWYV*Unknown residue: %d
width=%d seqs=%d%s: %s not found
  %c  %c    %4d (Peptide) Length: %d
Cons  Gap Len ..
 100 100
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BLIMPS_DIR 	
 	
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Cannot open BL file %s
Cannot specify both DB and SQFR and QM required with SQw
Cannot open OU file %s

Cannot open ML file %s
Missing OU output file nameMissing BL input file nameProfile written to %s
%s/docs/default.iij%s/docs/default.amino.frq%s/docs/default.qijConsensus written to %s

Cannot open LL file %s
FR and QM required with MA
Cannot open SQ file %s
Invalid consensus type: %d
Missing SU input file nameDB required with LLDB required with ML
Cannot open DB file %s
PSIPFS
Cannot open FR file %s

Cannot open SU file %s

Cannot open MA file %s
BLI
Cannot open QM file %s
 block=%s, pos=%d
 with counts + pseudo-countsSequence %s not found
Configuration file errorsCOBBLER Version %s
USAGE:  cobbler 
Cannot open file %s
>%s %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000%s %s	is first sequence most like consensus (%d %d)
%s %s	is first sequence least like consensus (%d %d)
%s %s from %d to %d with embedded PSSM>%s %s from %d to %d with embedded consensus blocks
#COBBLER Profile for %s %s from %d to %d
#
      COBBLER Profile for %s %s from %d to %d
Most like consensus written to %s
Least like consensus written to %s
FR and QM required with Type 3FR and QM required with Type 4WARNING: Aligned blocks overlap!!!  block=%s, pos=%d, last pos = %d
Query sequence %s is shorter than minimum path width
Type 2: Consensus based on substitution matrix with counts (no pseudo-counts)Type 4: Consensus based on PSSMType 1: Consensus based on percentage: %d
Type 3: Consensus based on substitution matrixCOPYRIGHT 1999 Fred Hutchinson Cancer Research CenterMake a consensus sequence and PSSM from a family of blocks
Enter name of configuration file: G.$@??B0B%lgfield has no effect.
load_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
pb_weights:%d ignored for %s
.+-0123456789%s/docs/default.sijMixture=Alpha=	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIX?R?@3333@3333ABzDMATRIX4444444444444444444444444444ID   AC   DE   BL   block=(block=(%d,%d);CC   motifwidth=width=%d;seqs=99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
Allocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
%fNo width field for matrix %s  |% 4d--+----%c |% 6.4fMA   %s
  %c     %c       A   C   G   T
%3d   *   -
% 9.4f % 9.4f
    *         -
 *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFastaUniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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          The order of the arguments is not important but the
          first name is for the input file and the second for the output.
pssm_type = 2 odds ratios normalized to 100
	3 pseudos, log odds, nats
	5 pseudos, log odds, half bits
	6 pseudos, log odds, third bits
	10 pseudos, odds ratios, nats
	20 just counts+pseudo counts
	30 average score
Genetic code type = 0 Standard
	1 Vertebrate Mitochondrial
	2 Yeast Mitochondrial
	3 Mold Mitochondrial and Mycoplasma
	4 Invertebrate Mitochondrial
	5 Ciliate Nuclear
	6 Echinoderm Mitochondrial
	7 Euplotid Nuclear
	8 Bacterial and Plant Plastid
	9 Alternative Yeast Nuclear
	10 Ascidian Mitochondrial
	11 Flatworm Mitochondrial
	12 Blepharisma Macronuclear
	13 Chlorophycean Mitochondrial
	14 Trematode Mitochondrial
	15 Scenedesmus obliquus mitochondrial
	16 Thraustochytrium mitochondrial
Degeneracy parameters=0.0 all nucleotides that actually appear are counted
	1.0 only nucleotide with highest value counted
	Between 0 and 1 nucleotides with high values counted,
	 if value/highest-value >= degeneracy parameter
Clamp temperature     Target melting temperature for clamp in degC 
Concentration         Probe concentration in nM
Rose restrictions     If set, uses Tim Rose's restrictions on boundaries
                      of core degenerate region.
Most common codons    If set, uses most common codons in clamp.
Begin oligo           If set, oligo must start on a conserved column,
                       otherwise core strictness is applied.
Apoly-x       Maxiumum number of consecutive nucleotides of same type.

Warning: Unspecified gcode type (%d) requested.
Using default gcode type (%d).
"%s help" for help.

Warning: Clamp temperature requested (%3.2f) is negative
Using default value (%3.2f).
Warning: Concentration requested (%3.2f) is negative
Using default value (%3.2f).
Warning: Clamp strictness parameter requested (%3.2f) is less than core strictness parameter (%3.2f)
Using default values (%3.2f, %3.2f).

No correctly formatted blocks found to processWarning: Unspecified pssm type (%d) requested.
Using default pssm type (%d).
"%s help" for help.

gWF)ؐȐiY<stdinstdoutdefault.codon.useuUuURVpVuUVVuUuUuUVuUuUuUuUuUuUuUuUuUVuUuUuUuUuUuUuUuUuUVL4@333333 @Xn?fffffq@0@??BzD>@@@pBHB%lgfield has no effect.
%s/docs/default.amino.frq%s/docs/default.qijload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
pb_weights:%d ignored for %s
 ,
.+-0123456789%s/docs/default.sijMixture=Alpha=	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIX?R?@3333@3333ABMATRIXm}]ID   AC   DE   BL   block=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
Allocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
rkaSE>-Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
%fNo width field for matrix %s% 6.4fMA   %s
  %c     %c       A   C   G   T
%3d   *   -
% 9.4f % 9.4f
    *         -
 %c   *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..>--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000 Fred Hutchinson Cancer Research CenterEnter organism name (leave blank for first organism in file): Looking for organism %s in %s

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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000COPYRIGHT 1998, Fred Hutchinson Cancer Research Centerfastaseqs: Converts a file of sequences to FASTA formatUSAGE: fastaseqs       = input file of seqences in a common format    = output file of sequences in FASTA format
Enter name of input sequence file: LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
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translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
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Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
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Warning: %s
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Information: %s
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Cannot open file "%s"

BL   
MA   %s%s;%s%s%s; ProDom_mul%s.biassed_blockswBLIMPS_DIR%s/docs/%sTrying %s...
 %2d %2d  %.3f
%-10s (%2d columns)

%s
Output written in file %s.
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Column score cutoff has to be between -1 and 1 !The value given (%f) is out of range.

Enter name of a file with blocks or block matrices: 
Bias fraction cutoff has to be between 0 and 1 !Input file doesn't have any entries !First entry in input file has neither block nor matrix lines !First entry in input file has both block and matrix lines !Unable to recover enough memory to continue.  Aborting.
Error ! Problem in ProDom entry %s
second word in description line doesn't begin with a (second word in description line doesn't end with a )Error ! Problem in format of ProDom entry %s sequence-line %d
A non-digit in the sequence start position %s
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.read_a_prodom_entry(): Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.
Error ! Problem in format of ProDom entry %s
A non-digit in the number-of-sequences field "%s"
 distance from previous block=(%d,%d)adapted from ProDom entry; width=%d; seqs=%d;Error ! Problem in format of ProDom entry sequence-line %d
Sequence %s has length of %d instead of expected %d
Error ! Actual number of sequences in ProDom entry %s
different than what the entry reportsError ! Problem in format of ProDom entry description -lineError ! Not enough sequences (%d) in ProDom entry %s
Error ! Number of sequences in ProDom entry %s (%d) is less than 2
Error ! Problem in format of ProDom entry description-lineError. variable db_type (%c) is of unknown type !

%s blocks_db [column score cutoff [bias fraction cutoff [min biased cols [debug level]]]]

Cannot open output file file "%s"
Normalized Sum-of-Products column score
Column score cutoff %.3f. Bias-fraction cutoff %2d percent (minimum %d columns).
               Pairs                 Columns         ClumpsBlock    Width Total Biassed Percent Biassed Percent Biassed Percent%-10s %2d   %4d  %4d   %3d      %4d   %3d      %4d   %3d%-10s %2d   %4d  %4d   %3d      %4d   %3d      %4d   %3d
%d biassed blocks found in the %d blocks.%d biassed blocks found in the %d blocks from file %s.@FB?AY@%lgfield has no effect.
%s/docs/default.amino.frq%s/docs/default.qijload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
pb_weights:%d ignored for %s
 ,
.+-0123456789%s/docs/default.sijMixture=Alpha=	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIX??R?@3333@3333ABzDMATRIX
-05:?DINSID   AC   DE   block=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
Allocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
%fNo width field for matrix %s% 6.4fMA   %s
  %c     %c       A   C   G   T
%3d   *   -
% 9.4f % 9.4f
    *         -
 %c   *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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    Warning
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    Error
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    Sequence %d not found.
    
%s %s %s %s %s > /dev/nullSequences weighted by (GIF image)]
     Vingron & Argos weights %% clustering position-based weights Voronoi weightsContent-type: text/html

REQUEST_METHODPOSTCONTENT_TYPEumask 006FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Error reading sequence %d. It is shorter (%d) than the apparent alignment length. Padding the end of the sequence with gaps.
    
%s; distance from previous block = (%dSequence names box is used and the alignment is in FASTA format.
    Sequence names will be taken from the alignment
    (first word in the sequence header lines -
    '>seq_name 123 aa example protein').
    The alignment width you gave (%s) is different than the first sequence length (%d).
    
Error reading sequence %d.
    
Error reading sequence %d. %d more residues in the sequence than the expected %d.
    
Number of sequence start positions (%d) is different than number of sequences (%d).
    
The number of sequences you gave (%s) is different from the number found (%d).
    
Number of sequence names (%d) is different than number of sequences (%d).
    
Sequence (%d) is too short (%d). The minimal length is %d.
    
Judging by the first sequence length (%d) the alignment is too short. The minimal length is %d.
    
Judging by the first sequence length (%d) the alignment is too long. The maximal length is %d.
    
No name found for sequence %d.
    
No start position found for sequence %d.
    
An error occured weighting the block.Please try again at a later time.If it fails again contact the maintainer of these pagesand describe what caused the problem with an example.
    Block Formatter output
    Block Formatter output
    . The weights were scaled to 1-100, 100 having most weight.
    [block logo [block PSSM (what is a PSSM)][block logo [block PSSM (what is a PSSM)]application/x-www-form-urlencodedThis script can only be used to decode form results. This script should be referenced with a METHOD of POST.If you don't understand this, see this forms overview.%c
    What could have happened is that you just reloaded this page rather than redoing the search.
    If you use NETSCAPE it has a tendency to try to reload a page when you go back to it.  This may be why you have this error.ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d ?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFastaUniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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%d blocks processed

COBBLER sequence:end cobblerend mapend treeend prowebend blinksend pdbend cyrcablinks.datproweb.datcobbler.pros/howard/btest/bin/blocks.datVersion %s
[prosite_dir]
Enter Block accession number: 
Enter name of Blocks database file [%s]:
GETBLOCK: (C) Copyright 1992-1999, Fred Hutchinson Cancer Research CenterUSAGE:  getblock AC blocks cobb maps trees proweb blinks blk2pdb cyrca 		AC = block accession (eg BL00094 or IPB001525)		blocks = name of blocks database file		cobb = name of cobbler database file		maps = name of map structure database file		trees = name of tree structure database file		proweb = name of Proweb database file		blinks = name of file of links to ProDom		blk2pdb = name of PDB cross-reference file		cyrca = name of CYRCA cross-reference file		prosite_dir = name of directory containing prosite.dat and prosite.doc files
Cannot open blocks database %s

Cannot open prosite.dat file %s

Cannot open prosite.doc file %s
*XVWPFMGArtprotomat.stpSCOREHIGH ,	
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Created directory %s
 	
FRAGMENTBLOCKLSTPS=LENGTH=
Processing input file as %s 
	

%d. Entry %s found...ARNDCQEGHILKMFPSTWYVBZXactgDR   PIR;.

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Protein files will be placed in current directory
%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P
 WARNING: Titles are sometimes truncated in this format;
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Cannot determine type of input file.
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Enter name of interpro xml file: INTERPRO: Copyright 2000 Fred Hutchinson Cancer Research Center
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Enter name of interpro entry or all : aFatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
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Enter name of block file: 
Reading %s...
  %d sequences in %sw+t
Cannot open file %s
No block found in %s

Cannot open file %s%d sequences written to %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
LISBLK: (C) Copyright 1995-2000, Fred Hutchinson Cancer Research Center %d sequences from %s
  were found in %s

Enter name of file containing list of sequences: ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d ?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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Created directory %s
 	
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Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directory~tcYO>4	sD\.@
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CLUSTALSTOCKHOLM%s.%dw 	
ClustalStockholmERROR reading Clustal file
%s\rm %s as proteinTrying  MSF format.
mablock.%dERROR reading MSF file
%sUNK motif; width=%d; seqs=%d;%s %d : %s %d
>%20s          from blocks
%5d P1;Non-unique sequence name: %s
%s%dModified name to %s
%s; BLOCK
Cannot open file %s

Enter name of output file: 

FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Trying CLUSTAL/STOCKHOLM format.
WARNING: Sequences appear to be DNA but will be treated%s; distance from previous block=(%d,%d)WARNING: sequence segments are of different lengths

Enter name of blocks database: MABLOCK: Copyright 2001 Fred Hutchinson Cancer Research Center
USAGE: mablock         = file of fasta or clustal multiple alignments             Clustal format must have CLUSTAL on first non-blank line      = output file of blocks             Puts blocks in out.blks & sequences in out.seqs      = output type, B=blocks, F=fasta    = minimum ungapped width to define a block    = maximum block width%d blocks found with minimum width %d and maximum with %d
Output written to %s.blks and %s.seqs

Enter type of output file [B=blocks|F=fasta]: WARNING: Maximum number of sequences = %d
no blocks found with minimum width %d
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
pb_weights:%d ignored for %s
 ,
.+-0123456789BLIMPS_DIR%s/docs/default.sijMixture=Alpha=	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankSIFT_pssm(): Cannot open %s
; MATRIX??R?@3333@3333BABzDMATRIX((((((((((((((((((((((((((((ID   AC   DE   BL   block=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d ?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
%fNo width field for matrix %s  |% 4d--+----%c |% 6.4fMA   %s
  %c     %c       A   C   G   T
%3d   *   -
% 9.4f % 9.4f
    *         -
 %c   *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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0call_gmon_startcrtstuff.c__CTOR_LIST____DTOR_LIST____JCR_LIST__p.0completed.1__do_global_dtors_auxframe_dummy__CTOR_END____DTOR_END____FRAME_END____JCR_END____do_global_ctors_auxmablock.cconvert.cbasic_matrix_constructionmake_colpre_weighted_sequencesmake_work_pssmcountscount_residuespseudo_altscompute_BZXblocks.cBlockBufLengthBlockBuffererrors.cErrorFilematrix.cmemory.cRecFuncsequences.clbuff.0first_time.1strutil.cgcode.cgctrans.0nt_atobread_block_bodytry_clustalremove_trailing_whitespaceaa_btoafree_sequencesimilarity_dependent_scale__strtod_internal@@GLIBC_2.0ABRT_signal_handlerstrncat@@GLIBC_2.0strchr@@GLIBC_2.0MinWidthpre_weighted_conversion_methodfeof@@GLIBC_2.0SIFT_conversion_methodfrequencyorder_seqgetpid@@GLIBC_2.0_DYNAMICmake_gribsmake_blockfree_matrixBlock_ACstrcmp@@GLIBC_2.0log10@@GLIBC_2.0original_conversion_method_cleaned_upinit_reclaim_spaceset_error_file_name_fp_hwaa_atobBlock_DEfprintf@@GLIBC_2.0getenv@@GLIBC_2.0fflush@@GLIBC_2.0__fini_array_endcodon2aant_arevcompaa2codonread_a_matrixgcodes__dso_handlent_bdegen__libc_csu_finifind_blocksoutput_block_sputchar@@GLIBC_2.0ErrorLevelReportgets@@GLIBC_2.0aafqsequence_typerewind@@GLIBC_2.0block_to_matrixftell@@GLIBC_2.0resize_sequencesystem@@GLIBC_2.0next_clusteroutput_blocksQijputs@@GLIBC_2.0_initaltschul_data_dependent_conversion_methodmalloc@@GLIBC_2.0output_matrix_stfasta_seqsfix_namesinit_gcodeseq_type_dbsstderr@@GLIBC_2.0output_blockaa_adegennew_blockfseek@@GLIBC_2.0gribskov_conversion_methodread_block_header_startprint_blockfgets@@GLIBC_2.0resize_block_sequencesfree_blockErrorBufferstrstr@@GLIBC_2.0output_fastaErrorReport__strtol_internal@@GLIBC_2.0output_sequenceMaxWidthblock_comparisonntfqlgamma@@GLIBC_2.0load_qijtranslate_sequencestrncmp@@GLIBC_2.0__fini_array_startmatrix_comparisonfputc@@GLIBC_2.0__libc_csu_initread_a_sequenceOutName__bss_startmaintry_msfmake_blisttype_dbseat_whitespace__libc_start_main@@GLIBC_2.0__init_array_endread_sequencefree_blistprint_sequenceexp@@GLIBC_2.0sequence_comparisonrealloc@@GLIBC_2.0strcat@@GLIBC_2.0get_tokenDbInfodata_startBlock_IDoutput_matrix_scounts_nogapsprintf@@GLIBC_2.0blank_lineread_to_block_finimemcpy@@GLIBC_2.0fclose@@GLIBC_2.1__ctype_toupper_loc@@GLIBC_2.3strrchr@@GLIBC_2.0__preinit_array_endadd_logsfree_work_pssmreclaim_spaceBufferfind_max_aa_colload_diristrspn@@GLIBC_2.0exit@@GLIBC_2.0insert_blistcalloc@@GLIBC_2.0nt_brevcompsscanf@@GLIBC_2.0_edata_GLOBAL_OFFSET_TABLE_free@@GLIBC_2.0_endpseudo_dirifind_max_aa_pssmnew_matrixstrncpy@@GLIBC_2.0fopen@@GLIBC_2.1__init_array_start_IO_stdin_useduntranslate_sequencenormalizestrtok@@GLIBC_2.0original_conversion_methodRTotSIFT_pssmread_a_block_fastersprintf@@GLIBC_2.0fwrite@@GLIBC_2.0resize_block_clustersnt_btoa__data_startoutput_matrix_Jv_RegisterClasses__ctype_b_loc@@GLIBC_2.3nt_adegen__preinit_array_startlog@@GLIBC_2.0print_matrixread_a_blockpb_weights__gmon_start__strcpy@@GLIBC_2.0blimps-3.9/bin/Linux/makeblockmap000075500001460000012000001507421062462471100174050ustar00jorjastaff00000400000027ELF(4D4 (444  $  (((  Qtd/lib/ld-linux.so.2GNU%0-,.)+*/
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vЋuX[US[Ó%PY[StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialAAGACATAGTACTACGACGTIMFPWDNEQARNDCQEGHILKMFPSTWYV*does not end with an "A".
block %s.
>%s %d %d %d %s
%s
%s %d %d
%c %d %d
//
wCannot open input file %s

Output in file %s.
Unable to allocate idsCannot open output file %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Warning ! The name of the first block in family %s
Note - Not all sequences in family %s contain all the blocks.
Error ! Block %s is not the block expected to follow (by name)
Note - Block %c PRECEDES block %c in sequence %s of family %s.
Note - Blocks %c (%d-%d) and %c (%d-%d) in sequence %s
of family %s overlap.
Note - Sequence %s in family %s does not contain block %c.
Note, first block (%c %d-%d) in sequence %s of family %s
begins BEFORE the first aa of the sequence !
Error ! Couldn't find all %d sequences.
Error ! Last block (%c, %d-%d) in sequence %s of family %s
is out of bounds.
Warning unrecognized parameter - "%s".
Input file "%s" processed by program "%s"

Couldn't find or process block family %s !
Couldn't make a block map for block family %s.
A program to create block map description(s) from block family(ies) data:
%s blocks-input_file_name [output_file_name] [-Fblock_family_name] [-Lsequence_length_file]
Defaults: in-"%s" out-"%s" block_family_name-"%s"

Comments: "-" instead of an input/output file name => stdin/stdout
           The order of the arguments is not important but the
           first name is for the input file and the second for the output.
          block_family_name = "" : all block families in input

((input now expected from screen; CTRL-C to quit))


%d block family(ies) processed into maps.
%d block family(ies) could not be processed.Note: The sequence lengths shown are the 'right-most' sequence positions found in the blocks.
Couldn't make a block map for block family %s.

Error ! Input file %s does not contain any blocks.
stdinstdoutID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d ?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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mkdir %s
Created directory %s
 	
FRAGMENTBLOCKLSTPS=LENGTH=zsle^WPIB;4-&<GNjc\U5.' q@cWK?3'| 
	
Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directorywpf\KA7&i[,D.p
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%19s...FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000First 20 characters of sequence name must be unique.
Unable to read sequence file: %s to determine the type of database
Unknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Sequences appear to be DNA: Block Maker is designed for protein.Only %d sequence found, need at least 3
get_file_list(): Unknown file group %d.Unable to recover enough memory to continue.  Aborting.
Already have a frequency file: %sinsert_file(): Bad file list, not entering filename "%s"               into a file list
get_file(): Unknown file group            Unable to open a file
Unable to read pattern file: %s
Unable to read sequence file: %s
Unable to open frequency file: %s
Unable to open database file: %s
Unable to open matrix file: %s
Unable to open block file: %s
Unable to read pattern file: %sUnable to read sequence file: %sAssuming there is no title and just sequence.
get_file(): Bad file list, unable to open a file
rewind_file(): Bad file group, unable to rewind file list
get_current_file_name(): No files in the file group                         Unable to return a file name
get_current_file_name(): Bad file group, unable to return a file name
get_file_name(): Requested file out of the range of the files                 in the file groupget_file_name(): No files in the file groupget_file_name(): Bad file group, unable to return a file name
number_of_files(): Bad file group, unable to report number of files
close_file() : Bad file group, unable to rewind file list
 , לp>The file %s will be ignored.
Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:%s >--- sequence --->%s 	( %d:??) 	>--- -------- ---NA) 	AA) 	>%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

>?Nthsl.cp->key != ((void *)0)Invalid matrix-sequence scoring method specified, %d.Setting the method to the default value and using theNo pattern for matrix %s, Scoring the entire matrix
score_and_enter(): Tried to score a sequence that is not an                   amino acid sequence.  Not scoring the                   sequence %s
---------------------------------------------%-8s %4u %-45s      %4d   %4d %2d %6d %s
%-8s vs %-7s   %-20s... & %-20s... %4d %4d %2d %6d %6d %s
%-11.11s %-50.50s      %4d   %4d %2d %6d %s
%-20.20s %-62.62s %4d %2d %5d %6d %s
default scoring method.
--------enter_score(): Error placing matrix score into list
default_scoring_method(): matrix %s has length <= 0default_scoring_method(): Not scoring the sequence.
default_scoring_method(): sequence %s has length (amino acids) <= 0zD@lD?Histogram:
   %5d - %-5d : %d
   %5d -       : %d
residue_compare_functionscan_patternsscan_patternparse_residueUnable to find pattern for PSSM %s
pattern.cNumInSL(residue_list) == 0pat_file != ((void *)0)AC   BL   ; MATRIXblock=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, --- ----- ---ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d 1' ~m\E>0Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
%fNo width field for matrix %s  |% 4d--+%c |% 6.4fMA   %s
  %c     %c       A   C   G   T
%3d   *   -
% 9.4f % 9.4f
    *         -
 %c   *  % 6.4f % 6.4f
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/cm {cmfactor mul} bind def %% defines centimeters

/rotation %*.*f def %% degrees
/knirhs 1 shrink sub 2 div def
/charwidth4 charwidth 4 div def
/charwidth2 charwidth 2 div def

%% Since outlining goes around the inner edge of the character
%% make the thickness of the character bigger to compensate.
/setthelinewidth {2 setlinewidth} def
setthelinewidth %% set to normal linewidth

%% Set up the font size for the graphics
(*[[ This special comment allows deletion of the repeated
/charparams { %% char charparams => uy ux ly lx
%% takes a single character and returns the coordinates that
%% defines the outer bounds of where the ink goes
    %% take the character off the stack and use it here:
    pathbbox %% compute bounding box of 1 pt. char => lx ly ux uy
    %% the path is here, but toss it away ...
/dashbox { %% xsize ysize dashbox -
%% draw a dashed box of xsize by ysize (in points)
  /ysize exch def %% the y size of the box
  /xsize exch def %% the x size of the box
    %% Define the width of the dashed lines for boxes:
/boxshow { %% xsize ysize char boxshow
%% show the character with a box around it, sizes in points
  /tc exch def %% define the character
  /ysize exch def %% the y size of the character
  /xsize exch def %% the x size of the character
  /xmulfactor 1 def /ymulfactor 1 def

  %% if ysize is negative, make everything upside down!
    %% put ysize normal in this orientation
  %% Don't show the box if it is a vertical bar, otherwise do.
  showingbox {tc (|) ne {xsize ysize dashbox} if} if

    xsize knirhs mul ysize knirhs mul translate
    xmulfactor ymulfactor scale
    ysize %% desired size of character in points
    uy ly sub %% height of character in points
      div %% factor by which to scale up the character
    xsize %% desired size of character in points
    ux lx sub %% width of character in points
  %% Adjust horizontal position if the symbol is an I
  tc (I) eq {charwidth 2 div %% half of requested character width
             ux lx sub 2 div %% half of the actual character
                sub      0 translate} if
  tc (I) eq {/xmulfactor 1 def} if

  /xmove xmulfactor lx mul neg def
  /ymove ymulfactor ly mul neg def

  xmulfactor ymulfactor scale

  gsave 1 setgray fill grestore

WARNING: Outlined characters will not display at all under NeWSbut will print fine on an Apple LaserWriter IIntx
/numchar{ %% charheight character numchar
%% Make a character of given height in cm,
%% then move vertically by that amount
/setthelinewidth {1 setlinewidth} def
    charwidth charheight char boxshow
  charheight abs 1 gt {0 charheight abs translate} if
  %% create the user defined strings

    stringwidth pop stringscale mul neg stacksperline
    stringscale stringscale scale

WARNING: if you don't see centered string number %ld:
it may be off the page because stacksperline is large (%ld) relative to the
FROM-TO range (%ld to %ld) and centering is based on stacks-per-line.  To
solve this, reduce parameter stacksperline to FROM-TO+1 = %ld


WARNING: rotations that are not multiples ofof 90 degrees are likely to be scaledincorrectly, due to a PostScript limitation.See the description of the pathbbox functioncharwidth parameter must be > 0 cmbarheight parameter must be > 0 cmbarwidth parameter must be > 0 cm
WARNING: are you SURE you don't want to show the variation due to a smallnumber of samples (i.e. the I-beam error bars)?
Reminder: the I-beam error bars show thevariation of the entire stack not just the highestsymbol, even though it may look like that.linemove parameter must be positiveShrink parameter must be less than or equal to 1.This way, you won't create a misleading logowhich has an apparent height larger than it should.missing a user defined string coordinatebarbits parameter must not be zeromissing bar coordinate parametermissing corner coordinate parametersnumbering parameters are missingnumber of user defined strings must be givenshowingbox parameter is missingmissing barheight and barwidth parametersShrinking can only be done when showing the dashed box.which has an apparent height smaller than it should.stacksperline parameter is missinglinesperpage parameter is missing getstring: a line exceeds maximum string size (%ld)
linesperpage parameter must be positivestacksperline parameter must be positive in the range from %ld to %ld
 bits (sample error not known)%% amplitude  phase  wavelength  base:
 %*.*f cm %*.*f cm %*.*f cm %*.*f cm
 %*.*f cm %*.*f cm %*.*f cm %*.*f cm %ld
mark symbol in file marks must be one of: "of" %*.*f cm %*.*f cm %*.*f cm circle
At position %ld the sum of symbols found is %ld
******************************************************************************
* NOTE: since the data come from the sites program, the error bar is not     *
* printed on the sequence logo.                                              *
This is a Chilogo! - Upside down letterswill be produced
WARNING: symvec does not contain data for position %ld
WARNING: negative Rs variation found in symvec,but the data are not from the sites programpossible program or data error.%% before coordinate %ld: make the bar
It seems that you don't have a zero coordinate."... the invention, probably by the Hindus, of the digit zero has beendescribed as one of the greatest importance in the history of mathematics."--- Encyclopaedia Britannica (1:1175, 1982)
WARNING: Highest position requested was not found in symvec
%% find out how high the bar is in centimeters:
/barincm barheight cmfactor div def
  gsave barincm (%c) numchar grestore shift
Half-White Ibeams are used because the symbols are solid black.%% bar at end of logo: make the bar before position %ld
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WARNING: Highest position requested was not found in symvec
%% find out how high the bar is in centimeters:
/barincm barheight cmfactor div def
  gsave barincm (%c) numchar grestore shift
Half-White Ibeams are used because the symbols are solid black.%% bar at end of logo: make the bar before position %ld
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Cannot open file "%s"

Enter file name suffix: Research Center%d number of symbols
%*ld %*.0lf %*.*f % .1E
%c %4d
col   %c   info.  sum%2d| %3d  %6.3f  %3.0f  %2d/%d %6.3f %6.3fcolors.%scp 'colors.%s' 'colors.%s'%s %*s; MATRIXMATRIX inputsymvecw* %s %s
%s/makelogob '%s' > /dev/nulllogo.%s
Cannot open file %s
cp %s/colors %stouch wavetouch marks   P to print logo (%s %s).)
%s %s %s
File %s sent to printer.
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Enter AC in %s or - to make logos for all: 
Enter name of BLOCK or MATRIX file: Logos will be written to logo.%s
MATRIX_LOGOB: Copyright 1995-8 Fred Hutchinson Cancer USAGE: matrix_logob blocks|pssms AC|- suffix   pssms must be in blimps format and consist of values betwen 0 and 100
    which sum to 100 in each column.These files must be in the current directory:   makelogob, colors, default.amino.frq* position, samples, information, variance

small sample correction (e) : %6.3f, variance (avarhnb) : %6.3f
(these are are actually the values for the last column and will be different for the other columns if they contain a different number of unspecified residues - gaps, Xs, etc.)
     residues   #_of_specified_residues/#_of_seqs   e   var* PSSM of block %s (%s) from file %s.
PSSM of %s (%s) %d sequences.
No block with name %s found in file %s !

The created sequence-logo file (%s) is a PostScript file.
  (V to view logo with program %s (%s %s %s))
     after viewing you can also choose to print,A?%lgfield has no effect.
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
Unable to recover enough memory to continue.  Aborting.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
pb_weights:%d ignored for %s
 ,
.+-0123456789%s/docs/default.sijMixture=Alpha=	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankSIFT_pssm(): Cannot open %s
BLOCK??R?@3333@3333BABzDMATRIX"xx',xxxxxxxxx16xxxxxxxx;xxxxxxxxxID   AC   DE   BL   block=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
Allocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
%fNo width field for matrix %s  |% 4d--+----%c |% 6.4fMA   %s
  %c     %c       A   C   G   T
%3d   *   -
% 9.4f % 9.4f
    *         -
 %c   *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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r***%s not found
   %5d %5.3f :
cutting %d %d: %d

Couldn't allocate GROUPS.
Motif: + .   %3ld (%3d)  %3ld (%3d)  %s (Motif at %d)--  Most common amino acids
*  	
Couldn't allocate Seq[%d]
motifj.motw+b
Unable to open file %s>%s %d%1s MAXIMUM
.motifj.pros MINIMUM

MOTIFJ Version %s PNAS 87 (1990), pp. 826-830.
Using RunType=%d
Reading batch file %s

Enter input file name: 
filepath=%s
Sequence #%d:	%s		Length of sequence #%d =  %d
MOTIFJ=[Couldn't allocate MOTIF.
Reading sequence file %s
%s,]
CANNOT ALLOCATE SMatrix Enter new level [2-%d; %d]:  Enter new number [0-;%d]:  Using previous distance  %d
 with shuffled sequences.
Found %d motifs.
Starting motomat...1motomat
Starting motifj...3 or 0 to assemble blocks: Enter 'l' for long form:  Total amino acids in %d proteins: %d

 last score = %d, groups = %d
                    Protein %s:
 in %d proteins (%d duplicates), Merged %d, Score %d
  Score (Position) for best two fits.ERROR reading %s, sequence longer than %d, truncated
Use shuffled sequences [y/n; n]? 
Please cite Hamilton O. Smith, et al,
NumSeqs=%d batch=%d Title=%s
Allocating and initializing arrays...Enter search width [1-24; 17]: Enter drop score [0-18540; %d]: Enter number of allowable internal duplicates [0-%d; 0]: 
Enter significance level [2-%d; %d]: Couldn't allocate AA3_OBS array.Couldn't allocate AA3_OBS pointer.
Too few sequences to process(need at least 2).Cannot open file %s not found

Previous significance level was %d.Previous number of internal duplications was %d.
RunType = %d, Normalized drop score = %d
Motif parameters = [%d, %d, %d]
CPU time to find and sort motifs: %ld seconds.
___________________________________________________________________________
Printed %d motifs out of %d total.
Mean score: %ld 
Enter number of motif groups to map (maximum %d)Enter 'g' to print first motif in each group: 
_________________________________Group #%d_________________________________

 Enter number to save or -1 to redo [1-%d; %d]: ?B*XVWPFMGArtprotomat.stpSCOREHIGH ,	
+-0123456789GENBANKLOCUSDEFINITIONORIGINACCESSIONENTRYTITLESEQUENCE///EMBLSQUNI>VMSPROCLASSPCF_ACPCF_DEPCS_IDmkdir %s
Created directory %s
FRAGMENTBLOCKLSTPS=LENGTH=
Processing input file as %s
%d. Entry %s found...ARNDCQEGHILKMFPSTWYVBZXactgDR   PIR;.

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Using BLOSUM62 scoring matrix.
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Protein files will be placed in current directory
%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P
 WARNING: Titles are sometimes truncated in this format;
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)|4 C{H0call_gmon_startcrtstuff.c__CTOR_LIST____DTOR_LIST____JCR_LIST__p.0completed.1__do_global_dtors_auxframe_dummy__CTOR_END____DTOR_END____FRAME_END____JCR_END____do_global_ctors_auxmotifj.cmotmisc.cwrite_prosmap_seqsBatsplitgetscorestrncat@@GLIBC_2.0strchr@@GLIBC_2.0pamidxfeof@@GLIBC_2.0_DYNAMICscore_motDistancestrcmp@@GLIBC_2.0strnjcmpcompare_subgrps_fp_hwNumSeqsfprintf@@GLIBC_2.0fflush@@GLIBC_2.0__fini_array_endprint_statscheck_dupbl62_highpassSMatrix__dso_handle__libc_csu_finicompare_motgrpsputchar@@GLIBC_2.0gets@@GLIBC_2.0Batch_Filenamerewind@@GLIBC_2.0num_to_aacharsystem@@GLIBC_2.0TitleShort_Formputs@@GLIBC_2.0_initMot_FilenameSignifRunTypemalloc@@GLIBC_2.0Firstpr_num_to_aa_spacestrpbrk@@GLIBC_2.0LenDropSeqstdout@@GLIBC_2.0bl62_matrixrealigntime@@GLIBC_2.0_startfgets@@GLIBC_2.0dir_unixexeclp@@GLIBC_2.0wpamidxfputs@@GLIBC_2.0strstr@@GLIBC_2.0strcspn@@GLIBC_2.0__strtol_internal@@GLIBC_2.0qsort@@GLIBC_2.0bl60_highpasscompare_scoresstrncmp@@GLIBC_2.0__fini_array_startpr_num_to_aafputc@@GLIBC_2.0__libc_csu_initSeqname__bss_startmainget_counttype_dbs__libc_start_main@@GLIBC_2.0makedbidcut_motifs__init_array_endprint_motifget_idsstrcat@@GLIBC_2.0extract_seqssplit_namesdata_startprintf@@GLIBC_2.0_finisqrt@@GLIBC_2.0fclose@@GLIBC_2.1kr_atoigetseqscheck_entry__preinit_array_endsrand@@GLIBC_2.0opendir@@GLIBC_2.0compare_groupsVersionstrspn@@GLIBC_2.0exit@@GLIBC_2.0_edatawrite_motifs_GLOBAL_OFFSET_TABLE_free@@GLIBC_2.0_endgetfilestrncpy@@GLIBC_2.0init_dbsfopen@@GLIBC_2.1__init_array_startkr_itoa_IO_stdin_usedstrtok@@GLIBC_2.0bl60_matrixaachar_to_numsprintf@@GLIBC_2.0fwrite@@GLIBC_2.0__data_start_Jv_RegisterClasses__ctype_b_loc@@GLIBC_2.3shuffle__preinit_array_startrand@@GLIBC_2.0pb_weights__gmon_start__Dupsstrcpy@@GLIBC_2.0d
 with shuffled sequences.
Found %d motifs.
Starting motomat...1motomat
Starting motifj...3 or 0 to assemblimps-3.9/bin/Linux/motomat000075500001460000012000001404341062462471100164340ustar00jorjastaff00000400000027ELF84T4 (444  @T5  (((  Qtd/lib/ld-linux.so.2GNU%0-,.(*)/ +"#%!	
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NumSeqs=%d, Total_Motifs=%d
Sequence #%d: %20s %d %.5s

MOTIF %d: %d(%d)%d(%d)%d
%20s (% 5d) 
                   
Path: % 3d
Score              %1s
Saving block %.1s%.1s%.1sID   %s; BLOCK
AC   %s;DE   %s
 width=%d seqs=%d


//

>>>MOTOMAT out of memory!
seq=%d: 
Revised TopScore=%ld
row %.3d:  %.3d   x
 (%d, %d) B%d %.1s%.1s%.1s
   thisb: %d=%d 
    allb: 
best_path: paths->nblocks=%d
 , total sequences=%d, prop=%d
   saveb, allb: %d=%d,%d 
 >>>NEW BESTPATH

follow:  row=%d, ntemp=%d
 curpath blocks=
 curpath_seqs:
End of follow_arcs for %d
find_paths: single %d

find_paths: more-----------%d  %d
, total conserved=%d
Sequences in the best path:%.3d:%20s 
MOTOMAT %s: ls -al *.motrb
%s

%d blocks read %d sequences.asisamotomat.err
Extending blocks...%s.blksw+t
Cannot open %s

Assuming input from Gibbs

Merging raw blocks...
Cannot open file %s

CANNOT ALLOCATE SMatrixSaving blocks to %s

Block %d: %.1s%.1s%.1s has been merged.
Extended width was %d
Block %d:

Looking for best path..., npath=%d

Merging extended blocks...., nseqs=%d

No surviving blocks, reduced significance=%d
Reducing block overlaps ...  domain=%d, score=%d, freq=%d, dups=%d, mots=%d
 %.1s%.1s%.1s (extended width=%d, score=%d  motifs=%d, motif width=%d, conserved=%d)
merged_motif: Unable to allocate merged_motif structure!
Blocks %d and %d have been divided
Merging motif %d into motif %d distance from previous block=(%d,%d)
BL   %.1s%.1s%.1s gibbs=[%d,%d,%d] motomat=[%d,%d,%d]BL   %.1s%.1s%.1s motif=[%d,%d,%d] motomat=[%d,%d,%d]
cluster_seqs: Unable to allocate pair structure!Block %d has been trimmed by %d to eliminate overlap with Block %d.
  Restarting with DropScore = %d
 makepath: Unable to allocate path structure!
 order_blocks: Unable to allocate temp structure!
 prune_blocks: Unable to allocate temp structure!
 check_seqs: Unable to allocate temp structure!
 makematrix: Unable to allocate matrix structure!
 ***MOTOMAT STOPPING BECAUSE >1500 PATHS*** makebllist: Unable to allocate block_list structure!

 New path: nblocks=%d, tots=%dBest sub-path:%d blocks, %d AAs, total score=%ld,
 total motifs=%d, total idents=%d
 row=%d temp[i].index=%d nseq=%d follow_arcs: Unable to allocate temp structure!
 find_paths: Unable to allocate temp structure!

Best path has %d sequences out of %d:
%d blocks, %d AAs, total score=%ld, total motifs=%d
 total sequences=%d out of %d
Sequences not in the best path:(C) Copyright 1991 by Fred Hutchinson Cancer Research Center
Please cite: S.Henikoff & J.Henikoff, NAR 19:6565-6572 (1991).
Enter name of file containing motifs:  using parameters [%d, %d, %d].
Processing blocks in %s using a cut-off score of %d 
   and a clustering threshold of %d percent.
Recalculating block column scores

Input file was created using wrong motifj version!
Enter minimum block extension column score or 1 for best block [100-2500 or 1; %d]: Enter clustering identity threshold [1-100; %d]: 
Processing block %d in %s using a cut-off score of %d 

Type S[ENTER] to save this block, or N[ENTER] to skip to next block,
or anything else[ENTER] to re-extend this block...

Removing duplicate blocks....
Using a drop score of %d standard deviations or %d., re-extending with cutoff score of %d.
Block %d has been dropped for low width:
Quitting becasuse no motifs to work on.
Mean score=%.2f, standard deviation=%.2f
Surviving blocks=%d, max dups=%d%s %d %d %d %d %d %d %d %d %d %d %d %d %ld %d %d %d

Enter drop standard deviations [-30 to 30; %d]: 
Block %d has been dropped for low score:
Dropping blocks with score below %ld...
 unless they have more than one merged motif?{Gz?B? A*XVWPFMGArtprotomat.stpSCOREHIGH ,	
+-0123456789GENBANKLOCUSDEFINITIONORIGINACCESSIONENTRYTITLESEQUENCE///EMBLSQUNI>VMSPROCLASSPCF_ACPCF_DEPCS_IDmkdir %s
Created directory %s
 	
FRAGMENTBLOCKLSTPS=LENGTH=
Processing input file as %s 
	

%d. Entry %s found...ARNDCQEGHILKMFPSTWYVBZXactgDR   PIR.

>%s
fragmentCreating %s>%sJC<5.' xx	x2;zqh_VMD2| 
	
Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directory
%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.
Cannot determine type of input file3p
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		GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2)GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2)GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2)GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2)GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2)GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2)GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2).symtab.strtab.shstrtab.interp.note.ABI-tag.hash.dynsym.dynstr.gnu.version.gnu.version_r.rel.dyn.rel.plt.init.text.fini.rodata.eh_frame.ctors.dtors.jcr.dynamic.got.got.plt.data.bss.comment#(( 1HH\7?GoHH`To`c	l	  Pupp	p	{88ȋ      ! @%@0 @;{-	d(HH 	p
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3# 6>|FTcql~#T1! z* @J|Uk_ajuTzUP{ PU0call_gmon_startcrtstuff.c__CTOR_LIST____DTOR_LIST____JCR_LIST__p.0completed.1__do_global_dtors_auxframe_dummy__CTOR_END____DTOR_END____FRAME_END____JCR_END____do_global_ctors_auxmotomat.cmotmisc.cGibbsgetscorestrncat@@GLIBC_2.0strchr@@GLIBC_2.0print_pathfeof@@GLIBC_2.0MinDist_DYNAMICbest_pathsscore_blockDistancestrcmp@@GLIBC_2.0strnjcmpMaxDisttempcmp_fp_hwNumSeqsArgv0fprintf@@GLIBC_2.0__fini_array_endIDfreopen@@GLIBC_2.0save_plotbl62_highpassACSMatrix__dso_handleright__libc_csu_finiputchar@@GLIBC_2.0gets@@GLIBC_2.0find_pathsrewind@@GLIBC_2.0num_to_aacharDagsystem@@GLIBC_2.0VerDatefollow_arcsputs@@GLIBC_2.0_initMot_FilenameSignifleftMinScoreRSignifRunTypecluster_seqsmalloc@@GLIBC_2.0pr_num_to_aa_spaceClThresfread@@GLIBC_2.0Overlapstrpbrk@@GLIBC_2.0stderr@@GLIBC_2.0extend_blockmerge_blocksbl62_matrixTopScore_startscore_colsprint_blockfgets@@GLIBC_2.0dir_unixexeclp@@GLIBC_2.0reduce_overlapfputs@@GLIBC_2.0strstr@@GLIBC_2.0strcspn@@GLIBC_2.0__strtol_internal@@GLIBC_2.0qsort@@GLIBC_2.0bl60_highpassprint_headstrncmp@@GLIBC_2.0__fini_array_startpr_num_to_aafputc@@GLIBC_2.0__libc_csu_initDE__bss_startmainmakematrixtype_dbs__libc_start_main@@GLIBC_2.0makedbid__init_array_endDropScoreget_idsstrcat@@GLIBC_2.0extract_seqssplit_namesfree_pathdata_startbuild_dagprintf@@GLIBC_2.0_finisqrt@@GLIBC_2.0copypathAsIsfclose@@GLIBC_2.1strrchr@@GLIBC_2.0ACNamekr_atoicheck_entryTotal_Motifs__preinit_array_endopendir@@GLIBC_2.0ins_bllistdup_blocksstrcasecmp@@GLIBC_2.0Versionprune_blocksstrspn@@GLIBC_2.0check_alignexit@@GLIBC_2.0_edata_GLOBAL_OFFSET_TABLE_free@@GLIBC_2.0_endstdin@@GLIBC_2.0Debugprint_seqprint_bestorder_blocksmakepathstrncpy@@GLIBC_2.0init_dbsrestartfopen@@GLIBC_2.1__init_array_startkr_itoainit_mmcheck_overlap_IO_stdin_usedins_pathstrtok@@GLIBC_2.0best_pathbl60_matrixaachar_to_numwrite_seqsprintf@@GLIBC_2.0fwrite@@GLIBC_2.0__data_start_IO_getc@@GLIBC_2.0_Jv_RegisterClasses__ctype_b_loc@@GLIBC_2.3save_block__preinit_array_startdump_datacheck_seqscheck_postrim_blockpb_weightsFblkBlk_Filenamemakebllist__gmon_start__Dupsstrcpy@@GLIBC_2.0ng with cutoff score of %d.
Block %d has been dropped for low width:
Quitting becasuse no motifs to work on.
Mean score=%.2f, standard deviation=%.2f
Surviving blocks=%d, max dups=%d%s %d %d %d %d %d %d %d %d %d %dblimps-3.9/bin/Linux/multimat000075500001460000012000001166411062462471200166140ustar00jorjastaff00000400000027ELF4T4 (444@|@|@(((  Qtd/lib/ld-linux.so.2GNU%*'&(#%$)	 
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Y[?zDpBAVersion 3.2.3Version 3.2.2Version 3.2.1Version 3.2.4Version 3.2.5Records Searched:Scores Done:blksrch.stp truncated to fit the page column of the block.
%-20s %-20s %s
() 	
AC   BL   99.5%=strength=,
OUT OF MEMORY


P<%6.2g for 
                %sin support of %s
%s
%s
%-20s%c<->%c%6d(%d,%d):%dResearch CenterVersion %s
amultimat.dat%d IDs in %s
wmultimat.mismultimat.fnd
%d scores read from %s

Reading %s...
Cannot open file %s;
Cannot open file %s blocks vs sequence db
No results files specified.AC family name = %s

Cannot open file %s
	FRAGMENT	BLOCK

NOT ENOUGH MEMORY!?MbP?
===============================================================================
Search results from the BLOCKS e-mail searcher.
Please report problems to jorja@sparky.fhcrc.org, include your query
and this output. To obtain help, send the word HELP on a single
line to blocks@howard.fhcrc.org
Copyright (c) 1992 by the Fred Hutchinson Cancer Research Center
If you use BLOCKS in your research, please cite:
Steven Henikoff and Jorja G. Henikoff, Automated assembly of protein
blocks for database searching, NAR 19:23 (1991), 6565-6572.
Each numbered result consists of one or more blocks from a PROSITE group
found in the query sequence. One set of the highest-scoring blocks that
are in the correct order and separated by distances comparable to the BLOCKS
database is selected for analysis. If this set includes multiple blocks
the probability that the lower scoring blocks support the highest scoring
block is reported. Maps of the database blocks and query sequence are shown:
  < indicates the sequence has been
  : indicates the minimum distance between blocks in the database
  . indicates the maximum distance
The maps are aligned on the highest scoring block. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database
is shown. Upper case in the query sequence indicates at least one
occurrence of the residue in that
                         |-----%5d residues----|
No blocks for family %s found in database.%s %s %d %d %d %d %d %d %6.2g %s


No P-value computed for single block hits.

ERROR: Anchor block not found in blocks database.

Top %d sequences sorted by maximum normalized score:
(the normalized score is the Score divided by the99.5 score in the block if available, or by thesmallest Score in the search results file for the block)

Block     Rank Frame Score      Location(aa) Sequence
%d.----------------------------------------------------------------------------------
%8s  %4d  %2d    %4d  %7ld-%7ld %s %s

Block     Rank Frame Score      Location(bp) Sequence%s %d %d %d %d %d %d %d %d %d %d %d %f
MULTIMAT: (C) Copyright 1991 by Fred Hutchinson Cancer 
Search results will be compared with %s
Search results will be compared with %s;
only hits not in this list will be reported
Enter name of file containing list of true positives:
search results will not be compared with true positive list.
Enter name of BLIMPS results file: 
Enter name of blocks database:;
search results will not be compared with blocks database.
Enter maximum number of hits to report [%d]: USAGE:   multimat                  = Maximum # of hits to report             = File containing blocks for comparison               = File containing list of TP sequences             = Blimps search result files, 
WARNING: AC family name truncated to 9 characters. *XVWPFMGArtprotomat.stpSCOREHIGH ,	
+-0123456789GENBANKLOCUSDEFINITIONORIGINACCESSIONENTRYTITLESEQUENCE///EMBLSQUNI>VMSPROCLASSPCF_ACPCF_DEPCS_IDmkdir %s
Created directory %s
LSTPS=LENGTH=
Processing input file as %s 
	

%d. Entry %s found...ARNDCQEGHILKMFPSTWYVBZXactgDR   PIR.

>%s
fragmentCreating %sw+t
Cannot open %s
>%s}vohaZSLE>70)"8CJf_XQ1*#m<_SG;/#| 
	
Using scoring matrix from %s
Could not open %s, using default BLOSUM scoring matrix

Using BLOSUM62 scoring matrix.
Unable to create directory %s
Protein files will be placed in current directory
%d. Entry %s found...but not extracted because FRAGMENT or PROSITE=P
 WARNING: Titles are sometimes truncated in this format;
          I may not be able to distinguish fragments.
Cannot determine type of input file.|
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Enter name of BLIMPS results file: 
Enter name of blocks database:;
search resultsblimps-3.9/bin/Linux/narrow000075500001460000012000002114401062462471200162610ustar00jorjastaff00000400000027ELF44 (444``T``(((  Qtd/lib/ld-linux.so.2GNU%/+,-')
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vЋuX[US[*P6VY[StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialAAGACATAGTACTACGACGTHIMFPWDNEQARNDCQEGHILKMFPSTWYV*% 6.3f ALPHABETlog-oddsfrequency 
	

Enter name of input file: 					F or W in MAST format%s.mastw%s.blimps 	
seqs=%d; width=%d;
Cannot open file %s
alength=alength= %d w=%d
Problem finding width in %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Unable to recover enough memory to continue.  Aborting.
ALPHABET= ARNDCQEGHILKMFPSTWYVBZX
log-odds matrix: alength= 23 w= %d

Enter type of input file (Block|Frequencies|Weights): COPYRIGHT 2000 Fred Hutchinson Cancer Research CenterUSAGE:  narrow  		file_type = B|F|W	B=block, F=frequencies, W=weightsWrites a positive PSSM to stdout in BLIMPS format
Problem finding value for pos=%d aa=%c
Not sure about the format of %s, assuming first line contains alphabetCould not find alphabet or width in %s
ERROR: Negative frequencies readPlease verify input format type
Problem finding ALPHABET in %s
ERROR:No block found in file %s
ERROR: All values read as zero
ALPHABET length (%d) not alength (%d)
A@FB?R?@3333@3333{cA{c%lgfield has no effect.
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
gribskov_conversion_method: default.sij matrix missing, Cannot continue.
dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
pb_weights:%d ignored for %s
 ,
.+-0123456789%s/docs/default.sijMixture=Alpha=	

 dirichlet(): OUT OF MEMORY
%s/docs/default.diri%s/docs/default.rankSIFT_pssm(): Cannot open %s
BLOCK; MATRIX?BzDMATRIXaqQID   AC   DE   BL   block=(block=(%d,%d);CC   motifwidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
Allocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d ?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
%fNo width field for matrix %s  |% 4d--+----%c |% 6.4fMA   %s
  %c     %c       A   C   G   T
%3d   *   -
% 9.4f % 9.4f
    *         -
 %c   *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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vЋuX[US[ëPY[StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialAGACATAGTACTACGACGTHIKMFPWDNEQARNDCQEGHILKMFPSTWYV*Length=%d, clamp=%d
References:OLIGO_MELT %s
 Center, Seattle, WA, USACannot open %s

Oligo in reverse order:FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Estimated melting temperatures of non-degenerate clamp region (C=%.2fnM):

-----------------------------------------------------------
---Using Breslauer's entropy=-%.1f & enthalpy=-%.1f
AT/GC=%.1f, NAR=%.1f, PRIMER3=%.1f
---Using SantaLucia's entropy=-%.1f & enthalpy=-%.1f
Entropy/Enthalpy: Table 2 from Breslauer, et al, (1986) PNAS 83:3746-3750Entropy/Enthalpy: Table 2 from SantaLucia, (1998) PNAS 95:1460-1465AT/GC: Suggs, et al, (1981) ICN-UCLA Symp.Dev.Biol. 23:683-693NAR: Eqn [2] from Freier, et al, (1986) PNAS 83:9373-9377PRIMER3: Eqn (ii) from Rychlik, et al, (1990) NAR 18:6409-6412COPYRIGHT 1997, Fred Hutchinson Cancer Research
USAGE:  oligo_melt  [DNA conc in nM]Enter name of file containing oligos: zD>n?fffffq@0@@@Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:%d, ??) 	>--- -------- ---NA) 	AA) 	>%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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Cannot open BL file %s
w
Cannot open EX file %s

Cannot open OU file %s

Cannot open FR file %s

Cannot open AL file %s
GRGQDICLLO
No valid PSSM type specified
Cannot open AQ file %s

Cannot open DI file %s

Cannot open GR file %s

Cannot open GQ file %s
BR
Cannot open CL file %s
HYNNFPHCGI
read_cf: OUT OF MEMORYPA
Cannot open PA file %s

Cannot open file %s
Mixture=Alpha=	

 
OUT OF MEMORYmake_col:  OUT OF MEMORYmake_pssm: OUT OF MEMORY%lgfield has no effect.
 ,
.+-0123456789
float_qij: OUT OF MEMORY ,	
BLOCKseqs=

%s seqs=%ddata%10s 
Executing rind ....positionID   %s
AC   %s
DE   %s
PA   %s
//

Configuration file errorsUsing Steve's method...Using Dirichlet pseudo-countsUsing Gribskov algorithm...Using PATMAT algorithm...FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Missing BL (input block) file
Missing EX (output PSSM) fileUncounted character for %s: %d

clump_seqs: Unable to allocate pair structure!Read a frequency of value of %f for: %c
Read a frequency of value of %f for: not a residue
The value for the non-amino acid will be the last weight seen.Currently the program ignores non-residue characters so thisThe non-amino acid codes U and J weights are differentThe non-amino acid codes O and U weights are differentThe non-amino acid codes J and O weights are different
bruno_rind(): Cannot open file data
bruno_rind(): Cannot open file counts
bruno_rind(): Execution of rind failed
Enter name of configuration file: WARNING: Parameters are not checked for validity!Using Gribskov algorithm with qij...Using background pseudo-counts (like Gibbs)Using Claverie pseudo-counts...Using Altschul's pseudo-counts...MATRIXyy][=? A@@HBBBPERT!	@3333@3333??33333?33333?@ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motifwidth=width=%d;99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
Allocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	BL   %s%-20s (%4d)  %3d
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
%fNo width field for matrix %s  |% 4d--+----%c |% 6.4fMA   %s
  %c     %c       A   C   G   T
%3d   *   -
% 9.4f % 9.4f
    *         -
 %c   *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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vЋuX[US[c6PY[StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialAAGACATAGTACTACGACGTHIMFPWDNEQARNDCQEGHILKMFPSTWYV*gc;fc;Extra motif: %s
gx;gn;SIMPLEgt;%s%c%s;%s; BLOCKmotif %d of Prints entry %s.
is shorter than 7 characters.fm;gp;PROSITEfl;bb;fd;BLOCKSPRINTSCOMPOUNDSequence not found in line.can't find the general codein Prints entry %s.
can't find closing )%s.datw%s.info
Cannot open output file %s

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FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000Unable to recover enough memory to continue.  Aborting.
Error ! Problem in format of final motif length line (fl; ...) inNote - the accesion code of Prints %s ("%s")
%-12s %-20s %5d  %-10s %-10s %s
 distance from previous block=(%d,%d)adapted from PRINTS entry; width=%d; seqs=%d;not enough residues to fill the sequence.Filling the rest of the sequence with blanks.read_a_prodom_entry(): Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.
Error ! Problem in format of sequence line %d (%s) in
Error reading sequence start position.Error ! Problem in format of sequence line %d in
Sequence name not found in line.Error ! Sequence %d in motif %d of Prints entry %s.
is %d chars long, instead of the %d expected
Error ! Accession line (gx; ...) not found in Prints entry %s.
Error ! Final motifs line (fm; ...) not found in Prints entry %s.
Error reading sequence distance from last motif.Error ! Type line (gn; ...) not found in Prints entry %s.
Error ! title line (gt; ...) not found in Prints entry %s.
Error ! Problem in motif %d of Prints entry %s.
  The motif's code line (fc; ...) does not contain the entry name = %s
Error ! final motif code line (fc; ...) not found inError ! final motif length line (fl; ...) not found inError ! Problem in format of Prints entry gc line,Error ! End of file reached while readingError ! Problem in format of gn line, can't find (Error ! Problem in format of Prints entry %s gx line.
Can't find the accession code.Error ! Problem in format of gn line in Prints entry %s -
Error ! Type line (gn; ...) is neither SIMPLE or COMPOUND
Enter name of input file (Prints protein motifs database): Block family PRINTS entry name    # of   Cross references to -
                                  blocks PROSITE    BLOCKS     PRINTS
------------ -------------------- ------ ---------- ---------- ----------

%d entries with %d motifs read from Prints database %s
and written as blocks in file %s.
Information about the processed entries written in file %s.
-ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d ?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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Cannot open file %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000%s; width=%d; seqs=%d; 99.5%%=%d; strength=%d;
Enter name of blocks database: 
Enter name of pssmdist.dat file: 
Enter name of new blocks database: ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d ?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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vЋuX[US[%PBY[StandardVertebrate MitochondrialYeast MitochondrialInvertebrate MitochondrialCiliate NuclearEchinoderm MitochondrialEuplotid NuclearBacterial and Plant PlastidAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma MacronuclearChlorophycean MitochondrialTrematode MitochondrialAAGACATAGTACTACGACGTRDEHILKMFPSWYDNEQARNDCQEGHILKMFPSTWYV*
Random distributionminscore without ends=%d

True positive distribution%d %6.2g
Sum of probabilities = %8.4f
%8.4f %4d %8.4f
%lgfield has no effect.

Cannot open file %s
%s.data
======>%s
 ;%s %d %d  %d %.4lf %d %d
%s.cum
Cannot open file ctempFFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000minvalue=%d maxvalue=%d minscore=%d maxscore=%d
maxscore is too big, increase MAXSCORE from %d
Score range  log(Possible ways)  Probability  Expected scores%4d %4d  %8.4f      %11.8f      %8.2f

CumScrs  Score   ExpectedScrs%4d %4d       0.0000       0.000000
99.5 TN score = %d, 80.0 = %d
Median TP score = %d, TPabove = %lf
Read a frequency of value of %f for: %c
Read a frequency of value of %f for: not a residue
The value for the non-amino acid will be the last weight seen.Currently the program ignores non-residue characters so thisThe non-amino acid codes U and J weights are differentThe non-amino acid codes O and U weights are differentThe non-amino acid codes J and O weights are different
Enter name of observed frequencies database: 
Enter name of matrix database: 
Enter name of frequency file: 
Cannot open file %s, TP distribution not computed.
Assuming %.0f sequences, %.0f amino acids in a search
and 100 true positive alignments
Enter number of amino acids in a typical database [%.0f]: 
Enter number of sequences in a typical search [%.0f]: BHBA?A BAFӦKzD{Gzt?{Gz?Mb@?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Unable to recover enough memory to continue.  Aborting.
Error in matrix file format.  No ID line.
Error in matrix file format.  No AC line.
Error in matrix file format.  No DE line.
Error in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
resize_matrix() not finished.  Exiting.
Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
width=%d;%fmotifwidth=seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for matrix %sSetting width to zero
  |% 4d--+----%c |% 6.4fID   %s
AC   %s
DE   %s
MA   %s
  %c     %c       A   C   G   T
%3d   *   -
//
% 9.4f % 9.4f
%3d
    *         -
 %c   *  % 6.4f % 6.4f
Reclaim space function is not defined.  No memory will be reclaimed.
 	

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Unknown sequence type: %d, using amino acid
Unknown output style: %d, using integer output
    A         C         G         T
Unknown output type: %d, using integer output
width=%d;%fmotifwidth=blimps-3.9/bin/Linux/rank_matrix000075500001460000012000001150431062462471200172720ustar00jorjastaff00000400000027ELF04(4 (444kkp`p(((  Qtd/lib/ld-linux.so.2GNU%&"#$
 
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Center		-f	=> floating point outputFFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Enter AC of blocks to extract, or all [%s]: RETBLOCK: Copyright 1997 Fred Hutchinson Cancer Research Extract blocks from a Blocks DatabaseUSAGE:  retblock   [[-n] -f]           = file of blocks           => extract AC or all blocks          -n       => output to stdout, otherwise each block                      will be written to AC?.blk
Enter name of blocks database: ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d ?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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                   aligned:
Cannot open file %s
FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG0000000000000000000000000000000011110000000000000001000000000000FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000110000000000000000000000000000Mold Mitochondrial and MycoplasmaFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0011000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG0001000000000000000000000000000011110000000000000001000000000000FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG0000000000000000000000000000000000010000000000000001000000000000FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0001000000000000000100000000000011110000000000000001000000000000FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000100000000000000010000000000000000000000000000FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGGFFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGGFFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGFFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGGScenedesmus obliquus mitochondrialFFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGThraustochytrium mitochondrial codeFF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG0000000000000000000000000000000010010000000000000001000000000000
Block %s not found in file %s
Something seems wrong in the alignment coordinates !!!


Sixth argument should be the start position of the aligned region in block 2

Seventh argument should be the alignment length
%s  blocks_file  block1_accession  block1_alignment_start  blocks_file  block2_accession  block2_alignment_start  alignment_length

Third argument should be the start position of the aligned region in block 1
ID   AC   DE   BL   ; MATRIXblock=(block=(%d,%d);CC   motifwidth=width=%d;seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dNo width field for block %sSetting width to zero
%lgAllocating more space
(%d)Resetting block width to %d.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
%s 	( %d:%d, ??) 	--- ----- ---AA) 	NA) 	ID   %s
AC   %s
DE   %s
BL   %s%-20s (%4d)  %3d
//
 %f
 ; width=%d; seqs=%d; %s (%d) %s %sError in block %s: seq %s
MATRIX on ID line; not a BLOCKError in block file format.  No ID line.
Error in block file format.  No BL line.
Error in block file format.  No DE line.
none; distance from previous block=( , )Error in block file format.  No AC line.
Error in block file format.  Invalid ID line:Error in block file format.  Invalid AC line:Error in block file format.  Invalid BL line:Error in block file format.  Invalid DE line:Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
No space allocated for sequence %s in block %s.not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%d more residues in the sequence than the expected %d.next_cluster(): Unknown sequence type, assuming an amino acid sequence.
Allocating more space for clusters in block %s.
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
Unknown output type: %d, using integer output
 width=%d; seqs=%d; 99.5%%=%d; strength=%d ?Fatal Error: %s
Program Error: %s
Warning: %s
Serious: %s
Information: %s
Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
Reclaim space function is not defined.  No memory will be reclaimed.
LOCUSDEFINITIONORIGINENTRYTITLESEQUENCE///EMBL/SwissProtSQGCGGCG-GenBankGCG-PIRGCG-EMBLIDDEFasta>UniversaFlat-file, no titleLength:Check:..%s >--- sequence --->%s 	( %d:>--- -------- --->%s  %s
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333? 	

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  and deposit into file %s
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MOTIFJ=[,]%s MOTIFJ=[%s,%s,%s,%s];$

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%sauextract.dat%s %d %d %s %s %s
motifj
Cannot open file %s

UEXTRACT %s: (C) Copyright 1991-2000 by
 Fred Hutchinson Cancer Research Center
Enter name of database file to extract entries from: 
%d sequences requested for extract from %s
Enter name of file containing list of entries to extract: USAGE: uextract   [-f -o -n]        = file listing sequence names to extract                   in PROTOMAT format         = sequence database       -f          to extract FRAGMENTs       -o to have all sequences put in        -n          to NOT execute motifj or create .lst file       -l          to NOT execute motifj but create .lst file       -k          to NOT execute motifj but create .lst file                    with fewer sequences than -l
Extracting all sequences to %sThe following sequences were not found:
  and deposit into directory %s
Cannot open file %s for update
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 WARNING: Titles are sometimes truncated in this format;
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		GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2)GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2)GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2)GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2)GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2)GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2)GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2).symtab.strtab.shstrtab.interp.note.ABI-tag.hash.dynsym.dynstr.gnu.version.gnu.version_r.rel.dyn.rel.plt.init.text.fini.rodata.eh_frame.ctors.dtors.jcr.dynamic.got.got.plt.data.bss.comment#(( 1HH87p?cGoTTNTo@c	l	up@{\\
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|ЪV"`P'/AQ@X܋aw|341$6C Wzp 0call_gmon_startcrtstuff.c__CTOR_LIST____DTOR_LIST____JCR_LIST__p.0completed.1__do_global_dtors_auxframe_dummy__CTOR_END____DTOR_END____FRAME_END____JCR_END____do_global_ctors_auxuextract.cmotmisc.cgetscorestrncat@@GLIBC_2.0strchr@@GLIBC_2.0feof@@GLIBC_2.0_DYNAMICstrcmp@@GLIBC_2.0strnjcmp_fp_hwfprintf@@GLIBC_2.0__fini_array_endbl62_highpass__dso_handle__libc_csu_finiputchar@@GLIBC_2.0gets@@GLIBC_2.0rewind@@GLIBC_2.0num_to_aacharsystem@@GLIBC_2.0lis_listputs@@GLIBC_2.0_initmalloc@@GLIBC_2.0pr_num_to_aa_spacestrpbrk@@GLIBC_2.0bl62_matrix_startfgets@@GLIBC_2.0dir_unixexeclp@@GLIBC_2.0fputs@@GLIBC_2.0strstr@@GLIBC_2.0strcspn@@GLIBC_2.0__strtol_internal@@GLIBC_2.0bl60_highpassstrncmp@@GLIBC_2.0__fini_array_startpr_num_to_aafputc@@GLIBC_2.0__libc_csu_init__bss_startmaintype_dbs__libc_start_main@@GLIBC_2.0makedbid__init_array_endget_idsstrcat@@GLIBC_2.0extract_seqssplit_namesdata_startprintf@@GLIBC_2.0_finifclose@@GLIBC_2.1kr_atoicheck_entry__preinit_array_endopendir@@GLIBC_2.0ProsVersionstrspn@@GLIBC_2.0exit@@GLIBC_2.0_edatalst_list_GLOBAL_OFFSET_TABLE__endgetcwd@@GLIBC_2.0strncpy@@GLIBC_2.0init_dbsfopen@@GLIBC_2.1__init_array_startkr_itoa_IO_stdin_usedstrtok@@GLIBC_2.0bl60_matrixaachar_to_numsprintf@@GLIBC_2.0fwrite@@GLIBC_2.0__data_start_Jv_RegisterClasses__ctype_b_loc@@GLIBC_2.3__preinit_array_start__gmon_start__strcpy@@GLIBC_2.0}GuQ*hPVhj<e8 P=PU}_tHSRhuR(WHPH1fDŽ)G M^_xWHPY[hHRXZHQ(WUQuhR#h(Q7DžWblimps-3.9/blimps/000075500001460000012000000000001062462127300144375ustar00jorjastaff00000400000027blimps-3.9/blimps/LAMA.h000064400001460000012000000065170774312247200153400ustar00jorjastaff00000400000027struct algnmnt_data_struct {
  double score;                      /* the score between the matrices of the
                                        aligned blocks */
  int positionE0;                    /* the alignment end position in the first 
                                        matrix */
  int positionE1;                    /* the alignment end position in the second 
                                        matrix */
  int complength;                    /* the alignment width */
};
typedef struct algnmnt_data_struct algnmnt;


struct blocks_algnmnt_struct {
  int  reported_alignments;          /* how many reported alignments in the 
                                        structure */
  char matrix0_number[NUMBER_WIDTH]; /* the first matrix/block number(accession)*/
  char matrix1_number[NUMBER_WIDTH]; /* the second matrix/block number(accession)*/
  algnmnt *alignment;                /* pointer to array of alignment structures - 
                                        each pair of blocks might have a number of
					significant non-overlapping alignments. */
};
typedef struct blocks_algnmnt_struct BlocksAlgnmnt;


struct stat_struct {
  double mean ;                      /* the mean score */
  double variance ;                  /* the variance of the scores */
  double cutoff ;                    /* the score reporting cutoff */
};
typedef struct stat_struct Stat ;


struct ZvsPRCNTL_struct {
  double Z ;                         /* the Z score */
  double prcntl ;                    /* the percentile in scores from shuffled 
                                        unbiassed blocks*/
};
typedef struct ZvsPRCNTL_struct ZvsPRCNTL ;




#define AA_FREQUENCY_FNAME "default.amino.frq"
                                     /* file name of aa frequencies for 
					load_frequencies procedure */

#define MAXNAME 100 	             /* Maximum file name length */

#define MAXLINELEN 5000 	     /* Maximum line length */

#define ALGNMNTS_ALLOC 10            /* Initial number of alignment
                                        data structures allocated to
                                        alignment structure. */
#define ENTRYSIZE 5000

#define OK    0

#define ERROR 1

#define WIDTHS 56                    /* block widths range. 0 can be used 
					for data from all the scores. 
					Currently the narrowest BLOCKS block 
					is 4 and the widest is 55. */ 

#define NARROWEST_WIDTH 4            /* default narrowest alignment to calculate */

#define Z_CUTOFF 5.6                   /* default Z score cutoff to report */

#define PERSEARCHES 5000             /* number of searches the expected number 
                                        of scores is calculated for.
                                        BLOCKS 9.0 has 3179 blocks.*/

#define MATRIX_CMPRD_WIDTH 21        /* compared "width" (possible chars in
                                        each position) of matrices - 
					20 aa and gap. */

#define BLOCK_DB 'B'

#define MATRIX_DB 'M'

#define ProDom_mul_DB 'P'

#define BLOCK_SEQUENCE_INCREASE_SIZE 20 /* default number of sequences to */
                                   /* allocate if the number of sequences */
                                   /* in the block is not specified */

#define POS_SUM 10000.0            /* sum of all counts in a matrix position */
                                   /* for matrix with probability values. */
blimps-3.9/blimps/blimps-mem.h000064400001460000012000000045250774312247300166660ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* blimps_mem.h: Memory management function for blimps. */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef BLIMPS_MEM_H_
#define BLIMPS_MEM_H_

/*
 * Exported variables and data structures
 */

/*
 * Exported macros
 */

/*
 * Exported functions
 */

/*
 * blimps_reclaim_space
 *   Tries to reclaim some of the allocated memory.  It tries to
 *   reclaim the memory from the various lists that are used by
 *   decreasing the elements that can be stored in the lists.
 *   NOTE: This function assumes that the searching has already begun.
 *         If that is not the case it will report that it was unable
 *         to get space because the list size and the NumberToReport
 *         will likely be zero.  This doesn't really matter much
 *         because if we have to reclaim space that early in the run, 
 *         there are problems.
 *   NOTE: Because of the SavedNodes list in the skiplist package many
 *         calls to blimps_reclaim_space may be needed before the free lists
 *         are filled and actual memory is freed.  This is not that
 *         big of a problem, considering that a balance will be
 *         reached with the nodes in the free lists.  The only time
 *         this would cause the Scores list size to reduce to zero is
 *         if there is so little memory that there can be only about
 *         20 scores in the list.  That amount of memory is about 100
 *         Kbytes. 
 *   Parameters: none
 *   Return codes: TRUE if it was able to get free some space, FALSE
 *                 if not.
 *   Error codes:  FALSE if it unable to get space.
 */


extern Boolean blimps_reclaim_space();


#endif /*  BLIMPS_MEM_H_ */




/* Change log information follows. */
/* 
 *
 * Revision 2.1017  1994/04/27  02:29:29  billa
 * Removed RECLAIM_SPACE define.
 *
 * Revision 2.1011  1994/04/26  02:39:09  billa
 * Removed BLIMPS dependent variables from global.[ch] and put in blimps.[ch].
 *
 * Revision 1.1000  1993/08/27  16:56:34  billa
 * Creation.  Added the function reclaim_space() and the macro CheckMem(A)
 * to handle the situation when there is no more memory to allocate.
 *
 */

blimps-3.9/blimps/blimps.h000064400001460000012000000044510774312247300161100ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* blimps.h: */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef BLIMPS_H_
#define BLIMPS_H_

/*
 * Default score reporting settings
 */
/*
 * Algorithm for computing the default size of the output:
 *  Query = block:
 *     Save 200 results
 *  Query = sequence:
 *    Protein: save 400 results
 *    DNA:     roof(length in nts/1000) x 4, max = 4000, min = 400
 */
#define MIN_DEFAULT_MATRIX_SEARCH_NUM_TO_REPORT 200
#define MAX_DEFAULT_MATRIX_SEARCH_NUM_TO_REPORT 200
#define MIN_DEFAULT_BLOCK_SEARCH_NUM_TO_REPORT  400
#define MAX_DEFAULT_BLOCK_SEARCH_NUM_TO_REPORT 4000

#define DEFAULT_MATRIX_SEARCH_NUMBER_TO_REPORT(b)        \
  MAX_DEFAULT_MATRIX_SEARCH_NUM_TO_REPORT

#define DEFAULT_MATRIX_SEARCH_NUMBER_TO_REPORT_M(m)      \
  MAX_DEFAULT_MATRIX_SEARCH_NUM_TO_REPORT

#define DEFAULT_BLOCK_SEARCH_NUMBER_TO_REPORT(s)         \
  ((s->type == NA_SEQ) ?                                 \
   (min(                                                 \
	(max(                                            \
	     MIN_DEFAULT_BLOCK_SEARCH_NUM_TO_REPORT,     \
	     (int)(ceil((double)s->length/1000.0)) * 4)) \
	, MAX_DEFAULT_BLOCK_SEARCH_NUM_TO_REPORT)) :     \
   MIN_DEFAULT_BLOCK_SEARCH_NUM_TO_REPORT )



/* variables set when reading configuration file */

/*
 * search types allowed
 */
#define SEARCH_TYPE_UNSET  -1	/* search type not set yet */
#define SEARCH_TYPE_UNKNOWN 0	/* unknown search type given */
#define SEARCH_TYPE_MATRIX  1	/* sequences vs databases */
#define SEARCH_TYPE_BLOCK   2	/* blocks vs databases */
extern int SearchType;

/*
 *  SequenceType 
*/
extern int SequenceType;

/* 
 * site specific scoring matrix types
 */
#define SSSM_BLOCK       0
#define SSSM_PRECOMP_MAT 1
extern int SiteSpecificScoringMatrixType;

extern int StrandsToSearch;
extern int NumberToReport;

extern Boolean RepeatsAllowed;

extern int GeneticCodeInitializer;

extern int BlockToMatrixConversionMethod;
extern int SequenceMatrixScoringMethod;


#endif /*  BLIMPS_H_ */

/* Change log information follows. */
/* Changes since version 3.0.0:
  4/24/96 Addeded SequenceType
*/
blimps-3.9/blimps/blkvblk.h000064400001460000012000000134340774312247300162520ustar00jorjastaff00000400000027struct algnmnt_data_struct {
  double score;                      /* the score between the matrices of the
                                        aligned blocks */
  int positionE0;                    /* the alignment end position in the first 
                                        matrix */
  int positionE1;                    /* the alignment end position in the second 
                                        matrix */
  int complength;                    /* the alignment width */
};
typedef struct algnmnt_data_struct algnmnt;


struct blocks_algnmnt_struct {
  int  reported_alignments;          /* how many reported alignments in the 
                                        structure */
  char matrix0_number[NUMBER_WIDTH]; /* the first matrix/block number(accession)*/
  char matrix1_number[NUMBER_WIDTH]; /* the second matrix/block number(accession)*/
  algnmnt *alignment;                /* pointer to array of alignment structures - 
                                        each pair of blocks might have a number of
					significant non-overlapping alignments. */
};
typedef struct blocks_algnmnt_struct BlocksAlgnmnt;


struct blocks_score_struct1 {
  double score;                      /* the score between the matrices of the*/
                                     /* aligned blocks */
  int complength;                    /* the alignment width */
  char matrix0_number[NUMBER_WIDTH]; /* the first matrix/block number(accession) */
  int positionE0;                    /* the alignment end position in the first 
                                        matrix */
  char matrix1_number[NUMBER_WIDTH]; /* the second matrix/block number(accession)*/
  int positionE1;                    /* the alignment end position in the second 
                                        matrix */
};
typedef struct blocks_score_struct1 BlocksScore1;


struct blocks_score_struct {
  int score;                         /* the score between the matrices of the*/
                                     /* aligned blocks */
  int complength;                    /* the alignment width */
  char matrix0_number[NUMBER_WIDTH]; /* the scanning matrix/block number (accession) */
  int positionS0;                    /* the alignment start position in the scanning matrix */
  int strength0;                     /* the scanning block/matrix strength */
  char matrix1_number[NUMBER_WIDTH]; /* the scanned matrix/block number (accession) */
  int positionS1;                    /* the alignment start position in the scanned matrix */
  int strength1;                     /* the scanned block/matrix strength */
};
typedef struct blocks_score_struct BlocksScore;


struct confidence_limits_struct {
  double low_score ;                 /* the low limit score */
  double high_score ;                /* the high limit score */
  double P ;                         /* the confidence */
};
typedef struct confidence_limits_struct Conf_limits ;


struct stat_struct {
  double mean ;                      /* the mean score */
  double variance ;                  /* the variance of the scores */
  double cutoff ;                    /* the score reporting cutoff */
};
typedef struct stat_struct Stat ;

struct ZvsPRCNTL_struct {
  double Z ;                         /* the Z score */
  double prcntl ;                    /* the percentile in scores from shuffled 
                                        unbiassed blocks*/
};
typedef struct ZvsPRCNTL_struct ZvsPRCNTL ;

struct line_struct {
  double intrcpt ;                /* the intercept (a, y=a+bx) */
  double slope ;                  /* the slope     (b, y=a+bx) */
  double std ;                    /* the standard deviation of y values  */
  double cutoff ;                 /* the score reporting cutoff */
};
typedef struct line_struct Line ;

#define AA_FREQUENCY_FNAME "default.amino.frq"
                                     /* file name of aa frequencies for 
					load_frequencies procedure */

#define MAXNAME 100 	             /* Maximum file name length */

#define MAXLINELEN 5000 	     /* Maximum line length */

#define ALGNMNTS_ALLOC 10            /* Initial number of alignment
                                        data structures allocated to
                                        alignment structure. */
#define OK    0

#define ERROR 1

#define WIDTHS 56                    /* block widths range. 0 can be used 
					for data from all the scores. 
					Currently the narrowest BLOCKS block 
					is 4 and the widest is 55. */ 

#define NARROWEST_WIDTH 4            /* default narrowest alignment to calculate */

#define Z_CUTOFF 5.6                   /* default Z score cutoff to report */

#define LOW_SCORE  5.6   /* scores with lower Z values are probably 
                            not significant in searching Blocks DB vs itself. */
#define HIGH_SCORE 8.3   /* scores with equal or higher Z values are probably 
                            significant in searching Blocks DB vs itself. */

#define PERSEARCHES 3179             /* number of searches the expected number 
                                        of scores is calculated for.
                                        BLOCKS 9.0 has 3179 blocks.*/

#define MATRIX_CMPRD_WIDTH 21        /* compared "width" (possible chars in
                                        each position) of matrices - 
					20 aa and gap. */

#define SMALL_VAL 0.000001

#define ENTRYSIZE 5000

#define BLOCK_DB 'B'

#define MATRIX_DB 'M'

#define ProDom_mul_DB 'P'

#define Conservative 'C'

#define Liberal 'L'

#define BLOCK_SEQUENCE_INCREASE_SIZE 20 /* default number of sequences to */
                                   /* allocate if the number of sequences */
                                   /* in the block is not specified */

#define POS_SUM 10000.0            /* sum of all counts in a matrix position */
                                   /* for matrix with probability values. */
blimps-3.9/blimps/blockmap.h000064400001460000012000000027670774312247300164220ustar00jorjastaff00000400000027/* COPYRIGHT 1997 Fred Hutchinson Cancer Research Center, Seattle, WA USA */
/*	blockmap.h	Used by block_vis.c               */

struct block_pos_struct {
  char code ;                        /* the block's code */
  int  start ;                       /* the block's start position */
  int  end ;                         /* the block's end position */
};
typedef struct block_pos_struct block_pos ;


struct seq_map_struct {
  char seq_name[SMALL_BUFF_LENGTH] ; /* sequence name */
  int seq_len ;                      /* sequence length */
  int num_blocks ;                   /* number of blocks in this sequence */
  block_pos *blocks ;                /* pointer to array of block positions */
};
typedef struct seq_map_struct sequence_map ;


struct blocks_map_struct {
  char block_family[SMALL_BUFF_LENGTH] ; /* the blocks family code */
  char description[SMALL_BUFF_LENGTH] ; /* the family description */
  char id[SMALL_BUFF_LENGTH] ;       /* the short family description */
  int num_seqs ;                     /* number of sequences */
  int tot_num_blocks ;               /* number of blocks */
  int max_seq_len ;                  /* longest sequence length */
  sequence_map *seq_map ;            /* pointer to array of sequence maps */
};
typedef struct blocks_map_struct blocks_map ;


#define MAXNAME 80	/* Maximum file name length */

#define BLOCKS_ALLOC 10 /* Initial number of block data structures 
                           to be allocated to blocks family array. */
#define OK    0

#define ERROR 1

blimps-3.9/blimps/codehop.h000064400001460000012000000157161013352226400162360ustar00jorjastaff00000400000027/* COPYRIGHT 1997 Fred Hutchinson Cancer Research Center
	codehop.h
   Header file for codehop.c
 8/18/01 Updated list of genetic codes
10/14/04 Updated list of genetic codes (see ../include/gcode.h)
==========================================================================*/
#include 

#define MAXNAME 80	/* Maximum file name length */

#define BLOCKS_ALLOC 10 /* Initial number of block data structures 
                           to be allocated to blocks family array. */
#define REGIONS_ALLOC 20 /* Initial number of region structures 
                           to be allocated to core degenerate regions array. */
#define OK    0

#define ERROR 1

#define BLOCK_AC_LEN 8

#define COMMENTS "Comments: \"-\" instead of a input/output file name => stdin/stdout\n          The order of the arguments is not important but the\n          first name is for the input file and the second for the output.\npssm_type = 2 odds ratios normalized to 100\n\t3 pseudos, log odds, nats\n\t5 pseudos, log odds, half bits\n\t6 pseudos, log odds, third bits\n\t10 pseudos, odds ratios, nats\n\t20 just counts+pseudo counts\n\t30 average score\nGenetic code type = 0 Standard\n\t1 Vertebrate Mitochondrial\n\t2 Yeast Mitochondrial\n\t3 Mold Mitochondrial and Mycoplasma\n\t4 Invertebrate Mitochondrial\n\t5 Ciliate Nuclear\n\t6 Echinoderm Mitochondrial\n\t7 Euplotid Nuclear\n\t8 Bacterial and Plant Plastid\n\t9 Alternative Yeast Nuclear\n\t10 Ascidian Mitochondrial\n\t11 Flatworm Mitochondrial\n\t12 Blepharisma Macronuclear\n\t13 Chlorophycean Mitochondrial\n\t14 Trematode Mitochondrial\n\t15 Scenedesmus obliquus mitochondrial\n\t16 Thraustochytrium mitochondrial\nDegeneracy parameters=0.0 all nucleotides that actually appear are counted\n\t1.0 only nucleotide with highest value counted\n\tBetween 0 and 1 nucleotides with high values counted,\n\t if value/highest-value >= degeneracy parameter\nClamp temperature     Target melting temperature for clamp in degC \nConcentration         Probe concentration in nM\nRose restrictions     If set, uses Tim Rose's restrictions on boundaries\n                      of core degenerate region.\nMost common codons    If set, uses most common codons in clamp.\nBegin oligo           If set, oligo must start on a conserved column,\n                       otherwise core strictness is applied.\nApoly-x       Maxiumum number of consecutive nucleotides of same type.\n\n"

#define AA_FREQUENCY_FNAME "default.amino.frq"
#define ID_FREQUENCY_FNAME "identity.frq"

#define ALPHABET 14 /* position in structure array nt_adegen (ntbet.h) with
                       number (4) and chars (A,C,G,T) of non-degenerate nucleotides. */

#define PSSM_TYPE_DFLT 2

#define PSSM_TYPES " 2 3 5 6 10 20 30 " /* each type must be flanked by blanks ! */

#define PSSM_DEFS {"","","odds ratios normalized to 100","pseudos, log odds, nats","","pseudos, log odds, half bits","pseudos, log odds, third bits","","","","pseudos, odds ratios, nats","","","","","","","","","","just counts+pseudo counts","","","","","","","","","","average score"}

#define GCODE_TYPE_DFLT 0

#define CODON_USAGE_FILE_DFLT "default.codon.use"

#define MIN_STRICTNESS 0.0  /* these 2 values are by definition and */
#define MAX_STRICTNESS 1.0  /* should not be changed.               */

#define CORE_MIN_LEN 11   /* minimal length of core degenerate regions */
#define CORE_MAX_LEN 12   /* maximal length of core degenerate regions */

#define CLAMP_MIN_LEN 17    /* min length of clamp (non-degenerate) region*/
#define CLAMP_MAX_LEN 165    /* max length of clamp (non-degenerate) region*/

#define DEFAULT_CORE_DEG 128    /* default degeneracy of core region */
#define DEFAULT_TEMP 60.0	/* default clamp temperature in degC */
#define DEFAULT_CONC 50.0	/* default concentration in nM units */
#define DEFAULT_KONC 50		/* default salt concentration in mM units */
#define DEFAULT_POLYX 5		/* default max run of any nuc in clamp */
#define DEFAULT_PRODLEN 200	/* default product length */

#define INT_TO_LOG2 {DBL_MIN, 0., 1., 1.5850, 2.} /* a table to find log2(X) */

/* # of positions (4 chars each) per line */
#define WWW_MATRIX_PRINT_WIDTH 240
#define SHL_MATRIX_PRINT_WIDTH 18

#define HELP_REQUEST " ? help HELP usage USAGE "   /* flanking blanks required */


/***** Structure type definitions *****/

struct position_degeneracy_struct {
  int degeneracy;                    /* the number of residues deemed to 
                                        appear in the position */
  char *residues;                    /* a pointer to a cahr array with the 
                                        residues appearing in the position */
};
typedef struct position_degeneracy_struct PosDegen;


struct degeneracy_struct {
  double strictness;                 /* the strictness value used to
                                        calculate the degeneracy 
                                        (see procedure J_degeneracy) */
  int  length;                       /* number of positions in this array */
  PosDegen **positions;              /* pointer to array of position degeneracy
                                        structure pointers */
};
typedef struct degeneracy_struct Dgnrcy;

struct region_struct {
  int start;                         /* region start position */

  int len;                           /* region length */

  int degen;                         /* degeneracy of region */
};
typedef struct region_struct Region;

/*	Modified matrix structure for DNA PSSMs  */
struct dna_matrix {
   Block *block;
   int strand;
   int length;
   MatType *weights[4];		/* ACGT weights for each column */
   MatType *max_weight;		/* Max weight for each column */
   int *nres;			/* Number of actual different residues in col */
   int *nsres;		/* Num of diff residues in col using strictness */
   int *nt_core;		/* Pointer into nt_btoa for degenerate res */
   int *nt_clamp;		/* Pointer into nt_btoa for nondegenerate res */
   int *nt_common;		/* Pointer into nt_btoa for most common codon */
   int *nt_max;		/* Pointer into nt_btoa for max PSSM weight */
};

/*		Temporary sort structure  */
struct sort_array {
   int clump, number;
   double core_score, clamp_score;
   struct oligo_list *oligo;
};

/*		Sorted list of oligos  */
struct oligo_list {
   struct dna_matrix *pssm;	/*  Pointer to the DNA PSSM */
   int strand;			/*  Negative is complemented PSSM */
   int core_first;		/*  1st position of core region */
   int core_last;		/*  Last position of core region */
   double core_score;		/*  Degen. score of core region (log base 4) */
   int clamp_first;		/*  1st position of clamp region */
   int clamp_last;		/*  Last position of clamp region */
   double clamp_score;		/*  Degen. score of clamp region (log base 4) */
   double clamp_prob;		/*  Clamp probability score */
   double clamp_temp;		/*  Clamp temperature */
   double clamp_temp_nn;	/*  Nearest neighbor clamp temperature */
   int clump;			/*  Left to right clump number */
   int number;			/*  Left to right display number */
   int out_order;		/*  Printing order  */
   struct oligo_list *next_oligo;
};

blimps-3.9/blimps/config.h000064400001460000012000000020260774312247300160630ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* config.h: reads the configuration file. */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef CONFIG_H_
#define CONFIG_H_

/*
 * Exported variables and data structures
 */
 
/*
 * Exported functions
 */
 
/*
 * read_config_file
 *   reads the configuration file given by the filename
 *   Parameters:
 *     char * filename  : the configuration filename
 *   Error codes:
 */

extern int read_config_file ();


#endif /*  CONFIG_H_ */

/* Change log information follows. */
/* 
 * System version 2.1 A [2.1000]
 * Added reading and scoring of precomputed site specific scoring matricies.
 * Reconfigured files.[ch] into files.[ch] and config.[ch].
 *
 * Revision 2.1  1994/02/23  20:42:46  billa
 * Creation.  Moved the configuration file stuff from files.[ch] to
 * config.[ch].
 *
 */
blimps-3.9/blimps/lists.h000064400001460000012000000047020774312247300157570ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* lists.h: definitions and functions for various ordered lists */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef LISTS_H_
#define LISTS_H_

#include 

/*
 * Exported variables and data structures
 */


typedef SkipList ScoreList;
typedef SkipList MatrixList;
typedef SkipList BlockList;
typedef SkipList SequenceList;


extern ScoreList    Scores;
extern ScoreList    PrintScores;
extern MatrixList   Matrices;
extern BlockList    Blocks;
extern SequenceList Sequences;
extern Boolean SavedScoresFlag;

extern int MinScoreOfList;	/* the minimum score of the score list */
				/* didn't make a function to do this */
				/* because it would be worse than just */
				/* having a global variable */



/*
 * Exported functions
 */


/* 
 * initialize_lists
 *   initializes the lists.
 *   Parameters: none
 *   Error codes:
 */

extern void initialize_lists();

#ifndef NO_SCORES
/* 
 * enter_score_into_print_scores
 *   Places the score from Scores into PrintScores.  PrintScores is a reverse
 *   ordered list so that the printing comes out with the largest score
 *   first.
 *   Parameters:
 *     Score *score: the score list entry
 *     void *arg: unused, here to match the procedure call in DoForSL
 *   Return code: SL_CONTINUE always.
 *   Error codes: none
 */

extern int enter_score_into_print_scores();

/*
 * insert_in_score_list
 *   Inserts the score entry into the score list and makes sure that the 
 *   number of elements n the list are fewer than the NumberToReport if there
 *   is a limit.
 *   Parameters:
 *     Score score: the score entry.
 *   Return codes: the same as InsertSL.
 *   Error codes: none
 */

extern int insert_in_score_list();

/* 
 * limit_Scores_list_size
 *   Used in insert_in_score_list to limit the size of the score list.
 *   Parameters: 
 *     Score *score: the score list entry
 *     void *arg: unused, here to match the procedure call in DoForSL
 *   Return codes: SL_DELETE if the list is too big, SL_QUIT otherwise.
 *   Error codes: none
 */

int limit_Scores_list_size();

#endif



#endif /*  LISTS_H_ */

/* Change log information follows. */
/* 
  Changes since version 3.2.5:
  1/23/99 Added SavedScoresFlag, used by lists.c, blimps.c, scoring.c, config.c
*/
able */



/*
 * Exported functions
 */


/* 
 * initialize_liblimps-3.9/blimps/p2c.h000064400001460000012000000261060774312247300153070ustar00jorjastaff00000400000027#ifndef P2C_H
#define P2C_H


/* Header file for code generated by "p2c", the Pascal-to-C translator */

/* "p2c"  Copyright (C) 1989 Dave Gillespie, version 1.18.
 * This file may be copied, modified, etc. in any way.  It is not restricted
 * by the licence agreement accompanying p2c itself.
 */


#include 



/* If the following heuristic fails, compile -DBSD=0 for non-BSD systems,
   or -DBSD=1 for BSD systems. */

#ifdef M_XENIX
# define BSD 0
#endif

#ifdef FILE       /* a #define in BSD, a typedef in SYSV (hp-ux, at least) */
# ifndef BSD	  /*  (a convenient, but horrible kludge!) */
#  define BSD 1
# endif
#endif

#ifdef BSD
# if !BSD
#  undef BSD
# endif
#endif


#ifdef __STDC__
# include 
# include 
# define HAS_STDLIB
# define __CAT__(a,b)a##b
#else
# ifndef BSD
#  include 
# endif
# include 
# define __ID__(a)a
# define __CAT__(a,b)__ID__(a)b
#endif


#ifdef BSD
# include 
# define memcpy(a,b,n) (bcopy(b,a,n),a)
# define memcmp(a,b,n) bcmp(a,b,n)
# define strchr(s,c) index(s,c)
# define strrchr(s,c) rindex(s,c)
#else
# include 
#endif

#include 
#include 
#include 
#include 


typedef struct __p2c_jmp_buf {
    struct __p2c_jmp_buf *next;
    jmp_buf jbuf;
} __p2c_jmp_buf;


/* Warning: The following will not work if setjmp is used simultaneously.
   This also violates the ANSI restriction about using vars after longjmp,
   but a typical implementation of longjmp will get it right anyway. */

#ifndef FAKE_TRY
# define TRY(x)         do { __p2c_jmp_buf __try_jb;  \
			     __try_jb.next = __top_jb;  \
			     if (!setjmp((__top_jb = &__try_jb)->jbuf)) {
# define RECOVER(x)	__top_jb = __try_jb.next; } else {
# define RECOVER2(x,L)  __top_jb = __try_jb.next; } else {  \
			     if (0) { L: __top_jb = __try_jb.next; }
# define ENDTRY(x)      } } while (0) 
#else
# define TRY(x)         if (1) {
# define RECOVER(x)     } else do {
# define RECOVER2(x,L)  } else do { L: ;
# define ENDTRY(x)      } while (0)
#endif



#ifdef M_XENIX  /* avoid compiler bug */
# define SHORT_MAX  (32767)
# define SHORT_MIN  (-32768)
#endif


/* The following definitions work only on twos-complement machines */
#ifndef SHORT_MAX
# define SHORT_MAX  (((unsigned short) -1) >> 1)
# define SHORT_MIN  (~SHORT_MAX)
#endif

#ifndef INT_MAX
# define INT_MAX    (((unsigned int) -1) >> 1)
# define INT_MIN    (~INT_MAX)
#endif

#ifndef LONG_MAX
# define LONG_MAX   (((unsigned long) -1) >> 1)
# define LONG_MIN   (~LONG_MAX)
#endif

#ifndef SEEK_SET
# define SEEK_SET   0
# define SEEK_CUR   1
# define SEEK_END   2
#endif

#ifndef EXIT_SUCCESS
# define EXIT_SUCCESS  0
# define EXIT_FAILURE  1
#endif


#define SETBITS  32


#ifdef __STDC__
# define Signed     signed
# define Void       void      /* Void f() = procedure */
# ifndef Const
#  define Const     const
# endif
# ifndef Volatile
# define Volatile  volatile
# endif
# define PP(x)      x         /* function prototype */
# define PV()       (void)    /* null function prototype */
typedef void *Anyptr;
#else
# define Signed
# define Void       void
# ifndef Const
#  define Const
# endif
# ifndef Volatile
#  define Volatile
# endif
# define PP(x)      ()
# define PV()       ()
typedef char *Anyptr;
#endif

#ifdef __GNUC__
# define Inline     inline
#else
# define Inline
#endif

#define Register    register  /* Register variables */
#define Char        char      /* Characters (not bytes) */

#ifndef Static
# define Static     static    /* Private global funcs and vars */
#endif

#ifndef Local
# define Local      static    /* Nested functions */
#endif

typedef Signed   char schar;
typedef unsigned char uchar;
typedef unsigned char boolean;

#ifndef true
# define true    1
# define false   0
#endif


typedef struct {
    Anyptr proc, link;
} _PROCEDURE;

#ifndef _FNSIZE
# define _FNSIZE  120
#endif


extern Void    PASCAL_MAIN  PP( (int, Char **) );
extern Char    **P_argv;
extern int     P_argc;
extern short   P_escapecode;
extern int     P_ioresult;
extern __p2c_jmp_buf *__top_jb;


#ifdef P2C_H_PROTO   /* if you have Ansi C but non-prototyped header files */
extern Char    *strcat      PP( (Char *, Const Char *) );
extern Char    *strchr      PP( (Const Char *, int) );
extern int      strcmp      PP( (Const Char *, Const Char *) );
extern Char    *strcpy      PP( (Char *, Const Char *) );
extern size_t   strlen      PP( (Const Char *) );
extern Char    *strncat     PP( (Char *, Const Char *, size_t) );
extern int      strncmp     PP( (Const Char *, Const Char *, size_t) );
extern Char    *strncpy     PP( (Char *, Const Char *, size_t) );
extern Char    *strrchr     PP( (Const Char *, int) );

extern Anyptr   memchr      PP( (Const Anyptr, int, size_t) );
extern Anyptr   memmove     PP( (Anyptr, Const Anyptr, size_t) );
extern Anyptr   memset      PP( (Anyptr, int, size_t) );
#ifndef memcpy
extern Anyptr   memcpy      PP( (Anyptr, Const Anyptr, size_t) );
extern int      memcmp      PP( (Const Anyptr, Const Anyptr, size_t) );
#endif

extern int      atoi        PP( (Const Char *) );
extern double   atof        PP( (Const Char *) );
extern long     atol        PP( (Const Char *) );
extern double   strtod      PP( (Const Char *, Char **) );
extern long     strtol      PP( (Const Char *, Char **, int) );
#endif /*P2C_H_PROTO*/

#ifndef HAS_STDLIB
extern Anyptr   malloc      PP( (size_t) );
extern Void     free        PP( (Anyptr) );
#endif

extern int      _OutMem     PV();
extern int      _CaseCheck  PV();
extern int      _NilCheck   PV();
extern int	_Escape     PP( (int) );
extern int	_EscIO      PP( (int) );

extern long     ipow        PP( (long, long) );
extern Char    *strsub      PP( (Char *, Char *, int, int) );
extern Char    *strltrim    PP( (Char *) );
extern Char    *strrtrim    PP( (Char *) );
extern Char    *strrpt      PP( (Char *, Char *, int) );
extern Char    *strpad      PP( (Char *, Char *, int, int) );
extern int      strpos2     PP( (Char *, Char *, int) );
extern long     memavail    PV();
extern int      P_peek      PP( (FILE *) );
extern int      P_eof       PP( (FILE *) );
extern int      P_eoln      PP( (FILE *) );
extern Void     P_readpaoc  PP( (FILE *, Char *, int) );
extern Void     P_readlnpaoc PP( (FILE *, Char *, int) );
extern long     P_maxpos    PP( (FILE *) );
extern Char    *P_trimname  PP( (Char *, int) );
extern long    *P_setunion  PP( (long *, long *, long *) );
extern long    *P_setint    PP( (long *, long *, long *) );
extern long    *P_setdiff   PP( (long *, long *, long *) );
extern long    *P_setxor    PP( (long *, long *, long *) );
extern int      P_inset     PP( (unsigned, long *) );
extern int      P_setequal  PP( (long *, long *) );
extern int      P_subset    PP( (long *, long *) );
extern long    *P_addset    PP( (long *, unsigned) );
extern long    *P_addsetr   PP( (long *, unsigned, unsigned) );
extern long    *P_remset    PP( (long *, unsigned) );
extern long    *P_setcpy    PP( (long *, long *) );
extern long    *P_expset    PP( (long *, long) );
extern long     P_packset   PP( (long *) );
extern int      P_getcmdline PP( (int l, int h, Char *line) );
extern Void     TimeStamp   PP( (int *Day, int *Month, int *Year,
				 int *Hour, int *Min, int *Sec) );
extern Void	P_sun_argv  PP( (char *, int, int) );


/* I/O error handling */
#define _CHKIO(cond,ior,val,def)  ((cond) ? P_ioresult=0,(val)  \
					  : P_ioresult=(ior),(def))
#define _SETIO(cond,ior)          (P_ioresult = (cond) ? 0 : (ior))

/* Following defines are suitable for the HP Pascal operating system */
#define FileNotFound     10
#define FileNotOpen      13
#define FileWriteError   38
#define BadInputFormat   14
#define EndOfFile        30

/* Creating temporary files */
#if (defined(BSD) || defined(NO_TMPFILE)) && !defined(HAVE_TMPFILE)
# define tmpfile()  (fopen(tmpnam(NULL), "w+"))
#endif

/* File buffers */
#define FILEBUF(f,sc,type) sc int __CAT__(f,_BFLAGS);   \
			   sc type __CAT__(f,_BUFFER)

#define RESETBUF(f,type)   (__CAT__(f,_BFLAGS) = 1)
#define SETUPBUF(f,type)   (__CAT__(f,_BFLAGS) = 0)

#define GETFBUF(f,type)    (*((__CAT__(f,_BFLAGS) == 1 &&   \
			       ((__CAT__(f,_BFLAGS) = 2),   \
				fread(&__CAT__(f,_BUFFER),  \
				      sizeof(type),1,(f)))),\
			      &__CAT__(f,_BUFFER)))
#define AGETFBUF(f,type)   ((__CAT__(f,_BFLAGS) == 1 &&   \
			     ((__CAT__(f,_BFLAGS) = 2),   \
			      fread(&__CAT__(f,_BUFFER),  \
				    sizeof(type),1,(f)))),\
			    __CAT__(f,_BUFFER))

#define PUTFBUF(f,type,v)  (GETFBUF(f,type) = (v))
#define CPUTFBUF(f,v)      (PUTFBUF(f,char,v))
#define APUTFBUF(f,type,v) (memcpy(GETFBUF(f,type), (v),  \
				   sizeof(__CAT__(f,_BUFFER))))

#define GET(f,type)        (__CAT__(f,_BFLAGS) == 1 ?   \
			    fread(&__CAT__(f,_BUFFER),sizeof(type),1,(f)) :  \
			    (__CAT__(f,_BFLAGS) = 1))

#define PUT(f,type)        (fwrite(&__CAT__(f,_BUFFER),sizeof(type),1,(f)),  \
			    (__CAT__(f,_BFLAGS) = 0))
#define CPUT(f)            (PUT(f,char))

#define BUFEOF(f)	   (__CAT__(f,_BFLAGS) != 2 && P_eof(f))
#define BUFFPOS(f)	   (ftell(f) - (__CAT__(f,_BFLAGS) == 2))

typedef struct {
    FILE *f;
    FILEBUF(f,,Char);
    Char name[_FNSIZE];
} _TEXT;

/* Memory allocation */
#ifdef __GCC__
# define Malloc(n)  (malloc(n) ?: (Anyptr)_OutMem())
#else
extern Anyptr __MallocTemp__;
# define Malloc(n)  ((__MallocTemp__ = malloc(n)) ? __MallocTemp__ : (Anyptr)_OutMem())
#endif
#define FreeR(p)    (free((Anyptr)(p)))    /* used if arg is an rvalue */
#define Free(p)     (free((Anyptr)(p)), (p)=NULL)

/* sign extension */
#define SEXT(x,n)   ((x) | -(((x) & (1L<<((n)-1))) << 1))

/* packed arrays */   /* BEWARE: these are untested! */
#define P_getbits_UB(a,i,n,L)   ((int)((a)[(i)>>(L)-(n)] >>   \
				       (((~(i))&((1<<(L)-(n))-1)) << (n)) &  \
				       (1<<(1<<(n)))-1))

#define P_getbits_SB(a,i,n,L)   ((int)((a)[(i)>>(L)-(n)] <<   \
				       (16 - ((((~(i))&((1<<(L)-(n))-1))+1) <<\
					      (n)) >> (16-(1<<(n))))))

#define P_putbits_UB(a,i,x,n,L) ((a)[(i)>>(L)-(n)] |=   \
				 (x) << (((~(i))&((1<<(L)-(n))-1)) << (n)))

#define P_putbits_SB(a,i,x,n,L) ((a)[(i)>>(L)-(n)] |=   \
				 ((x) & (1<<(1<<(n)))-1) <<   \
				 (((~(i))&((1<<(L)-(n))-1)) << (n)))

#define P_clrbits_B(a,i,n,L)    ((a)[(i)>>(L)-(n)] &=   \
				 ~( ((1<<(1<<(n)))-1) <<   \
				   (((~(i))&((1<<(L)-(n))-1)) << (n))) )

/* small packed arrays */
#define P_getbits_US(v,i,n)     ((int)((v) >> ((i)<<(n)) & (1<<(1<<(n)))-1))
#define P_getbits_SS(v,i,n)     ((int)((long)(v) << (SETBITS - (((i)+1) << (n))) >> (SETBITS-(1<<(n)))))
#define P_putbits_US(v,i,x,n)   ((v) |= (x) << ((i) << (n)))
#define P_putbits_SS(v,i,x,n)   ((v) |= ((x) & (1<<(1<<(n)))-1) << ((i)<<(n)))
#define P_clrbits_S(v,i,n)      ((v) &= ~( ((1<<(1<<(n)))-1) << ((i)<<(n)) ))

#define P_max(a,b)   ((a) > (b) ? (a) : (b))
#define P_min(a,b)   ((a) < (b) ? (a) : (b))


/* Fix toupper/tolower on Suns and other stupid BSD systems */
#ifdef toupper
# undef toupper
# undef tolower
# define toupper(c)   my_toupper(c)
# define tolower(c)   my_tolower(c)
#endif

#ifndef _toupper
# if 'A' == 65 && 'a' == 97
#  define _toupper(c)  ((c)-'a'+'A')
#  define _tolower(c)  ((c)-'A'+'a')
# else
#  define _toupper(c)  toupper(c)
#  define _tolower(c)  tolower(c)
# endif
#endif


#endif    /* P2C_H */



/* End. */


EK_END   2
#endif

#ifndef EXIT_SUCCESS
# define EXIT_SUCCESS  0
# define EXIT_FAILURE  1
#endif


#define SETBITS  32


#ifdef __STDC__
# define Signed     signed
# define Void       void      /* Void f() = procedure */
# ifndef Const
#  define Const     const
# endif
# ifndef Volatile
# define Volatile  volatile
# endif
# define PP(x)      x         /* function prototype */
# define PV()       (void)    /* null function prototype */
typblimps-3.9/blimps/scores.h000064400001460000012000000111450774312247300161160ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* scores.h: score structure manipulation and scoring routines */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef SCORES_H_
#define SCORES_H_

#include 

/*
 * Exported variables and data structures
 */

struct score_struct {
  int score;			/* the score of the matrix, used as the key */
  int strength;			/* the block/matrix strength */
  int position;			/* the position in the sequence where we */
				/* started comparing */
  int seq_length;		/* the length of the sequence scored */
  int frame;			/* translated nucleic acid frame (1, 2, 3, */
				/* -1, -2, -3). a frame of zero is an amino */
				/* acid sequence */
  char matrix_number[NUMBER_WIDTH]; /* the matrix/block number */
  char sequence_number[NUMBER_WIDTH]; /* the sequence number/name */
  char matrix_desc[DESC_WIDTH];	/* the matrix/block description */
  char sequence_desc[DESC_WIDTH]; /* the sequence description */
  char consensus[DESC_WIDTH];	/* the "consensus" sequence */
};
typedef struct score_struct Score;


/*
 * Exported functions
 */

/* 
 * score_and_enter
 *   computes the score of the sequence against the matrix.  If repeats is
 *   TRUE, all of the pairwise scores are entered into the score_list, 
 *   otherwise only the best score is entered.
 *   The scoring algorithm is selected by setting SequenceMatrixScoringMethod
 *   appropriately.  
 *   Note: the sequence must be an AA_SEQ.
 *   Parameters:
 *     Sequence *seq: the sequence to score
 *     Matrix *matrix: the matrix used for scoring
 *     int frame: the frame we are looking at (0 = aa seq.,
 *                1, 2, 3, -1, -2, -3 = na seqs.)
 *     Boolean repeats: enter repeats into the score_list?
 *     int search_type: the type of search we are doing.  If it is a 
 *                      SEARCH_TYPE_MATRIX search (block vs sequences), 
 *                      do NOT divide by the block percentile.  If it is a 
 *                      SEARCH_TYPE_BLOCK search (sequence vs blocks), DO 
 *                      divide by the block percentile. 
 *   Return Codes: TRUE if the sequence is an AA_SEQ, FALSE otherwise.  The
 *                 score is inserted into the scores list.
 *   Error Codes: returns FALSE if the sequence was not an AA_SEQ and does not 
 *                score the sequence.
 */

extern int score_and_enter();


/*
 * score_comparison
 *   Compares two score records.   It compares by the value in the score
 *   field.  
 *   Parameters:
 *     ScoreListEntry a, b: the entries to compare
 *   Return codes:  a return value > 0 if a > b, a return value = 0 if a == b,
 *                  and a return value < 0 if a < b
 *   Error codes: none
 */

extern int score_comparison();


/*
 * neg_score_comparison
 *   Returns the negative of score_comparison.  Effectively the opposite
 *   logic of score_comparison. 
 *   Parameters:
 *     ScoreListEntry a, b: the entries to compare
 *   Return codes:  a return value < 0 if a < b, a return value = 0 if a == b,
 *                  and a return value > 0 if a > b
 *   Error codes: none
 */
extern int neg_score_comparison();


/* 
 * free_score
 *   Deletes the score list entry and the sub elements.
 *   Parameters: 
 *     Score *score: the score to free
 *   Return code: none
 *   Error code: none
 */

extern void free_score();


/* 
 * output_scores
 *   Prints out the score list in the final format.
 *   Parameters:
 *     int num_to_report: the number of scores to report, if <1 reports all.
 *     FILE *ofp:         the file to output scores to.
 *   Error codes: none
 */

extern void output_scores();



#endif /*  SCORES_H_ */

/* Change log information follows. */
/* 
 *
 * Revision 0.110  1993/08/10  02:50:53  billa
 * System version update.  Added convert.[ch], scoring.[ch] and version.[ch].
 *
 * Revision 0.106  1993/08/10  02:26:37  billa
 * Moved the code in score_and_enter that did the scoring of a sequence and
 * a matrix into the function default_scoring_method in scoring.[ch].
 * Also moved create_score_list_entry from scores.c to scoring.c.
 *
 * Revision 0.101  1993/08/04  19:47:14  billa
 * Reorganized file structure and changed includes.
 * Moved to scores.[ch] from lists.[ch]:
 *   score_comparison, neg_score_comparison, free_score,
 *   create_score_list_entry
 * Moved to scores.[ch] from matrix.[ch]:
 *   score_and_enter
 *
 * Revision 0.100  1993/08/03  17:47:24  billa
 * Creation.  System version 0.100.  Pre file structure reorganization.
 *
 */

blimps-3.9/blimps/scoring.h000064400001460000012000000046360774312247300162730ustar00jorjastaff00000400000027/* (C) Copyright 1993-9, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* scoring.h: functions for different methods of scoring a sequence against */
/*            a matrix */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef SCORING_H_
#define SCORING_H_

/*
 * Exported variables and data structures
 */

#define MIN_SAVE_SCORE 945	/* If SV option used, never save lower score*/
#define MAX_HIST_SCORE  6000	/* the top of the histogram */
/* MAX_HIST_SCORE is 6000 = 60 x 100 = max block width x max weight */
#define HIST_BOX_SIZE   20	/* must evenly divide MAX_HIST_SCORE */
#define NUM_HIST_COLS   ( MAX_HIST_SCORE / HIST_BOX_SIZE )

extern double Alignments_Done;
extern double Scores_Done;
extern int histogram[];
extern Boolean DoHistogram;


/*
 * Exported functions
 */

/*
 * default_scoring_method
 *   The default scoring method.  Basically a score is the sum of the scores 
 *   in the matrix at each position-amino acid pair for one alignment.
 *   Parameters:
 *     Sequence *seq: the sequence to score
 *     Matrix *matrix: the matrix used for scoring
 *     int frame: the frame we are looking at (0 = aa seq.,
 *                1, 2, 3, -1, -2, -3 = na seqs.)
 *     Boolean repeats: enter repeats into the score_list?
 *     int search_type: the type of search we are doing.  If it is a 
 *                      SEARCH_TYPE_MATRIX search (block vs sequences), 
 *                      do NOT divide by the block percentile.  If it is a 
 *                      SEARCH_TYPE_BLOCK search (sequence vs blocks), DO 
 *                      divide by the block percentile. 
 *   Error codes: none
 */

extern void default_scoring_method();


/* 
 * print_histogram
 *   ouputs the histogram array from scoring.[ch] to the output stream ofp.
 *   Parameters:
 *     FILE *ofp: the output file pointer
 *   Return codes: none
 *   Error codes: none
 */

extern void print_histogram();




#endif /*  SCORING_H_ */

/* Change log information follows. */
/*
   Changes since version 3.2.5:
    5/25/99 Renamed scores_done to Scores_Done & alignemnts_done
	    to Alignments_Done & changed them from unsigned long to double
    2/ 3/99 Added MIN_SAVE_SCORE
   10/19/94 Increased MAX_HIST_SCORE from 2000 to 6000 = 60 x 100 =
	    max block width x max weight
 */

blimps-3.9/blimps/tree.h000064400001460000012000000002020774312247300155470ustar00jorjastaff00000400000027(
(
LACB_BOVIN:0.54708,
(
ICYA_MANSE:0.11010,
BBP_PIEBR:0.51596)
77:0.29262)
56:0.13501,
MUP2_MOUSE:0.99157,
RETB_BOVIN:0.48100);
blimps-3.9/blimps/LAMA.c000064400001460000012000002504300774312247600153320ustar00jorjastaff00000400000027/* Copyright 1994-2002: Fred Hutchinson Cancer Research Center, Seattle, WA USA
 LAMA.c Compare pairs of matrix blocks.
   Author: Shmuel Pietrokovski, pietro@bioinfo.weizmann.ac.il
   Reference: NAR (1996) 24:3836-3845.

-----------------------------------------------------------------------------
4/28/00 Update for longer ACs. Fix DBtype(); removed Prodom check since
	format has changed.
2/15/02 Fix bug with freeing matrix[1] too soon.
-----------------------------------------------------------------------------*/

#define EXTERN

#define SEARCH_TYPE_UNSET  -1

#define HELPLINES "\
Usage: \n\
LAMA inp_file1[,inp_file2] out_file [min_algn_wdth] [dbg_lvl] [scrn] [cutoff] [expected target]\n\
\n\
The program must have the names of one or two files with entry(ies) to compare\n\
and an output file name. These can be specified on the command line or\n\
interactively. On the command line the first argument is the entry(ies) file\n\
name(s), if two files are specified they should be separated by a comma\n\
with no spaces. Each file can be of either block, matrix, ProDom \n\
multiple alignment entry(ies). The second argument is the output file name,\n\
it will be overwritten if it already exists. Optional arguments are 3rd -\n\
minimal alignment width (0 for default), 4th - the debug level, 5th -\n\
screen output (0 to forbid, anything else to allow), 6th - score\n\
cutoff (in Z units [std's from mean], >=0, 0 for default), and 7th - for\n\
how many searched blocks to calculate the number a score is expected to appear\n\
(0 for default).\n"

#include 
#include "LAMA.h"

/* variables set by the configuration file in blimps program */

int StrandsToSearch;
int NumberToReport;
int SearchType;
int GeneticCodeInitializer;
int SiteSpecificScoringMatrixType;
int BlockToMatrixConversionMethod; /* default method is two */
int SequenceMatrixScoringMethod;   /* default method is zero */

/*
 * Local variables and data structures
 */

int    getargs(), data_read() ;

void   set_defaults(), load_stats3(), SW_matrices() ;
void   fprint_matrix(), load_ZvsPrcntl1() ;

double cols_score(), ZtoPrcntl(), extrpltd_mean(), extrpltd_var() ;

char   DBtype() ;

Block  *read_a_prodom_entry() ;

int         alloctd_algnmnts, alloctd_zVsPrcntl ;
int         alignments_done = 0 ;
int         dbg_lvl = 0, min_algnmnt_width = NARROWEST_WIDTH ;
double      Z_cutoff ;
ZvsPRCNTL   *zVsPrcntl ;
Stat        stats[WIDTHS] ;
Boolean     screen_out = TRUE, WWW_FLAG = TRUE ;

/*=======================================================================*/
/*
 * main
 *   controls flow of program
 *   Parameters: argc, argv
 *   Error codes:
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  int           i1, inpfiles ;
  int           read_entries = 0, entries_compared = 0, hits = 0, persearches = PERSEARCHES ;
  FILE          *bfp[2], *out ;
  Block         *block[2] ;
  Matrix        *matrix[2] ;
  BlocksAlgnmnt *scorePrpo ;
  char          bdbname[2][MAXNAME], outname[MAXNAME] ;
  char          version[40], line[MAXLINELEN], db_type[2], significance[9];
  char		*blimps_dir;	/* BLIMPS_DIR environment variable */
  char		ctemp[MAXNAME];
  double        percentile, expected, Z_score, shfl_mean, shfl_var ;


             /* allocate memory for the structures which are only pointed-to */
  scorePrpo = (BlocksAlgnmnt *) malloc(sizeof(BlocksAlgnmnt)) ;

  scorePrpo->alignment = (algnmnt *) calloc(ALGNMNTS_ALLOC, sizeof(algnmnt)) ;
  alloctd_algnmnts = ALGNMNTS_ALLOC ;

  strcpy(version,"28 Apr 00") ;

         /* load the mean and variance values for scores of different widths */
  load_stats3() ;

       /* load the Z score vs shuffled and unbiassed score percentile values */
  load_ZvsPrcntl1() ;

  Z_cutoff = Z_CUTOFF ;     /* set the Z value for score cutoff. */

                /* If no parameters passed on command line show how to do it */
  if (argc == 1) printf("\n%s", HELPLINES) ;

                                      /* getting input and output file names */
  if ((getargs(argc,argv,bdbname,bfp,&inpfiles,outname,&out,&Z_cutoff, &persearches)) != OK) 
     exit(ERROR) ; 

                                                    /*set the default values */
  set_defaults();

                                    /* set the score reporting cutoff values */
                   /* (avoid negative values which won't show up in S matrix)*/
  for (i1=0; i1width < min_algnmnt_width)
        {
        if (screen_out)
           {
           printf("\nComparisons skipped !\n") ;
           printf(
           "Block matrix %s shorter (%d) than narrowest width allowed (%d)\n",
                  matrix[0]->number, matrix[0]->width,  
       	          min_algnmnt_width) ;
	   }
                                /* free memory allocated to structure */
        if (db_type[0] != MATRIX_DB) free_block(block[0]) ;
        free_matrix(matrix[0]) ;

        continue ;
        }

          /* if only one input files is used begin using second block/matrix 
                      from the block/matrix following the first block/matrix */
     if (inpfiles == 1) 
        for(i1 = 0; i1 < read_entries; i1++)
           {
           data_read(&bfp[1],&block[1],&matrix[1],db_type[1]) ;
                                      /* free memory allocated to structures */
           if (db_type[1] != MATRIX_DB) free_block(block[1]) ;
           free_matrix(matrix[1]) ;
           }

     while (data_read(&bfp[1],&block[1],&matrix[1],db_type[1]) == OK) 
        {
      
                 /* skip comparison if the width of second matrix is less than 
                    narrowest allowed allowed alignment (min_algnmnt_width). */
        if (matrix[1]->width < min_algnmnt_width)
           {
           if (screen_out)
              {
              printf("\nComparison skipped !\n") ;
              printf(
           "Block matrix %s shorter (%d) than narrowest width allowed (%d)\n",
                     matrix[1]->number, matrix[1]->width, 
       	             min_algnmnt_width) ;
	      }
                                /* free memory allocated to structure */
           if (db_type[1] != MATRIX_DB) free_block(block[1]) ;
           free_matrix(matrix[1]) ;

           continue ;
	   }

        if (dbg_lvl >= 7) /*-------------------------------------------------*/
           {
	   if (db_type[0] != MATRIX_DB) print_block(block[0]) ;
	   if (db_type[1] != MATRIX_DB) print_block(block[1]) ;
           printf("\n") ;
	   } /*--------------------------------------------------------------*/

        if (dbg_lvl >= 6) /*------------------------------------------------*/
           {
           printf("\n%s", matrix[0]->number) ;
           fprint_matrix(matrix[0],stdout) ;
           if (WWW_FLAG) 
              {
              fprintf(out,"\n%s", matrix[0]->number) ;
              fprint_matrix(matrix[0],out) ;
	      }

           printf("\n\n%s", matrix[1]->number) ;
           fprint_matrix(matrix[1],stdout) ;
           printf("\n") ;
           if (WWW_FLAG) 
              {
              fprintf(out,"\n\n%s", matrix[1]->number) ;
              fprint_matrix(matrix[1],out) ;
              fprintf(out,"\n") ;
	      }
           } /*--------------------------------------------------------------*/


                                                         /* compare matrices */
        SW_matrices (matrix[0], matrix[1], min_algnmnt_width, scorePrpo, &out) ;

        entries_compared++ ;

                                      /* free memory allocated to structures */
        if (db_type[1] != MATRIX_DB) free_block(block[1]) ;

        hits += scorePrpo->reported_alignments ;
                                                /* print reported alignments */
        for (i1=0; i1reported_alignments; i1++)
           {
/* If width of comparison is more than the longest width for which statistics 
   were scored - use mean and variance from extrapolation formulas.          */

           if (min(matrix[0]->width, matrix[1]->width) > WIDTHS-1)
	      {
              shfl_mean = 
                     extrpltd_mean(min(matrix[0]->width, matrix[1]->width)) ;
              shfl_var = 
                     extrpltd_var(min(matrix[0]->width, matrix[1]->width)) ;
	      }
           else
	      {
              shfl_mean = 
                        stats[min(matrix[0]->width, matrix[1]->width)].mean ;
              shfl_var = 
                    stats[min(matrix[0]->width, matrix[1]->width)].variance ;
	      }

                                           /* calculate the score's Z value. */
           Z_score = 
(scorePrpo->alignment[i1].score * scorePrpo->alignment[i1].complength / 100. -
                                                       shfl_mean) / shfl_var ;

           percentile = ZtoPrcntl(Z_score) ;
           if (percentile > 0)
              {
              expected = (1 - percentile) * (float) persearches ;
              sprintf(significance, "%.1e", expected) ;
	      }
           else
              {
              expected = -1 ;
              sprintf(significance,"-") ;
	      }


           sprintf (line,
"%-10s  %3d : %3d and %-10s  %3d : %3d (%2d) score %3.0f (%4.1f  %s)",
 scorePrpo->matrix0_number, 
 scorePrpo->alignment[i1].positionE0 - scorePrpo->alignment[i1].complength + 1,
 scorePrpo->alignment[i1].positionE0,
 scorePrpo->matrix1_number, 
 scorePrpo->alignment[i1].positionE1 - scorePrpo->alignment[i1].complength + 1,
 scorePrpo->alignment[i1].positionE1,
 scorePrpo->alignment[i1].complength, 
 scorePrpo->alignment[i1].score, Z_score, significance) ;

           if (screen_out) printf("%s\n",line) ;
           fprintf(out,"%s\n",line) ;
           }
        }

                                      /* free memory allocated to structures */
     if (db_type[0] != MATRIX_DB) free_block(block[0]) ;
     free_matrix(matrix[0]) ;
     free_matrix(matrix[1]) ;

     rewind(bfp[1]) ;
     }

  if (hits == 0) 
     {
     sprintf(line,"No hits found above score cutoff %.1f.", Z_cutoff) ;
     printf("%s\n",line) ;
     if (WWW_FLAG) fprintf(out,"%s\n",line) ;
     }


  fclose(bfp[0]); fclose(bfp[1]); fclose(out);               /* close files */

  printf ("Output written in file %s.\n", outname) ;
  exit(0);

}  /* end of main */


/*****************************************************************************
 * get input and output file names and other program parameters interactively
 * or from command line. 
 * WARNING: argv[] only expands ~s in first filename, so
	~btest/...,~btest/... works for the first first filename but
	not for the second filename
 *****************************************************************************/

int getargs(argc,argv,bdbname,bfp,inpfiles,outname,out,Z_cutoff, persearches)

int    argc;
char   *argv[];
char   bdbname[][MAXNAME], outname[] ;
FILE   *bfp[], **out;
int    *inpfiles, *persearches ;
double *Z_cutoff ;

{
   int i1, i2;

/* ------------1st arg = block file(s) --------------------------------------*/
   if (argc > 1)
      if (strstr(argv[1],",") == NULL)             /* if only one input file */
         {
         strcpy(bdbname[0], argv[1]);
         *inpfiles = 1 ;
         }
      else                             /* if two input files ("file1,file2") */
         {
         for(i1 = 0; argv[1][i1] != ',' && argv[1][i1] != '\0' && i1 < MAXNAME;
             bdbname[0][i1] = argv[1][i1++]) ;
         if (argv[1][i1] != ',') 
            {
            printf(
              "Error in reading first file name from first argument !\n") ;
            return(ERROR) ;
            }
         bdbname[0][i1] = '\0' ;

         for(i1 = i1++, i2 = 0; argv[1][i1] != '\0' && i2 < MAXNAME; 
             bdbname[1][i2++] = argv[1][i1++]) ;
         if (argv[1][i1] != '\0') 
            {
            printf(
              "Error in reading second file name from first argument !\n") ;
            return(ERROR) ;
            }
         bdbname[1][i2] = '\0' ;

         *inpfiles = 2 ;
         }
   else                                   /* get input file(s) interactively */
      {
      printf("\nEnter name of a file with blocks or block matrices: ");
      gets(bdbname[0]);

      printf("\nThe blocks/matrices in this file will be intercompared.\n");
      printf("If you wish to compare them against blocks/matrices in\n");
      printf("another file enter that file name (else just hit ).\n");
      gets(bdbname[1]);

      if (bdbname[1][0] == '\0') *inpfiles = 1 ;
      else                       *inpfiles = 2 ;
      }

   if (*inpfiles == 1) strcpy(bdbname[1],bdbname[0]) ;

   for (i1 = 0; i1 < 2; i1++)                  /* opening input files */
      if ( (bfp[i1]=fopen(bdbname[i1], "r")) == NULL)
         {
         printf("\nCannot open file \"%s\"\n", bdbname[i1]);
         return(ERROR);
         }

/* ------------2nd arg = output file name -----------------------------------*/
   if (argc > 2)
      strcpy(outname, argv[2]);
   else
      {
      printf("\nEnter name of output file: ");
      gets(outname);
      }

   if ( (*out=fopen(outname, "w")) == NULL)
      {
      printf("\nCannot open file \"%s\"\n", outname);
      return(ERROR);
      }

/* ------------optional 3rd arg = minimal alignment width ------------------*/

   if (argc > 3) min_algnmnt_width = atoi(argv[3]) ;

   if (min_algnmnt_width == 0)
      min_algnmnt_width = NARROWEST_WIDTH ;
   else if (min_algnmnt_width < 0)
      {
      printf("\nMinimal alignment width can not be negative !\n") ;
      printf("The value given (%d) is out of range.\n", min_algnmnt_width) ;
      return(ERROR) ;
      }
   else if (min_algnmnt_width < NARROWEST_WIDTH)
      {
      printf("\nMinimal alignment width can not be less \n") ;
      printf("than narrowest allowed blocks (%d).\n", NARROWEST_WIDTH) ;
      return(ERROR) ;
      }

/* ------------optional 4th arg = debug level ------------------------------*/

   if (argc > 4) dbg_lvl = atoi(argv[4]) ;


/* ------------optional 5th arg = screen output ----------------------------*/

   if (argc > 5) screen_out = atoi(argv[5]) ;


/* -- optional 6th arg = Z score reporting level, 0 or less sets default ---*/
/*  If the Z cutoff wasn't given on the command line
    it would be been given a default value specified in the header file. */

   if (argc > 6) 
      if ((*Z_cutoff = atof(argv[6])) <= 0) *Z_cutoff = Z_CUTOFF ;


          /* If negative Z cutoff was passed print out why that was wrong. */

   if (argc > 6 && atof(argv[6]) < 0.)
      {
      printf("\nCutoff score should be specified as a Z score (mean+Z*std).\n") ;
      printf(
"The Z score must be positive (corresponding to the 50 percentile or higher).\n") ;
      printf(
        "A negative cutoff score (%f) was specified, default value (%.2f) used.\n",
         atof(argv[6]), (float) Z_CUTOFF) ;
      }

/* -- optional 7th arg = persearches number, the number of blocks for calculating the
   expected times a score would occur searching that number of blocks. */
/*  If it wasn't given on the command line or 0 or a non integer specified
    it would be been given a default value specified in the header file. */

   if (argc > 7) 
      if ((*persearches = atoi(argv[7])) <= 0) *persearches = PERSEARCHES ;


   return(OK) ;

}



/****************************************************************************
 * set the default values for some of the variables.
 ****************************************************************************/

void set_defaults()
{

  GeneticCodeInitializer = 0;           /* the standard genetic code */

  StrandsToSearch = 2;          /* == 2 if want to search both strands */
  NumberToReport  = 0;          /* <0 means all, 0 means judge, */
                                /* >0 means use that number */
  SearchType      = SEARCH_TYPE_UNSET;

  BlockToMatrixConversionMethod = 2; /* default method is two */
  SequenceMatrixScoringMethod   = 0; /* default method is zero */

  ErrorLevelReport = 5;		/* don't want to see BLIMPS errors */

}


/*****************************************************************************
 * SW_matrices
 * A modified (no gaps, alignments retained if they are above a cutoff value -
 * more than one alignment can be found for a pair of matrices) Smith Waterman 
 * optimal local alignment for matrices.
 *
 * Algorithm :
 * S matrix constructed. Highest score (=optimal alignment) found. For the
 * current score (starting with the highest) - while the score is above the 
 * minimal score cutoff (cutoff value for shortest allowed alignment) the 
 * following is done -
 *  The alignment and its width are found by doing a trace back along the
 *   diagonal in the S matrix from the score position,
 *  The S matrix is modified to remove the scores of the current alignment,
 *  The alignment is retained if its score is above the cutoff for its width
 *   (hence an alignment may be initially retained because of the score 
 *   (which might be significant for a short alignment) but later discarded 
 *   because it is not significant for its actual width), 
 *  The next best score is found in the modified S matrix.
 *
 * Dynamic programing algorithm based on Pearson & Miller,
 *  Meth. Enz. 210:575 92'.
 *****************************************************************************/

void SW_matrices(matrix0, matrix1, min_algnmnt_width, scorePrpo, out)

Matrix        *matrix0, *matrix1 ;
BlocksAlgnmnt *scorePrpo ;
int           min_algnmnt_width ;
FILE          **out;

{
  double  **s_matrix, *tmp_ptr1, Z_score, best_score, cutoff ;
  algnmnt *tmp_ptr2 ;
  int     i0, i1, i2, j, use_width ;

/* for cases where shortest block is longer the WIDTHS stat data will be 
   received by extrapolation formulas */

   use_width = min(matrix0->width, matrix1->width) ;

/* get cutoff score - from shuffled data for blocks <= 55 from extrapolation
   formulas for longer blocks */
  if (min(matrix0->width, matrix1->width) > WIDTHS-1)
     cutoff = max (0, 
                    extrpltd_mean(min(matrix0->width, matrix1->width)) + 
                     (Z_cutoff * 
                      extrpltd_var(min(matrix0->width, matrix1->width)) 
                     )) ;
  else
     cutoff = stats[use_width].cutoff ;


                                         /* allocate memory for score matrix */
                                              /* get memory for all elements */
  tmp_ptr1 = (double *) 
           calloc ((matrix0->width+1) * (matrix1->width+1), sizeof(double)) ;

	                                /* initialize the elements 2-d array */
  s_matrix = (double **) calloc (matrix0->width+1, sizeof(double *)) ;
  for (i0=0; i0 <= matrix0->width; i0++)
     s_matrix[i0] = &(tmp_ptr1[i0 * (matrix1->width+1)]) ;

                                 /* use j to simplify the way the code looks */
  j = scorePrpo->reported_alignments = 0 ;

  best_score = 0. ;

  strcpy(scorePrpo->matrix0_number, matrix0->number) ;
  strcpy(scorePrpo->matrix1_number, matrix1->number) ;

   /* initialize outer edges of S matrix to 0 and calculate rest of matrix and
      find best score.                                                       */
  for (i1=0; i1 <= matrix1->width; i1++)
     s_matrix[0][i1] = 0. ;

  for (i0=1; i0 <= matrix0->width; i0++)
     {
     s_matrix[i0][0] = 0. ;
     for (i1=1; i1 <= matrix1->width; i1++)
        {
        s_matrix[i0][i1] = max(0, s_matrix[i0-1][i1-1] + 
                     cols_score(matrix0->weights,i0-1,matrix1->weights,i1-1)) ;
        if (s_matrix[i0][i1] > best_score)
	   {
           best_score = s_matrix[i0][i1] ;
           scorePrpo->alignment[0].positionE0 = i0 ;
           scorePrpo->alignment[0].positionE1 = i1 ;
	   }
        }
     }

  if (dbg_lvl >= 5) /*-------------------------------------------------------*/
     {
     printf("Column scores for %s and %s -\n", 
            matrix0->number, matrix1->number) ;

     for (i0=1; i0 <= matrix0->width; i0++)
        {
        for (i1=1; i1 <= matrix1->width; i1++)
           printf("%6.3f ",
                  cols_score(matrix0->weights,i0-1,matrix1->weights,i1-1)) ;

        printf("\n") ;
        }

     printf("\n") ;
     }
  /*-------------------------------------------------------------------------*/


/* while best score is more than lowest possible score cutoff for this matrix 
   pair find the next best (sub optimal) scores found in decreasing values. */

  while (best_score > 0. && best_score > cutoff)
    {

/* Do a trace back along the S matrix to find the alignment's width.        */
/* trace-back procedure - go back along the diagonal from the best score's 
   position and stop when a value of 0 or an edge of the matrix is reached. */

    for (scorePrpo->alignment[j].complength = 1 ;
         (s_matrix[scorePrpo->alignment[j].positionE0 - 
                   scorePrpo->alignment[j].complength]
                  [scorePrpo->alignment[j].positionE1 - 
                   scorePrpo->alignment[j].complength] > 0.) &&
         (scorePrpo->alignment[j].positionE0 - 
          scorePrpo->alignment[j].complength > 0) &&
         (scorePrpo->alignment[j].positionE1 - 
          scorePrpo->alignment[j].complength > 0) ;
         scorePrpo->alignment[j].complength++) ;


    if (dbg_lvl >= 4) /*----------------------------------------------------*/
       {
       printf("S matrix for %s and %s -\n", 
              matrix0->number, matrix1->number) ;
       for (i0=1; i0 <= matrix0->width; i0++)
          {
          for (i1=1; i1 <= matrix1->width; i1++)
             printf("%6.3f ",s_matrix[i0][i1]) ;
          printf("\n") ;
          }

       printf("\n") ;
       }
    /*-----------------------------------------------------------------------*/

  if (dbg_lvl >= 3) /*-------------------------------------------------------*/
     {
     printf("\nColumn scores for optimal alignment of %s and %s -\n", 
            matrix0->number, matrix1->number) ;
     if (WWW_FLAG)  
        fprintf(*out,"\nColumn scores for optimal alignment of %s and %s -\n", 
                matrix0->number, matrix1->number) ;

     for (i2=0, 
          i0=scorePrpo->alignment[j].positionE0 - 
             scorePrpo->alignment[j].complength + 1, 
          i1=scorePrpo->alignment[j].positionE1 - 
             scorePrpo->alignment[j].complength + 1;
          i2 < scorePrpo->alignment[j].complength; i2++)
       {
       printf("%3d,%2d ",i0+i2, i1+i2) ;
       if (WWW_FLAG) fprintf(*out,"%3d,%2d ",i0+i2, i1+i2) ;
       }

     printf("\n") ;
     if (WWW_FLAG)  fprintf(*out,"\n") ;

     for (i2=0, 
          i0=scorePrpo->alignment[j].positionE0 - 
             scorePrpo->alignment[j].complength + 1, 
          i1=scorePrpo->alignment[j].positionE1 - 
             scorePrpo->alignment[j].complength + 1;
          i2 < scorePrpo->alignment[j].complength; i2++)
        {
        printf("%6.3f ",
              cols_score(matrix0->weights,i0-1+i2,matrix1->weights,i1-1+i2)) ;
        if (WWW_FLAG) fprintf(*out,"%6.3f ",
              cols_score(matrix0->weights,i0-1+i2,matrix1->weights,i1-1+i2)) ;
        }

     printf("\n") ;
     if (WWW_FLAG)  fprintf(*out,"\n") ;

     }

  /*-------------------------------------------------------------------------*/

    if (dbg_lvl >= 2) /*-----------------------------------------------------*/
       {
                                                        /* calculate Z value */
       if (min(matrix0->width, matrix1->width) > WIDTHS-1)
          Z_score = (best_score - 
                    extrpltd_mean(min(matrix0->width, matrix1->width))) /
                     extrpltd_var(min(matrix0->width, matrix1->width)) ;
       else
          Z_score = (best_score - stats[use_width].mean) / 
                    stats[use_width].variance ;

       printf("%-10s %3d %3d %-10s %3d %3d %2d Prpo %6.2f (%4.1f)\n",
           matrix0->number, 
   scorePrpo->alignment[j].positionE0 - scorePrpo->alignment[j].complength + 1,
           scorePrpo->alignment[j].positionE0, 
           matrix1->number, 
   scorePrpo->alignment[j].positionE1 - scorePrpo->alignment[j].complength + 1,
           scorePrpo->alignment[j].positionE1,
           scorePrpo->alignment[j].complength, 
           best_score * 100. / scorePrpo->alignment[j].complength,
           Z_score) ;
       }
    /*-----------------------------------------------------------------------*/

                                                     /* find next best score */

       /* change values of S matrix elements of current best alignment to 0s */
    for (i0 = scorePrpo->alignment[j].positionE0,
         i1 = scorePrpo->alignment[j].positionE1; 
         i0 >= scorePrpo->alignment[j].positionE0 -
               scorePrpo->alignment[j].complength + 1 ;
         i0--, i1--)
         s_matrix[i0][i1] = 0. ; 

/* recalculate  values of S matrix elements on the diagonal beyond the end of 
   the current best alignment alignment                                      */

    for (i0 = scorePrpo->alignment[j].positionE0 + 1, 
         i1 = scorePrpo->alignment[j].positionE1 + 1; 
         i0 <= matrix0->width && i1<= matrix1->width ;
         i0++, i1++)
        s_matrix[i0][i1] = max(0, s_matrix[i0-1][i1-1] + 
                     cols_score(matrix0->weights,i0-1,matrix1->weights,i1-1)) ;


  /* if the width of the alignment is more than the narrowest allowed 
     alignment save and normalize score and advance reported scores index.   */

    if (scorePrpo->alignment[j].complength >= min_algnmnt_width)
       {
         
/* Normalize the score by dividing it with the alignment width and multiplying 
   by 100. Since the score of each column pair ranges -1 to +1 this makes the 
   range of the normalized score -100 to +100.                               */

       scorePrpo->alignment[j].score = best_score * 100. / 
                                       scorePrpo->alignment[j].complength ;

       j = ++scorePrpo->reported_alignments ;        /* advance scores index */

      /* check if more memory needed for alignments array in score structure */
       if (scorePrpo->reported_alignments == alloctd_algnmnts)
         {
         alloctd_algnmnts += ALGNMNTS_ALLOC ;
         tmp_ptr2 = (algnmnt *) 
              realloc(scorePrpo->alignment, alloctd_algnmnts*sizeof(algnmnt)) ;
         scorePrpo->alignment = tmp_ptr2 ; 
         }

       }

                                /* find best score in the modified S matrix */
    best_score = 0. ;
    for (i0=1; i0 <= matrix0->width; i0++)
       for (i1=1; i1 <= matrix1->width; i1++)
          if (s_matrix[i0][i1] > best_score)
    	     {
             best_score = s_matrix[i0][i1] ;
             scorePrpo->alignment[j].positionE0 = i0 ;
             scorePrpo->alignment[j].positionE1 = i1 ;
             }
    }

  free(tmp_ptr1) ; free(s_matrix) ;                           /* free memory */
  return ;
}

/*****************************************************************************
 * cols_score
 * compare a pair of matrix columns (positions)
 ****************************************************************************/

double cols_score(mat1,col1,mat2,col2)

MatType *mat1[], *mat2[] ;
int     col1, col2 ;

{
   double score ;
   double p1=0.0, p2=0.0, p3a=0.0, p3b=0.0, p4a=0.0, p4b=0.0 ;
   int    aa ;

                 /* Calculate Pearson's r score between the 2 matrix columns */

   for (aa=0; aa zVsPrcntl[alloctd_zVsPrcntl-1].Z) return(1.0) ;

/* if Zscore larger then lowest noted Z score go down the array (whose values 
   are sorted) until reaching a Zscore smaller then the searched one. This is 
   conservative since we find a smaller value not the closest one. */

   if (Zscore >= zVsPrcntl[0].Z)
      {
      for (i1=alloctd_zVsPrcntl-1; i1 >= 0 && Zscore <= zVsPrcntl[i1].Z; i1--) ;
      return(zVsPrcntl[i1].prcntl) ;
      }

/* for very low scores return value for unknown percentile */

   if (Zscore < 0) return(-1.0) ;

/* else fit with a formula */

   if (Zscore < 2) return(1.0 - 0.473 * exp(-1.150*Zscore)) ;

   if (Zscore < 5) return(1.0 - 0.901 * exp(-1.582*Zscore)) ;

/* if this part reached something is probably wrong, return -1 */

   return(-1.0) ;
 }

/***************************************************************************
 * A procedure to give the extrapolated mean-of-suffled-PSSMs for a given
 * block width. The extrapolation was done by fitting the actual values 
 * found for widths 4-55 (see procedure load_stats) to a formula :
 * mean = A1 + A2 * sqrt(width), the values found are 
 * mean = -0.134758 + 0.702457*sqrt(width).
 * The use of this procedure is for approximating the mean for widths
 * longer than 55. */

double extrpltd_mean(blk_width)

int blk_width ;

{
   if (blk_width 5 from the following score data -
 * The compared data was BLOCKS 8.0 with a shuffled version of itself.
 * For each block the order of columns in its PSSM was randomly changed
 * and the resulting PSSM saved. This resulted in 8.2 million (8,233,820)
 * scores. These were purged from all scores that contained any one of 215
 * biassed blocks or their shuffled versions and from scores between blocks
 * and their own shuffled version. This resulted in 7,048,856 scores. 
 ****************************************************************************/

void load_ZvsPrcntl1() 
{
            /* Allocate memory to array of structures according to the data */
   alloctd_zVsPrcntl = 471 ;
   zVsPrcntl = (ZvsPRCNTL *) calloc(alloctd_zVsPrcntl, sizeof(ZvsPRCNTL)) ;

   zVsPrcntl[0].Z = 5.000 ;  zVsPrcntl[0].prcntl = 0.9997645 ;
   zVsPrcntl[1].Z = 5.000 ;  zVsPrcntl[1].prcntl = 0.9997650 ;
   zVsPrcntl[2].Z = 5.000 ;  zVsPrcntl[2].prcntl = 0.9997655 ;
   zVsPrcntl[3].Z = 5.000 ;  zVsPrcntl[3].prcntl = 0.9997660 ;
   zVsPrcntl[4].Z = 5.000 ;  zVsPrcntl[4].prcntl = 0.9997665 ;
   zVsPrcntl[5].Z = 5.000 ;  zVsPrcntl[5].prcntl = 0.9997670 ;
   zVsPrcntl[6].Z = 5.000 ;  zVsPrcntl[6].prcntl = 0.9997675 ;
   zVsPrcntl[7].Z = 5.000 ;  zVsPrcntl[7].prcntl = 0.9997680 ;
   zVsPrcntl[8].Z = 5.006 ;  zVsPrcntl[8].prcntl = 0.9997685 ;
   zVsPrcntl[9].Z = 5.006 ;  zVsPrcntl[9].prcntl = 0.9997690 ;
   zVsPrcntl[10].Z = 5.007 ;  zVsPrcntl[10].prcntl = 0.9997695 ;
   zVsPrcntl[11].Z = 5.011 ;  zVsPrcntl[11].prcntl = 0.9997700 ;
   zVsPrcntl[12].Z = 5.012 ;  zVsPrcntl[12].prcntl = 0.9997705 ;
   zVsPrcntl[13].Z = 5.013 ;  zVsPrcntl[13].prcntl = 0.9997710 ;
   zVsPrcntl[14].Z = 5.013 ;  zVsPrcntl[14].prcntl = 0.9997715 ;
   zVsPrcntl[15].Z = 5.014 ;  zVsPrcntl[15].prcntl = 0.9997720 ;
   zVsPrcntl[16].Z = 5.016 ;  zVsPrcntl[16].prcntl = 0.9997725 ;
   zVsPrcntl[17].Z = 5.018 ;  zVsPrcntl[17].prcntl = 0.9997730 ;
   zVsPrcntl[18].Z = 5.018 ;  zVsPrcntl[18].prcntl = 0.9997735 ;
   zVsPrcntl[19].Z = 5.018 ;  zVsPrcntl[19].prcntl = 0.9997740 ;
   zVsPrcntl[20].Z = 5.019 ;  zVsPrcntl[20].prcntl = 0.9997745 ;
   zVsPrcntl[21].Z = 5.023 ;  zVsPrcntl[21].prcntl = 0.9997750 ;
   zVsPrcntl[22].Z = 5.025 ;  zVsPrcntl[22].prcntl = 0.9997755 ;
   zVsPrcntl[23].Z = 5.026 ;  zVsPrcntl[23].prcntl = 0.9997760 ;
   zVsPrcntl[24].Z = 5.026 ;  zVsPrcntl[24].prcntl = 0.9997765 ;
   zVsPrcntl[25].Z = 5.028 ;  zVsPrcntl[25].prcntl = 0.9997770 ;
   zVsPrcntl[26].Z = 5.031 ;  zVsPrcntl[26].prcntl = 0.9997775 ;
   zVsPrcntl[27].Z = 5.032 ;  zVsPrcntl[27].prcntl = 0.9997780 ;
   zVsPrcntl[28].Z = 5.033 ;  zVsPrcntl[28].prcntl = 0.9997785 ;
   zVsPrcntl[29].Z = 5.033 ;  zVsPrcntl[29].prcntl = 0.9997790 ;
   zVsPrcntl[30].Z = 5.034 ;  zVsPrcntl[30].prcntl = 0.9997795 ;
   zVsPrcntl[31].Z = 5.036 ;  zVsPrcntl[31].prcntl = 0.9997800 ;
   zVsPrcntl[32].Z = 5.036 ;  zVsPrcntl[32].prcntl = 0.9997805 ;
   zVsPrcntl[33].Z = 5.037 ;  zVsPrcntl[33].prcntl = 0.9997810 ;
   zVsPrcntl[34].Z = 5.040 ;  zVsPrcntl[34].prcntl = 0.9997815 ;
   zVsPrcntl[35].Z = 5.042 ;  zVsPrcntl[35].prcntl = 0.9997820 ;
   zVsPrcntl[36].Z = 5.042 ;  zVsPrcntl[36].prcntl = 0.9997825 ;
   zVsPrcntl[37].Z = 5.043 ;  zVsPrcntl[37].prcntl = 0.9997830 ;
   zVsPrcntl[38].Z = 5.045 ;  zVsPrcntl[38].prcntl = 0.9997835 ;
   zVsPrcntl[39].Z = 5.046 ;  zVsPrcntl[39].prcntl = 0.9997840 ;
   zVsPrcntl[40].Z = 5.047 ;  zVsPrcntl[40].prcntl = 0.9997845 ;
   zVsPrcntl[41].Z = 5.050 ;  zVsPrcntl[41].prcntl = 0.9997850 ;
   zVsPrcntl[42].Z = 5.051 ;  zVsPrcntl[42].prcntl = 0.9997855 ;
   zVsPrcntl[43].Z = 5.054 ;  zVsPrcntl[43].prcntl = 0.9997860 ;
   zVsPrcntl[44].Z = 5.055 ;  zVsPrcntl[44].prcntl = 0.9997865 ;
   zVsPrcntl[45].Z = 5.057 ;  zVsPrcntl[45].prcntl = 0.9997870 ;
   zVsPrcntl[46].Z = 5.059 ;  zVsPrcntl[46].prcntl = 0.9997875 ;
   zVsPrcntl[47].Z = 5.059 ;  zVsPrcntl[47].prcntl = 0.9997880 ;
   zVsPrcntl[48].Z = 5.060 ;  zVsPrcntl[48].prcntl = 0.9997885 ;
   zVsPrcntl[49].Z = 5.061 ;  zVsPrcntl[49].prcntl = 0.9997890 ;
   zVsPrcntl[50].Z = 5.061 ;  zVsPrcntl[50].prcntl = 0.9997895 ;
   zVsPrcntl[51].Z = 5.063 ;  zVsPrcntl[51].prcntl = 0.9997900 ;
   zVsPrcntl[52].Z = 5.064 ;  zVsPrcntl[52].prcntl = 0.9997905 ;
   zVsPrcntl[53].Z = 5.066 ;  zVsPrcntl[53].prcntl = 0.9997910 ;
   zVsPrcntl[54].Z = 5.068 ;  zVsPrcntl[54].prcntl = 0.9997915 ;
   zVsPrcntl[55].Z = 5.069 ;  zVsPrcntl[55].prcntl = 0.9997920 ;
   zVsPrcntl[56].Z = 5.069 ;  zVsPrcntl[56].prcntl = 0.9997925 ;
   zVsPrcntl[57].Z = 5.071 ;  zVsPrcntl[57].prcntl = 0.9997930 ;
   zVsPrcntl[58].Z = 5.071 ;  zVsPrcntl[58].prcntl = 0.9997935 ;
   zVsPrcntl[59].Z = 5.073 ;  zVsPrcntl[59].prcntl = 0.9997940 ;
   zVsPrcntl[60].Z = 5.074 ;  zVsPrcntl[60].prcntl = 0.9997945 ;
   zVsPrcntl[61].Z = 5.077 ;  zVsPrcntl[61].prcntl = 0.9997950 ;
   zVsPrcntl[62].Z = 5.077 ;  zVsPrcntl[62].prcntl = 0.9997955 ;
   zVsPrcntl[63].Z = 5.078 ;  zVsPrcntl[63].prcntl = 0.9997960 ;
   zVsPrcntl[64].Z = 5.078 ;  zVsPrcntl[64].prcntl = 0.9997965 ;
   zVsPrcntl[65].Z = 5.078 ;  zVsPrcntl[65].prcntl = 0.9997970 ;
   zVsPrcntl[66].Z = 5.080 ;  zVsPrcntl[66].prcntl = 0.9997975 ;
   zVsPrcntl[67].Z = 5.082 ;  zVsPrcntl[67].prcntl = 0.9997980 ;
   zVsPrcntl[68].Z = 5.086 ;  zVsPrcntl[68].prcntl = 0.9997985 ;
   zVsPrcntl[69].Z = 5.087 ;  zVsPrcntl[69].prcntl = 0.9997990 ;
   zVsPrcntl[70].Z = 5.089 ;  zVsPrcntl[70].prcntl = 0.9997995 ;
   zVsPrcntl[71].Z = 5.090 ;  zVsPrcntl[71].prcntl = 0.9998000 ;
   zVsPrcntl[72].Z = 5.090 ;  zVsPrcntl[72].prcntl = 0.9998005 ;
   zVsPrcntl[73].Z = 5.091 ;  zVsPrcntl[73].prcntl = 0.9998010 ;
   zVsPrcntl[74].Z = 5.093 ;  zVsPrcntl[74].prcntl = 0.9998015 ;
   zVsPrcntl[75].Z = 5.094 ;  zVsPrcntl[75].prcntl = 0.9998020 ;
   zVsPrcntl[76].Z = 5.095 ;  zVsPrcntl[76].prcntl = 0.9998025 ;
   zVsPrcntl[77].Z = 5.097 ;  zVsPrcntl[77].prcntl = 0.9998030 ;
   zVsPrcntl[78].Z = 5.100 ;  zVsPrcntl[78].prcntl = 0.9998035 ;
   zVsPrcntl[79].Z = 5.103 ;  zVsPrcntl[79].prcntl = 0.9998040 ;
   zVsPrcntl[80].Z = 5.104 ;  zVsPrcntl[80].prcntl = 0.9998045 ;
   zVsPrcntl[81].Z = 5.105 ;  zVsPrcntl[81].prcntl = 0.9998050 ;
   zVsPrcntl[82].Z = 5.107 ;  zVsPrcntl[82].prcntl = 0.9998055 ;
   zVsPrcntl[83].Z = 5.108 ;  zVsPrcntl[83].prcntl = 0.9998060 ;
   zVsPrcntl[84].Z = 5.110 ;  zVsPrcntl[84].prcntl = 0.9998065 ;
   zVsPrcntl[85].Z = 5.110 ;  zVsPrcntl[85].prcntl = 0.9998070 ;
   zVsPrcntl[86].Z = 5.110 ;  zVsPrcntl[86].prcntl = 0.9998075 ;
   zVsPrcntl[87].Z = 5.112 ;  zVsPrcntl[87].prcntl = 0.9998080 ;
   zVsPrcntl[88].Z = 5.113 ;  zVsPrcntl[88].prcntl = 0.9998085 ;
   zVsPrcntl[89].Z = 5.115 ;  zVsPrcntl[89].prcntl = 0.9998090 ;
   zVsPrcntl[90].Z = 5.117 ;  zVsPrcntl[90].prcntl = 0.9998095 ;
   zVsPrcntl[91].Z = 5.119 ;  zVsPrcntl[91].prcntl = 0.9998100 ;
   zVsPrcntl[92].Z = 5.121 ;  zVsPrcntl[92].prcntl = 0.9998105 ;
   zVsPrcntl[93].Z = 5.123 ;  zVsPrcntl[93].prcntl = 0.9998110 ;
   zVsPrcntl[94].Z = 5.124 ;  zVsPrcntl[94].prcntl = 0.9998115 ;
   zVsPrcntl[95].Z = 5.125 ;  zVsPrcntl[95].prcntl = 0.9998120 ;
   zVsPrcntl[96].Z = 5.125 ;  zVsPrcntl[96].prcntl = 0.9998125 ;
   zVsPrcntl[97].Z = 5.126 ;  zVsPrcntl[97].prcntl = 0.9998130 ;
   zVsPrcntl[98].Z = 5.127 ;  zVsPrcntl[98].prcntl = 0.9998135 ;
   zVsPrcntl[99].Z = 5.127 ;  zVsPrcntl[99].prcntl = 0.9998140 ;
   zVsPrcntl[100].Z = 5.128 ;  zVsPrcntl[100].prcntl = 0.9998145 ;
   zVsPrcntl[101].Z = 5.133 ;  zVsPrcntl[101].prcntl = 0.9998150 ;
   zVsPrcntl[102].Z = 5.134 ;  zVsPrcntl[102].prcntl = 0.9998155 ;
   zVsPrcntl[103].Z = 5.137 ;  zVsPrcntl[103].prcntl = 0.9998160 ;
   zVsPrcntl[104].Z = 5.137 ;  zVsPrcntl[104].prcntl = 0.9998165 ;
   zVsPrcntl[105].Z = 5.138 ;  zVsPrcntl[105].prcntl = 0.9998170 ;
   zVsPrcntl[106].Z = 5.141 ;  zVsPrcntl[106].prcntl = 0.9998175 ;
   zVsPrcntl[107].Z = 5.141 ;  zVsPrcntl[107].prcntl = 0.9998180 ;
   zVsPrcntl[108].Z = 5.142 ;  zVsPrcntl[108].prcntl = 0.9998185 ;
   zVsPrcntl[109].Z = 5.143 ;  zVsPrcntl[109].prcntl = 0.9998190 ;
   zVsPrcntl[110].Z = 5.143 ;  zVsPrcntl[110].prcntl = 0.9998195 ;
   zVsPrcntl[111].Z = 5.147 ;  zVsPrcntl[111].prcntl = 0.9998200 ;
   zVsPrcntl[112].Z = 5.147 ;  zVsPrcntl[112].prcntl = 0.9998205 ;
   zVsPrcntl[113].Z = 5.149 ;  zVsPrcntl[113].prcntl = 0.9998210 ;
   zVsPrcntl[114].Z = 5.150 ;  zVsPrcntl[114].prcntl = 0.9998215 ;
   zVsPrcntl[115].Z = 5.154 ;  zVsPrcntl[115].prcntl = 0.9998220 ;
   zVsPrcntl[116].Z = 5.155 ;  zVsPrcntl[116].prcntl = 0.9998225 ;
   zVsPrcntl[117].Z = 5.157 ;  zVsPrcntl[117].prcntl = 0.9998230 ;
   zVsPrcntl[118].Z = 5.157 ;  zVsPrcntl[118].prcntl = 0.9998235 ;
   zVsPrcntl[119].Z = 5.158 ;  zVsPrcntl[119].prcntl = 0.9998240 ;
   zVsPrcntl[120].Z = 5.158 ;  zVsPrcntl[120].prcntl = 0.9998245 ;
   zVsPrcntl[121].Z = 5.158 ;  zVsPrcntl[121].prcntl = 0.9998250 ;
   zVsPrcntl[122].Z = 5.159 ;  zVsPrcntl[122].prcntl = 0.9998255 ;
   zVsPrcntl[123].Z = 5.161 ;  zVsPrcntl[123].prcntl = 0.9998260 ;
   zVsPrcntl[124].Z = 5.162 ;  zVsPrcntl[124].prcntl = 0.9998265 ;
   zVsPrcntl[125].Z = 5.163 ;  zVsPrcntl[125].prcntl = 0.9998270 ;
   zVsPrcntl[126].Z = 5.166 ;  zVsPrcntl[126].prcntl = 0.9998275 ;
   zVsPrcntl[127].Z = 5.167 ;  zVsPrcntl[127].prcntl = 0.9998280 ;
   zVsPrcntl[128].Z = 5.169 ;  zVsPrcntl[128].prcntl = 0.9998285 ;
   zVsPrcntl[129].Z = 5.171 ;  zVsPrcntl[129].prcntl = 0.9998290 ;
   zVsPrcntl[130].Z = 5.175 ;  zVsPrcntl[130].prcntl = 0.9998295 ;
   zVsPrcntl[131].Z = 5.178 ;  zVsPrcntl[131].prcntl = 0.9998300 ;
   zVsPrcntl[132].Z = 5.179 ;  zVsPrcntl[132].prcntl = 0.9998305 ;
   zVsPrcntl[133].Z = 5.184 ;  zVsPrcntl[133].prcntl = 0.9998310 ;
   zVsPrcntl[134].Z = 5.184 ;  zVsPrcntl[134].prcntl = 0.9998315 ;
   zVsPrcntl[135].Z = 5.186 ;  zVsPrcntl[135].prcntl = 0.9998320 ;
   zVsPrcntl[136].Z = 5.186 ;  zVsPrcntl[136].prcntl = 0.9998325 ;
   zVsPrcntl[137].Z = 5.189 ;  zVsPrcntl[137].prcntl = 0.9998330 ;
   zVsPrcntl[138].Z = 5.191 ;  zVsPrcntl[138].prcntl = 0.9998335 ;
   zVsPrcntl[139].Z = 5.191 ;  zVsPrcntl[139].prcntl = 0.9998340 ;
   zVsPrcntl[140].Z = 5.192 ;  zVsPrcntl[140].prcntl = 0.9998345 ;
   zVsPrcntl[141].Z = 5.195 ;  zVsPrcntl[141].prcntl = 0.9998350 ;
   zVsPrcntl[142].Z = 5.198 ;  zVsPrcntl[142].prcntl = 0.9998355 ;
   zVsPrcntl[143].Z = 5.200 ;  zVsPrcntl[143].prcntl = 0.9998360 ;
   zVsPrcntl[144].Z = 5.201 ;  zVsPrcntl[144].prcntl = 0.9998365 ;
   zVsPrcntl[145].Z = 5.202 ;  zVsPrcntl[145].prcntl = 0.9998370 ;
   zVsPrcntl[146].Z = 5.203 ;  zVsPrcntl[146].prcntl = 0.9998375 ;
   zVsPrcntl[147].Z = 5.204 ;  zVsPrcntl[147].prcntl = 0.9998380 ;
   zVsPrcntl[148].Z = 5.206 ;  zVsPrcntl[148].prcntl = 0.9998385 ;
   zVsPrcntl[149].Z = 5.208 ;  zVsPrcntl[149].prcntl = 0.9998390 ;
   zVsPrcntl[150].Z = 5.209 ;  zVsPrcntl[150].prcntl = 0.9998395 ;
   zVsPrcntl[151].Z = 5.211 ;  zVsPrcntl[151].prcntl = 0.9998400 ;
   zVsPrcntl[152].Z = 5.214 ;  zVsPrcntl[152].prcntl = 0.9998405 ;
   zVsPrcntl[153].Z = 5.214 ;  zVsPrcntl[153].prcntl = 0.9998410 ;
   zVsPrcntl[154].Z = 5.215 ;  zVsPrcntl[154].prcntl = 0.9998415 ;
   zVsPrcntl[155].Z = 5.216 ;  zVsPrcntl[155].prcntl = 0.9998420 ;
   zVsPrcntl[156].Z = 5.217 ;  zVsPrcntl[156].prcntl = 0.9998425 ;
   zVsPrcntl[157].Z = 5.220 ;  zVsPrcntl[157].prcntl = 0.9998430 ;
   zVsPrcntl[158].Z = 5.222 ;  zVsPrcntl[158].prcntl = 0.9998435 ;
   zVsPrcntl[159].Z = 5.224 ;  zVsPrcntl[159].prcntl = 0.9998440 ;
   zVsPrcntl[160].Z = 5.225 ;  zVsPrcntl[160].prcntl = 0.9998445 ;
   zVsPrcntl[161].Z = 5.229 ;  zVsPrcntl[161].prcntl = 0.9998450 ;
   zVsPrcntl[162].Z = 5.230 ;  zVsPrcntl[162].prcntl = 0.9998455 ;
   zVsPrcntl[163].Z = 5.232 ;  zVsPrcntl[163].prcntl = 0.9998460 ;
   zVsPrcntl[164].Z = 5.237 ;  zVsPrcntl[164].prcntl = 0.9998465 ;
   zVsPrcntl[165].Z = 5.238 ;  zVsPrcntl[165].prcntl = 0.9998470 ;
   zVsPrcntl[166].Z = 5.239 ;  zVsPrcntl[166].prcntl = 0.9998475 ;
   zVsPrcntl[167].Z = 5.241 ;  zVsPrcntl[167].prcntl = 0.9998480 ;
   zVsPrcntl[168].Z = 5.241 ;  zVsPrcntl[168].prcntl = 0.9998485 ;
   zVsPrcntl[169].Z = 5.244 ;  zVsPrcntl[169].prcntl = 0.9998490 ;
   zVsPrcntl[170].Z = 5.247 ;  zVsPrcntl[170].prcntl = 0.9998495 ;
   zVsPrcntl[171].Z = 5.250 ;  zVsPrcntl[171].prcntl = 0.9998500 ;
   zVsPrcntl[172].Z = 5.252 ;  zVsPrcntl[172].prcntl = 0.9998505 ;
   zVsPrcntl[173].Z = 5.253 ;  zVsPrcntl[173].prcntl = 0.9998510 ;
   zVsPrcntl[174].Z = 5.254 ;  zVsPrcntl[174].prcntl = 0.9998515 ;
   zVsPrcntl[175].Z = 5.258 ;  zVsPrcntl[175].prcntl = 0.9998520 ;
   zVsPrcntl[176].Z = 5.260 ;  zVsPrcntl[176].prcntl = 0.9998525 ;
   zVsPrcntl[177].Z = 5.261 ;  zVsPrcntl[177].prcntl = 0.9998530 ;
   zVsPrcntl[178].Z = 5.263 ;  zVsPrcntl[178].prcntl = 0.9998535 ;
   zVsPrcntl[179].Z = 5.265 ;  zVsPrcntl[179].prcntl = 0.9998540 ;
   zVsPrcntl[180].Z = 5.265 ;  zVsPrcntl[180].prcntl = 0.9998545 ;
   zVsPrcntl[181].Z = 5.269 ;  zVsPrcntl[181].prcntl = 0.9998550 ;
   zVsPrcntl[182].Z = 5.271 ;  zVsPrcntl[182].prcntl = 0.9998555 ;
   zVsPrcntl[183].Z = 5.275 ;  zVsPrcntl[183].prcntl = 0.9998560 ;
   zVsPrcntl[184].Z = 5.275 ;  zVsPrcntl[184].prcntl = 0.9998565 ;
   zVsPrcntl[185].Z = 5.277 ;  zVsPrcntl[185].prcntl = 0.9998570 ;
   zVsPrcntl[186].Z = 5.280 ;  zVsPrcntl[186].prcntl = 0.9998575 ;
   zVsPrcntl[187].Z = 5.281 ;  zVsPrcntl[187].prcntl = 0.9998580 ;
   zVsPrcntl[188].Z = 5.284 ;  zVsPrcntl[188].prcntl = 0.9998585 ;
   zVsPrcntl[189].Z = 5.286 ;  zVsPrcntl[189].prcntl = 0.9998590 ;
   zVsPrcntl[190].Z = 5.288 ;  zVsPrcntl[190].prcntl = 0.9998595 ;
   zVsPrcntl[191].Z = 5.290 ;  zVsPrcntl[191].prcntl = 0.9998600 ;
   zVsPrcntl[192].Z = 5.293 ;  zVsPrcntl[192].prcntl = 0.9998605 ;
   zVsPrcntl[193].Z = 5.295 ;  zVsPrcntl[193].prcntl = 0.9998610 ;
   zVsPrcntl[194].Z = 5.296 ;  zVsPrcntl[194].prcntl = 0.9998615 ;
   zVsPrcntl[195].Z = 5.298 ;  zVsPrcntl[195].prcntl = 0.9998620 ;
   zVsPrcntl[196].Z = 5.300 ;  zVsPrcntl[196].prcntl = 0.9998625 ;
   zVsPrcntl[197].Z = 5.302 ;  zVsPrcntl[197].prcntl = 0.9998630 ;
   zVsPrcntl[198].Z = 5.305 ;  zVsPrcntl[198].prcntl = 0.9998635 ;
   zVsPrcntl[199].Z = 5.306 ;  zVsPrcntl[199].prcntl = 0.9998640 ;
   zVsPrcntl[200].Z = 5.308 ;  zVsPrcntl[200].prcntl = 0.9998645 ;
   zVsPrcntl[201].Z = 5.309 ;  zVsPrcntl[201].prcntl = 0.9998650 ;
   zVsPrcntl[202].Z = 5.310 ;  zVsPrcntl[202].prcntl = 0.9998655 ;
   zVsPrcntl[203].Z = 5.310 ;  zVsPrcntl[203].prcntl = 0.9998660 ;
   zVsPrcntl[204].Z = 5.313 ;  zVsPrcntl[204].prcntl = 0.9998665 ;
   zVsPrcntl[205].Z = 5.318 ;  zVsPrcntl[205].prcntl = 0.9998670 ;
   zVsPrcntl[206].Z = 5.318 ;  zVsPrcntl[206].prcntl = 0.9998675 ;
   zVsPrcntl[207].Z = 5.322 ;  zVsPrcntl[207].prcntl = 0.9998680 ;
   zVsPrcntl[208].Z = 5.322 ;  zVsPrcntl[208].prcntl = 0.9998685 ;
   zVsPrcntl[209].Z = 5.323 ;  zVsPrcntl[209].prcntl = 0.9998690 ;
   zVsPrcntl[210].Z = 5.324 ;  zVsPrcntl[210].prcntl = 0.9998695 ;
   zVsPrcntl[211].Z = 5.324 ;  zVsPrcntl[211].prcntl = 0.9998700 ;
   zVsPrcntl[212].Z = 5.327 ;  zVsPrcntl[212].prcntl = 0.9998705 ;
   zVsPrcntl[213].Z = 5.329 ;  zVsPrcntl[213].prcntl = 0.9998710 ;
   zVsPrcntl[214].Z = 5.329 ;  zVsPrcntl[214].prcntl = 0.9998715 ;
   zVsPrcntl[215].Z = 5.330 ;  zVsPrcntl[215].prcntl = 0.9998720 ;
   zVsPrcntl[216].Z = 5.331 ;  zVsPrcntl[216].prcntl = 0.9998725 ;
   zVsPrcntl[217].Z = 5.332 ;  zVsPrcntl[217].prcntl = 0.9998730 ;
   zVsPrcntl[218].Z = 5.333 ;  zVsPrcntl[218].prcntl = 0.9998735 ;
   zVsPrcntl[219].Z = 5.336 ;  zVsPrcntl[219].prcntl = 0.9998740 ;
   zVsPrcntl[220].Z = 5.337 ;  zVsPrcntl[220].prcntl = 0.9998745 ;
   zVsPrcntl[221].Z = 5.341 ;  zVsPrcntl[221].prcntl = 0.9998750 ;
   zVsPrcntl[222].Z = 5.343 ;  zVsPrcntl[222].prcntl = 0.9998755 ;
   zVsPrcntl[223].Z = 5.345 ;  zVsPrcntl[223].prcntl = 0.9998760 ;
   zVsPrcntl[224].Z = 5.346 ;  zVsPrcntl[224].prcntl = 0.9998765 ;
   zVsPrcntl[225].Z = 5.348 ;  zVsPrcntl[225].prcntl = 0.9998770 ;
   zVsPrcntl[226].Z = 5.349 ;  zVsPrcntl[226].prcntl = 0.9998775 ;
   zVsPrcntl[227].Z = 5.349 ;  zVsPrcntl[227].prcntl = 0.9998780 ;
   zVsPrcntl[228].Z = 5.351 ;  zVsPrcntl[228].prcntl = 0.9998785 ;
   zVsPrcntl[229].Z = 5.353 ;  zVsPrcntl[229].prcntl = 0.9998790 ;
   zVsPrcntl[230].Z = 5.355 ;  zVsPrcntl[230].prcntl = 0.9998795 ;
   zVsPrcntl[231].Z = 5.356 ;  zVsPrcntl[231].prcntl = 0.9998800 ;
   zVsPrcntl[232].Z = 5.358 ;  zVsPrcntl[232].prcntl = 0.9998805 ;
   zVsPrcntl[233].Z = 5.361 ;  zVsPrcntl[233].prcntl = 0.9998810 ;
   zVsPrcntl[234].Z = 5.362 ;  zVsPrcntl[234].prcntl = 0.9998815 ;
   zVsPrcntl[235].Z = 5.365 ;  zVsPrcntl[235].prcntl = 0.9998820 ;
   zVsPrcntl[236].Z = 5.367 ;  zVsPrcntl[236].prcntl = 0.9998825 ;
   zVsPrcntl[237].Z = 5.368 ;  zVsPrcntl[237].prcntl = 0.9998830 ;
   zVsPrcntl[238].Z = 5.368 ;  zVsPrcntl[238].prcntl = 0.9998835 ;
   zVsPrcntl[239].Z = 5.370 ;  zVsPrcntl[239].prcntl = 0.9998840 ;
   zVsPrcntl[240].Z = 5.371 ;  zVsPrcntl[240].prcntl = 0.9998845 ;
   zVsPrcntl[241].Z = 5.372 ;  zVsPrcntl[241].prcntl = 0.9998850 ;
   zVsPrcntl[242].Z = 5.376 ;  zVsPrcntl[242].prcntl = 0.9998855 ;
   zVsPrcntl[243].Z = 5.378 ;  zVsPrcntl[243].prcntl = 0.9998860 ;
   zVsPrcntl[244].Z = 5.381 ;  zVsPrcntl[244].prcntl = 0.9998865 ;
   zVsPrcntl[245].Z = 5.383 ;  zVsPrcntl[245].prcntl = 0.9998870 ;
   zVsPrcntl[246].Z = 5.385 ;  zVsPrcntl[246].prcntl = 0.9998875 ;
   zVsPrcntl[247].Z = 5.388 ;  zVsPrcntl[247].prcntl = 0.9998880 ;
   zVsPrcntl[248].Z = 5.389 ;  zVsPrcntl[248].prcntl = 0.9998885 ;
   zVsPrcntl[249].Z = 5.391 ;  zVsPrcntl[249].prcntl = 0.9998890 ;
   zVsPrcntl[250].Z = 5.394 ;  zVsPrcntl[250].prcntl = 0.9998895 ;
   zVsPrcntl[251].Z = 5.397 ;  zVsPrcntl[251].prcntl = 0.9998900 ;
   zVsPrcntl[252].Z = 5.397 ;  zVsPrcntl[252].prcntl = 0.9998905 ;
   zVsPrcntl[253].Z = 5.404 ;  zVsPrcntl[253].prcntl = 0.9998910 ;
   zVsPrcntl[254].Z = 5.407 ;  zVsPrcntl[254].prcntl = 0.9998915 ;
   zVsPrcntl[255].Z = 5.410 ;  zVsPrcntl[255].prcntl = 0.9998920 ;
   zVsPrcntl[256].Z = 5.413 ;  zVsPrcntl[256].prcntl = 0.9998925 ;
   zVsPrcntl[257].Z = 5.415 ;  zVsPrcntl[257].prcntl = 0.9998930 ;
   zVsPrcntl[258].Z = 5.416 ;  zVsPrcntl[258].prcntl = 0.9998935 ;
   zVsPrcntl[259].Z = 5.421 ;  zVsPrcntl[259].prcntl = 0.9998940 ;
   zVsPrcntl[260].Z = 5.424 ;  zVsPrcntl[260].prcntl = 0.9998945 ;
   zVsPrcntl[261].Z = 5.432 ;  zVsPrcntl[261].prcntl = 0.9998950 ;
   zVsPrcntl[262].Z = 5.436 ;  zVsPrcntl[262].prcntl = 0.9998955 ;
   zVsPrcntl[263].Z = 5.444 ;  zVsPrcntl[263].prcntl = 0.9998960 ;
   zVsPrcntl[264].Z = 5.445 ;  zVsPrcntl[264].prcntl = 0.9998965 ;
   zVsPrcntl[265].Z = 5.448 ;  zVsPrcntl[265].prcntl = 0.9998970 ;
   zVsPrcntl[266].Z = 5.449 ;  zVsPrcntl[266].prcntl = 0.9998975 ;
   zVsPrcntl[267].Z = 5.452 ;  zVsPrcntl[267].prcntl = 0.9998980 ;
   zVsPrcntl[268].Z = 5.453 ;  zVsPrcntl[268].prcntl = 0.9998985 ;
   zVsPrcntl[269].Z = 5.457 ;  zVsPrcntl[269].prcntl = 0.9998990 ;
   zVsPrcntl[270].Z = 5.460 ;  zVsPrcntl[270].prcntl = 0.9998995 ;
   zVsPrcntl[271].Z = 5.460 ;  zVsPrcntl[271].prcntl = 0.9999000 ;
   zVsPrcntl[272].Z = 5.464 ;  zVsPrcntl[272].prcntl = 0.9999005 ;
   zVsPrcntl[273].Z = 5.469 ;  zVsPrcntl[273].prcntl = 0.9999010 ;
   zVsPrcntl[274].Z = 5.473 ;  zVsPrcntl[274].prcntl = 0.9999015 ;
   zVsPrcntl[275].Z = 5.475 ;  zVsPrcntl[275].prcntl = 0.9999020 ;
   zVsPrcntl[276].Z = 5.477 ;  zVsPrcntl[276].prcntl = 0.9999025 ;
   zVsPrcntl[277].Z = 5.478 ;  zVsPrcntl[277].prcntl = 0.9999030 ;
   zVsPrcntl[278].Z = 5.483 ;  zVsPrcntl[278].prcntl = 0.9999035 ;
   zVsPrcntl[279].Z = 5.484 ;  zVsPrcntl[279].prcntl = 0.9999040 ;
   zVsPrcntl[280].Z = 5.487 ;  zVsPrcntl[280].prcntl = 0.9999045 ;
   zVsPrcntl[281].Z = 5.488 ;  zVsPrcntl[281].prcntl = 0.9999050 ;
   zVsPrcntl[282].Z = 5.489 ;  zVsPrcntl[282].prcntl = 0.9999055 ;
   zVsPrcntl[283].Z = 5.492 ;  zVsPrcntl[283].prcntl = 0.9999060 ;
   zVsPrcntl[284].Z = 5.501 ;  zVsPrcntl[284].prcntl = 0.9999065 ;
   zVsPrcntl[285].Z = 5.502 ;  zVsPrcntl[285].prcntl = 0.9999070 ;
   zVsPrcntl[286].Z = 5.509 ;  zVsPrcntl[286].prcntl = 0.9999075 ;
   zVsPrcntl[287].Z = 5.513 ;  zVsPrcntl[287].prcntl = 0.9999080 ;
   zVsPrcntl[288].Z = 5.514 ;  zVsPrcntl[288].prcntl = 0.9999085 ;
   zVsPrcntl[289].Z = 5.515 ;  zVsPrcntl[289].prcntl = 0.9999090 ;
   zVsPrcntl[290].Z = 5.520 ;  zVsPrcntl[290].prcntl = 0.9999095 ;
   zVsPrcntl[291].Z = 5.525 ;  zVsPrcntl[291].prcntl = 0.9999100 ;
   zVsPrcntl[292].Z = 5.526 ;  zVsPrcntl[292].prcntl = 0.9999105 ;
   zVsPrcntl[293].Z = 5.530 ;  zVsPrcntl[293].prcntl = 0.9999110 ;
   zVsPrcntl[294].Z = 5.533 ;  zVsPrcntl[294].prcntl = 0.9999115 ;
   zVsPrcntl[295].Z = 5.537 ;  zVsPrcntl[295].prcntl = 0.9999120 ;
   zVsPrcntl[296].Z = 5.538 ;  zVsPrcntl[296].prcntl = 0.9999125 ;
   zVsPrcntl[297].Z = 5.540 ;  zVsPrcntl[297].prcntl = 0.9999130 ;
   zVsPrcntl[298].Z = 5.545 ;  zVsPrcntl[298].prcntl = 0.9999135 ;
   zVsPrcntl[299].Z = 5.550 ;  zVsPrcntl[299].prcntl = 0.9999140 ;
   zVsPrcntl[300].Z = 5.551 ;  zVsPrcntl[300].prcntl = 0.9999145 ;
   zVsPrcntl[301].Z = 5.557 ;  zVsPrcntl[301].prcntl = 0.9999150 ;
   zVsPrcntl[302].Z = 5.557 ;  zVsPrcntl[302].prcntl = 0.9999155 ;
   zVsPrcntl[303].Z = 5.557 ;  zVsPrcntl[303].prcntl = 0.9999160 ;
   zVsPrcntl[304].Z = 5.561 ;  zVsPrcntl[304].prcntl = 0.9999165 ;
   zVsPrcntl[305].Z = 5.564 ;  zVsPrcntl[305].prcntl = 0.9999170 ;
   zVsPrcntl[306].Z = 5.567 ;  zVsPrcntl[306].prcntl = 0.9999175 ;
   zVsPrcntl[307].Z = 5.569 ;  zVsPrcntl[307].prcntl = 0.9999180 ;
   zVsPrcntl[308].Z = 5.571 ;  zVsPrcntl[308].prcntl = 0.9999185 ;
   zVsPrcntl[309].Z = 5.574 ;  zVsPrcntl[309].prcntl = 0.9999190 ;
   zVsPrcntl[310].Z = 5.580 ;  zVsPrcntl[310].prcntl = 0.9999195 ;
   zVsPrcntl[311].Z = 5.582 ;  zVsPrcntl[311].prcntl = 0.9999200 ;
   zVsPrcntl[312].Z = 5.585 ;  zVsPrcntl[312].prcntl = 0.9999205 ;
   zVsPrcntl[313].Z = 5.586 ;  zVsPrcntl[313].prcntl = 0.9999210 ;
   zVsPrcntl[314].Z = 5.588 ;  zVsPrcntl[314].prcntl = 0.9999215 ;
   zVsPrcntl[315].Z = 5.591 ;  zVsPrcntl[315].prcntl = 0.9999220 ;
   zVsPrcntl[316].Z = 5.596 ;  zVsPrcntl[316].prcntl = 0.9999225 ;
   zVsPrcntl[317].Z = 5.599 ;  zVsPrcntl[317].prcntl = 0.9999230 ;
   zVsPrcntl[318].Z = 5.601 ;  zVsPrcntl[318].prcntl = 0.9999235 ;
   zVsPrcntl[319].Z = 5.609 ;  zVsPrcntl[319].prcntl = 0.9999240 ;
   zVsPrcntl[320].Z = 5.613 ;  zVsPrcntl[320].prcntl = 0.9999245 ;
   zVsPrcntl[321].Z = 5.615 ;  zVsPrcntl[321].prcntl = 0.9999250 ;
   zVsPrcntl[322].Z = 5.619 ;  zVsPrcntl[322].prcntl = 0.9999255 ;
   zVsPrcntl[323].Z = 5.623 ;  zVsPrcntl[323].prcntl = 0.9999260 ;
   zVsPrcntl[324].Z = 5.625 ;  zVsPrcntl[324].prcntl = 0.9999265 ;
   zVsPrcntl[325].Z = 5.626 ;  zVsPrcntl[325].prcntl = 0.9999270 ;
   zVsPrcntl[326].Z = 5.632 ;  zVsPrcntl[326].prcntl = 0.9999275 ;
   zVsPrcntl[327].Z = 5.635 ;  zVsPrcntl[327].prcntl = 0.9999280 ;
   zVsPrcntl[328].Z = 5.638 ;  zVsPrcntl[328].prcntl = 0.9999285 ;
   zVsPrcntl[329].Z = 5.647 ;  zVsPrcntl[329].prcntl = 0.9999290 ;
   zVsPrcntl[330].Z = 5.649 ;  zVsPrcntl[330].prcntl = 0.9999295 ;
   zVsPrcntl[331].Z = 5.651 ;  zVsPrcntl[331].prcntl = 0.9999300 ;
   zVsPrcntl[332].Z = 5.659 ;  zVsPrcntl[332].prcntl = 0.9999305 ;
   zVsPrcntl[333].Z = 5.662 ;  zVsPrcntl[333].prcntl = 0.9999310 ;
   zVsPrcntl[334].Z = 5.664 ;  zVsPrcntl[334].prcntl = 0.9999315 ;
   zVsPrcntl[335].Z = 5.666 ;  zVsPrcntl[335].prcntl = 0.9999320 ;
   zVsPrcntl[336].Z = 5.669 ;  zVsPrcntl[336].prcntl = 0.9999325 ;
   zVsPrcntl[337].Z = 5.674 ;  zVsPrcntl[337].prcntl = 0.9999330 ;
   zVsPrcntl[338].Z = 5.675 ;  zVsPrcntl[338].prcntl = 0.9999335 ;
   zVsPrcntl[339].Z = 5.681 ;  zVsPrcntl[339].prcntl = 0.9999340 ;
   zVsPrcntl[340].Z = 5.684 ;  zVsPrcntl[340].prcntl = 0.9999345 ;
   zVsPrcntl[341].Z = 5.685 ;  zVsPrcntl[341].prcntl = 0.9999350 ;
   zVsPrcntl[342].Z = 5.690 ;  zVsPrcntl[342].prcntl = 0.9999355 ;
   zVsPrcntl[343].Z = 5.694 ;  zVsPrcntl[343].prcntl = 0.9999360 ;
   zVsPrcntl[344].Z = 5.698 ;  zVsPrcntl[344].prcntl = 0.9999365 ;
   zVsPrcntl[345].Z = 5.699 ;  zVsPrcntl[345].prcntl = 0.9999370 ;
   zVsPrcntl[346].Z = 5.708 ;  zVsPrcntl[346].prcntl = 0.9999375 ;
   zVsPrcntl[347].Z = 5.712 ;  zVsPrcntl[347].prcntl = 0.9999380 ;
   zVsPrcntl[348].Z = 5.718 ;  zVsPrcntl[348].prcntl = 0.9999385 ;
   zVsPrcntl[349].Z = 5.723 ;  zVsPrcntl[349].prcntl = 0.9999390 ;
   zVsPrcntl[350].Z = 5.725 ;  zVsPrcntl[350].prcntl = 0.9999395 ;
   zVsPrcntl[351].Z = 5.730 ;  zVsPrcntl[351].prcntl = 0.9999400 ;
   zVsPrcntl[352].Z = 5.735 ;  zVsPrcntl[352].prcntl = 0.9999405 ;
   zVsPrcntl[353].Z = 5.735 ;  zVsPrcntl[353].prcntl = 0.9999410 ;
   zVsPrcntl[354].Z = 5.740 ;  zVsPrcntl[354].prcntl = 0.9999415 ;
   zVsPrcntl[355].Z = 5.741 ;  zVsPrcntl[355].prcntl = 0.9999420 ;
   zVsPrcntl[356].Z = 5.746 ;  zVsPrcntl[356].prcntl = 0.9999425 ;
   zVsPrcntl[357].Z = 5.750 ;  zVsPrcntl[357].prcntl = 0.9999430 ;
   zVsPrcntl[358].Z = 5.752 ;  zVsPrcntl[358].prcntl = 0.9999435 ;
   zVsPrcntl[359].Z = 5.758 ;  zVsPrcntl[359].prcntl = 0.9999440 ;
   zVsPrcntl[360].Z = 5.762 ;  zVsPrcntl[360].prcntl = 0.9999445 ;
   zVsPrcntl[361].Z = 5.768 ;  zVsPrcntl[361].prcntl = 0.9999450 ;
   zVsPrcntl[362].Z = 5.771 ;  zVsPrcntl[362].prcntl = 0.9999455 ;
   zVsPrcntl[363].Z = 5.771 ;  zVsPrcntl[363].prcntl = 0.9999460 ;
   zVsPrcntl[364].Z = 5.777 ;  zVsPrcntl[364].prcntl = 0.9999465 ;
   zVsPrcntl[365].Z = 5.782 ;  zVsPrcntl[365].prcntl = 0.9999470 ;
   zVsPrcntl[366].Z = 5.784 ;  zVsPrcntl[366].prcntl = 0.9999475 ;
   zVsPrcntl[367].Z = 5.793 ;  zVsPrcntl[367].prcntl = 0.9999480 ;
   zVsPrcntl[368].Z = 5.795 ;  zVsPrcntl[368].prcntl = 0.9999485 ;
   zVsPrcntl[369].Z = 5.796 ;  zVsPrcntl[369].prcntl = 0.9999490 ;
   zVsPrcntl[370].Z = 5.799 ;  zVsPrcntl[370].prcntl = 0.9999495 ;
   zVsPrcntl[371].Z = 5.801 ;  zVsPrcntl[371].prcntl = 0.9999500 ;
   zVsPrcntl[372].Z = 5.806 ;  zVsPrcntl[372].prcntl = 0.9999505 ;
   zVsPrcntl[373].Z = 5.810 ;  zVsPrcntl[373].prcntl = 0.9999510 ;
   zVsPrcntl[374].Z = 5.813 ;  zVsPrcntl[374].prcntl = 0.9999515 ;
   zVsPrcntl[375].Z = 5.822 ;  zVsPrcntl[375].prcntl = 0.9999520 ;
   zVsPrcntl[376].Z = 5.824 ;  zVsPrcntl[376].prcntl = 0.9999525 ;
   zVsPrcntl[377].Z = 5.828 ;  zVsPrcntl[377].prcntl = 0.9999530 ;
   zVsPrcntl[378].Z = 5.838 ;  zVsPrcntl[378].prcntl = 0.9999535 ;
   zVsPrcntl[379].Z = 5.844 ;  zVsPrcntl[379].prcntl = 0.9999540 ;
   zVsPrcntl[380].Z = 5.845 ;  zVsPrcntl[380].prcntl = 0.9999545 ;
   zVsPrcntl[381].Z = 5.853 ;  zVsPrcntl[381].prcntl = 0.9999550 ;
   zVsPrcntl[382].Z = 5.857 ;  zVsPrcntl[382].prcntl = 0.9999555 ;
   zVsPrcntl[383].Z = 5.862 ;  zVsPrcntl[383].prcntl = 0.9999560 ;
   zVsPrcntl[384].Z = 5.871 ;  zVsPrcntl[384].prcntl = 0.9999565 ;
   zVsPrcntl[385].Z = 5.877 ;  zVsPrcntl[385].prcntl = 0.9999570 ;
   zVsPrcntl[386].Z = 5.882 ;  zVsPrcntl[386].prcntl = 0.9999575 ;
   zVsPrcntl[387].Z = 5.884 ;  zVsPrcntl[387].prcntl = 0.9999580 ;
   zVsPrcntl[388].Z = 5.893 ;  zVsPrcntl[388].prcntl = 0.9999585 ;
   zVsPrcntl[389].Z = 5.901 ;  zVsPrcntl[389].prcntl = 0.9999590 ;
   zVsPrcntl[390].Z = 5.905 ;  zVsPrcntl[390].prcntl = 0.9999595 ;
   zVsPrcntl[391].Z = 5.913 ;  zVsPrcntl[391].prcntl = 0.9999600 ;
   zVsPrcntl[392].Z = 5.917 ;  zVsPrcntl[392].prcntl = 0.9999605 ;
   zVsPrcntl[393].Z = 5.933 ;  zVsPrcntl[393].prcntl = 0.9999610 ;
   zVsPrcntl[394].Z = 5.942 ;  zVsPrcntl[394].prcntl = 0.9999615 ;
   zVsPrcntl[395].Z = 5.948 ;  zVsPrcntl[395].prcntl = 0.9999620 ;
   zVsPrcntl[396].Z = 5.955 ;  zVsPrcntl[396].prcntl = 0.9999625 ;
   zVsPrcntl[397].Z = 5.962 ;  zVsPrcntl[397].prcntl = 0.9999630 ;
   zVsPrcntl[398].Z = 5.974 ;  zVsPrcntl[398].prcntl = 0.9999635 ;
   zVsPrcntl[399].Z = 5.983 ;  zVsPrcntl[399].prcntl = 0.9999640 ;
   zVsPrcntl[400].Z = 5.990 ;  zVsPrcntl[400].prcntl = 0.9999645 ;
   zVsPrcntl[401].Z = 5.996 ;  zVsPrcntl[401].prcntl = 0.9999650 ;
   zVsPrcntl[402].Z = 6.003 ;  zVsPrcntl[402].prcntl = 0.9999655 ;
   zVsPrcntl[403].Z = 6.007 ;  zVsPrcntl[403].prcntl = 0.9999660 ;
   zVsPrcntl[404].Z = 6.014 ;  zVsPrcntl[404].prcntl = 0.9999665 ;
   zVsPrcntl[405].Z = 6.019 ;  zVsPrcntl[405].prcntl = 0.9999670 ;
   zVsPrcntl[406].Z = 6.026 ;  zVsPrcntl[406].prcntl = 0.9999675 ;
   zVsPrcntl[407].Z = 6.034 ;  zVsPrcntl[407].prcntl = 0.9999680 ;
   zVsPrcntl[408].Z = 6.048 ;  zVsPrcntl[408].prcntl = 0.9999685 ;
   zVsPrcntl[409].Z = 6.059 ;  zVsPrcntl[409].prcntl = 0.9999690 ;
   zVsPrcntl[410].Z = 6.069 ;  zVsPrcntl[410].prcntl = 0.9999695 ;
   zVsPrcntl[411].Z = 6.081 ;  zVsPrcntl[411].prcntl = 0.9999700 ;
   zVsPrcntl[412].Z = 6.096 ;  zVsPrcntl[412].prcntl = 0.9999705 ;
   zVsPrcntl[413].Z = 6.104 ;  zVsPrcntl[413].prcntl = 0.9999710 ;
   zVsPrcntl[414].Z = 6.115 ;  zVsPrcntl[414].prcntl = 0.9999715 ;
   zVsPrcntl[415].Z = 6.129 ;  zVsPrcntl[415].prcntl = 0.9999720 ;
   zVsPrcntl[416].Z = 6.139 ;  zVsPrcntl[416].prcntl = 0.9999725 ;
   zVsPrcntl[417].Z = 6.139 ;  zVsPrcntl[417].prcntl = 0.9999730 ;
   zVsPrcntl[418].Z = 6.158 ;  zVsPrcntl[418].prcntl = 0.9999735 ;
   zVsPrcntl[419].Z = 6.180 ;  zVsPrcntl[419].prcntl = 0.9999740 ;
   zVsPrcntl[420].Z = 6.187 ;  zVsPrcntl[420].prcntl = 0.9999745 ;
   zVsPrcntl[421].Z = 6.188 ;  zVsPrcntl[421].prcntl = 0.9999750 ;
   zVsPrcntl[422].Z = 6.194 ;  zVsPrcntl[422].prcntl = 0.9999755 ;
   zVsPrcntl[423].Z = 6.197 ;  zVsPrcntl[423].prcntl = 0.9999760 ;
   zVsPrcntl[424].Z = 6.206 ;  zVsPrcntl[424].prcntl = 0.9999765 ;
   zVsPrcntl[425].Z = 6.221 ;  zVsPrcntl[425].prcntl = 0.9999770 ;
   zVsPrcntl[426].Z = 6.235 ;  zVsPrcntl[426].prcntl = 0.9999775 ;
   zVsPrcntl[427].Z = 6.240 ;  zVsPrcntl[427].prcntl = 0.9999780 ;
   zVsPrcntl[428].Z = 6.251 ;  zVsPrcntl[428].prcntl = 0.9999785 ;
   zVsPrcntl[429].Z = 6.271 ;  zVsPrcntl[429].prcntl = 0.9999790 ;
   zVsPrcntl[430].Z = 6.276 ;  zVsPrcntl[430].prcntl = 0.9999795 ;
   zVsPrcntl[431].Z = 6.285 ;  zVsPrcntl[431].prcntl = 0.9999800 ;
   zVsPrcntl[432].Z = 6.297 ;  zVsPrcntl[432].prcntl = 0.9999805 ;
   zVsPrcntl[433].Z = 6.303 ;  zVsPrcntl[433].prcntl = 0.9999810 ;
   zVsPrcntl[434].Z = 6.310 ;  zVsPrcntl[434].prcntl = 0.9999815 ;
   zVsPrcntl[435].Z = 6.331 ;  zVsPrcntl[435].prcntl = 0.9999820 ;
   zVsPrcntl[436].Z = 6.342 ;  zVsPrcntl[436].prcntl = 0.9999825 ;
   zVsPrcntl[437].Z = 6.345 ;  zVsPrcntl[437].prcntl = 0.9999830 ;
   zVsPrcntl[438].Z = 6.362 ;  zVsPrcntl[438].prcntl = 0.9999835 ;
   zVsPrcntl[439].Z = 6.365 ;  zVsPrcntl[439].prcntl = 0.9999840 ;
   zVsPrcntl[440].Z = 6.395 ;  zVsPrcntl[440].prcntl = 0.9999845 ;
   zVsPrcntl[441].Z = 6.406 ;  zVsPrcntl[441].prcntl = 0.9999850 ;
   zVsPrcntl[442].Z = 6.424 ;  zVsPrcntl[442].prcntl = 0.9999855 ;
   zVsPrcntl[443].Z = 6.434 ;  zVsPrcntl[443].prcntl = 0.9999860 ;
   zVsPrcntl[444].Z = 6.453 ;  zVsPrcntl[444].prcntl = 0.9999865 ;
   zVsPrcntl[445].Z = 6.467 ;  zVsPrcntl[445].prcntl = 0.9999870 ;
   zVsPrcntl[446].Z = 6.473 ;  zVsPrcntl[446].prcntl = 0.9999875 ;
   zVsPrcntl[447].Z = 6.476 ;  zVsPrcntl[447].prcntl = 0.9999880 ;
   zVsPrcntl[448].Z = 6.525 ;  zVsPrcntl[448].prcntl = 0.9999885 ;
   zVsPrcntl[449].Z = 6.526 ;  zVsPrcntl[449].prcntl = 0.9999890 ;
   zVsPrcntl[450].Z = 6.575 ;  zVsPrcntl[450].prcntl = 0.9999895 ;
   zVsPrcntl[451].Z = 6.594 ;  zVsPrcntl[451].prcntl = 0.9999900 ;
   zVsPrcntl[452].Z = 6.600 ;  zVsPrcntl[452].prcntl = 0.9999905 ;
   zVsPrcntl[453].Z = 6.606 ;  zVsPrcntl[453].prcntl = 0.9999910 ;
   zVsPrcntl[454].Z = 6.635 ;  zVsPrcntl[454].prcntl = 0.9999915 ;
   zVsPrcntl[455].Z = 6.655 ;  zVsPrcntl[455].prcntl = 0.9999920 ;
   zVsPrcntl[456].Z = 6.676 ;  zVsPrcntl[456].prcntl = 0.9999925 ;
   zVsPrcntl[457].Z = 6.703 ;  zVsPrcntl[457].prcntl = 0.9999930 ;
   zVsPrcntl[458].Z = 6.741 ;  zVsPrcntl[458].prcntl = 0.9999935 ;
   zVsPrcntl[459].Z = 6.767 ;  zVsPrcntl[459].prcntl = 0.9999940 ;
   zVsPrcntl[460].Z = 6.801 ;  zVsPrcntl[460].prcntl = 0.9999945 ;
   zVsPrcntl[461].Z = 6.834 ;  zVsPrcntl[461].prcntl = 0.9999950 ;
   zVsPrcntl[462].Z = 6.891 ;  zVsPrcntl[462].prcntl = 0.9999955 ;
   zVsPrcntl[463].Z = 6.963 ;  zVsPrcntl[463].prcntl = 0.9999960 ;
   zVsPrcntl[464].Z = 7.064 ;  zVsPrcntl[464].prcntl = 0.9999965 ;
   zVsPrcntl[465].Z = 7.121 ;  zVsPrcntl[465].prcntl = 0.9999970 ;
   zVsPrcntl[466].Z = 7.151 ;  zVsPrcntl[466].prcntl = 0.9999975 ;
   zVsPrcntl[467].Z = 7.238 ;  zVsPrcntl[467].prcntl = 0.9999980 ;
   zVsPrcntl[468].Z = 7.252 ;  zVsPrcntl[468].prcntl = 0.9999985 ;
   zVsPrcntl[469].Z = 7.442 ;  zVsPrcntl[469].prcntl = 0.9999990 ;
   zVsPrcntl[470].Z = 7.837 ;  zVsPrcntl[470].prcntl = 0.9999995 ;

   return ;
}

Block *read_a_prodom_entry(db)

FILE   *db ;

{
   Block    *block ;
   char     line[MAXLINELEN], word[MAXLINELEN], entry_name[MAXLINELEN] ;
   char     *ptr, *iptr ;
   int      i1, i2, num_seqs, rc, max_pos, min_pos, temp ;
   Sequence *sequence_pointer ;
   Residue  *residue_pointer ;


                 /* read until a prodom entry first line - begins with a ">" */
   while((fgets(line, MAXLINELEN, db)) != NULL && line[0] != '>') ;

   if (line[0] != '>') return(NULL) ;

                                                /* allocate space for block */
     CheckMem(block = (Block *) malloc(sizeof(Block))) ;

/* process first line - the description line */

   line[0] = ' ' ;                                        /* get rid of '>' */
                                          /* get first word - sequence name */
   if ((ptr = get_token(line)) == NULL) 
      {
      printf("Error ! Problem in format of ProDom entry description -line\n") ;
      return(NULL) ;
      }

                            /* create accession prefix - "PD" + preceding 0s,
                                entry presumed not to be longer then 5 chars */
   word[0] = 'P' ;   word[1] = 'D' ; 
   i2 = 2 ;
   for(i1=0; i1<(5 - (int) strlen(ptr)); i1++) word[i2++] = '0' ;
   word[i2] = '\0' ;

   strcpy(entry_name, ptr) ;
                                       /* save first word in block accession */
   sprintf(block->ac, "%s%s;", word, entry_name) ;
   sprintf(block->number, "%s%s", word, entry_name) ;

                                              /* save first word in block ID */
   sprintf(block->id, "%s; ProDom_mul", entry_name) ;

                 /* get second word - number of sequences between parethesis */
   if ((ptr = get_token(NULL)) == NULL) 
      {
      printf("Error ! Problem in format of ProDom entry description-line\n") ;
      return(NULL) ;
      }

                                                        /* strip parenthesis */
   if (ptr[0] != '(')
      {
      printf("Error ! Problem in ProDom entry %s\n", entry_name) ;
      printf("second word in description line doesn't begin with a (\n") ;
      return(NULL) ;
      }
   else
      ptr[0] = '0' ;

   if (ptr[strlen(ptr)-1] != ')')
      {
      printf("Error ! Problem in ProDom entry %s\n", entry_name) ;
      printf("second word in description line doesn't end with a )\n") ;
      return(NULL) ;
      }
   else
      ptr[strlen(ptr)-1] = ' ' ;

               /* check that second word is composed of digits and copy it */
   for(iptr=ptr; *iptr != ' ' && isdigit(*iptr); iptr++) ;
   if (*iptr != ' ')
      {
      printf("Error ! Problem in format of ProDom entry %s\n", entry_name) ;
      printf("A non-digit in the number-of-sequences field \"%s\"\n", ptr) ;
      return(NULL) ;
      }

   block->num_sequences = atoi(ptr) ;

   if (block->num_sequences <= 1) 
      {
      printf(
       "Error ! Number of sequences in ProDom entry %s (%d) is less than 2\n",
       entry_name, block->num_sequences) ;
      return(NULL) ;
      }
   else 
      block->max_sequences = block->num_sequences ;

                                                        /* get rest of line */
   for(iptr=ptr; *iptr != '\0'; iptr++) ;       /* find end of current word */

                            /* get rid of leading and trailing white spaces */
   ptr = eat_whitespace(iptr+1) ;
   remove_trailing_whitespace(ptr) ;

                                   /* save string in block description line */
   strncpy(block->de, ptr, SMALL_BUFF_LENGTH) ;
                           /* in case word is longer than SMALL_BUFF_LENGTH 
                                      and thus the last char copied isnt \0 */ 
   block->de[SMALL_BUFF_LENGTH-1] = '\0' ;

   block->num_clusters = block->max_clusters = 1 ; 
   block->motif[0] = '\0';
   block->percentile = 0 ;
   block->strength = 0 ;

                                         /* allocate space for the clusters */
   CheckMem(block->clusters = (Cluster *) 
                             calloc(block->max_clusters, sizeof(Cluster))) ;

/* process next lines - the sequence lines */
  
          /* read all lines until a line starting with a space, EOL or '>' */
/* Note that if a line begining with '>' was read (the description line of 
   the next entry) it won't be read in fetching the next entry and that 
   entry will be lost */

   
   for(num_seqs=0;
       (fgets(line, MAXLINELEN, db)) != NULL && 
       line[0] != '\n' && line[0] != ' '  && line[0] != '>' ;
       num_seqs++)
      {
                                          /* get first word - sequence name */
      if ((ptr = get_token(line)) == NULL) 
         {
         printf(
            "Error ! Problem in format of ProDom entry %s sequence-line %d\n",
                entry_name, num_seqs+1) ;
         return(NULL) ;
         }

           /* temporarily store sequence name, if this is first sequence 
              the sequences length isn't known and no memory allocated yet, 
              place it in block sequence structure after memory is allocated */
      strcpy(word, ptr) ;

                               /* get second word - sequence start position */
      if ((ptr = get_token(NULL)) == NULL) 
         {
         printf(
            "Error ! Problem in format of ProDom entry %s sequence-line %d\n",
                entry_name, num_seqs+1) ;
         return(NULL) ;
         }

           /* temporarily store start position, if this is first sequence 
              the sequences length isn't known and no memory allocated yet, 
              place it in block sequence structure after memory is allocated */

      for(iptr=ptr; *iptr != '\0' && isdigit(*iptr); iptr++) ;
      if (*iptr != '\0')
         {
         printf(
            "Error ! Problem in format of ProDom entry %s sequence-line %d\n",
                entry_name, num_seqs+1) ;
         printf("A non-digit in the sequence start position %s\n", ptr) ;
         return(NULL) ;
         }

      temp = atoi(ptr) ;

                    /* get 3rd word - sequence end position (no use for it) */
      if ((ptr = get_token(NULL)) == NULL) 
         {
         printf(
            "Error ! Problem in format of ProDom entry %s sequence-line %d\n",
                entry_name, num_seqs+1) ;
         return(NULL) ;
         }

                                              /* get 4th word - the sequence */
      if ((ptr = get_token(NULL)) == NULL) 
         {
         printf(
            "Error ! Problem in format of ProDom entry %s sequence-line %d\n",
                entry_name, num_seqs+1) ;
         return(NULL) ;
         }


           /* should have arrived at the begining of 4th word - the sequence */
                /* find out from the first sequence the sequence length 
                   and use it to allocate memory for the sequence structures */
      if (num_seqs == 0)
	 {
         block->width = strlen(ptr) ;

                          /* following part adapted from 
                             blimps procedure read_block_body by Bill Alford */

         /* allocate space for all the Sequences of the block sequence array */
         CheckMem(
             sequence_pointer = 
                  (Sequence *) 
		  calloc(block->max_sequences,sizeof(Sequence))) ;

	                             /* initialize the block sequences array */
	 block->sequences = sequence_pointer ;

	                                  /* allocate space for all residues */
	 CheckMem(
             residue_pointer = 
                 (Residue *) 
                 calloc(block->width * block->max_sequences, 
			sizeof(Residue))) ;

	                                /* initialize the residues 2-d array */
	 CheckMem(
             block->residues = 
                 (Residue **) calloc(block->max_sequences, sizeof(Residue *))) ;

	                                /* initialize sequences and residues */
         for(i1=0; i1max_sequences; i1++) 
            {
	    sequence_pointer[i1].length = block->width;
	    sequence_pointer[i1].sequence =
 		              &(residue_pointer[i1 * block->width]) ;
	    block->residues[i1] = 
                              &(residue_pointer[i1 * block->width]) ;
	    }
         }

                         /* memory now allocated to block sequence structure 
                                              copy name, position and length */
      strncpy(block->sequences[num_seqs].name, word, SMALL_BUFF_LENGTH) ;
                           /* in case word is longer than SMALL_BUFF_LENGTH 
                                      and thus the last char copied isnt \0 */ 
      block->sequences[num_seqs].name[SMALL_BUFF_LENGTH-1] = '\0' ; 

      block->sequences[num_seqs].position = temp ;

      block->sequences[num_seqs].length = block->width ;

/* process next word - the sequence, check length, change gap symbol "." to "-" */

      if (strlen(ptr) != block->width)
	 {
         printf(
            "Error ! Problem in format of ProDom entry sequence-line %d\n",
                num_seqs+1) ;
         printf("Sequence %s has length of %d instead of expected %d\n",
                block->sequences[num_seqs].name, strlen(ptr), 
	        block->width) ;
         return(NULL) ;
         }

      for(iptr=ptr; *iptr != '\0'; iptr++) if (*iptr == '.') *iptr = '-' ;

    /* next part adopted from blimps  procedure next_cluster by Bill Alford */
                     /* read the sequence from the string into the Sequence */

       rc = read_sequence(&(block->sequences[num_seqs]), AA_SEQ, 0, ptr) ; 
				   /* the Sequence, sequence type, starting */
   				   /* position, string with the sequence    */

                                      /* check to see if there was an error */    
       if (rc < 0) 
          {
                      /* Error, more residues in the sequence than expected */
          printf("Error reading sequence %s in block %s,", 
                 block->sequences[num_seqs].name, block->number) ;
          printf("%d more residues in the sequence than the expected %d.\n",
	         -rc, block->sequences[num_seqs].length) ;
          }
       else if (rc < block->sequences[num_seqs].length) 
          {
        /* Error, not enough residues for the sequence, filling with blanks */
          printf("Error reading sequence %s in block %s,", 
                 block->sequences[num_seqs].name, block->number) ;
          printf("not enough residues to fill the sequence.");
          printf("Filling the rest of the sequence with blanks.\n");

                                                     /* filling with blanks */
    	  for(i1=rc; i1sequences[num_seqs].length; i1++) 
	     block->sequences[num_seqs].sequence[i1] = aa_atob['-'];
          }
       else if (rc > block->sequences[num_seqs].length) 
          {
              /* BIG Error, an undocumented return value from read_sequence */
          printf(
              "read_a_prodom_entry(): Error reading sequence %s in block %s,",
 	         block->sequences[num_seqs].name,
                 block->number) ;
          printf("Undocumented return value, %d, from read_sequence().\n",
                 rc) ;
          } /* else, ret_value == seq.length, OK */

                 /* sequences have no weights give all equal weights of 100 */
       block->sequences[num_seqs].weight =  100.0 ;

          /* assign the sequences to the cluster (space has been allocated) */

       block->clusters[0].num_sequences = block->num_sequences ;

       block->clusters[0].sequences = &(block->sequences[0]) ;

       }

      if (num_seqs < 2)
	 {
         printf("Error ! Not enough sequences (%d) in ProDom entry %s\n",
                num_seqs, block->number) ;
         return(NULL) ;
         }
      else if (num_seqs != block->num_sequences)
         {
         printf("Error ! Actual number of sequences in ProDom entry %s\n",
                block->number) ;
         printf("different than what the entry reports\n") ;
         return(NULL) ;
         }

      min_pos = 10000 ;  /* find min and max start positions of sequences */
      max_pos = 0 ;
      for(i1=0; i1sequences[i1].position > max_pos) 
            max_pos = block->sequences[i1].position ;
         if (block->sequences[i1].position < min_pos) 
            min_pos = block->sequences[i1].position ;
	 }

/* add min and max distance from previous block (sequence start) to Ac line */
      sprintf(word, " distance from previous block=(%d,%d)", 
              min_pos, max_pos);
      strcat(block->ac, word) ;

      sprintf(block->bl, "adapted from ProDom entry; width=%d; seqs=%d;",
              block->width, block->num_sequences) ; 

   return(block) ;
}


/*
 * fprint_matrix
 *   Prints a Matrix data structure to a file.  Primarily for debugging purposes.
 * adapted from blimps3.0.0 print_matrix
 *   Parameters: 
 *     Matrix *matrix:  the matrix to print
 *     FILE   *omfp:   the output matrix file pointer
 *   Error Codes: none
 */

void fprint_matrix(matrix,omfp)
     Matrix *matrix;
     FILE *omfp;
{
  int pos;
  int low, high;
  char c;

  int MATRIX_PRINT_WIDTH ;

  if (WWW_FLAG)
     MATRIX_PRINT_WIDTH = 55 ;
  else
     MATRIX_PRINT_WIDTH = 18 ;

  high = MATRIX_PRINT_WIDTH;
  for (low=0; 
       lowwidth; 
       low = (high+=MATRIX_PRINT_WIDTH) - MATRIX_PRINT_WIDTH) {



  fprintf(omfp,"\n");

/* modified following statements to 
  print matrix column number starting from 1 not 0*/

  if (matrix->width > 99) {
    fprintf(omfp,"  |");
    for (pos=low; poswidth; pos++) {
      if (pos+1 > 99) {
	fprintf(omfp,"% 4d", (pos+1)%100);
      }
      else {
	fprintf(omfp,"    ");
      }
    }
  }

  fprintf(omfp,"\n");
  if (matrix->width > 9) {
    fprintf(omfp,"  |");
    for (pos=low; poswidth; pos++) {
      if (pos+1 > 9) {
	fprintf(omfp,"% 4d", (pos+1-(((pos+1)/100)*100)) / 10);
      }
      else {
	fprintf(omfp,"    ");
      }
    }
  }
  
  fprintf(omfp,"\n");
  fprintf(omfp,"  |");
  for (pos=low; poswidth; pos++) {
    fprintf(omfp,"%4d", ((pos-((pos/10)*10))+1)%10);
  }
  
  fprintf(omfp,"\n");
  fprintf(omfp,"--+");
  for (pos=low; poswidth; pos++) {
    fprintf(omfp,"----");
  }

  fprintf(omfp,"\n");
  
/* following part modified not to show B, J, O, U and Z */
  for (c='A'; c<='Y'; c++) {
    switch (c)
      {
      case 'B' : continue ;
      case 'J' : continue ;
      case 'O' : continue ;
      case 'U' : continue ;
      }
    fprintf(omfp,"%c |", c);
    for (pos=low; poswidth; pos++) {
      fprintf(omfp,"% 4d", round(matrix->weights[aa_atob[c]][pos]));
    }
    fprintf(omfp,"\n");
  }

/* removed printing of c='*' */

  c = '-';
  fprintf(omfp,"%c |", c);
  for (pos=low; poswidth; pos++) {
    fprintf(omfp,"% 4d", round(matrix->weights[aa_atob[c]][pos]));
  }
  fprintf(omfp,"\n");

  }

}


                entry_name, num_seqs+1) ;
         return(NULL) ;
         }

           /* temporarily store sequence name, if this is first sequence 
              the sequences length isn't known and no memory allocated yet, 
  blimps-3.9/blimps/LAMA_search.c000064400001460000012000000460550776115711500166630ustar00jorjastaff00000400000027/* COPYRIGHT 1999-2003 Fred Hutchinson Cancer Research Center

      LAMA_search.c
  Processes LAMA_search.sh form
  Executes the following programs which must be in the same directory:
	LAMA
	htmlize-blimps.pl
	htmlize-LAMA
	/blocks/icons/cyrcashLogo.gif
	/blocks-bin/cyrcaLama.pl
	/blocks/tmp/

   WARNING! This is not a very robust piece of code.  If the data in the 
            entry.val field overflows the allowed space it will be truncated
	    by the following entry and have the following entry.name appended 
	    to the truncation.
	    Because of this the sequence needs to be the last entry in the
	    html form because there is no entry following it to truncate 
	    the sequence data.
*/
/* 5/02/95  Modified chmod calls to give proper permissions to log files. 
	    Wouldn't compile: had to remove calls to "remove_trailing_
	    whitespace(); also a problem with Buffer[], changed to buf[] JGH
   5/ 6/95  Modified .cs file to search mats.dat instead of blocks.dat
   7/11/95  Added "umask 006" to prevent general read on wwwuser files
	    Added more "chmod"s for .cs, seq, .out
   7/19/95  Changed the error message when the page is not accessed by a post.
            Netscape does this sometimes when backing up to a page.
   9/ 5/95  Changed blimps search to search a blocks db using pseudo-counts.
	    Added option to search the Prints database in blocks format.
   9/23/95  Fixed problem introduced 9/5 with blimps options.
   9/25/95  Changed log file entry to indicate blocks or prints
  12/ 2/95  Changed SMALL_BUFF_LENGTH to LARGE_BUFF_LENGTH everywhere
	    blksort_output, etc. was getting corrupted ...
  12/ 3/95  Changed to look for environment variables BLOCKS_HOME &
            BLOCKS_EMAIL before using values here.
 May/ 8/96  Changed the database searched when prints is specified to 
            actually be prints (it was small test database until now).
   8/22/96  Log to the general file.
   3/22/97  Changed location of prints db, JGH.
   4/ 2/97  Changed location of blocks db. JGH
  10/29/97  Recompiled - unknown problem with version of 6/28/97?
   11/15/97 Moved home directory definitions to homdir.h
   3/ 6/98  Added "nice" to execution of LAMA
   12/22/98 Removed all hard-coded file names; assumes execution is from
	    bin/ sub-directory. Added blocks+ searching option.
    6/20/99 Execute htmlize-LAMA instead of htmlink_LAMA-out.
    23/8/00 Execute CYRCA and add icon linking to results if there are any.
    5/21/03 Stop logging
    8/17/03 Don't execute CYRCA if user blocks
===========================================================================*/
/* blimps stuff */
#define EXTERN

#include 

typedef struct {
    char *name;
    char *val;
} entry;

/* from util.c */
char *makeword(char *line, char stop);
char *fmakeword(FILE *f, char stop, int *len);
char x2c(char *what);
void unescape_url(char *url);
void plustospace(char *str);
 
entry entries[10000];
 
/*	Assumes execution is from the bin/ directory  */
#define HOME ".."
#define BIN_SUBDIR   "."
#define TMP_SUBDIR   "../tmp"
#define LOG_SUBDIR   "../log"
#define BLOCKS_SUBDIR "../data-blocks"
#define PRINTS_SUBDIR "../data-prints"
#define BLPLUS_SUBDIR "../data-blplus"
#define BLOCKS_EMAIL "blocks@fhcrc.org"
#define WWW_ADDRESS "blocks"
#define LAMA_HELP_PAGE "../help/LAMA_help.html"
#define LAMA_HELP_ICON "?"

#define MAX_BLOCKS 10

#define CYRCA_ZSCORE "5.6"
#define CYRCA_LOGO "/blocks/icons/cyrcashLogo.gif"
#define CYRCA "./cyrcaLama.pl"

char LAMA[LARGE_BUFF_LENGTH];
char LAMA_queue[LARGE_BUFF_LENGTH];
char add_queue_entry[LARGE_BUFF_LENGTH];
char extblock_stdout[LARGE_BUFF_LENGTH];
char Qblock_file[LARGE_BUFF_LENGTH];
char log_dir[LARGE_BUFF_LENGTH];
char log_file[LARGE_BUFF_LENGTH];
char error_file[LARGE_BUFF_LENGTH];
char LAMA_output[LARGE_BUFF_LENGTH];
char cyrcaOutputFile[LARGE_BUFF_LENGTH];
char database[LARGE_BUFF_LENGTH];		/* searched database of blocks */
char blocksdbase[LARGE_BUFF_LENGTH];		/* Blocks Database*/
char printsdbase[LARGE_BUFF_LENGTH];		/* Prints blocks db */
char blplusdbase[LARGE_BUFF_LENGTH];		/* Blocks+ db */
char targetdbase[LARGE_BUFF_LENGTH];		/* user target blocks db */
char mail_file[LARGE_BUFF_LENGTH];
char email_addr[LARGE_BUFF_LENGTH];
char buf[LARGE_BUFF_LENGTH];

int pid;

entry *Targetblock_Ptr = NULL;
entry *Qblock_Ptr = NULL;
entry *Title_Ptr = NULL;
entry *Address_Ptr = NULL;



int Debug_Level = 0;
float Score_Cutoff_Level = 0;


Boolean Mail_Flag = FALSE;
Boolean Prints_Flag = FALSE;
Boolean Blplus_Flag = FALSE;
Boolean No_DB_Flag = FALSE;
 
/*FILE *jgh;
*/

void read_startup_info()
{
  int i;
  char *script, *ptr;
  FILE *logdate, *curr_year_month;

  ptr = getenv("BLOCKS_EMAIL");
  if (ptr != NULL) sprintf(email_addr, "%s", ptr);
  else  sprintf(email_addr, "%s", BLOCKS_EMAIL);
/*fprintf(jgh, "%s %s\n", ptr, email_addr);
*/

  pid = getpid();
  curr_year_month = popen("date '+%y%m'", "r");
  logdate = popen("date \"+%y%m%d\"", "r");

  sprintf(LAMA, "%s/LAMA", BIN_SUBDIR);
  sprintf(add_queue_entry, "%s/add_queue_entry.pl", BIN_SUBDIR);
  sprintf(LAMA_queue, "%s/LAMA_queue", BIN_SUBDIR);
  sprintf(extblock_stdout, "%s/extblock_stdout", BIN_SUBDIR);
  sprintf(blocksdbase, "%s/blocks.dat", BLOCKS_SUBDIR);
  sprintf(printsdbase, "%s/prints.dat", PRINTS_SUBDIR);
  sprintf(blplusdbase, "%s/blocks.dat", BLPLUS_SUBDIR);
/* '_tmp' string added to Qblock and target names so they won't be removed and be available for making logos */
  sprintf(targetdbase, "%s/%d_tmp.dat", TMP_SUBDIR, pid);
  sprintf(Qblock_file, "%s/%d_tmp.blk", TMP_SUBDIR, pid); 
  fgets(buf, LARGE_BUFF_LENGTH, curr_year_month);
  remove_trailing_whitespace(buf);
  sprintf(log_dir, "%s/%s", LOG_SUBDIR, buf);
  fgets(buf, LARGE_BUFF_LENGTH, logdate);
  remove_trailing_whitespace(buf);
  sprintf(log_file, "%s/%s", log_dir, buf);
  sprintf(mail_file, "%s/%d.mail", TMP_SUBDIR, pid);
  sprintf(LAMA_output, "%s/%d.out", TMP_SUBDIR, pid);

  pclose(curr_year_month);
  pclose(logdate);
}   /*  end of read_startup_info */


int parse()
{
/* parse the input
   while parsing
    set the email flag if there is an address, remember which entry it is in.
    set the pointer to the sequence 
*/

  register int i,num_entries=0;
  char *entry_string;
  int cl;

  /* check that there is something to use. */
  entry_string = getenv("QUERY_STRING");
/*  if (entry_string != NULL) fprintf(jgh, "%s", entry_string);
*/

/*
  if (entry_string == NULL) 
     {
     printf("No query information to decode.\n");
     exit(1);
     }
*/

  /* parse the query string into individual entries */

  cl = atoi(getenv("CONTENT_LENGTH"));

  for(i=0;cl && (!feof(stdin));i++) 
     {
     num_entries=i;
     entries[i].val = fmakeword(stdin,'&', &cl);
     plustospace(entries[i].val);
     unescape_url(entries[i].val);
     entries[i].name = makeword(entries[i].val,'=');

/*    fprintf(jgh, "%s %s\n", entries[i].name, entries[i].val);
*/

     if (!strncmp(entries[i].name, "User_target_block", 14)) 
        {
	Targetblock_Ptr = &entries[i]; 
        }


     if (!strncmp(entries[i].name, "User_query_block", 16)) 
        {
        Qblock_Ptr = &entries[i];
        }

     if (!strncmp(entries[i].name, "debug_level", 16)) 
        {
	  Debug_Level = atoi(entries[i].val);
        }

     if (!strncmp(entries[i].name, "score_cutoff_level", 16)) 
        {
	  Score_Cutoff_Level = atof(entries[i].val);
        }

     else if (!strncmp(entries[i].name, "address", 7)) 
        {
        Address_Ptr = &entries[i];
        if ( (int) strlen(entries[i].val) > 0) 
           {
  	   Mail_Flag = TRUE;
           }
        }

     else if (!strncmp(entries[i].name, "database", 8)) 
       {
	 if (!strncmp(entries[i].val, "prints-db", 9))
           {
	     strncpy(database, printsdbase,LARGE_BUFF_LENGTH) ;
	     Prints_Flag = TRUE;
           }
	 else if (!strncmp(entries[i].val, "blplus-db", 9))
           {
	     strncpy(database, blplusdbase,LARGE_BUFF_LENGTH) ;
	     Blplus_Flag = TRUE;
           }
	 else if (!strcmp(entries[i].val, "no-db")) 
	   {
	     strncpy(database, targetdbase,LARGE_BUFF_LENGTH) ;
	     No_DB_Flag = TRUE;
	   }
	 else 
	   { /* assume the blocks database by default */
	     strncpy(database, blocksdbase, LARGE_BUFF_LENGTH) ;
	   }
       }
    }


  return num_entries;
} /*  end of parse */


void clean_temp_files()
{
  sprintf(buf, "rm -f %s/%d.*", TMP_SUBDIR, pid); 
  system(buf);
}


void write_Qblock()
{
  FILE  *bfp, *efp ;
  Block *block ;
  int   blocks_num ;


  /* check that a block was specified */
  if (Qblock_Ptr->val[0] == NULL) 
    {
      printf("
      Search Error
      \n");
      printf("You need to enter a block to search with by writing or pasting a block in the query block window.
      \n");
      exit(0);
    }
  

  /* open error_file so that error messages from read_a_block can be examined*/
  sprintf(error_file, "%s/%d.LAMA_Qblock_errors", TMP_SUBDIR, pid);
  set_error_file_name(error_file) ;     



  /* if block was pasted/written - */
  if (Qblock_Ptr->val[0] != NULL)
    {
      
      /* open up the block file to write to */
      bfp = fopen(Qblock_file, "w");
      
      fprintf(bfp, "%s\n",Qblock_Ptr->val);

/* add "//" to the file end. 
   This is done to over come the fact that read_a_block does not detect if the 
   end of block signal (//) is missing and the program crashes later. */
      fprintf(bfp, "//\n");

      /* close and reopen block file in a read mode */
      fclose(bfp);
      bfp = fopen(Qblock_file, "r");
      
      
      blocks_num = 0 ;
      
      /* read-in blocks to check their format and content */
      while ((block = read_a_block(bfp)) != NULL)
        {
	  blocks_num++ ;
	  
	  /* try and open error file to see if there were any errors */
	  if ((efp = fopen(error_file, "r")) != NULL) 
	    {
	      printf("
      Search Error
      \n");
	      printf("There seems to be an error in the format of query block number %d:
      ", blocks_num);
	      
	      printf("
      \n");
	      while((buf[0]=getc(efp)) != EOF) putchar(buf[0]) ; 
	      printf("
      ") ;
	      
	      fclose(efp) ;
	      
	      clean_temp_files() ;
	      
	      exit(1);
	    }
	  
        }
      
      if (blocks_num <= 0) 
	{
	  printf("
      Search Error
      \n");
	  printf("No blocks were read from the query.\n");
	  clean_temp_files() ;
	  exit(1);
	}

      if (blocks_num > MAX_BLOCKS) 
	{
	  printf("
      Search Error
      \n");
	  printf("Sorry, you can not compare more than %d query blocks in each run.\n", 
                 MAX_BLOCKS);
	  clean_temp_files() ;
	  exit(1);
	}
      
      
      fclose(bfp);
    } /* end if (Qblock_Ptr->val[0] == NULL) */
  
  
  if (No_DB_Flag)
    {
      /* open file, write data from target into the temp target file */
      bfp = fopen(targetdbase, "w");
      fprintf(bfp, "%s\n",Targetblock_Ptr->val);

/* add "//" to the file end. 
   This is done to over come the fact that read_a_block does not detect if the 
   end of block signal (//) is missing and the program crashes later. */
      fprintf(bfp, "//\n");

      fclose(bfp);
      
      /* check that the DB is of the right format first (see above) */
      bfp = fopen(targetdbase, "r");
      
      blocks_num = 0 ;
      
      /* read-in blocks to check their format and content */
      while ((block = read_a_block(bfp)) != NULL) 
	{
	  blocks_num++ ;
	  
	  /* try and open error file to see if there were any errors */
	  if ((efp = fopen(error_file, "r")) != NULL) 
	    {
	      printf("
      Search Error
      \n");
	      printf("There seems to be an error in the format of target block number %d:
      ", blocks_num);
	      
	      printf("
      \n");
	      while((buf[0]=getc(efp)) != EOF) putchar(buf[0]) ; 
	      printf("
      ") ;
	      
	      fclose(efp) ;
	      
	      clean_temp_files() ;
	      
	      exit(1);
	    }
	}
      
      fclose(bfp);
      
      if (blocks_num <= 0) 
	{
	  printf("
      Search Error
      \n");
	  printf("No blocks were read from the target data.\n");
	  clean_temp_files() ;
	  exit(1);
	}

      if (blocks_num > MAX_BLOCKS) 
	{
	  printf("
      Search Error
      \n");
	  printf("Sorry, you can not compare more than %d target blocks in each run.\n", 
                 MAX_BLOCKS);
	  clean_temp_files() ;
	  exit(1);
	}

    } /* end if a target DB */
}


 

/*
+Run search
-
if submitted in the background, check the load level before running
  if have waited for more than half an hour?, then submit.
run LAMA and keep track of where the output goes

*/
void run_search()
{
  FILE *dfp;
  char datein[LARGE_BUFF_LENGTH];
  char dateout[LARGE_BUFF_LENGTH];
  char db[80];

  dfp = popen("date", "r");
  remove_trailing_whitespace(fgets(datein, LARGE_BUFF_LENGTH, dfp));
  pclose(dfp);

  sprintf(buf, "/usr/bin/nice -5 %s %s,%s %s 0 %d 0 %f > /dev/null 2>&1",
	  LAMA, Qblock_file, database, LAMA_output, Debug_Level, 
	  Score_Cutoff_Level);

  if (system(buf)) {
    printf("
      Search Error
      \n");
    printf("An error occured during the search.\n");
    printf("Please try your search again at a later time.\n");
    printf("If it fails again contact the maintainer of these pages\n");
    printf("and describe what caused the problem with an example.
      \n");

    clean_temp_files() ;

    exit(0);
  }

  dfp = popen("date", "r");
  remove_trailing_whitespace(fgets(dateout, LARGE_BUFF_LENGTH, dfp));
  pclose(dfp);

  /* OK, I know you can do this with system calls, but this was easier. */
  /* make the path if needed (and make sure of the protection) */
/*
  sprintf(buf, "mkdir -p %s", log_dir);
  system(buf);
  sprintf(buf, "chmod -f 775 %s", log_dir);
  system(buf);
*/

  /* enter the data into the log file (and make sure of the protection) */
/*
  if (Prints_Flag) {
    strcpy(db, "Prints");
  }
  if (Blplus_Flag) {
    strcpy(db, "Blplus");
  }
  else if (No_DB_Flag) {
    strcpy(db, "user_target");
  }
  else {
    strcpy(db, "Blocks");
  }
  sprintf(buf, 
	  "echo \"%s\tLAMA %s: `grep \'Probe Size\' %s`\t%s\t%s\" >> %s",
	  WWW_ADDRESS, db, LAMA_output, datein, dateout, log_file);

  system(buf);
  sprintf(buf, "chmod -f 664 %s", log_file);
  system(buf);
*/

}  /*  end of run_search */


void convert_LAMA_output()
{
  FILE *outf;
/** either **/
  FILE *fp;

  if ((outf = fopen(LAMA_output, "r")) == NULL)
     {
     printf("Error opening LAMA output file.\n") ;

     clean_temp_files() ;

     exit(1) ;
     }

/*
  printf("
      \n");
  while (!feof(outf) && fgets(buf, LARGE_BUFF_LENGTH, outf) != NULL)
     printf(buf) ; 
  printf("
      \n"); */

  fclose(outf);

  sprintf(buf, "%s/htmlize-blimps.pl %s | %s/htmlize-LAMA %s %s - -", 
          BIN_SUBDIR, LAMA_output, 
          BIN_SUBDIR, Qblock_file, database) ;

  if (!(fp = popen(buf, "r"))) printf("Error opening pipe\n") ;

  printf("
      \n");

  while (!feof(fp) &&
	 fgets(buf, LARGE_BUFF_LENGTH, fp) != NULL)
     printf(buf) ;

  printf("
      \n");

  pclose(fp);

} /* end of convert_LAMA_output */




void display_output()
{

  printf("LAMA Search Results\n");
  printf("
      LAMA Search Results (%s)
      \n",
         LAMA_HELP_PAGE, LAMA_HELP_ICON);
    
}

/*====================================================================
   Every email request generates 3 entries in the bin/LAMA_queue file,
   which should be processed in order by the bin/run_queue script:
	1. execute LAMA, 2. mail the results, 3. remove the files
============================================================================*/
void queue_to_mail()
{
  char db[80];
  char datein[LARGE_BUFF_LENGTH];

  FILE *dfp;
  dfp = popen("date", "r");
  remove_trailing_whitespace(fgets(datein, LARGE_BUFF_LENGTH, dfp));
  pclose(dfp);

  /* put the commands into the queue */
  /*    run LAMA */
  sprintf(buf, "%s %s \"/usr/bin/nice -10 %s %s,%s %s 0 %d 0 %f > /dev/null 2>&1\"", add_queue_entry, LAMA_queue, LAMA, Qblock_file, database, LAMA_output, Debug_Level, Score_Cutoff_Level);
  system(buf);


  /*    mail the person the results */
  /*    NOTE: need to echo the header lines for the LAMA output :P */
  /*    NOTE: all this should need to do is to cat the ouput file. */
  sprintf(buf, "%s %s '(cat %s) | /usr/bin/mailx -s \"LAMA Results\" -r \"blocks\@fhcrc.org\" %s'", add_queue_entry, LAMA_queue, LAMA_output, Address_Ptr->val);
  system(buf);
  


  /*   clean up the files */
  sprintf(buf, "%s %s 'rm -f %s/%d.*'", add_queue_entry, LAMA_queue, 
	  TMP_SUBDIR, pid); 
  system(buf);


  /* enter the queued info into the LOG */
  /* OK, I know you can do this with system calls, but this was easier. */
  /* make the path if needed (and make sure of the protection) */
/*
  sprintf(buf, "mkdir -p %s", log_dir);
  system(buf);
  sprintf(buf, "chmod -f 775 %s", log_dir);
  system(buf);
*/

  /* enter the data into the log file (and make sure of the protection) */
/*
  if (Prints_Flag) {
    strcpy(db, "Prints");
  }
  if (Blplus_Flag) {
    strcpy(db, "Blplus");
  }
  else if (No_DB_Flag) {
    strcpy(db, "user_target");
  }
  else {
    strcpy(db, "Blocks");
  }
  sprintf(buf, 
	  "echo \"%s\tLAMA %s: `grep \'Probe Size\' %s`\t%s\t%s\" >> %s",
	  WWW_ADDRESS, db, LAMA_output, datein, "queued", log_file);

  system(buf);
  sprintf(buf, "chmod -f 664 %s", log_file);
  system(buf);
*/



  /* announce it is queued */
  printf("LAMA Search Submitted\n");
  printf("
      LAMA Search Submitted
      \n");
  printf("Your search has been submitted.\n");
  printf(
"You will receive the results via email to the address you gave (\"%s\").\n", 
         Address_Ptr->val);

  /* exit */
  exit(1);
}


void runCyrca ()
{
  int returnCode;
  char fname[20];

  sprintf(fname, "%dC.html", pid);
  sprintf (cyrcaOutputFile, "%s/%s", TMP_SUBDIR, fname);
  sprintf (buf, "%s %s %s %s",
	   CYRCA, LAMA_output, CYRCA_ZSCORE, cyrcaOutputFile); 

  returnCode = system(buf);

/*
printf("%s=%d\n", buf, returnCode);
*/

  /* examine the CYRCA output error code. */
  if (returnCode == 0)
    {
/*
      printf ("CYRCA results\n", SHOW_CYRCA_RESULTS, cyrcaOutputFile, CYRCA_LOGO); 
*/
      printf ("CYRCA results\n", 
    		fname, CYRCA_LOGO); 
    }

} /* end of run Cyrca */

void main(int argc, char *argv[]) {

  printf("Content-type: text/html\n\n\n");


  if(strcmp(getenv("REQUEST_METHOD"),"POST")) {
    printf("This script should be referenced with a METHOD of POST.\n");
    printf("If you don't understand this, see this ");
    printf("forms overview.%c",10);

    printf("
      What could have happened is that you just reloaded this page rather than redoing the search.\n");

    printf("
      If you use NETSCAPE it has a tendency to try to reload a page when you go back to it.  This may be why you have this error.\n");

    exit(1);
  }

  if(strcmp(getenv("CONTENT_TYPE"),"application/x-www-form-urlencoded")) {
    printf("This script can only be used to decode form results. \n");
    exit(1);
  }

  /*    Set file permissions to "rw-rw----"     */
  system("umask 006");

  read_startup_info();

  parse();

  write_Qblock();

  if (Mail_Flag) {
    queue_to_mail();
  }
  
  run_search();

  display_output(); 

  /* Cyrca execution, added by Victor Kunin */
  if (!No_DB_Flag)
  {   runCyrca();   }
    
  convert_LAMA_output() ;

  /* End of modification*/

  clean_temp_files() ;

  exit(0) ;
}
t read_a_block does not detect if the 
   end of block signal (//) is missing and the program crashes later. */
      fprintf(bfp, "//\n");

      /* close and reopen block file in a read mode */
      fclose(bfp);
      bfp = fopen(Qblock_file, "r");
      
      
      blocks_num = 0 ;
      
      /* read-in blocks to check their format and content */
      while ((block = read_a_block(bfp)) != NULL)
        {
	  blocks_num++ ;
	  
	  /* try and open error filblimps-3.9/blimps/addseqs.c000064400001460000012000001206021035631526200162300ustar00jorjastaff00000400000027/*  Copyright 2000-2006 Fred Hutchinson Cancer Research Center
    addseqs.c   Reads a file of blocks and a sequence not in the
			blocks.
		  Aligns the sequence to the blocks.

           addseqs    []

blksonly: (for protomat) Align sequences with blocks & add them to
	  blocks only if ALL are in order and ALL score above a cutoff.
          Use to output blocks with sequences added to all blocks.

For seqsonly & simionly, all  sequences are added to the blocks,
but then assembled & out of order segments flagged:
seqsonly: Align sequences with blocks and print out  sequences
	  from min block pos to max block pos in fasta format.
          Use to output sequences added to some blocks,
	  not necessarily to all.
          
simionly: Assumes only one sequence in ; it will be
	  added to the blocks scoring above cutoff and in order.
          Use to output blocks with sequences added to some blocks,
	  not necessarily to all.
--------------------------------------------------------------------
 9/30/99 J. Henikoff
11/29/99 Put in btest for tree_add.csh
12/15/99.1 Added Version.
 3/13/00.1 List blocks to which sequence was added if simionly
 3/22/00.1 Added compute_dist(); distance matrix calculation
 5/ 2/00.1 Don't add seqs if they're off the ends of the blocks (blksonly)
		or are documented FRAGMENTs
10/ 1/02.1 Fixed bug checking sequence names. More output info.
10/11/02.1 Allow 1 aa overlap between adjacent blocks
10/11/02.2 Pad if starts before first block or ends after last block
 6/ 8/03.1 Compare multi-part sequence names - compare_names()
 1/ 2/06.1 Match Q9KWE2 with Q9KWE2_AGRRH, etc. - compare_names()
====================================================================*/

#define ADDSEQS_C_
#define EXTERN
#define MAXNAME 80	/* Maximum file name length */
#define MAXWIDTH 60     /* Max block width */
#define MAXAA 26	/* alphabet size */
#define AASALL 26	/* alphabet size */
#define AAS 21	
#define MAXWIDTH 60
#define CUTOFF 800	/* Min. calibrated cutoff score */
#define MAXSEQ 1000

/*		Stuff for pssmdist()   */
#define TPS 100			/* number of known TPs */
#define Search 185371		/* number of seqs in database */
#define SearchAA 58639837	/* number of aas in database */
#define MAXSCORE 6000

#include 

struct blocks_list {
   int nblock;		/* number of blocks in family */
   int nseq;		/* number of seqs originally in blocks */
   int nadd;		/* number of seqs added to blocks */
   int mindist;		/* min dist from last block */
   int maxdist;		/* max dist from last block */
   int bestpos;		/* for current sequence */
   int endpos;		/* for current sequence */
   int bestscore;	/* for current sequence */
   Block *block;
   Matrix *pssm, *pssm_frq;
   struct blocks_list *next;
};

struct seqseq {		/* to reorder sequences */
   int seq, minseq, clump;
   double maxscore, minscore;
};

struct btemp {		/* sort hit structure */
   double score;
   int bnum;			/* order of blist->block in family */
   struct blocks_list *blist;
};

void addseq();
void assemble_hit();
void best_pos();
void scale_weights();
void fix_ac();
void add_cluster();
void write_seq();
void order_seq();
int btempcmp();
void compute_dist();
int compare_names();

/*		List of blocks routines  */
struct blocks_list *make_blist();
void insert_blist();
void free_blist();
/*		Block calibration routine */
struct score_struct {
	double ways, prob;
};
int pssmdist();

char Version[12] = " 1/ 2/06.1"; 		/* Version number */
int NumSeqs, TN995, TPabove, CutOff;
double QMax;				/* Max possible query similarity */

/*=======================================================================*/
/*
 * main
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
   FILE *fseq, *fblk, *fout, *fqij, *fdat;
   Block *block;
   Sequence *sequence;
   struct blocks_list *blist, *bcur, *bprev;
   char frqname[MAXNAME], qijname[MAXNAME], siminame[MAXNAME];
   char infile[MAXNAME], outfile[MAXNAME], seqsfile[MAXNAME];
   char  *blimps_dir;
   int i, j, not_in, in_order, above_cut, endpos;
   int fragment, iblock, pad1, pad2;
   int maxpos, minpos;
   int seqsonly, simionly, blksonly;

   ErrorLevelReport = 2;	/* 5 for No blimps errors */

   printf("ADDSEQS Version %s\n", Version);
   if (argc < 3)
   {
      printf("ADDSEQS: Copyright 1999 by the Fred Hutchinson Cancer");
      printf(" Research Center\n");
      printf("Adds sequences to blocks.\n");
      printf("USAGE:  addseqs   \n");
      printf("                 = input blocks\n");
      printf("		           = fasta format sequences\n");
      printf("                      = output file\n");
      printf("                = processing option\n");
      printf("                   blks = add sequences to blocks & output blocks\n");
      printf("                   seqs = add sequences to blocks & output sequences\n");
      printf("                   simi = add sequences to blocks & do similarity analysis\n");
   }
 
/*----------------Get the input blocks------------------------------*/
   if (argc > 1)
      strcpy(infile, argv[1]);
   else
   {
      printf("\nEnter name of file containing blocks: ");
      gets(infile);
   }
   if ( (fblk=fopen(infile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", infile);
      exit(-1);
   }

/* ------------2nd arg = sequence file -----------------------*/
   if (argc > 2)
      strcpy(seqsfile, argv[2]);
   else
   {
      printf("\nEnter name of sequence file: ");
      gets(seqsfile);
   }
   if ( (fseq=fopen(seqsfile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", seqsfile);
      exit(-1);
   }
   /* ------------3rd arg = output seqs -----------------------*/
   if (argc > 3)
      strcpy(outfile, argv[3]);
   else
   {
      printf("\nEnter name of output seqs file: ");
      gets(outfile);
   }
   if ( (fout=fopen(outfile, "w")) == NULL)
   {
      printf("\nCannot open file %s\n", outfile);
      exit(-1);
   }
   /* ------------4th arg = optional processing----------------*/
   blksonly = YES; seqsonly = NO; simionly = NO;
   if (argc > 4)
   {
      if (strcasecmp(argv[4], "seqs") == 0)
      {
         blksonly = NO; seqsonly = YES; simionly = NO;
      }
      else if (strcasecmp(argv[4], "simi") == 0)
      {
         blksonly = NO; seqsonly = NO; simionly = YES;
      }
   }
   CutOff = CUTOFF;
/*
   if (blksonly) CutOff = CUTOFF;
   else          CutOff = 0;
*/

   /*--------- Get the information to make PSSMs ---------------------*/
   blimps_dir = getenv("BLIMPS_DIR");
   frqname[0] = '\0';
   if (blimps_dir != NULL) sprintf(frqname, "%s/docs/", blimps_dir);
   strcat(frqname, "default.amino.frq");
   /*  Creates global array frequency[]  */
   load_frequencies(frqname);
   qijname[0] = '\0';
   if (blimps_dir != NULL) sprintf(qijname, "%s/docs/", blimps_dir);
   strcat(qijname, "default.qij");
   Qij = NULL;
   if ( (fqij=fopen(qijname, "r")) != NULL) Qij = load_qij(fqij);
   fclose(fqij);
   RTot = LOCAL_QIJ_RTOT;

   /*=======================================================================*/

   /*  Read all of the blocks into memory  */
   blist = make_blist();
   while ((block = read_a_block(fblk)) != NULL)
   {
       pb_weights(block);		  /* add position-based weights */
       scale_weights(block, 1);	           /* weights add to # of seqs */
       insert_blist(blist, block);	 /* also computes PSSMs & calibrates */
   }
   fclose(fblk);
   if (blist->nblock == 0)
   {
      printf("No blocks found in %s .\n", infile);
      exit(-1);
   }

   /*======================================================================*/
   /*---- Process each block for every sequence ---------------------------*/
   NumSeqs = 0;
   while (!feof(fseq) &&
      (sequence = read_a_sequence(fseq, FASTA, AA_SEQ)) != NULL)
   {
     NumSeqs += 1;
     fragment = FALSE;
     if (strstr(sequence->info, "FRAGMENT") != NULL) fragment = TRUE;
     /*---------------Process each block---------------------------------*/
     /*   Assumes all the blocks are from the same family!  */
     bcur = blist->next;
     minpos = 9999; maxpos = -9999;
     endpos = -9999;	/* first block is never out of order */
     not_in = in_order = above_cut = TRUE;
     iblock = pad1 = pad2 = 0;
     while (bcur != NULL && bcur->block != NULL)
     {
         iblock++;
         for (i = 0; i < bcur->block->num_sequences; i++)
         {
           if ((compare_names(sequence->name, bcur->block->sequences[i].name)) == 1)
           {
                printf("%s already in block\n", sequence->name), 
                not_in = FALSE;
           }
         }
         if (not_in)		/* sequence isn't in block */
         {
           /* Get best position & score for this block in this sequence */
	   bcur->bestpos = bcur->endpos = bcur->bestscore = -999; 
           best_pos(bcur, sequence);

           if (bcur->bestscore < CutOff) above_cut = FALSE;
           /*  Allow overlap of 1, motomat does?  */
           if (bcur->bestpos < (endpos-1))
           {
               printf(" out of order %d, previous end %d\n", 
		       bcur->bestpos, endpos);
               in_order = FALSE;
           }
           else
           {  endpos = bcur->bestpos + bcur->block->width; }

           /*>>>>pad seq with Xs if this is first or last block <<<*/
           if (bcur->bestpos < 0 && iblock == 1)
           {
              pad1 = 0 - bcur->bestpos;
              printf(" pad1=%d bestpos=%d endpos=%d seqlen=%d\n",
		       pad1, bcur->bestpos, endpos, sequence->length);
           }
           if (iblock == bcur->nblock && endpos > sequence->length)
           {
              printf(" pad2=%d bestpos=%d endpos=%d seqlen=%d\n",
		       pad2, bcur->bestpos, endpos, sequence->length); 
              pad2 = endpos - sequence->length;
           }
           if ( (iblock > 1 && bcur->bestpos < 0)  ||
                (iblock < bcur->nblock &&  endpos > sequence->length) )
           {
                printf(" bad bestpos=%d endpos=%d seqlen=%d\n",
			bcur->bestpos, endpos, sequence->length);
		fragment = TRUE;
           }

           if (bcur->bestpos < minpos) minpos = bcur->bestpos;
	   if ((bcur->bestpos + bcur->block->width) > maxpos)
		maxpos = bcur->bestpos + bcur->block->width - 1;
         }  /* end of not-in */
         bcur = bcur->next;
     }  /* end of block  */

     /*------Now all blocks have been examined for this sequence-----------*/
     /*  Add this sequence to the block, unless it's already in or
		blocks aren't in order or score is too low   */
     if ( (!blksonly && not_in) ||
           (blksonly && not_in && !fragment && in_order && above_cut) )
     {
        bcur = blist->next; bprev = NULL;
        while (bcur != NULL && bcur->block != NULL)
        {
            addseq(bprev, bcur, sequence);
            if (!blist->nadd) add_cluster(bcur->block);
	    bprev = bcur;
            bcur = bcur->next;
        }
        blist->nadd += 1;	/* #seqs added to all blocks */
        /*  Check to see if blocks are in order for sequence just added:
            flags block->undefined & block->sequences[].undefined */
        if (!blksonly && blist->nblock > 1)
           assemble_hit(blist, &minpos, &maxpos);
     }
     if (seqsonly)  
     {
        write_seq(fout, sequence, minpos, maxpos);
     }

     /*  save the name of the last sequence added */
     if (simionly) strcpy(siminame, sequence->name);
     free_sequence(sequence);
   }  /* end of sequence */

   if (NumSeqs == 0)
   {
      printf("No sequences found in %s .\n", seqsfile);
      exit(-1);
   }
   fclose(fseq);
   printf("\n");

   /*-------------Add sequence weights & output the final blocks----------*/
   /*  if simionly, just skips blocks out of order for last sequence added */
   if (!seqsonly)
   {
      bcur = blist->next;
      while (bcur != NULL && bcur->block != NULL)
      {
         if (blksonly ||
             (simionly && bcur->block->undefined))
         {
            pb_weights(bcur->block);	/* add position-based weights */
            scale_weights(bcur->block, 0);    /* max weight = 100 */
            fix_ac(bcur);
            output_block(bcur->block, fout);
            if (simionly)
            {
		printf("Query added to %s\n", bcur->block->number);
            }
         }
         bcur = bcur->next;
      }  /* end of block  */
   }
   fclose(fout);
   if (!simionly)
      printf("%d sequences added\n", blist->nadd);

   /*----------Append statistics to addseqs.dat----------------------*/
   if (blksonly)
   {
      if ( (fdat=fopen("addseqs.dat", "a")) != NULL)
      {
         fprintf(fdat, "%s %d %d %d %d\n",
              blist->next->block->number, blist->nblock, blist->nseq, 
              blist->next->block->num_sequences, NumSeqs);
         fclose(fdat);
      }
   }

   exit(0);

}  /* end of main */

/*=======================================================================
	Add sequence to the end of the blist block
        blist is current block, bprev is previous block
========================================================================*/
void addseq(bprev, blist, seq)
struct blocks_list *bprev, *blist;
Sequence *seq;
{
   int j, pos, posj, prevdist, clmax, newseq;

/*
      printf("%s: ", blist->block->number);
      printf("Adding %s at position %4d\n", seq->name, pos);
*/
      pos = blist->bestpos;
      if (blist->block->num_sequences + 1 > blist->block->max_sequences)
      {
         resize_block_sequences(blist->block);
         /*  resize() doesn't fix cluster pointers?  */
/*
         blist->block->clusters[0].sequences = &(blist->block->sequences[0]);
*/
      }

      newseq = blist->block->num_sequences;
      /*  Block points to first position */
      blist->block->sequences[newseq].position = pos + 1;
      strcpy(blist->block->sequences[newseq].name, seq->name);
      strcpy(blist->block->sequences[newseq].info, seq->info);
      blist->block->sequences[newseq].undefined = YES; /* block is in seq */
      blist->block->sequences[newseq].max_length =
             blist->block->width;
/*    blist->block->sequences[newseq].length =
             blist->block->width; 
*/
      blist->block->num_sequences += 1;

      clmax = blist->block->num_clusters - 1;
      blist->block->clusters[clmax].num_sequences += 1; 

      /*  Force all sequences into a single cluster */
/*
      blist->block->num_clusters = 1;
      blist->block->clusters[0].num_sequences = blist->block->num_sequences;
      blist->block->clusters[0].sequences = &(blist->block->sequences[0]);
*/

      for (j=0; j< blist->block->width; j++)
      {
         if (blist->bestscore >= CutOff)
         {
            posj = pos + j;
            if (posj >= 0 && posj < seq->length)
               blist->block->sequences[newseq].sequence[j] =
                      seq->sequence[posj];
            else
               blist->block->sequences[newseq].sequence[j] = 23;    /*   X */
         }
         else
         {
            blist->block->sequences[newseq].sequence[j] = 23;    /*   X */
         }
      }

      /*   Update distance from previous block if necessary  */
      prevdist = pos;
      if (bprev != NULL)
      {
         prevdist -= (bprev->block->sequences[newseq].position + bprev->block->width);
      }
      if (prevdist < blist->mindist) blist->mindist = prevdist;
      if (prevdist > blist->maxdist) blist->maxdist = prevdist;
    
}  /* end of addseq */

/*======================================================================
      Scale sequence weights so maximum value is 100
=======================================================================*/
void scale_weights(block, stype)
Block *block;
int stype;
{
   double maxweight, minweight, sumweight, factor;
   int seq;

   sumweight = maxweight = 0.0; minweight = 999999.9;
   for (seq = 0; seq < block->num_sequences; seq++)
   {
      sumweight += block->sequences[seq].weight;
      if (block->sequences[seq].weight > maxweight) 
           maxweight = block->sequences[seq].weight;
      if (block->sequences[seq].weight < minweight) 
           minweight = block->sequences[seq].weight;
   }

   factor = 1.0;
   /*    Force maximum weight to be 100  */
   if (stype == 0)  factor = 100. / maxweight;
   /*    Force sum of weights to be number of sequences */
   else if (stype == 1) factor = (double) block->num_sequences / sumweight;
   /*    Force sum of weights to be stype */
        else if (stype > 1) factor = (double) stype / sumweight;

   for (seq = 0; seq < block->num_sequences; seq++)
   {
      block->sequences[seq].weight *= factor;
   }
}  /* end of scale_weights */

/*=======================================================================
            Score all alignments of matrix with sequence & return
	     position of best alignment
============================================================================*/
void best_pos(blist, seq)
struct blocks_list *blist;
Sequence *seq;
{
  int scan_pos, seq_pos, mat_pos, best_position;
  double seq_score, max_seq_score;

  max_seq_score = 0.0;
  
  /* for every alignment of the matrix and sequence score the alignment. */
  /* there are (seq_length + matrix_length  - 1) different alignments. */
  /* Note: seq_pos is the relative position of the 1st matrix column to the */
  /*       1st sequence column */
  /* Note: the indexing is shifted to make the calculation of scan_pos */
  /*       (see below) easier/faster */
  for (seq_pos= -blist->pssm->width+1; seq_pos < seq->length; seq_pos++) {


    /* 
     * score this alignment
     */
    seq_score = 0.0;

    /* for each position in the matrix add the weight to the total score */
    /* Note: mat_pos is the current column of the matrix */
    for (mat_pos=0; mat_pos < blist->pssm->width; mat_pos++) {

      /* make sure the sequence and the matrix overlap at this point */
      /* Note: scan_pos is where the current matrix column is in the */
      /*       sequence */
      scan_pos = seq_pos + mat_pos;
      if ((scan_pos >= 0) && (scan_pos < seq->length)) { /* if in the seq */
	seq_score += blist->pssm->weights[seq->sequence[scan_pos]][mat_pos];
      }
      else {			/* not in the sequence */
	seq_score += blist->pssm->weights[aa_atob['-']][mat_pos]; 
	/* score as if it was a gap */
      }

    } /* end score this alignment */

    
      if (seq_score > max_seq_score) {
	max_seq_score = seq_score;
	best_position = seq_pos;
      }
    
  } /* end of pairwise lineup */
  
  /*  Normalize score */
  if (blist->pssm->percentile > 0)
  {
     printf("%s %s calibrated ", seq->name, blist->block->number);
     max_seq_score *= 1000.0;
     max_seq_score /= (double) blist->pssm->percentile;
  }
  blist->bestpos = best_position;
  blist->endpos = best_position + blist->block->width - 1;
  blist->bestscore = round(max_seq_score);
  printf("best score = %5d at %d\n", blist->bestscore, blist->bestpos);

}  /* end of best_pos */

/*=======================================================================
     routines for a list of blocks
========================================================================*/
struct blocks_list *make_blist()
{
   struct blocks_list *new;
   
   new = (struct blocks_list *) malloc (sizeof(struct blocks_list));
   new->nblock = new->nseq = new->nadd = 0;
   new->bestscore = new->bestpos = new->maxdist = -9999;
   new->mindist = 9999;
   new->block = NULL;
   new->next = NULL;

   return(new);
}  /* end of make_blist */

/*=======================================================================
  PSSMs are computed & block calibrated here. The 99.5
  and strength values are not separate fields in the block record, but
  are extra fields stored in the PSSM record.
=======================================================================*/
void insert_blist(blist, block)
struct blocks_list *blist;
Block *block;
{
   struct blocks_list *cur;
   char *ptr, ctemp[80];

   cur = blist;
   while (cur->next != NULL) cur = cur->next;
   cur->next = make_blist();
   cur->next->block = block;

   cur->next->pssm = block_to_matrix(block, 3);		/* log odds  PSSM */
   cur->next->pssm_frq = block_to_matrix(block, 2);	/* frequency PSSM */

   /*   Get min & max distances:
	block->ac = "PS00094A; distance from previous block=(0,1141)"  */
   strcpy(ctemp, block->ac);
   ptr = strtok(ctemp, "(");
   if (ptr != NULL)
   { 
      ptr = strtok(NULL, ",");
      if (ptr != NULL)
      {
          cur->next->mindist = atoi(ptr);
          ptr = strtok(NULL, ")");
          if (ptr != NULL)
          { cur->next->maxdist = atoi(ptr);}
      }
   }

   /*  Calibrate the block if it isn't already & add to block->bl line */
   if (cur->next->pssm->percentile <= 0)
   {
      cur->next->pssm->percentile = pssmdist(cur->next->pssm, 0, frequency, NULL);
      block->percentile = cur->next->pssm->percentile;
/*
      ptr = strtok(block->bl, "\n\r");
      sprintf(block->bl, "%s; 99.5%%=%d", ptr, cur->next->pssm->percentile);
*/
   }
   if (cur->next->pssm->strength <= 0)
   {
      cur->next->pssm->strength = pssmdist(cur->next->pssm, 1, frequency, cur->next->pssm_frq);
      block->strength = cur->next->pssm->strength;
/*
      ptr = strtok(block->bl, "\n\r");
      sprintf(block->bl, "%s; strength=%d", ptr, cur->next->pssm->strength);
*/
   }

   /*  Update the list totals */
   blist->nblock += 1;
   blist->nseq = block->num_sequences;
 
}  /* end of insert_blist */

/*=======================================================================*/
void free_blist(blist)
struct blocks_list *blist;
{
   struct blocks_list *cur, *last;
   cur = last = blist;
   while (cur->next != NULL)
   {
      last = cur;  cur = cur->next;
   }
   if (cur != blist)
   {
      free(cur);
      last->next = NULL;
      free_blist(last);
   }
   else free(blist);

}  /* end of free_blist */

/*=======================================================================
    ftype == 0 => use freqs (TN distribution)
    ftype == 1 => use obs_freqs (TP distribution)
========================================================================*/
int pssmdist(matrix, ftype, freqs, obs_freqs)
Matrix *matrix, *obs_freqs;
int ftype;
double *freqs;
{
  struct score_struct *last, *this, ends[MAXSCORE];
  struct score_struct middle[MAXSCORE], scores[2][MAXSCORE];
  int col, aa, minvalue, maxvalue, minscore, maxscore, mincol, maxcol;
  int x, score, minfirst, minlast;
  double cum, aligns, report, ftemp, dtemp, probwt[MAXWIDTH];

  /*   compute which score to report */
  if (ftype == 1) report = (double) 0.5 * TPS;		/* median TP */
  else            report = (double) 0.005 * Search;	/* 99.5% TN  */
  minscore = maxscore = 0;
  maxvalue = -1;		/* assumes no negative scores */
  minvalue = 9999;
  probwt[0] = 20.0;
  for (col = 0; col < matrix->width; col++)
  {
     /*  Intialize probability weights with powers of 20 */
     if (col > 0) probwt[col] = probwt[col - 1] * 20.0;
     mincol = 9999; maxcol = -1;
/*   for (aa = 0; aa < AASALL; aa++) */
     for (aa = 1; aa <= 20; aa++)
     {
        if (matrix->weights[aa][col] > maxvalue)
            maxvalue = matrix->weights[aa][col];
	if (matrix->weights[aa][col] < minvalue)
	    minvalue = matrix->weights[aa][col];
        if (matrix->weights[aa][col] > maxcol)
            maxcol = matrix->weights[aa][col];
	if (matrix->weights[aa][col] < mincol)
	    mincol = matrix->weights[aa][col];
     }
     maxscore += maxcol;
     minscore += mincol;
     if (col == 0) minfirst = mincol;
     if (col == (matrix->width - 1) ) minlast = mincol;
   }
   /*    Probability weights: weights applied to probs depending
         on how many columns of the block are aligned, the
         full alignment width gets about 19/21 = .905, alignments
         off either end of the sequence get the remainder */
   dtemp = probwt[matrix->width - 1] * 21.0 - 40.0;
   cum = 0.0;
   for (col = 0; col < matrix->width; col++)
   {
      probwt[col] = probwt[col] * 19.0 / dtemp;
      cum += probwt[col];
      if (col < matrix->width - 1) cum += probwt[col];
   }
   /* ---- Min. score could be just first or last column ----*/
   if (minfirst < minscore) minscore = minfirst;
   if (minlast < minscore)  minscore = minlast;
/*
   if (ftype == 1) printf("\nTrue positive distribution\n");
   else            printf("\nRandom distribution\n");
   printf("minscore without ends=%d\n", minscore);
   printf("minvalue=%d maxvalue=%d minscore=%d maxscore=%d\n",
	   minvalue, maxvalue, minscore, maxscore);
*/
   /*-----------------------------------------------------------------*/
   if (maxscore > MAXSCORE) maxscore = MAXSCORE - 1;
   last = scores[0]; this = scores[1];
   for (x = minvalue; x <= maxscore; x++)
   {  last[x].ways = last[x].prob = this[x].ways = this[x].prob = 0.0; 
      ends[x].ways = ends[x].prob = middle[x].ways = middle[x].prob = 0.0; }

   /*---------Initialize from first column -------------------------------*/
   /*   use obs_freqs->weights[aa][col] instead of freqs[aa] for TP probs */
   col = 0;
/* for (aa=0; aa < AASALL; aa++) */
   for (aa=1; aa <= 20; aa++)
   {
      x = matrix->weights[aa][col];
      last[x].ways += 1.0;
      if (ftype == 1) ftemp = obs_freqs->weights[aa][col] / 100.;
      else            ftemp = freqs[aa];
      last[x].prob += ftemp;   
   }

   /*---- Now enumerate all possible scores, expanding one column
          at a time ----------*/
   for (col=1; col < matrix->width; col++)
   {
      /*--------- Save the alignments hanging off the left end ------*/
      /*    There are currently col+1 columns of the block aligned  */
      for (x=minvalue; x <= maxscore; x++)
      {
            ends[x].ways += last[x].ways;
            ends[x].prob += last[x].prob * probwt[col - 1];
      }
/*    for (aa=0; aa < AASALL; aa++) */
      for (aa=1; aa <= 20; aa++)
      {
         for (x=minvalue; x <= maxscore; x++)
         {
            if (last[x].ways > 0)
            {
               score = x + matrix->weights[aa][col];
               this[score].ways += last[x].ways;
               if (ftype == 1) ftemp = obs_freqs->weights[aa][col] / 100.;
               else            ftemp = freqs[aa];
               this[score].prob += last[x].prob * ftemp;
            }
         } /* end of score x */
      }  /* end of aa */
      /*---------   Switch the arrays ------------------------------*/
      if (this == scores[1])
      {  last = scores[1]; this = scores[0]; }
      else
      {  last = scores[0]; this = scores[1]; }
      for (x = minvalue; x <= maxscore; x++)
      {  this[x].ways = this[x].prob = 0.0;  }
   }  /* end of col */

   /*-------- last now has the final counts of all combinations
      of column scores for full blocks, and ends has the counts
      for alignments off the left end. Still have to get counts
      for alignments off the right end and need two arrays to do
      it. So have to keep last results in another array--------*/
   for (x=minvalue; x <= maxscore; x++)
   {
	middle[x].ways = last[x].ways;
	middle[x].prob = last[x].prob * probwt[matrix->width - 1];
	last[x].ways = last[x].prob = 0.0;
   }

   /*-------- Get the alignments hanging off the right end -------*/
   /*    Initialize with last column   */
   col = matrix->width - 1;
   for (aa=1; aa <= 20; aa++)
   {
      x = matrix->weights[aa][col];
      last[x].ways += 1.0;
      if (ftype == 1) ftemp = obs_freqs->weights[aa][col] / 100.;
      else            ftemp = freqs[aa];
      last[x].prob += ftemp;   
   }
   for (col = matrix->width - 2; col >= 1; col--)
   {
      /*--------- Save the gapped alignments off the right end ------*/
      /*  There are currently length-col columns of the block aligned */
      for (x=minvalue; x <= maxscore; x++)
      {
            ends[x].ways += last[x].ways;
            ends[x].prob += last[x].prob * probwt[matrix->width - col - 2];
      }
      for (aa=1; aa <= 20; aa++)
      {
         for (x=minvalue; x <= maxscore; x++)
         {
            if (last[x].ways > 0)
            {
               score = x + matrix->weights[aa][col];
               this[score].ways += last[x].ways;
               if (ftype == 1) ftemp = obs_freqs->weights[aa][col] / 100.;
               else            ftemp = freqs[aa];
               this[score].prob += last[x].prob * ftemp;
            }
         } /* end of score x */
      }  /* end of aa */
      /*---------   Switch the arrays ------------------------------*/
      if (this == scores[1])
      {  last = scores[1]; this = scores[0]; }
      else
      {  last = scores[0]; this = scores[1]; }
      for (x = minvalue; x <= maxscore; x++)
      {  this[x].ways = this[x].prob = 0.0;  }
   }  /* end of column */
   /*--------- Save the gapped alignments off the right end ------*/
   /*  Need to get the length - 1 counts from the right   */
   for (x=minvalue; x <= maxscore; x++)
   {
         ends[x].ways += last[x].ways;
         ends[x].prob += last[x].prob * probwt[matrix->width - 2];
   } 

   /*   number of alignments done in a hypothetical search   */
   /*   Always assume one alignment per TP sequence          */
   if (ftype == 1) aligns = TPS;
   else aligns = (double) SearchAA + Search * (matrix->width - 1); 

   /* Count the TP scores above 99.5% of TN scores, x is the score */
   if (ftype == 1 && TN995 > 0)
   {
      x = maxscore; TPabove = 0.0;
      while (x > TN995)
      {
         if (middle[x].prob > 0.0 || ends[x].prob > 0.0)
         {
            TPabove += (middle[x].prob + ends[x].prob) * aligns;
         }
         x--;
      }
   }

   /* Print the top scores, x is the score */
   x = maxscore; cum = 0.0;
/*
   printf("\nCum      Score   Expected\n");
*/
   while (cum < report && x >= 0)
   {
       if (middle[x].prob > 0.0 || ends[x].prob > 0.0)
       {
/*
          if (cum > 100.0)
             printf("%8.4f %4d %8.4f\n", 
		cum, x, (middle[x].prob + ends[x].prob) * aligns);
*/
          cum += (middle[x].prob + ends[x].prob) * aligns;
       }
       x--;
   }
   if (ftype == 1) printf("Median TP score = %d, TPabove = %d\n",
                           x, TPabove);
   else            printf("99.5 TN score = %d\n", x);
   return(x);
}  /* end of pssmdist */
/*================================================================
    fix_ac() updates distances on the block->ac line
	block->ac = "PS00094A; distance from previous block=(0,1141)"
================================================================*/
void fix_ac(blist)
struct blocks_list *blist;
{
   sprintf(blist->block->ac, "%s; distance from previous block=(%d,%d)",
           blist->block->number, blist->mindist, blist->maxdist);
} /* end of fix_ac */
/*=====================================================================
    Add a cluster pointing to the last sequence in the block
    Blimps assumes the sequences are in cluster order within the block
=======================================================================*/
void add_cluster(block)
Block *block;
{
   /*  Open up an extra cluster for the additional sequences */
   if (block->num_clusters + 1 > block->max_clusters)
   {
      resize_block_clusters(block);  /* updates block->max_clusters */
   }
   /*  First sequence will have been added to last cluster */
   block->clusters[ block->num_clusters - 1 ].num_sequences -= 1;
   block->clusters[ block->num_clusters ].num_sequences = 1;
   block->clusters[ block->num_clusters ].sequences = 
          &(block->sequences[ block->num_sequences - 1 ]);
   block->num_clusters += 1;
}  /* add_cluster */
/*=====================================================================
   Write sequence to fout in fasta format from inpos to maxpos
=======================================================================*/
void write_seq(fout, seq, minpos, maxpos)
FILE *fout;
Sequence *seq;
int minpos, maxpos;
{
   int min, max, pos;

   min = 9999; max = -9999;

   if ((minpos < 0) || (maxpos > seq->length) || (maxpos < minpos))
   {
	printf("Cannot write %s of length %d from %d to %d\n",
            seq->name, seq->length, minpos, maxpos);
   }
   else
   {
      min = minpos - 10;
      if (minpos < 0) minpos = 0;
      max = maxpos + 10;
      if (maxpos > seq->length) maxpos = seq->length;
      fprintf(fout, ">%s %s from %d to %d\n", 
	seq->name, seq->info, min+1, max+1);
      for (pos=min; pos < max; pos++)
      {
          /*  assuming seq->type == AA_SEQ here ... */
          fprintf(fout, "%c", aa_btoa[seq->sequence[pos]]);
          if ((pos+1)%60 == 0) { fprintf(fout, "\n");  }
      }
      fprintf(fout, "\n");
   }
}  /* end of write_seq  */

/*=======================================================================*/
/*  Sequences may not be in the same order both blocks. If not, then
    set sseq[s1] = s2  where
    b1->sequences[s1].name == b2->sequences[s2].name
=========================================================================*/
void order_seq(sseq, b1, b2)
struct seqseq *sseq;
Block *b1, *b2;
{
   int nseq, i1, i2;

   nseq = b1->num_sequences;
   if (b2->num_sequences < nseq) nseq = b2->num_sequences;
   for (i1 = 0; i1 < nseq; i1++)
   {
      if (b1 == b2) sseq[i1].seq = i1;
      else
      {
         sseq[i1].seq = -1;
         i2 = 0;
         while (sseq[i1].seq < 0 && i2 < nseq)
         {
            if (strcmp(b1->sequences[i1].name, b2->sequences[i2].name) == 0)
               sseq[i1].seq = i2;
            i2++;
         }
      }
   }
}  /*  end of order_seq */

/*=======================================================================
       Indicate which blocks are to be used for this
       sequence; in order, etc. if it matters 
       assemble_hit(blist): look at last sequence, 
        last = blist->block->num_sequences - 1
        look at blist->block->sequences[last].position,
                blist->bestscore, blist->bestpos
	flag    blist->block->sequences[last].undefined
=======================================================================*/
void assemble_hit(blist, minpos, maxpos)
struct blocks_list *blist;
int *minpos, *maxpos;
{
   struct blocks_list *bcur, *bprev;
   struct btemp *btemp;
   int i, j, qseq;

   btemp = (struct btemp *) malloc(blist->nblock * sizeof(struct btemp));

   bcur = blist->next; bprev = NULL;
   i = 0;
   while (bcur != NULL && bcur->block != NULL)
   {
      btemp[i].score = bcur->bestscore;
      btemp[i].bnum = i+1;
      btemp[i].blist = bcur;
      bcur->block->undefined = NO;
      i++;
      bprev = bcur;
      bcur = bcur->next;
   }
   /*	descending sort by maxscore  */
   qsort(btemp, blist->nblock, sizeof(struct btemp), btempcmp);

   /*  Just checking overlap not distance here   */
   btemp[0].blist->block->undefined = YES;		/* anchor block */
   qseq = btemp[0].blist->block->num_sequences - 1;
   for (i=1; inblock; i++)
   {
      btemp[i].blist->block->undefined = YES;
      for (j=0; jblock->undefined &&
             ( (btemp[j].blist->bestscore < CutOff) ||
               (btemp[i].bnum < btemp[j].bnum && 
                btemp[i].blist->endpos > btemp[j].blist->bestpos) ||
               (btemp[i].bnum > btemp[j].bnum &&
                btemp[i].blist->bestpos < btemp[j].blist->endpos) ) )
         {
               btemp[i].blist->block->sequences[qseq].undefined = NO;
               btemp[i].blist->block->undefined = NO;
         }
      }
   }
   /*---Not update minpos & maxpos for good blocks---------------*/
   *minpos = *maxpos; *maxpos = -999; 
   bcur = blist->next;
   while (bcur != NULL && bcur->block != NULL)
   {
      if (bcur->block->sequences[qseq].undefined)
      {
         if (bcur->block->sequences[qseq].position < *minpos)
                    *minpos = bcur->block->sequences[qseq].position;
         if (bcur->block->sequences[qseq].position > *maxpos)
                    *maxpos = bcur->block->sequences[qseq].position;
      }
      bcur = bcur->next;
   }

   free(btemp);
}  /* end of assemble_hit */

/*=====================================================================
   btempcmp sorts a btemp structure in descending order by value
=====================================================================*/
int btempcmp(t1, t2)
struct btemp *t1, *t2;
{
   double diff;
  
   diff = t2->score - t1->score;
   if (diff > 0.0) return(1);
   else if (diff < 0.0) return(-1);
   else return(0);

}  /*  end of btempcmp */

/*=========================================================================
???used in addseqs???
Computes and prints distance matrix
"Distances" are the segment pair scores.

"Correlations" are really percentages of max possible score of a given pair
of sequences: E.G. for:
	WIVNRA
	WLFKQA

	WW=11, II=4/LL=4, VV=4/FF=6, NN=6/KK=5, RR=5/QQ=5, AA=4 => 
		max score = 11+4+6+6+5+4 = 36
	IL=2, VF=-1, NK=0, RQ=1 =>
		act score = 11+2-1+0+1+4 = 17, 17/36 = 0.47 = "correlation"
Completely conserved segment pair always has corr = 1.0, but segment pair
scores could be negative ...

=========================================================================*/
void compute_dist(ofp, mtype, nseq, seqs, mat)
FILE *ofp;
int mtype;		/* output matrix type */
int nseq;
Sequence *seqs[MAXSEQ];
struct float_qij *mat;
{
   int length, s1, s2, aa1, aa2, pos;
   double dist[MAXSEQ][MAXSEQ], maxdist, meandist, maxscore, dtemp;

   maxdist = -999;
   meandist = 0.0;

   for (s1=0; s1length;
      for (s2=s1; s2length < length)
         {
            printf("WARNING: sequence segments are of different lengths\n");
            printf("%s %d : %s %d\n", seqs[s1]->name, seqs[s1]->length,
		                     seqs[s2]->name, seqs[s2]->length);
            length = seqs[s2]->length;
         }
         dist[s1][s2] = maxscore = 0.0;
         for (pos=0; possequence[pos];
            aa2 = seqs[s2]->sequence[pos];
            dist[s1][s2] += mat->value[aa1][aa2];
	    dtemp = mat->value[aa1][aa1];
	    if (mat->value[aa2][aa2] > dtemp) dtemp = mat->value[aa2][aa2];
	    maxscore += dtemp;
         }
         if (mtype == 3) 
         {
            dist[s1][s2] /= maxscore;
            /* This is not a proper "correlation" ... */
            if (dist[s1][s2] >  1.0) dist[s1][s2] =  1.0;
            if (dist[s1][s2] < -1.0) dist[s1][s2] = -1.0;
         }
    
      }
   }

   /*  Now dist is similarity matrix, probably
       with unequal diagonal values => some seqs
       are more similar to themselves than others.
       Subtract all entries from max value to make
       a dissimilarity matrix */
   for (s1=0; s1 maxdist)
              maxdist = dist[s1][s2];
         if (s1 != s2)
		 dist[s2][s1] = dist[s1][s2];
      }
   }
   /*  Average score includes diagonals   */
   dtemp = (double) nseq * (nseq + 1.0) / 2.0;
   meandist /= dtemp;
   printf("Mean dissimilarity distance = %.2f\n",
           (maxdist - meandist) );

   /*  Print dissim. matrix for SAS, requires full matrix, max linesize=256 */
   /*  Proc varclus requires a covariance matrix as input ... */
   for (s1=0; s1name);
      for (s2=0; s2 strlen(name2))
   {   strcpy(name2, name1);  }
   
   return(match);

}  /* end of compare_names */
 an extra cluster for the additional sequences */
   if (block->num_clusters + 1 > block->max_clusters)
   {
      resize_blocblimps-3.9/blimps/biassed_blocks_finder.c000064400001460000012000000155450775574277400211400ustar00jorjastaff00000400000027/*  Copyright 1997-2000: 
      Fred Hutchinson Cancer Research Center, Seattle, WA, USA
	biassed_blocks_finder   Find compositionally biassed blocks       */

/*--------------------------------------------------------------------------
11/15/97 Moved home directory defs to homedir.h
 6/ 4/00 Updated for new find_biassed_blocks
11/15/03 Add to blimps programs
===========================================================================*/
/* blimps stuff */
#define EXTERN

#include 

typedef struct {
    char *name;
    char *val;
} entry;

/* from util.c */
/*
char *makeword(char *line, char stop);
char *fmakeword(FILE *f, char stop, int *len);
char x2c(char *what);
void unescape_url(char *url);
void plustospace(char *str);
*/
 
entry entries[10000];

#define MAX_BLOCKS 10
#define PROGRAM_DBGLVL 3
#define PROGRAM_SCORECUTOFF 0.50
#define PROGRAM_FRACTIONCUTOFF 0.25

#define TMP_SUBDIR   "../tmp"
#define BIN_SUBDIR   "./blimps-bin"

char Block_file[LARGE_BUFF_LENGTH];
char find_biassed_blocks[LARGE_BUFF_LENGTH] ;
char program_output[LARGE_BUFF_LENGTH] ;
char error_file[LARGE_BUFF_LENGTH];
char tmp_dir[LARGE_BUFF_LENGTH];
char buf[LARGE_BUFF_LENGTH];

int pid;

entry *BLOCK_Ptr = NULL;

void read_startup_info()
{
  int i;
  char *script, *ptr;

  script = getenv("SCRIPT_NAME");

  pid = getpid();

  sprintf(find_biassed_blocks, "%s/find_biassed_blocks", BIN_SUBDIR);
  sprintf(program_output, "%s/%d.biassed_blocks_out", TMP_SUBDIR, pid);

  sprintf(Block_file, "%s/%d.blk", TMP_SUBDIR, pid);

  sprintf(tmp_dir, "%s", TMP_SUBDIR);

}   /*  end of read_startup_info */


int parse()
{
/* parse the input */

  register int i,num_entries=0;
  char *entry_string;
  int cl;

  /* check that there is something to use. */
  entry_string = getenv("QUERY_STRING");

/*
  if (entry_string == NULL) 
     {
     printf("No query information to decode.\n");
     exit(1);
     }
*/

  /* parse the query string into individual entries */

  cl = atoi(getenv("CONTENT_LENGTH"));

  for(i=0;cl && (!feof(stdin));i++) 
     {
     num_entries=i;
     entries[i].val = fmakeword(stdin,'&', &cl);
     plustospace(entries[i].val);
     unescape_url(entries[i].val);
     entries[i].name = makeword(entries[i].val,'=');

     if (!strncmp(entries[i].name, "BLOCK", 5)) 
        {
	BLOCK_Ptr = &entries[i]; 
        }

    }


  return num_entries;
} /*  end of parse */


void clean_temp_files()
{
  sprintf(buf, "rm -f %s/%d*temp", TMP_SUBDIR, pid); 
  system(buf);
}


void write_block()
{
  FILE  *bfp, *efp ;
  Block *block ;
  int   blocks_num ;


  /* check that a block was specified */
  if (BLOCK_Ptr->val[0] == NULL) 
    {
      printf("
      Error
      \n");
      printf("You need to enter a block by writing or pasting a block in the window.
      \n");
      exit(0);
    }
  

  /* open error_file so that error messages from read_a_block can be examined*/
  sprintf(error_file, "%s/%d.block_errors", TMP_SUBDIR, pid);
  set_error_file_name(error_file) ;     



  /* if block was pasted/written - */
  if (BLOCK_Ptr->val[0] != NULL)
    {
      
      /* open up the block file to write to */
      bfp = fopen(Block_file, "w");
      
      fprintf(bfp, "%s\n",BLOCK_Ptr->val);

/* add "//" to the file end. 
   This is done to over come the fact that read_a_block does not detect if the 
   end of block signal (//) is missing and the program crashes later. */
      fprintf(bfp, "//\n");

      /* close and reopen block file in a read mode */
      fclose(bfp);
      bfp = fopen(Block_file, "r");
      
      
      blocks_num = 0 ;
      
      /* read-in blocks to check their format and content */
      while ((block = read_a_block(bfp)) != NULL)
        {
	  blocks_num++ ;
	  
	  /* try and open error file to see if there were any errors */
	  if ((efp = fopen(error_file, "r")) != NULL) 
	    {
	      printf("
      Error
      \n");
	      printf("There seems to be an error in the format of block number %d:
      ", blocks_num);
	      
	      printf("
      \n");
	      while((buf[0]=getc(efp)) != EOF) putchar(buf[0]) ; 
	      printf("
      ") ;
	      
	      fclose(efp) ;
	      
	      clean_temp_files() ;
	      
	      exit(1);
	    }
	  
        }
      
      if (blocks_num <= 0) 
	{
	  printf("
      Error
      \n");
	  printf("No blocks were read.\n");
	  clean_temp_files() ;
	  exit(1);
	}

      if (blocks_num > MAX_BLOCKS) 
	{
	  printf("
      Error
      \n");
	  printf("Sorry, you can not check more than %d blocks each time.\n", 
                 MAX_BLOCKS);
	  clean_temp_files() ;
	  exit(1);
	}
      
      
      fclose(bfp);
    } /* end if (Block_Ptr->val[0] != NULL) */
} 
  

/**********************************************************************/
/*
run find_biassed_blocks
*/
void run_program()
{

  sprintf(buf, "%s %s %f %f %d > %s 2>&1", 
          find_biassed_blocks, Block_file, 
          PROGRAM_SCORECUTOFF, PROGRAM_FRACTIONCUTOFF, PROGRAM_DBGLVL, 
          program_output);

  if (system(buf)) {
    printf("
      Program Error
      \n");
    printf("An error occured during the execution.\n");
    printf("Please try again at a later time.\n");
    printf("If it fails again contact the maintainer of these pages\n");
    printf("and describe what caused the problem with an example.
      \n");

    clean_temp_files() ;

    exit(0);
  }

}  /*  end of run_program */

/**********************************************************************/

void display_output()
{

  FILE *outf;

  printf("Biassed Blocks Results\n");
  printf("
      Biassed Blocks Results
      \n");
  printf("
      \n") ;

  if ((outf = fopen(program_output, "r")) == NULL)
     {
     printf("Error opening program output file.\n") ;

     clean_temp_files() ;

     exit(1) ;
     }


  printf("
      \n");
  while (!feof(outf) && fgets(buf, LARGE_BUFF_LENGTH, outf) != NULL)
     printf(buf) ; 
  printf("
      \n"); 

  fclose(outf);

}

/**********************************************************************/

void main(int argc, char *argv[]) {

  printf("Content-type: text/html\n\n\n");


  if(strcmp(getenv("REQUEST_METHOD"),"POST")) {
    printf("This script should be referenced with a METHOD of POST.\n");
    printf("If you don't understand this, see this ");
    printf("forms overview.%c",10);

    printf("
      What could have happened is that you just reloaded this page rather than redoing the search.\n");

    printf("
      If you use NETSCAPE it has a tendency to try to reload a page when you go back to it.  This may be why you have this error.\n");

    exit(1);
  }

  if(strcmp(getenv("CONTENT_TYPE"),"application/x-www-form-urlencoded")) {
    printf("This script can only be used to decode form results. \n");
    exit(1);
  }

  /*    Set file permissions to "rw-rw----"     */
  system("umask 006");

  read_startup_info();

  parse();

  write_block();
  
  run_program();

  display_output(); 

  clean_temp_files() ;

  exit(0) ;
}

blimps-3.9/blimps/blDR.c000064400001460000012000000116561016241426100154310ustar00jorjastaff00000400000027/*   
  blDR.c:  blDR   
           Read blocks, look up sequences in a file of sequences,
	   rewrite sequence names in blocks, write an output file
           for the DR line of Swiss-Prot:

DR   BLOCKS; BL00405; 43_KD_POSTSYNAPTIC.
Q13702
P12672
P09108
//
--------------------------------------------------------------------
 6/ 9/99 J.Henikoff
 6/ 9/03 Free up memory
====================================================================*/

#define BLDR_C_
#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#include "blocksprogs.h"

struct name_list 
{ 
  char name[MAXNAME];
  struct name_list *next;
};
void revise_names();

/*=======================================================================*/
/*
 * main
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
   FILE *bfp, *sfp, *ofp;
   Block *block;
   int i;
   char bdbname[MAXNAME], sdbname[MAXNAME], outname[MAXNAME], ctemp[MAXNAME];
   char lastac[10];
   Sequence *seq;
   struct name_list *dbnames, *db, *new;

   ErrorLevelReport = 2;

   if (argc < 3)
   {
      printf("COPYRIGHT 1999, Fred Hutchinson Cancer Research Center\n");
      printf("blDR   \n");
   }
   /* ------------1st arg = blocks database -------------------------------*/
   if (argc > 1) strcpy(bdbname, argv[1]);
   else
   {
      printf("\nEnter name of blocks database: ");
      gets(bdbname);
   }
   if ( (bfp=fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbname);
      exit(-1);
   }
   /* ------------2nd arg = sequence database ---------------------*/
   if (argc > 2) strcpy(sdbname, argv[2]);
   else
   {
      printf("\nSequence database must be in fasta format:");
      printf("\nEnter name of sequence database: ");
      gets(sdbname);
   }
   if ( (sfp=fopen(sdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", sdbname);
      exit(-1);
   }
   /* ------------3rd arg = new blocks database ---------------------*/
   if (argc > 3) strcpy(outname, argv[3]);
   else
   {
      printf("\nEnter name of new blocks database: ");
      gets(outname);
   }
   if ( (ofp=fopen(outname, "w")) == NULL)
   {
      printf("\nCannot open file %s\n", outname);
      exit(-1);
   }

   /*------------------------------------------------------------------*/
   /* Make a list of all the database sequence names */
   dbnames = (struct name_list *) malloc (sizeof(struct name_list));
   dbnames->next = NULL;
   db = dbnames;
   while( (seq = read_a_sequence(sfp, FASTA, AA_SEQ)) != NULL)
   {
      if ((int) strlen(seq->name) > MAXNAME) { seq->name[MAXNAME] = '\0'; }
      new = (struct name_list *) malloc (sizeof(struct name_list));
      strcpy(new->name, seq->name);
      new->next = NULL;
      db->next = new;
      db = new;
      free_sequence(seq);
   }
   close(sfp);

   /*-----------------------------------------------------------------*/
   lastac[0] = '\0'; 
   while ((block = read_a_block(bfp)) != NULL)
   {
     strcpy(ctemp, block->ac); ctemp[7] = '\0';
     if (strcmp(lastac, ctemp) != 0)
     {
         revise_names(block, dbnames, TRUE);  /* DR output 1st block of fam */
         strcpy(lastac, ctemp);
     }
     else
     {
         revise_names(block, dbnames, FALSE);
     }
     output_block(block, ofp, INT_OUTPUT);
     free_block(block);
   }
   
   fclose(bfp); fclose(ofp);
   exit(0);

}  /* end of main */


/*=======================================================================
     Find ID in sequence database, which is assumed to have title lines:

	>ID|AC

     Then change names to from "ID" to "ID|AC" in block
*/
void revise_names(block, dbnames, drflag)
Block *block;
struct name_list *dbnames;
int drflag;
{
   int s, done;
   char ctemp[MAXNAME], *ptr;
   struct name_list *db;

   if (drflag)
   {
      strcpy(ctemp, block->ac); ctemp[7] = '\0';
      printf("DR   BLOCKS; %s; %s\n", ctemp, block->de);
   }

   /*  Compare each block seq name vs list of db seq names */
   for (s=0; s< block->num_sequences; s++)
   {
      done = 0;
      db = dbnames->next;
      while (!done && db != NULL)
      {
        strcpy(ctemp, db->name);
        ptr = strtok(ctemp, "|");
        if (ptr != NULL)  /* don't bother if no "|" in seq->name */
        {
           if (strcmp(block->sequences[s].name, ctemp) == 0)
           {
               /* only want ID|AC, not ID|AC|AC|...  */
               strcpy(block->sequences[s].name, db->name);
               done = 1;
               if (drflag)
               {
                  if (ptr != NULL)
                  { 
                     ptr = strtok(NULL, "\0");
                     if (ptr != NULL) printf("%s\n", ptr);
                     else { printf("%s\n", db->name); }
                  }
                  else { printf("%s\n", db->name); }
               }
           }
        }
        db = db->next;
      }  /* end of dbnames seq db */
   }   /* end of block seq s */

   if (drflag) printf("//\n");
}  /*end of revise_names */
fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbnameblimps-3.9/blimps/blalign.c000064400001460000012000000660431054326002600162170ustar00jorjastaff00000400000027/*  COPYRIGHT 1994-2003 Fred Hutchinson Cancer Research Center
    blalign.c    Print blocks as multiple alignment      
        blalign  -[p|s|f|m|g]
          = name of blocks db file, aligns each group
         p|s|f = p for Posfai style, s for short style, f for fasta style,
		 m for MSF style, for giant block

	Requires blimps 3.2.6+ to compile.
--------------------------------------------------------------------
 4/21/94 J. Henikoff (from blcovar.c)
 4/26/94 Added option for "Posfai" or abbreviated style of output
 6/23/94 Print number of sequences and block widths
 8/12/96 Added fasta style output
 2/19/97 Added output width parameter = OutWidth
 8/27/97 More spaces in name for format -f
 2/25/98 Format changes for -f per Shmuel
10/20/98 Fix abort problem if different #seqs in blocks
 1/29/99 Longer sequence names (10->15)
 5/19/99 Added MSF format
 6/14/99 Adjustments for longer sequence names (10->18 chars)
 8/23/99 Add offset to seqname when fasta style so clustalw is sure
	 to get unique names from prints blocks
12/14/99 Added g option to output one giant block.
12/17/99 Accomodate ACs from 7 to 10 chars wide.
12/18/02 Output STOCKHOLM format for quicktree
 8/11/03.1 Fix STOCKHOLM format when blocks overlap: format_seqs().
 8/24/03.1 STOCKHOLM format without gaps (style=q=6)
 8/25/03.1 Pre-sort sequences in each block (namecmp())
 8/27/03.1 Fix block->residues in sorted blocks
12/23/06.1 Increased sequence name length
====================================================================*/

#define BLALIGN_C_
#define EXTERN
#define MAXNAME 80	/* Maximum file name length */
#define MAXAA 25	/* Dimension of aa_ arrays */
#define MAXWIDTH 60	/* Maximum block width */
#define OUTWIDTH 80	/* Default output line */
#define OUTMAX 240	/* Maximum output line width */
#define MAXLEN 4000	/* Maximum sequence length */
#define FLZERO 0.0000001
#define INDEX(n, col, row) (col*n + row - (col*(col+1))/2)

#include 


/*
 * Local variables and data structures
 */

/*  first entry has no block, just nblock & totwidth, other entries
    in list have just pointers to the blocks */
/* >>> NOT the same as block_list in protomat.h <<< */
struct blocks_list {		/* list of blocks for a family */
   int nblock;				/* number of blocks in family */
   char fam[MAXAC+1];			/* family name */
   int nseq;				/* number of sequences in blocks */
   int totwidth;			/* total width of the blocks */
   Block *block;
   struct blocks_list *next;
};
struct seqseq {			/* reorder sequences */
   int seq;
   int pos;
};
struct align {			/* alignment line */
   char line[MAXLEN];
};

struct blocks_list *make_blist();
void insert_blist();
void free_blist();
void order_seq();
int print_align();
void format_seqs();
void posfai_seqs();
void short_seqs();
void fasta_seqs();
void msf_seqs();
void stockholm_seqs();
void giant();
int namecmp();

int OutWidth;			/* width of output */

double frequency[MATRIX_AA_WIDTH];    /* for frequency.c */
char Version[12] = "12/23/06.1";                /* Version date */


/*=======================================================================
 * main
 =======================================================================*/

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *bfp;
  Block *block;
  struct blocks_list *blist;
  int np, style;
  char bdbname[MAXNAME], save_family[MAXAC+1];

   if (argc < 2)
   {
      printf("BLALIGN Version %s\n", Version);
      printf("Copyright 1999-2003 Fred Hutchinson Cancer Research ");
      printf("Center\nPrints blocks as a multiple alignment.\n");
      printf("USAGE:  blalign  [-p|s|f|m|h|q|g] [width]\n");
      printf("          p=Posfai style, s=short style, f=fasta style,\n");
      printf("          m=MSF style, h=STOCKHOLM style, q=ungapped STOCKHOLM,\n");
      printf("          g=giant block\n");
      printf("          defaults are short style, width = 66\n");
   }

/* ------------1st arg = blocks database -------------------------------*/
   if (argc > 1)
      strcpy(bdbname, argv[1]);
   else
   {
      printf("\nEnter name of file of blocks: ");
      gets(bdbname);
   }
   if ( (bfp=fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbname);
      exit(-1);
   }
/*----------2nd arg = p or s -------------------------------------------*/
   style = 0; 			/* short*/
   if (argc > 2 && argv[2][0] == '-')
   {
	if      (argv[2][1] == 'p' || argv[2][1] == 'P') style = 1;
	else if (argv[2][1] == 'f' || argv[2][1] == 'F') style = 2;
	else if (argv[2][1] == 'm' || argv[2][1] == 'M') style = 3;
	else if (argv[2][1] == 'g' || argv[2][1] == 'G') style = 4;
	else if (argv[2][1] == 'h' || argv[2][1] == 'H') style = 5;
	else if (argv[2][1] == 'q' || argv[2][1] == 'Q') style = 6;
   }
   
/*-----------3rd arg = output width -----------------------------------*/
   OutWidth = OUTWIDTH;
   if (argc > 3) OutWidth = atoi(argv[3]);
   if (OutWidth < 1 || OutWidth > OUTMAX) OutWidth = OUTWIDTH;

/*----------------------------------------------------------------------*/
  save_family[0] = '\0';
  blist = NULL;
  while ((block = read_a_block(bfp)) != NULL)
  {
     if (strcmp(save_family, block->family) != 0)
     {       /*  new family  */
        /*  process last family */
        if (blist != NULL && blist->nblock > 0)
        {
           np = print_align(blist, style);
           free_blist(blist);
        }
        strcpy(save_family, block->family);
        if (style < 2) printf(">%s %s\n", save_family, block->de);
        blist = make_blist();
        insert_blist(blist, block);
     }
     else    
     {     /*  same family */
        insert_blist(blist, block);
     }
  }
  /*  process final family */
  if (blist != NULL && blist->nblock > 0)
  {
     np = print_align(blist, style);
     free_blist(blist);
  }

  fclose(bfp);
  exit(0);

}  /* end of main */
/*=======================================================================
     routines for a list of blocks
========================================================================*/
struct blocks_list *make_blist()
{
   struct blocks_list *new;
   
   new = (struct blocks_list *) malloc (sizeof(struct blocks_list));
   new->nblock = new->nseq = new->totwidth = 0;
   new->fam[0] = '\0';
   new->block = NULL;
   new->next = NULL;

   return(new);
}  /* end of make_blist */

void insert_blist(blist, block)
struct blocks_list *blist;
Block *block;
{
   struct blocks_list *cur;
   int seq, pos;

   cur = blist;
   while (cur->next != NULL)
      cur = cur->next;
   cur->next = make_blist();
   cur->next->block = block;
   strcpy(cur->fam, block->family); 
   blist->nblock += 1;
   if (block->num_sequences > blist->nseq)
      blist->nseq = block->num_sequences;
   blist->totwidth += block->sequences[0].length;
   
   /* sort the sequences in the block by name and collapse to 1 cluster*/
/*output_block(block,stdout);*/
   qsort(block->sequences, block->num_sequences, sizeof(Sequence), namecmp);
   block->num_clusters = block->max_clusters = 1;
   block->clusters[0].num_sequences = block->num_sequences;
/*
   block->clusters[0].sequences = block->sequences;
*/
  /*  fix up the residue pointers */
   for(seq=0; seqnum_sequences; seq++)
   {
      block->residues[seq] = block->sequences[seq].sequence; 
   }
/*output_block(block,stdout);*/

}  /* end of insert_blist */

void free_blist(blist)
struct blocks_list *blist;
{
   struct blocks_list *cur, *last;
   cur = last = blist;
   while (cur->next != NULL)
   {
      last = cur;  cur = cur->next;
   }
   if (cur != blist)
   {
      free(cur);
      last->next = NULL;
      free_blist(last);
   }
   else free(blist);

}  /* end of free_blist */
/*=======================================================================
	blist = list of blocks for a group
========================================================================*/
int print_align(blist, style)
struct blocks_list *blist;
int style;
{
   int np, seq;
   int nseq;
   struct blocks_list *bcur, *bfirst;
   struct seqseq *sseq;

   /*     Initialize */
   nseq = blist->nseq;
   sseq = (struct seqseq *) malloc (nseq * sizeof(struct seqseq));
  
   /*   Sequences aren't in the same order in different blocks */
   /*   They are printed in the order of the first block       */

   /*   Do the first block                                     */
   bfirst = blist->next;
   if (bfirst->block == NULL) return(0);

   /*   sseq should be the same for every block after namecmp() */
   for (seq = 0; seq < nseq; seq++)
   {
      sseq[seq].seq = seq;
      sseq[seq].pos = 0;
   }
   format_seqs(sseq, bfirst->block);
   np = 1;

   bcur = bfirst->next;
   while (bcur != NULL && bcur->block != NULL)
   {
      /*  Guard against sets of blocks with unequal numbers of 
	  sequences */
      if (bcur->block->num_sequences == blist->nseq)
      {
         /*  sequences may not be in the same order */
/*
         order_seq(sseq, bfirst->block, bcur->block);
*/
         format_seqs(sseq, bcur->block);
      }
      else
      {
         printf("ERROR in block %s: %d sequences found but ",
		bcur->block->number, bcur->block->num_sequences);
         printf(" %d expected\n", blist->nseq);
      }
      np++;
      bcur = bcur->next;
   } /* end of block */

   if (style < 2)
      printf("%d sequences are included in %d blocks\n", 
           blist->nseq, blist->nblock);
   if (style == 1)      posfai_seqs(sseq, blist);
   else if (style == 2) fasta_seqs(sseq, blist);
   else if (style == 3) msf_seqs(sseq, blist);
   else if (style == 4) giant(sseq, blist);
   else if (style == 5) stockholm_seqs(sseq, blist, 1);
   else if (style == 6) stockholm_seqs(sseq, blist, 0);
   else                 short_seqs(sseq, blist);
   return(np);

}  /* end of print_align */

/*=======================================================================*/
/*  Sequences may not be in the same order both blocks. If not, then
    set sseq[s1] = s2  where
    b1->sequences[s1].name == b2->sequences[s2].name
=========================================================================*/
void order_seq(sseq, b1, b2)
struct seqseq *sseq;
Block *b1, *b2;
{
   int nseq, i1, i2;

   nseq = b1->num_sequences;
   if (b2->num_sequences < nseq) nseq = b2->num_sequences;
   for (i1 = 0; i1 < nseq; i1++)
   {
      if (b1 == b2) sseq[i1].seq = i1;
      else
      {
         sseq[i1].seq = -1;
         i2 = 0;
         while (sseq[i1].seq < 0 && i2 < nseq)
         {
            if (strcmp(b1->sequences[i1].name, b2->sequences[i2].name) == 0)
               sseq[i1].seq = i2;
            i2++;
         }
      }
   }
}  /*  end of order_seq */
/*=======================================================================
        Formats one block: determines how many gaps and unaligned
        positions are required to line up the block in each sequence.

	These values are stored as sequences[].type (gaps) and
        sequences[].max_length (unaligned).
        Updates sseq[].pos values
========================================================================*/
void format_seqs(sseq, b)
struct seqseq *sseq;
Block *b;
{
   int nseq, seq, seq1, posgap, posun;
   int between;

   nseq = b->num_sequences;
   /*    find maximum distance since last block in all sequences */
   between = 0;
   for (seq = 0; seq < nseq ; seq++)
   {
      seq1 = sseq[seq].seq;
      /* be careful, some seqs may overlap slightly in adjacent blocks */
      if (b->sequences[seq1].position > sseq[seq].pos)
      { posun = b->sequences[seq1].position - sseq[seq].pos; }
      else { posun = 0; }
      if (posun > between) between = posun;
   }
   for (seq=0; seq < nseq; seq++)
   {
      seq1 = sseq[seq].seq;
      /*   unaligned region between blocks */
      /* be careful, some seqs may overlap slightly in adjacent blocks */
      if (b->sequences[seq1].position > sseq[seq].pos)
      { posun = b->sequences[seq1].position - sseq[seq].pos; }
      else { posun = 0; }
      /*   gap to accomodate longest unaligned region */
      posgap = between - posun;
      sseq[seq].pos = b->sequences[seq1].position + b->width;
      /*    Reusing these fields !!! */
      b->sequences[seq1].type = posgap;
      b->sequences[seq1].max_length = posun;
   }
}   /* end of format_seqs */
/*==================================================================
      Prints the alignment in the style of Posfai (every position)
====================================================================*/
void posfai_seqs(sseq, blist)
struct seqseq *sseq;
struct blocks_list *blist;
{
   int alen, nseq, seq, seq1, pos, posgap, posun, curpos;
   char ctemp[OUTMAX];
   struct blocks_list *bcur;
   Block *b;
   struct align *out;

   nseq = blist->nseq;
   out = (struct align *) malloc(nseq * sizeof(struct align));
   if (out == NULL)
   {   printf("\nposfai_seqs: OUT OF MEMORY"); exit(-1); }
   for (seq=0; seq < nseq; seq++) out[seq].line[0] = '\0';

   bcur = blist->next;
   while (bcur != NULL && bcur->block != NULL)
   {
      b = bcur->block;
      for (seq=0; seq < nseq; seq++)
      {
/*
         if (bcur->block->num_sequences == blist->nseq)
         {
            order_seq(sseq, blist->next->block, bcur->block);
         }
         else
         {
            printf("ERROR in block %s, found %d sequences but ",
                   bcur->block->number, bcur->block->num_sequences);
            printf("expected %d\n", blist->nseq);
         }
*/
         seq1 = sseq[seq].seq;
         /*   unaligned region between blocks */
         posun = b->sequences[seq1].max_length;
         /*   gap to accomodate longest unaligned region */
         posgap = b->sequences[seq1].type;
         for (pos=0; pos < posgap; pos++)
            strcat(out[seq].line, " ");
         for (pos=0; pos < posun; pos++)
            strcat(out[seq].line, ".");
         sprintf(ctemp, "%5d ", b->sequences[seq1].position);
         strcat(out[seq].line, ctemp);
         for (pos=0; pos < b->width; pos++)
            ctemp[pos] = aa_btoa[b->sequences[seq1].sequence[pos]];
         ctemp[b->width] = '\0';
         strcat(out[seq].line, ctemp);
      }
      bcur = bcur->next;
   }

   alen = strlen(out[0].line);
   b = blist->next->block;
   for (curpos = 0; curpos < alen; curpos += OutWidth)
   {
      for (seq=0; seq < nseq; seq++)
      {
         printf("\n%20s ", b->sequences[seq].name);
         for (pos=curpos; pos < curpos+OutWidth; pos++)
            if (pos < alen)   printf("%c", out[seq].line[pos]);
      }
      printf("\n");
   }
   printf("\n");
}   /* end of posfai_seqs */
/*==================================================================
      Prints the alignment in short style (doesn't print spaces
      between blocks)
====================================================================*/
void short_seqs(sseq, blist)
struct seqseq *sseq;
struct blocks_list *blist;
{
   int alen, nseq, seq, seq1, pos, posun, curpos;
   char ctemp[OUTMAX], header[OUTMAX];
   struct blocks_list *bcur;
   Block *b;
   struct align *out;

   nseq = blist->nseq;
   out = (struct align *) malloc(nseq * sizeof(struct align));
   if (out == NULL)
   {   printf("\nshort_seqs: OUT OF MEMORY"); exit(-1); }
   for (seq=0; seq < nseq; seq++) out[seq].line[0] = '\0';
   header[0] = '\0';

   curpos = 19;   /* seq name width */
   bcur = blist->next;
   while (bcur != NULL && bcur->block != NULL)
   {
      b = bcur->block;

      /*  Page width required to print each block is
              name=19 + distance from last block=8 + offset=6 +
              max block width for blockmaker=55 => 88 max  */
      /*   Print full line */
      if ((curpos + 14 + b->width) > OutWidth)
      {
         printf("\n            %s", header);
         header[0] = '\0';
         for (seq=0; seq < nseq; seq++)
         {
            printf("\n%20s ", blist->next->block->sequences[seq].name);
            printf("%s", out[seq].line);
            out[seq].line[0] = '\0';
         }
         printf("\n");
         curpos = 19;
      }
      curpos += (14 + b->width);

      /*    Format the block  */
      strcat(header, b->number);
      sprintf(ctemp, ", width = %d", b->width);
      strcat(header, ctemp);
      for (seq=0; seq < nseq; seq++)
      {
/*
         if (bcur->block->num_sequences == blist->nseq)
         {
            order_seq(sseq, blist->next->block, bcur->block);
         }
         else
         {
            printf("ERROR in block %s, found %d sequences but ",
                   bcur->block->number, bcur->block->num_sequences);
            printf("expected %d\n", blist->nseq);
         }
*/
         seq1 = sseq[seq].seq;
         /*   unaligned region between blocks */
         posun = b->sequences[seq1].max_length;
         /*  print distance bewteen blocks for this sequence after 1st block*/
         if (bcur != blist->next)
         {
            sprintf(ctemp, " (%4d) ", posun);
            strcat(out[seq].line, ctemp);
         }
         sprintf(ctemp, "%5d ", b->sequences[seq1].position);
         strcat(out[seq].line, ctemp);
         for (pos=0; pos < b->width; pos++)
            ctemp[pos] = aa_btoa[b->sequences[seq1].sequence[pos]];
         ctemp[b->width] = '\0';
         strcat(out[seq].line, ctemp);
      }
      /*   Pad out the header line */
      alen = strlen(header);
      for (pos = alen; pos < strlen(out[0].line); pos++)
         strcat(header, " ");
      bcur = bcur->next;
   }
   /*   Print last block */
   printf("\n            %s", header);
   for (seq=0; seq < nseq; seq++)
   {
      printf("\n%20s ", blist->next->block->sequences[seq].name);
      printf("%s", out[seq].line);
   }

   printf("\n");
}   /* end of short_seqs */
/*==================================================================
      Prints the portion of the sequences in blocks in fasta format
====================================================================*/
void fasta_seqs(sseq, blist)
struct seqseq *sseq;
struct blocks_list *blist;
{
   int nseq, seq, seq1, pos, curpos, endpos;
   char header[OUTMAX], ctemp;
   struct blocks_list *bcur;
   Block *b;
   struct align *out;

   nseq = blist->nseq;
   out = (struct align *) malloc(nseq * sizeof(struct align));
   if (out == NULL)
   {   printf("\nfasta_seqs: OUT OF MEMORY"); exit(-1); }
   for (seq=0; seq < nseq; seq++) out[seq].line[0] = '\0';
   header[0] = '\0';

   for (seq=0; seq < nseq; seq++)
   {
      pos = blist->next->block->sequences[seq].position;
      /*  endpos is only for the first block   */
      endpos = pos + blist->next->block->width;
      printf(">%s|%d              from %10.10s blocks\n",
              blist->next->block->sequences[seq].name,
              pos,
              blist->fam);
      curpos = 0;
      bcur = blist->next;
      while (bcur != NULL && bcur->block != NULL)
      {
         b = bcur->block;
         if (b->num_sequences == blist->nseq)
         {
/*
            order_seq(sseq, blist->next->block, b);
*/
            seq1 = sseq[seq].seq;
/*
            printf("%5d ", b->sequences[seq1].position);
*/
            for (pos=0; pos < b->width; pos++)
            {  
ctemp = aa_btoa[b->sequences[seq1].sequence[pos]];
               printf("%c", aa_btoa[b->sequences[seq1].sequence[pos]]); 
            }
            printf("\n");
         }
/*
         else
         {
            printf("ERROR in block %s, found %d sequences but ",
                   b->number, b->num_sequences);
            printf("expected %d\n", blist->nseq);
         }
*/
         bcur = bcur->next;
      } /* end of blocks */
   }   /*  end of a sequence  */
}   /* end of fasta_seqs */
/*==================================================================
      Prints the alignment in MSF format
====================================================================*/
void msf_seqs(sseq, blist)
struct seqseq *sseq;
struct blocks_list *blist;
{
   int alen, nseq, seq, seq1, pos, posgap, posun, curpos;
   int first, msfwidth;
   char ctemp[OUTMAX];
   struct blocks_list *bcur;
   Block *b;
   struct align *out;

   msfwidth = OutWidth - 29;	/* subtract space required for seq name */
   if (msfwidth < 1) msfwidth = OutWidth;

   nseq = blist->nseq;
   out = (struct align *) malloc(nseq * sizeof(struct align));
   if (out == NULL)
   {   printf("\nmsf_seqs: OUT OF MEMORY"); exit(-1); }
   for (seq=0; seq < nseq; seq++) out[seq].line[0] = '\0';

   printf("//\n");

   bcur = blist->next;
   while (bcur != NULL && bcur->block != NULL)
   {
      b = bcur->block;
      for (seq=0; seq < nseq; seq++)
      {
/*
         if (bcur->block->num_sequences == blist->nseq)
         {
            order_seq(sseq, blist->next->block, bcur->block);
         }
         else
         {
            printf("ERROR in block %s, found %d sequences but ",
                   bcur->block->number, bcur->block->num_sequences);
            printf("expected %d\n", blist->nseq);
         }
*/
         seq1 = sseq[seq].seq;

         if (bcur != blist->next)
         {
            /*   gap to accomodate longest unaligned region */
            posgap = b->sequences[seq1].type;
            for (pos=0; pos < posgap; pos++)
               strcat(out[seq].line, "-");
            /*   unaligned region between blocks */
            posun = b->sequences[seq1].max_length;
            for (pos=0; pos < posun; pos++)
               strcat(out[seq].line, ".");
         }

         for (pos=0; pos < b->width; pos++)
            ctemp[pos] = aa_btoa[b->sequences[seq1].sequence[pos]];
         ctemp[b->width] = '\0';
         strcat(out[seq].line, ctemp);
      }
      bcur = bcur->next;
   }  /* end of a block */

   first = TRUE;
   alen = strlen(out[0].line);
   b = blist->next->block;
   for (curpos = 0; curpos < alen; curpos += msfwidth)
   {
      for (seq=0; seq < nseq; seq++)
      {
         /*   MSF requires names to be left-justified */
         if (first)	/* first set */
         {
            sprintf(ctemp, "%-s/%d",
               b->sequences[seq].name,
               b->sequences[seq].position);
            printf("\n%-28s ", ctemp); 
         }
         else
         {   printf("\n%-28s ", b->sequences[seq].name);   }
         for (pos=curpos; pos < curpos+msfwidth; pos++)
            if (pos < alen)   printf("%c", out[seq].line[pos]);
      }
      first = FALSE;
      printf("\n");
   }
   printf("\n");
}   /* end of msf_seqs  */
/*==================================================================
      Combines all of the blocks into one giant block
====================================================================*/
void giant(sseq, blist)
struct seqseq *sseq;
struct blocks_list *blist;
{
   int seq, seq1, pos, curpos, bpos;
   struct blocks_list *bcur;
   Block *fb, *b, *bgiant;

   fb = blist->next->block;
   if (blist->nblock < 2)
   {
      output_block(fb, stdout);
   }
   else
   {
      bgiant = new_block(blist->totwidth, blist->nseq);
      if (bgiant == NULL)
      {   printf("\ngiant: OUT OF MEMORY"); exit(-1); }

      /*   first block initializes giant block */
      bcur = blist->next;
      fb = bcur->block;
      strcpy(bgiant->id, fb->id);
      strcpy(bgiant->ac, fb->ac);
      strcpy(bgiant->number, fb->number);
      strcpy(bgiant->de, fb->de);
      strcpy(bgiant->bl, fb->bl);
      bgiant->min_prev = fb->min_prev;
      bgiant->max_prev = fb->max_prev;
      curpos = 0;
      for (seq=0; seq < blist->nseq; seq++)
      {
         strcpy(bgiant->sequences[seq].name, fb->sequences[seq].name);
         strcpy(bgiant->sequences[seq].info, fb->sequences[seq].info);
         bgiant->sequences[seq].position = fb->sequences[seq].position;
         bgiant->sequences[seq].length = blist->totwidth;
         bpos = curpos;
/*  bgiant->residues[seq] = bgiant->sequences[seq].sequence; new_block() did this ????*/
         for (pos=0; pos < fb->width; pos++)
         {
            bgiant->sequences[seq].sequence[bpos] =
                fb->sequences[seq].sequence[pos];
            bpos++;
         }
      }
      curpos = fb->width;

      bcur = bcur->next;		/* second and subsequent blocks */
      while (bcur != NULL && bcur->block != NULL)
      {
         b = bcur->block;
         for (seq=0; seq < blist->nseq; seq++)
         {
/*
            order_seq(sseq, blist->next->block, b);
*/
            seq1 = sseq[seq].seq;
            bpos = curpos;
            for (pos=0; pos < b->width; pos++)
            {
               bgiant->sequences[seq].sequence[bpos] =
                   b->sequences[seq1].sequence[pos];
               bpos++;
            }
         }
         curpos += b->width;
         bcur = bcur->next;
      }

      /* pb_weights() uses residues */
      pb_weights(bgiant);

      output_block(bgiant, stdout);
   }   /*  end of if more than one block  */

}   /* end of giant */
/*==================================================================
      Prints the alignment in STOCKHOLM format
# STOCKHOLM 1.0

seq1   ----NVY
seq2   MKMLLLL

seq1
seq2
//

====================================================================*/
void stockholm_seqs(sseq, blist, gap_flag)
struct seqseq *sseq;
struct blocks_list *blist;
int gap_flag;
{
   int alen, nseq, seq, seq1, pos, posgap, posun, curpos;
   int msfwidth;
   char ctemp[OUTMAX];
   struct blocks_list *bcur;
   Block *b;
   struct align *out;

   msfwidth = OutWidth - 29;	/* subtract space required for seq name */
   if (msfwidth < 1) msfwidth = OutWidth;

   nseq = blist->nseq;
   out = (struct align *) malloc(nseq * sizeof(struct align));
   if (out == NULL)
   {   printf("\nstockholm_seqs: OUT OF MEMORY"); exit(-1); }
   for (seq=0; seq < nseq; seq++) out[seq].line[0] = '\0';

   printf("# STOCKHOLM 1.0\n");

   bcur = blist->next;
   while (bcur != NULL && bcur->block != NULL)
   {
      b = bcur->block;
      for (seq=0; seq < nseq; seq++)
      {
/*
         if (bcur->block->num_sequences == blist->nseq)
         {
            order_seq(sseq, blist->next->block, bcur->block);
         }
         else
         {
            printf("ERROR in block %s, found %d sequences but ",
                   bcur->block->number, bcur->block->num_sequences);
            printf("expected %d\n", blist->nseq);
         }
*/
         seq1 = sseq[seq].seq;

         if (bcur != blist->next)
         {
            /*   gap to accomodate longest unaligned region */
            posgap = b->sequences[seq1].type;
            if (gap_flag == 1)
            {
               for (pos=0; pos < posgap; pos++)
               {  strcat(out[seq].line, "-");  }
            }
            /*   unaligned region between blocks */
            posun = b->sequences[seq1].max_length;
            if (gap_flag == 1)
            {
               for (pos=0; pos < posun; pos++)
               {  strcat(out[seq].line, "."); }
            }
         }

         for (pos=0; pos < b->width; pos++)
         {  ctemp[pos] = aa_btoa[b->sequences[seq1].sequence[pos]]; }
         ctemp[b->width] = '\0';
         strcat(out[seq].line, ctemp);
      }
      bcur = bcur->next;
   }  /* end of a block */

   alen = strlen(out[0].line);
   b = blist->next->block;
   for (curpos = 0; curpos < alen; curpos += msfwidth)
   {
      for (seq=0; seq < nseq; seq++)
      {
         printf("\n%-28s ", b->sequences[seq].name); 
         for (pos=curpos; pos < curpos+msfwidth; pos++)
            if (pos < alen)   printf("%c", out[seq].line[pos]);
      }
      printf("\n");
   }
   printf("//\n");
}   /* end of stockholm_seqs  */
/*=======================================================================*/
int namecmp(s1, s2)
Sequence *s1, *s2;
{
   return(strcmp(s1->name, s2->name));
}

    bcur = bcur->next;
   }
   /*   Print last block */
   printf("\n            %s", header);
   for (seq=0; seq < nseq; seq++)
   {
      printf("\n%20s ", blist->next->block->sequences[seq].name);
      printf("%s", out[seq].line);
   }

   printf("\n");
}   /* end of short_seqs */
/*==================================================================
      Prints the portion of the sequences in blocks in fasta format
======================================================blimps-3.9/blimps/bldist.c000064400001460000012000000232331042724122200160600ustar00jorjastaff00000400000027/*>>> make output in protdist format, /howard2/phylip/examples/outfile.protdist
	prodist values are all between 0 and 1?
  >>> allow other formats than fasta for input alignments? Gaps?
*/
/* BLDIST Copyright 1998 Fred Hutchinson Cancer Research Center
   Read a file of multiple alignments in fasta format and a substitution
	matrix and output a matrix of distances between pairs of sequences.

   NOTES: Requires version 3.2.3 or higher of BLIMPS libraries.

   bldist    
	Limit of 100 sequences in alignment

--------------------------------------------------------------------
 3/20/98  J. Henikoff
 3/23/98  Added correlation option
11/30/00  Added protdist option
====================================================================*/

#define EXTERN
#define MAXNAME 80	/* Maximum file name length */
#define MAXSEQ 100	/* Maximum number of sequences */

#include 

void compute_dist();
int OutType;

/*-------------------Blimps stuff----------------------------------------*/
extern int ErrorLevelReport;
extern struct float_qij *Qij;
extern struct float_qij *load_qij();
double frequency[MATRIX_AA_WIDTH];    /* for frequency.c */

/*=======================================================================*/
/*
 * main
 *   controls flow of program
 *   Parameters: argc, argv
 *   Error codes:
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
   FILE *ifp, *ofp, *sfp;
   Sequence *seqs[MAXSEQ];
   char sijname[MAXNAME], bdbname[MAXNAME], outname[MAXNAME], *blimps_dir;
   char ctemp[MAXNAME];
   int db_type, seq_type, nseq;

   ErrorLevelReport = 4;	/* BLIMPS error level */

   if (argc < 3)
   {
      printf("BLDIST: Copyright 1998 Fred Hutchinson Cancer Research");
      printf(" Center\nUSAGE: bldist   \n");
      printf("    = file of fasta multiple alignments (blocks)\n");
      printf("    = substitution matrix\n");
      printf("      = output distance matrix\n");
      printf("     = output matrix type:\n");
      printf("			S=similarity\n");
      printf("			D=dissimilarity\n");
      printf("			P=dissimilarity in protdist format\n");
      printf("			C=correlation\n");
   }
   /* ------------1st arg = fasta sequences -------------------------------*/
   if (argc > 1) { strcpy(bdbname, argv[1]); }
   else
   {
      printf("\nEnter name of file of fasta multiple alignments: ");
      gets(bdbname);
   }
   if ( (ifp=fopen(bdbname, "r")) == NULL)
   {
      printf("Cannot open file %s\n", bdbname);
      exit(-1);
   }
   db_type = type_dbs(ifp, DbInfo);
   seq_type = UNKNOWN_SEQ;
   seq_type = seq_type_dbs(ifp, DbInfo, db_type, seq_type);
   if (seq_type == NA_SEQ)
   {
      printf("WARNING: Sequences appear to be DNA but will be treated");
      printf(" as protein\n");
      seq_type = AA_SEQ;
   }
   rewind(ifp);

   /* ------------2nd arg = fasta sequences -------------------------------*/
   blimps_dir = getenv("BLIMPS_DIR");
   if (argc > 2) { strcpy(sijname, argv[2]); }
   else
   {
      printf("\nEnter name of file containing substitution matrix: ");
      gets(sijname);
   }
   if ( (sfp=fopen(sijname, "r")) == NULL)
   {
      printf("Cannot open file %s\n", sijname);
      if (blimps_dir != NULL) 
      {
	sprintf(ctemp, "%s/docs/%s", blimps_dir, sijname);
        if ( (sfp=fopen(ctemp, "r")) == NULL)
        {
           printf("Cannot open file %s\n", ctemp);
	   sprintf(ctemp, "%s/docs/default.iij", blimps_dir);
           if ( (sfp=fopen(ctemp, "r")) == NULL)
           {
              printf("Cannot open file %s\n", ctemp);
              exit(-1);
           }
           else
           {   strcpy(sijname, ctemp);   }
        }
      }
   }
   printf("Using %s\n", sijname);
   /*  Using load_qij() because want the option for floating point */
   /*  Qij->value[aa1][aa2]   */
   Qij = load_qij(sfp);
   fclose(sfp);

   /* ------------3rd arg = output file  -----------------------------------*/
   if (argc > 3) { strcpy(outname, argv[3]); }
   else
   {
      printf("\nEnter name of output file: ");
      gets(outname);
   }
   if ( (ofp=fopen(outname, "w")) == NULL)
   {
      printf("Cannot open file %s\n", outname);
      exit(-1);
   }

   /* ------------4th arg = output type  -----------------------------------*/
   if (argc > 4) { strcpy(ctemp, argv[4]); }
   else
   {
      printf("\nEnter type (S=similarity, D=dissimilarity, C=correlation): ");
      gets(ctemp);
   }
   OutType = 1;			/* similarity is default */
   if      (ctemp[0] == 'd' || ctemp[0] == 'D' || ctemp[0] == '2') OutType = 2;
   else if (ctemp[0] == 'c' || ctemp[0] == 'C' || ctemp[0] == '3') OutType = 3;
   else if (ctemp[0] == 'p' || ctemp[0] == 'P' || ctemp[0] == '4') OutType = 4;

   printf("Writing ");
   switch(OutType)
   {
      case 1:
	printf("similarity ");
	break;
      case 2:
	printf("dissimilarity ");
	break;
      case 3:
	printf("correlation ");
	break;
      case 4:
	printf("protdist ");
	break;
      default:
	break;
   }
   printf("matrix to %s\n", outname);

   /*=====================================================================*/
   nseq = 0;
   /*-----------------------------------------------------------------*/
   /*   First read all the sequences into memory                    */
   if (db_type >= 0)
   {
      while ( nseq < MAXSEQ &&
          (seqs[nseq] = read_a_sequence(ifp, db_type, seq_type)) != NULL)
      {
         nseq++;
      }
   }
   fclose(ifp);


   /*=====================================================================*/
   compute_dist(ofp, OutType, nseq, seqs, Qij);

   /*=====================================================================*/
   /*   Make a "mean" sequence, and compute how far each sequence is from
	it; have to use a different sequence representation since each
	position of the artificial sequence will be a blend of amino acids
   */

   /*=====================================================================*/
   fclose(ofp);
   exit(0);
}   /* end of main */

/*=========================================================================
"Distances" are the segment pair scores.

"Correlations" are really percentages of max possible score of a given pair
of sequences: E.G. for:
	WIVNRA
	WLFKQA

	WW=11, II=4/LL=4, VV=4/FF=6, NN=6/KK=5, RR=5/QQ=5, AA=4 => 
		max score = 11+4+6+6+5+4 = 36
	IL=2, VF=-1, NK=0, RQ=1 =>
		act score = 11+2-1+0+1+4 = 17, 17/36 = 0.47 = "correlation"
Completely conserved segment pair always has corr = 1.0, but segment pair
scores could be negative ...

=========================================================================*/
void compute_dist(ofp, mtype, nseq, seqs, mat)
FILE *ofp;
int mtype;		/* output matrix type */
int nseq;
Sequence *seqs[MAXSEQ];
struct float_qij *mat;
{
   int length, s1, s2, aa1, aa2, pos;
   double dist[MAXSEQ][MAXSEQ], maxdist, mindist, meandist, maxscore, dtemp;
   double range;

   maxdist = -999; mindist = 999;
   meandist = 0.0;

   for (s1=0; s1length;
      for (s2=s1; s2length < length)
         {
            printf("WARNING: sequence segments are of different lengths\n");
            printf("%s %d : %s %d\n", seqs[s1]->name, seqs[s1]->length,
		                     seqs[s2]->name, seqs[s2]->length);
            length = seqs[s2]->length;
         }
         dist[s1][s2] = maxscore = 0.0;
         for (pos=0; possequence[pos];
            aa2 = seqs[s2]->sequence[pos];
            dist[s1][s2] += mat->value[aa1][aa2];
	    dtemp = mat->value[aa1][aa1];
	    if (mat->value[aa2][aa2] > dtemp) dtemp = mat->value[aa2][aa2];
	    maxscore += dtemp;
         }
         if (mtype == 3) 		/* correlation */
         {
            dist[s1][s2] /= maxscore;
            /* This is not a proper "correlation" ... */
            if (dist[s1][s2] >  1.0) dist[s1][s2] =  1.0;
            if (dist[s1][s2] < -1.0) dist[s1][s2] = -1.0;
         }
    
      }
   }

   /*  Now dist is similarity matrix, probably
       with unequal diagonal values => some seqs
       are more similar to themselves than others.
       Subtract all entries from max value to make
       a dissimilarity matrix */
   for (s1=0; s1 maxdist) maxdist = dist[s1][s2];
         if (dist[s1][s2] < mindist) mindist = dist[s1][s2];
         if (s1 != s2) dist[s2][s1] = dist[s1][s2];
      }
   }
   /*  Average score includes diagonals   */
   dtemp = (double) nseq * (nseq + 1.0) / 2.0;
   meandist /= dtemp;
   printf("Mean dissimilarity distance = %.2f\n",
           (maxdist - meandist) );
   range = maxdist - mindist;

   /*  Print dissim. matrix for SAS, requires full matrix, max linesize=256 */
   /*  Proc varclus requires a covariance matrix as input ... */
   if (mtype == 4) fprintf(ofp, "%d\n", nseq);
   for (s1=0; s1name);
      for (s2=0; s2>>all diagonal values s.b. zero <<<*/
              fprintf(ofp, "%.5f ", (maxdist - dist[s1][s2])/range );
	      break;
            default:
	      break;
         }
         if ((s2 > 0) && (s2%25 == 0)) fprintf(ofp, "\n");
      }
      if (s2 == nseq) fprintf(ofp, "\n");
   }


}  /* end of compute_dist */
blimps-3.9/blimps/blexplode.c000064400001460000012000000036330774312247600165770ustar00jorjastaff00000400000027/*    blexplode.c  Explode a blocks db into individual blocks 
           blexplode  []
	   Creates files named AC.blk
--------------------------------------------------------------------
 8/24/95 J. Henikoff
11/18/99 Added 2nd argument to prefix directory of output block files
====================================================================*/

#define BLNORM_C_
#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#include 

/*=======================================================================*/

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *bfp, *ofp;
  Block *block;
  char bdbname[MAXNAME], conname[MAXNAME], prefix[MAXNAME];
  int len;

/* ------------1st arg = blocks database -------------------------------*/
   if (argc > 1)
      strcpy(bdbname, argv[1]);
   else
   {
      printf("\nEnter name of blocks database: ");
      gets(bdbname);
   }
   if ( (bfp=fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbname);
      exit(-1);
   }

/* ------------2nd optional argument = prefix name----------------------*/
   prefix[0] = '\0';
   if (argc > 2) strcpy(prefix, argv[2]);

/*-----------------------------------------------------------------*/

  while ((block = read_a_block(bfp)) != NULL)
  {
     if (strlen(prefix))
     {
        sprintf(conname,"%s/%s", prefix, block->number);
/*
        strcpy(conname, prefix);
        if (strlen(block->number) == 8)
        {
           len = strlen(conname);
           conname[len] = block->number[7];
           conname[len+1] = '\0';
        }
*/
     }
     else
     { strcpy(conname, block->number); }
     strcat(conname, ".blk");
     if ( (ofp=fopen(conname, "w")) == NULL)
     {
         printf("\nCannot open file %s\n", conname);
         exit(-1);
     }
     output_block(block, ofp);
     fclose(ofp);
  }
   
  fclose(bfp);
  exit(0);

}  /* end of main */
blimps-3.9/blimps/blimps-mem.c000064400001460000012000000211640774312247600166620ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* blimps-mem.c: Memory management function for blimps. */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */


/*	system headers not in global.h */
/*	blimps library headers not in global.h */
#include 
/*	headers in current directory */
#include "blimps-mem.h"
#include "blimps.h"
#include "lists.h"


/*
 * Exported variables and data structures
 */

/*
 * Local variables and data structures
 */

static int CallsWhenToReduce  = 10;
static int NumberOfTimesCalled = 0;
#define DECREASE_AMOUNT (CallsWhenToReduce*.25 + 1) /* 10 7 5 3 2 1 0 */
#define REPORT_DECREASE_AMOUNT  1  /* amount to decrease NumberToReport by */
				   /* if there is not enough room */
				   /* NOTE: MUST be greater than zero */



/*
 * Function definitions
 */

/*
 * blimps_reclaim_space
 *   Tries to reclaim some of the allocated memory.  It tries to
 *   reclaim the memory from the various lists that are used by
 *   decreasing the elements that can be stored in the lists.
 *   NOTE: This function assumes that the searching has already begun.
 *         If that is not the case it will report that it was unable
 *         to get space because the list size and the NumberToReport
 *         will likely be zero.  This doesn't really matter much
 *         because if we have to reclaim space that early in the run, 
 *         there are problems.
 *   NOTE: Because of the SavedNodes list in the skiplist package many
 *         calls to blimps_reclaim_space may be needed before the free lists
 *         are filled and actual memory is freed.  This is not that
 *         big of a problem, considering that a balance will be
 *         reached with the nodes in the free lists.  The only time
 *         this would cause the Scores list size to reduce to zero is
 *         if there is so little memory that there can be only about
 *         20 scores in the list.  That amount of memory is about 100
 *         Kbytes. 
 *   Parameters: none
 *   Return codes: TRUE if it was able to get free some space, FALSE
 *                 if not.
 *   Error codes:  FALSE if it unable to get space.
 */

Boolean blimps_reclaim_space()
{
  /* note for later.  make a skiplist function to turn on severe space */
  /* saving.  In the function it will empty out the saved empty list */
  /* nodes and set a variable that will turn off the saving of the */
  /* nodes.  This should free up a _small_ amount of space.  Might not */
  /* be worth doing.  This skiplist function would be called from here */
  /* when the space is very tight. */

  int list_size;
  int prev_report_size;
  int ret_val;

  /* increase the count of the number of times this has been called */
  if (!(NumberOfTimesCalled<0)) {
    NumberOfTimesCalled++;
  }

  /* get the size of the Scores list for future use */
  list_size = NumInSL(Scores);
  prev_report_size = NumberToReport;

  if ((NumberToReport == 0) &&
      (list_size == 0)) {
    /* There is nothing we can do to save memory.  NumberToReport is */
    /* non-zero once the runs start.  If the list_size is zero, we deleted */
    /* everything we could. */
    sprintf(ErrorBuffer,
	    "Unable to recover memory.\n");
    ErrorReport(SERIOUS_ERR_LVL);
    return FALSE;
  }
  else if (NumberToReport < 0) { /* trying to save all, but can't */
    /* reset the NumberToReport */
    if (SearchType == SEARCH_TYPE_MATRIX) { /* blk vs sequences */
      NumberToReport = MAX_DEFAULT_MATRIX_SEARCH_NUM_TO_REPORT;
    }
    else if (SearchType == SEARCH_TYPE_BLOCK) {	/* seq vs blocks */
      NumberToReport = MAX_DEFAULT_BLOCK_SEARCH_NUM_TO_REPORT;
    }
    else {
      NumberToReport = max(MAX_DEFAULT_BLOCK_SEARCH_NUM_TO_REPORT, 
			   MAX_DEFAULT_MATRIX_SEARCH_NUM_TO_REPORT);
    }

    NumberToReport = list_size - REPORT_DECREASE_AMOUNT;
    if ( NumberToReport < 0 ) {
      NumberToReport = 1;
    }

    /* report the error */
    sprintf(ErrorBuffer,
	    "Decreasing the NumberToReport from saving all (%d currently) to %d.",
	    list_size, NumberToReport);
    ErrorReport(INFO_ERR_LVL);
    sprintf(ErrorBuffer,
	    "Ran out of memory (1), fewer scores will be reported.\n");
    ErrorReport(WARNING_ERR_LVL);

    /* free up some space with the new NumberToReport */
    DoForSL(Scores, limit_Scores_list_size, NULL);

    return TRUE;
  }
  else if (list_size <= NumberToReport) { /* can not report as many */
					  /* scores as we wanted to */
    /* reset the NumberToReport */
    NumberToReport = list_size - REPORT_DECREASE_AMOUNT;
    if ( NumberToReport < 0 ) {
      /* if we have not totally decreased the saved nodes to none, lower */
      /* the amount of nodes to save and report one, otherwise report zero */
      if (NumberOfTimesCalled >= 0) { /* NumberOfTimesCalled <0 if there is */
				      /* no more decreasing possible */
	sprintf(ErrorBuffer,
		"Decreasing the number of saved nodes in the list.");
	ErrorReport(INFO_ERR_LVL);
	ret_val = LowerSavedNodesLevel();
	if (ret_val < 0) {
	  sprintf(ErrorBuffer,
		  "The saved nodes level of the list has been reduced to %d.", 
		  ret_val);
	  ErrorReport(INFO_ERR_LVL);
	  sprintf(ErrorBuffer,
		  "The list saved nodes cannot be reduced any more.\n");
	  ErrorReport(WARNING_ERR_LVL);
	  NumberOfTimesCalled = -1; /* set up to stop calling if nothing */
				    /* else can be done */
	}
	else {
	  sprintf(ErrorBuffer,
		  "The saved nodes level of the list has been reduced to %d.\n", 
		  ret_val);
	  ErrorReport(INFO_ERR_LVL);
	}
	NumberToReport = 1;
      }
      else {			/* Can't decrease the saved nodes anymore */
	NumberToReport = 0;	/* Don't want to overshoot zero and get into */
				/* an infinite loop */
				/* NOTE: This will allow it to keep going */
				/*       but no scores will be reported */
      }
    }

    /* if this function has been called too often, reduce the level of */
    /* saving in the skiplists */
    if ((NumberOfTimesCalled >= 0) &&
	(NumberOfTimesCalled > CallsWhenToReduce)) {
      NumberOfTimesCalled = 0;
      CallsWhenToReduce = CallsWhenToReduce - DECREASE_AMOUNT;
      sprintf(ErrorBuffer,
	      "Decreasing the number of saved nodes in the list.");
      ErrorReport(INFO_ERR_LVL);
      ret_val = LowerSavedNodesLevel();
      if (ret_val < 0) {
	sprintf(ErrorBuffer,
		"The saved nodes level of the list has been reduced to %d.", 
		ret_val);
	ErrorReport(INFO_ERR_LVL);
	sprintf(ErrorBuffer,
		"The list saved nodes cannot be reduced any more.\n");
	ErrorReport(WARNING_ERR_LVL);
	NumberOfTimesCalled = -1; /* set up to stop calling if nothing */
				  /* else can be done */
      }
      else {
	sprintf(ErrorBuffer,
		"The saved nodes level of the list has been reduced to %d.\n", 
		ret_val);
	ErrorReport(INFO_ERR_LVL);
      }
    }

    /* report the error */
    sprintf(ErrorBuffer,
	    "Decreasing the NumberToReport from %d to %d.",
	    prev_report_size, NumberToReport);
    ErrorReport(INFO_ERR_LVL);
    sprintf(ErrorBuffer,
	    "Ran out of memory (2), fewer scores will be reported.\n");
    ErrorReport(WARNING_ERR_LVL);

    /* free up some space with the new NumberToReport */
    DoForSL(Scores, limit_Scores_list_size, NULL);

    return TRUE;
  }
  else {			/* list_size > NumberToReport, need to */
				/* decrease the size of the list. */
    /* Should never get to this point.  The list size should always be */
    /* kept <= the NumberToReport. */

    /* report the error */
    sprintf(ErrorBuffer,
	    "blimps_reclaim_space(): NumInSL(Scores) is greater than NumberToReport.");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "                 NumInSL(Scores) is supposed to be maintained");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "                 less than or equal to the NumberToReport.");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "                 NumberToReport = %d, NumInSL(Scores) = %d.",
	    NumberToReport, NumInSL(Scores));
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "                 Ran out of memory, removing the excess scores");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "                 in the Scores list.\n");
    ErrorReport(PROGRAM_ERR_LVL);

    /* free up some space with the new NumberToReport */
    DoForSL(Scores, limit_Scores_list_size, NULL);

    return TRUE;
  }
}







/* Change log information follows. */
/* 
 * Revision 1.1000  1993/08/27  17:00:11  billa
 * Creation.  Added the function reclaim_space() and the macro CheckMem(A)
 * to handle the situation when there is no more memory to allocate.
 *
 */

t package many
 *         calls to blimps_reclaim_space may be needed before the free lists
 *         are filled and actual memory is freed.  This is not that
 *         big of a problem, considering that a balance will be
 *         reached with the nodes in the free lists.  The only time
 *         this would cause the Scores list size to reduce to zero is
 *         if there is so little mblimps-3.9/blimps/blimps.c000064400001460000012000001143020774312247600161030ustar00jorjastaff00000400000027/* (C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* blimps.c: main module of the BLIMPS blocks searcher.  */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#define EXTERN

/*	system headers not in global.h  */
#include 
#include 

/*	blimps headers */
#include 
#include 
#include 
#include 
#include 	/* includes sequences.h, output.h */
#include 	/* includes pattern.h */
#include 
#include 
#include 

/*	headers in current directory */
#include "blimps.h"
#include "blimps-mem.h"
#include "config.h"
#include "scores.h"
#include "scoring.h"		/* for Alignments_Done and Scores_Done */
#include "lists.h"



/*
 * Exported variables and data structures
 */

/* variables set by the configuration file */

int StrandsToSearch;
int NumberToReport;
int SearchType;
int SequenceType;
Boolean RepeatsAllowed;
Boolean SavedScoresFlag;
int GeneticCodeInitializer;
int SiteSpecificScoringMatrixType;
int BlockToMatrixConversionMethod; /* default method is two */
int SequenceMatrixScoringMethod;   /* default method is zero */



/*
 * Local variables and data structures
 */


static Block *block;
static Matrix *matrix;
static Sequence *sequence;
static Sequence *trans1, *trans2, *trans3;    
				/* translated DNA reading frames */
static Sequence *trans_1, *trans_2, *trans_3; 
				/* translated DNA reading frames */

static unsigned char gcode[64], revgcode[64]; 
				/* genetic codes for translation */

static int records_searched;


/* 
 * sequence_vs_blocks
 *   When SearchType is BLOCK, there is one sequence against a blocks 
 *   database.
 *   Parameters:
 *     FILE *emfp: the file to output the matrix information to.
 *   Error codes:
 */

static void sequence_vs_blocks(emfp)
     FILE *emfp;
{
  char prev_number[20];

  /* make sure we are at the beginning of the sequence data */
  rewind_file(SEQUENCE_FILES);
  
  /* read in the first sequence (if there are others, won't be processed */
  sequence = read_a_sequence(get_file(SEQUENCE_FILES), 
			     get_sequence_db_db_type(),
			     get_sequence_db_seq_type());
  
 if (sequence == NULL) {
    sprintf(ErrorBuffer, 
	    "Unable to read the sequence for scoring against the blocks.");
    ErrorReport(SERIOUS_ERR_LVL);
    return;
  }
 if (sequence->length <= 0) {
    sprintf(ErrorBuffer, 
	    "Query sequence has zero length, not scoring it.\n");
    ErrorReport(SERIOUS_ERR_LVL);
    return;
  }

  /*   Just translate the query sequence once  */
  /*   May take too much memory for long DNA sequences ... */
  trans1 = trans2 = trans3 = trans_1 = trans_2 = trans_3 = NULL;
  if (sequence->type == NA_SEQ) 
  {
     if (StrandsToSearch > 0)
     {
        trans1 = translate_sequence(sequence, 1, gcode, revgcode);
        trans2 = translate_sequence(sequence, 2, gcode, revgcode);
        trans3 = translate_sequence(sequence, 3, gcode, revgcode);
     }
     if (StrandsToSearch < 0 || StrandsToSearch == 2)
     {
        trans_1 = translate_sequence(sequence, -1, gcode, revgcode);
        trans_2 = translate_sequence(sequence, -2, gcode, revgcode);
        trans_3 = translate_sequence(sequence, -3, gcode, revgcode);
     }
  }

  if (NumberToReport == 0) {
    NumberToReport = DEFAULT_BLOCK_SEARCH_NUMBER_TO_REPORT(sequence);
  }

  /* inform what sequence the search is being done with */
/*	Trying to speed things up ...
  sprintf(ErrorBuffer,
	  "Searching sequence %s against the blocks database.\n",
	  sequence->name);
  ErrorReport(INFO_ERR_LVL);
*/

    records_searched = 0;

    /* make sure we are at the begining of the block data */
    rewind_file(BLOCK_FILES);

    /* ------------------------loop through all the blocks */
    prev_number[0] = '\0';
    /*  Assuming the database is correctly formatted  */
    while ((block = read_a_block_faster(get_file(BLOCK_FILES))) != NULL) 
    {
        /* inform which block scoring against */
/*  Trying to speed things up ...
        sprintf(ErrorBuffer, "Scoring vs block %s.\n", block->number);
	ErrorReport(INFO_ERR_LVL);
*/
/*		Check for new family
	if ((int) strlen(prev_number) < 7 ||
                  strncmp(block->number, prev_number, 7) != 0)
        {
		strcpy(prev_number, block->number);
        }
*/
        /* Compute a PSSM from the block */
	matrix = block_to_matrix(block, BlockToMatrixConversionMethod);
	if (emfp != NULL) { output_matrix(matrix, emfp); }


	/* score and enter the data into the list */
/*>>>>NOTE: just call default_scoring_method() instead of
	score_and_enter() since no other methods are implemented
 <<<<<< */

        if (sequence->type == NA_SEQ) 
        {
           if (StrandsToSearch > 0)
           {
/*
	      score_and_enter(trans1, matrix, 1, RepeatsAllowed, SearchType);
	      score_and_enter(trans2, matrix, 2, RepeatsAllowed, SearchType);
	      score_and_enter(trans3, matrix, 3, RepeatsAllowed, SearchType);
*/
              default_scoring_method(trans1, matrix, 1, RepeatsAllowed, SearchType, FALSE);
              default_scoring_method(trans2, matrix, 2, RepeatsAllowed, SearchType, FALSE);
              default_scoring_method(trans3, matrix, 3, RepeatsAllowed, SearchType, FALSE);
           }
           if (StrandsToSearch < 0 || StrandsToSearch == 2)
           {
/*
	      score_and_enter(trans_1, matrix, -1, RepeatsAllowed, SearchType);
	      score_and_enter(trans_2, matrix, -2, RepeatsAllowed, SearchType);
	      score_and_enter(trans_3, matrix, -3, RepeatsAllowed, SearchType);
*/
              default_scoring_method(trans_1, matrix, -1, RepeatsAllowed, SearchType, FALSE);
              default_scoring_method(trans_2, matrix, -2, RepeatsAllowed, SearchType, FALSE);
              default_scoring_method(trans_3, matrix, -3, RepeatsAllowed, SearchType, FALSE);
           }
        }
        else  /* AA  */
        {
/*
           score_and_enter(sequence, matrix, 0, RepeatsAllowed, SearchType);
*/
           default_scoring_method(sequence, matrix, 0, RepeatsAllowed, SearchType, FALSE);
        }

	records_searched++;
	free_block(block);
	free_matrix(matrix);
    } /* end while there are blocks */

    if (sequence->type == NA_SEQ) 
    {
       if (trans1 != NULL) free_sequence(trans1);
       if (trans2 != NULL) free_sequence(trans2);
       if (trans3 != NULL) free_sequence(trans3);
       if (trans_1 != NULL) free_sequence(trans_1);
       if (trans_2 != NULL) free_sequence(trans_2);
       if (trans_3 != NULL) free_sequence(trans_3);
    }

/*  free(sequence);  This is a global var, used later !!! */
  
}  /* end of sequence_vs_blocks */


/* 
 * block_vs_sequences
 *   When SearchType is MATRIX, there is one block against a sequences 
 *   database.
 *   Parameters:
 *     FILE *emfp: the file to output the matrix information to.
 *   Error codes:
 */

static void block_vs_sequences(emfp)
     FILE *emfp;
{
  /* make sure we are at the begining of the block data */
  rewind_file(BLOCK_FILES);
  
  /* loop through all the blocks (one) */
  block = read_a_block(get_file(BLOCK_FILES));

  if (block == NULL) {
    sprintf(ErrorBuffer, 
	    "Unable to read block for scoring against the sequences.");
    ErrorReport(SERIOUS_ERR_LVL);
    sprintf(ErrorBuffer, 
	    "Not scoring the block.\n");
    ErrorReport(SERIOUS_ERR_LVL);
    return;
  }
  
  if (NumberToReport == 0) {
    NumberToReport = DEFAULT_MATRIX_SEARCH_NUMBER_TO_REPORT(block);
  }

  /* inform what block the search is being done with */
  sprintf(ErrorBuffer,
	  "Searching block %s against the sequence database.\n",
	  block->number);
  ErrorReport(INFO_ERR_LVL);

  /* get the block matrix */
  matrix = block_to_matrix(block, BlockToMatrixConversionMethod);
  if (emfp != NULL) {
    output_matrix(matrix, emfp);
  }
  
  /* make sure we are at the beginning of the sequence data */
  rewind_file(SEQUENCE_FILES);
  
  records_searched = 0;

  /* loop through all the sequences */
  while ((sequence = read_a_sequence(get_file(SEQUENCE_FILES), 
				     get_sequence_db_db_type(),
				     get_sequence_db_seq_type())) != NULL) {
    
    /* inform which sequence scoring against */
    sprintf(ErrorBuffer,
	    "Scoring vs sequence %s.\n",
	    sequence->name);
    ErrorReport(INFO_ERR_LVL);

    /* is the sequence a NA_SEQ?  if so, translate */
    if (sequence->type == NA_SEQ) {
      /*   Search forward direction  */
      if (StrandsToSearch > 0)
      {
         /* translate */
         trans1 = translate_sequence(sequence, 1, gcode, revgcode);
         /* score and enter the data into the list */
         score_and_enter(trans1, matrix, 1, RepeatsAllowed, SearchType);
         /* free the translated sequences */
         free_sequence(trans1);

         trans2 = translate_sequence(sequence, 2, gcode, revgcode);
         score_and_enter(trans2, matrix, 2, RepeatsAllowed, SearchType);
         free_sequence(trans2);

         trans3 = translate_sequence(sequence, 3, gcode, revgcode);
         score_and_enter(trans3, matrix, 3, RepeatsAllowed, SearchType);
         free_sequence(trans3);
      }
      /*   Search reverse direction  */
      if (StrandsToSearch == 2 || StrandsToSearch < 0)
      {
	 trans_1 = translate_sequence(sequence, -1, gcode, revgcode);
	 score_and_enter(trans_1, matrix, -1, RepeatsAllowed, SearchType);
	 free_sequence(trans_1);

	 trans_2 = translate_sequence(sequence, -2, gcode, revgcode);
	 score_and_enter(trans_2, matrix, -2, RepeatsAllowed, SearchType);
	 free_sequence(trans_2);

	 trans_3 = translate_sequence(sequence, -3, gcode, revgcode);
	 score_and_enter(trans_3, matrix, -3, RepeatsAllowed, SearchType);
	 free_sequence(trans_3);
      }
    }  /* end of NA_SEQ  */
    /* otherwise, just use the sequence, assuming it is an AA_SEQ */
    else {
      /* score and enter the data into the list */
      score_and_enter(sequence, matrix, 0, RepeatsAllowed, SearchType);
    }

    free_sequence(sequence);
    
    records_searched++;

  } /* end while there are sequences */
  
  free_block(block);
  free_matrix(matrix);
}  /* end of block_vs_sequences */


/* 
 * blocks_vs_sequences
 *   When SearchType is UNKNOWN, there is probably a blocks database against
 *   a sequences database.  Score all pairwise matches of blocks and
 *   sequences.
 *   Parameters:
 *     FILE *emfp: the file to output the matrix information to.
 *   Error codes:
 */

static void blocks_vs_sequences(emfp)
     FILE *emfp;
{
  /* NOTE: If there are speed problems, might look at the SearchType */
  /*       variable in files.c to see which of sequences or blocks is */
  /*       considered the database.  The one that is the database is most */
  /*       likely to have the most elements, and should be in the outer */
  /*       loop to reduce "block->matrix" and "if NA_SEQ; NA_SEQ->AA_SEQ" */
  /*       overhead. */
  
  /* set the number to report */
  if (NumberToReport == 0) {
    rewind_file(BLOCK_FILES);
    block = read_a_block(get_file(BLOCK_FILES));
    rewind_file(SEQUENCE_FILES);
    sequence = read_a_sequence(get_file(SEQUENCE_FILES), 
			       get_sequence_db_db_type(),
			       get_sequence_db_seq_type());
    if (block == NULL) {
      if (sequence == NULL) {
	/* there are no comparisons to do */
	NumberToReport = 1;
      }
      else {
	NumberToReport = DEFAULT_BLOCK_SEARCH_NUMBER_TO_REPORT(sequence); 
	free_sequence(sequence);
      }
    }
    else {
      if (sequence == NULL) {
	/* there are no comparisons to do */
	NumberToReport = DEFAULT_MATRIX_SEARCH_NUMBER_TO_REPORT(block);
	free_block(block);
      }
      else {
	NumberToReport = 
	  max((DEFAULT_BLOCK_SEARCH_NUMBER_TO_REPORT(sequence)),
	      (DEFAULT_MATRIX_SEARCH_NUMBER_TO_REPORT(block)));
	free_block(block);
	free_sequence(sequence);
      }
    }
    rewind_file(BLOCK_FILES);
    rewind_file(SEQUENCE_FILES);
  }

  /* make sure we are at the begining of the block data */
  rewind_file(BLOCK_FILES);
  
  /* loop through all the blocks */
  while ((block = read_a_block(get_file(BLOCK_FILES))) != NULL) {
    
    /* get the block matrix */
    matrix = block_to_matrix(block, BlockToMatrixConversionMethod);
    if (emfp != NULL) {
      output_matrix_s(matrix, emfp, FLOAT_OUTPUT);
    }
    
    /* make sure we are at the beginning of the sequence data */
    rewind_file(SEQUENCE_FILES);
    
    /* loop through all the sequences */
    while ((sequence = read_a_sequence(get_file(SEQUENCE_FILES), 
				       get_sequence_db_db_type(),
				       get_sequence_db_seq_type())) != NULL) {
      
      /* inform which block and sequence are being scored */
      sprintf(ErrorBuffer,
	      "Scoring sequence %s vs block %s.\n",
	      sequence->name, block->number);
      ErrorReport(INFO_ERR_LVL);
      
      /* is the sequence a NA_SEQ?  if so, translate */
      if (sequence->type == NA_SEQ) {
	/* translate */
	trans1 = translate_sequence(sequence, 1, gcode, revgcode);
	trans2 = translate_sequence(sequence, 2, gcode, revgcode);
	trans3 = translate_sequence(sequence, 3, gcode, revgcode);
	/* score and enter the data into the list */
	score_and_enter(trans1, matrix, 1, RepeatsAllowed, SearchType);
	score_and_enter(trans2, matrix, 2, RepeatsAllowed, SearchType);
	score_and_enter(trans3, matrix, 3, RepeatsAllowed, SearchType);
	/* free the translated sequences */
	free_sequence(trans1);
	free_sequence(trans2);
	free_sequence(trans3);
	/* if we are supposed to search both strands, translate and score */
	if (StrandsToSearch == 2) {
	  /* translate */
	  trans_1 = translate_sequence(sequence, -1, gcode, revgcode);
	  trans_2 = translate_sequence(sequence, -2, gcode, revgcode);
	  trans_3 = translate_sequence(sequence, -3, gcode, revgcode);
	  /* score and enter the data into the list */
	  score_and_enter(trans_1, matrix, -1, RepeatsAllowed, SearchType);
	  score_and_enter(trans_2, matrix, -2, RepeatsAllowed, SearchType);
	  score_and_enter(trans_3, matrix, -3, RepeatsAllowed, SearchType);
	  /* free the translated sequences */
	  free_sequence(trans_1);
	  free_sequence(trans_2);
	  free_sequence(trans_3);
	}
      }
      /* otherwise, just use the sequence, assuming it is an AA_SEQ */
      else {
	/* score and enter the data into the list */
	score_and_enter(sequence, matrix, 0, RepeatsAllowed, SearchType);
      }
      
      free_sequence(sequence);
      
      records_searched++;

    } /* end while there are sequences */
    
    free_block(block);
    free_matrix(matrix);
    
  } /* end while there are blocks */
}  /* end of blocks_vs_sequences */



/* 
 * sequence_vs_matrices
 *   When SearchType is BLOCK, there is one sequence against a matrix 
 *   database.
 *   Parameters:
 *     FILE *emfp: the file to output the matrix information to.
 *   Error codes:
 */

static void sequence_vs_matrices(emfp)
     FILE *emfp;
{
  /* make sure we are at the beginning of the sequence data */
  rewind_file(SEQUENCE_FILES);
  
  /* loop through all the sequences (one) */
  sequence = read_a_sequence(get_file(SEQUENCE_FILES), 
			     get_sequence_db_db_type(),
			     get_sequence_db_seq_type());
  
 if (sequence == NULL) {
    sprintf(ErrorBuffer, 
	    "Unable to read the sequence for scoring against the matrices.");
    ErrorReport(SERIOUS_ERR_LVL);
    sprintf(ErrorBuffer, 
	    "Not scoring the sequence.\n");
    ErrorReport(SERIOUS_ERR_LVL);
    return;
  }

  if (NumberToReport == 0) {
    NumberToReport = DEFAULT_BLOCK_SEARCH_NUMBER_TO_REPORT(sequence);
  }

  /* inform what sequence the search is being done with */
  sprintf(ErrorBuffer,
	  "Searching sequence %s against the matrices database.\n",
	  sequence->name);
  ErrorReport(INFO_ERR_LVL);

  records_searched = 0;

  /* is the sequence a NA_SEQ?  if so, translate and score */
  if (sequence->type == NA_SEQ) {

    /* translate */
    trans1 = translate_sequence(sequence, 1, gcode, revgcode);
    trans2 = translate_sequence(sequence, 2, gcode, revgcode);
    trans3 = translate_sequence(sequence, 3, gcode, revgcode);

    /* if we are supposed to search both strands, translate and score */
    if (StrandsToSearch == 2) {

      /* translate */
      trans_1 = translate_sequence(sequence, -1, gcode, revgcode);
      trans_2 = translate_sequence(sequence, -2, gcode, revgcode);
      trans_3 = translate_sequence(sequence, -3, gcode, revgcode);
      
    } /* end if StrandsToSearch == 2 */

    /* make sure we are at the begining of the matrix data */
    rewind_file(MATRIX_FILES);

    if (StrandsToSearch != 2) {
      /* loop through all the matrices */
      while ((matrix = read_a_matrix(get_file(MATRIX_FILES))) != NULL) {
	/* inform which matrix scoring against */
	sprintf(ErrorBuffer,
		"Scoring vs matrix %s.\n",
		matrix->number);
	ErrorReport(INFO_ERR_LVL);
	if (emfp != NULL) {
	  output_matrix(matrix, emfp);
	}
	/* score and enter the data into the list */
	score_and_enter(trans1, matrix, 1, RepeatsAllowed, SearchType);
	score_and_enter(trans2, matrix, 2, RepeatsAllowed, SearchType);
	score_and_enter(trans3, matrix, 3, RepeatsAllowed, SearchType);

	records_searched++;

	free_matrix(matrix);
      } /* end while there are matrices */
    }
    else { /* StrandsToSearch == 2 */
      /* loop through all the matrices */
      while ((matrix = read_a_matrix(get_file(MATRIX_FILES))) != NULL) {
	/* inform which matrix scoring against */
	sprintf(ErrorBuffer,
		"Scoring vs matrix %s.\n",
		matrix->number);
	ErrorReport(INFO_ERR_LVL);
	if (emfp != NULL) {
	  output_matrix(matrix, emfp);
	}
	/* score and enter the data into the list */
	score_and_enter(trans1, matrix, 1, RepeatsAllowed, SearchType);
	score_and_enter(trans2, matrix, 2, RepeatsAllowed, SearchType);
	score_and_enter(trans3, matrix, 3, RepeatsAllowed, SearchType);
	score_and_enter(trans_1, matrix, -1, RepeatsAllowed, SearchType);
	score_and_enter(trans_2, matrix, -2, RepeatsAllowed, SearchType);
	score_and_enter(trans_3, matrix, -3, RepeatsAllowed, SearchType);
	
	records_searched++;
	
	free_matrix(matrix);
      } /* end while there are matrices */
    }
  
  } /* end if NA_SEQ */
  /* otherwise, just use the sequence, assuming it is an AA_SEQ */
  else {
    /* make sure we are at the begining of the matrix data */
    rewind_file(MATRIX_FILES);
    
    /* loop through all the matrices */
    while ((matrix = read_a_matrix(get_file(MATRIX_FILES))) != NULL) {
      /* inform which matrix scoring against */
      sprintf(ErrorBuffer,
	      "Scoring vs matrix %s.\n",
	      matrix->number);
      ErrorReport(INFO_ERR_LVL);
      if (emfp != NULL) {
	output_matrix(matrix, emfp);
      }
      /* score and enter the data into the list */
      score_and_enter(sequence, matrix, 0, RepeatsAllowed, SearchType);
      
      records_searched++;

      free_matrix(matrix);
    } /* end while there are matrices */
  } /* end else assuming an AA_SEQ */
  
/*  free(sequence); This is a global var. & is used later !!*/
  
}  /* end of sequence_vs_matrices */


/* 
 * matrix_vs_sequences
 *   When SearchType is MATRIX, there is one matrix against a sequences 
 *   database.
 *   Parameters:
 *     FILE *emfp: the file to output the matrix information to.
 *   Error codes:
 */

static void matrix_vs_sequences(emfp)
     FILE *emfp;
{
  /* make sure we are at the begining of the matrix data */
  rewind_file(MATRIX_FILES);
  
  /* loop through all the matrices (one) */
  matrix = read_a_matrix(get_file(MATRIX_FILES));

  if (matrix == NULL) {
    sprintf(ErrorBuffer, 
	    "Unable to read matrix for scoring against the sequences.");
    ErrorReport(SERIOUS_ERR_LVL);
    sprintf(ErrorBuffer, 
	    "Not scoring the matrix.\n");
    ErrorReport(SERIOUS_ERR_LVL);
    return;
  }
  
  if (NumberToReport == 0) {
    NumberToReport = DEFAULT_MATRIX_SEARCH_NUMBER_TO_REPORT_M(matrix);
  }

  /* inform what matrix the search is being done with */
  sprintf(ErrorBuffer,
	  "Searching matrix %s against the sequence database.\n",
	  matrix->number);
  ErrorReport(INFO_ERR_LVL);

  /* output the matrix */
  if (emfp != NULL) {
    output_matrix(matrix, emfp);
  }
  
  /* make sure we are at the beginning of the sequence data */
  rewind_file(SEQUENCE_FILES);
  
  records_searched = 0;

  /* loop through all the sequences */
  while ((sequence = read_a_sequence(get_file(SEQUENCE_FILES), 
				     get_sequence_db_db_type(),
				     get_sequence_db_seq_type())) != NULL) {
    
    /* inform which sequence scoring against */
    sprintf(ErrorBuffer,
	    "Scoring vs sequence %s.\n",
	    sequence->name);
    ErrorReport(INFO_ERR_LVL);

    /* is the sequence a NA_SEQ?  if so, translate */
    if (sequence->type == NA_SEQ) {
      /* translate */
      trans1 = translate_sequence(sequence, 1, gcode, revgcode);
      trans2 = translate_sequence(sequence, 2, gcode, revgcode);
      trans3 = translate_sequence(sequence, 3, gcode, revgcode);
      /* score and enter the data into the list */
      score_and_enter(trans1, matrix, 1, RepeatsAllowed, SearchType);
      score_and_enter(trans2, matrix, 2, RepeatsAllowed, SearchType);
      score_and_enter(trans3, matrix, 3, RepeatsAllowed, SearchType);
      /* free the translated sequences */
      free_sequence(trans1);
      free_sequence(trans2);
      free_sequence(trans3);
      /* if we are supposed to search both strands, translate and score */
      if (StrandsToSearch == 2) {
	/* translate */
	trans_1 = translate_sequence(sequence, -1, gcode, revgcode);
	trans_2 = translate_sequence(sequence, -2, gcode, revgcode);
	trans_3 = translate_sequence(sequence, -3, gcode, revgcode);
	/* score and enter the data into the list */
	score_and_enter(trans_1, matrix, -1, RepeatsAllowed, SearchType);
	score_and_enter(trans_2, matrix, -2, RepeatsAllowed, SearchType);
	score_and_enter(trans_3, matrix, -3, RepeatsAllowed, SearchType);
	/* free the translated sequences */
	free_sequence(trans_1);
	free_sequence(trans_2);
	free_sequence(trans_3);
      }
    }
    /* otherwise, just use the sequence, assuming it is an AA_SEQ */
    else {
      /* score and enter the data into the list */
      score_and_enter(sequence, matrix, 0, RepeatsAllowed, SearchType);
    }

    free_sequence(sequence);
    
    records_searched++;

  } /* end while there are sequences */
  
  free_matrix(matrix);
}


/* 
 * matrices_vs_sequences
 *   When SearchType is UNKNOWN, there is probably a matrices database against
 *   a sequences database.  Score all pairwise matches of matrices and
 *   sequences.
 *   Parameters:
 *     FILE *emfp: the file to output the matrix information to.
 *   Error codes:
 */

static void matrices_vs_sequences(emfp)
     FILE *emfp;
{
  /* NOTE: If there are speed problems, might look at the SearchType */
  /*       variable in files.c to see which of sequences or blocks is */
  /*       considered the database.  The one that is the database is most */
  /*       likely to have the most elements, and should be in the outer */
  /*       loop to reduce "block->matrix" and "if NA_SEQ; NA_SEQ->AA_SEQ" */
  /*       overhead. */
  
  /* set the number to report */
  if (NumberToReport == 0) {
    rewind_file(MATRIX_FILES);
    matrix = read_a_matrix(get_file(MATRIX_FILES));
    rewind_file(SEQUENCE_FILES);
    sequence = read_a_sequence(get_file(SEQUENCE_FILES), 
			       get_sequence_db_db_type(),
			       get_sequence_db_seq_type());
    if (matrix == NULL) {
      if (sequence == NULL) {
	/* there are no comparisons to do */
	NumberToReport = 1;
      }
      else {
	NumberToReport = DEFAULT_BLOCK_SEARCH_NUMBER_TO_REPORT(sequence); 
	free_sequence(sequence);
      }
    }
    else {
      if (sequence == NULL) {
	/* there are no comparisons to do */
	NumberToReport = DEFAULT_MATRIX_SEARCH_NUMBER_TO_REPORT_M(matrix);
	free_matrix(matrix);
      }
      else {
	NumberToReport = 
	  max((DEFAULT_BLOCK_SEARCH_NUMBER_TO_REPORT(sequence)),
	      (DEFAULT_MATRIX_SEARCH_NUMBER_TO_REPORT_M(matrix)));
	free_block(matrix);
	free_sequence(sequence);
      }
    }
    rewind_file(MATRIX_FILES);
    rewind_file(SEQUENCE_FILES);
  }

  /* make sure we are at the begining of the matrix data */
  rewind_file(MATRIX_FILES);
  
  /* loop through all the matrices */
  while ((matrix = read_a_matrix(get_file(MATRIX_FILES))) != NULL) {
    
    /* output the matrix */
    if (emfp != NULL) {
      output_matrix(matrix, emfp);
    }
    
    /* make sure we are at the beginning of the sequence data */
    rewind_file(SEQUENCE_FILES);
    
    /* loop through all the sequences */
    while ((sequence = read_a_sequence(get_file(SEQUENCE_FILES), 
				       get_sequence_db_db_type(),
				       get_sequence_db_seq_type())) != NULL) {
      
      /* inform which matrix and sequence are being scored */
      sprintf(ErrorBuffer,
	      "Scoring sequence %s vs matrix %s.\n",
	      sequence->name, matrix->number);
      ErrorReport(INFO_ERR_LVL);
      
      /* is the sequence a NA_SEQ?  if so, translate */
      if (sequence->type == NA_SEQ) {
	/* translate */
	trans1 = translate_sequence(sequence, 1, gcode, revgcode);
	trans2 = translate_sequence(sequence, 2, gcode, revgcode);
	trans3 = translate_sequence(sequence, 3, gcode, revgcode);
	/* score and enter the data into the list */
	score_and_enter(trans1, matrix, 1, RepeatsAllowed, SearchType);
	score_and_enter(trans2, matrix, 2, RepeatsAllowed, SearchType);
	score_and_enter(trans3, matrix, 3, RepeatsAllowed, SearchType);
	/* free the translated sequences */
	free_sequence(trans1);
	free_sequence(trans2);
	free_sequence(trans3);
	/* if we are supposed to search both strands, translate and score */
	if (StrandsToSearch == 2) {
	  /* translate */
	  trans_1 = translate_sequence(sequence, -1, gcode, revgcode);
	  trans_2 = translate_sequence(sequence, -2, gcode, revgcode);
	  trans_3 = translate_sequence(sequence, -3, gcode, revgcode);
	  /* score and enter the data into the list */
	  score_and_enter(trans_1, matrix, -1, RepeatsAllowed, SearchType);
	  score_and_enter(trans_2, matrix, -2, RepeatsAllowed, SearchType);
	  score_and_enter(trans_3, matrix, -3, RepeatsAllowed, SearchType);
	  /* free the translated sequences */
	  free_sequence(trans_1);
	  free_sequence(trans_2);
	  free_sequence(trans_3);
	}
      }
      /* otherwise, just use the sequence, assuming it is an AA_SEQ */
      else {
	/* score and enter the data into the list */
	score_and_enter(sequence, matrix, 0, RepeatsAllowed, SearchType);
      }
      
      free_sequence(sequence);
      
      records_searched++;

    } /* end while there are sequences */
    
    free_matrix(matrix);
    
  } /* end while there are matrices */
}





static void print_stats(ofp)
     FILE *ofp;
{
  fprintf(ofp, "Records Searched:   %d\n", records_searched);
  fprintf(ofp, "\n");
  fprintf(ofp, "Scores Done:        %16.0f\n", Scores_Done);
  fprintf(ofp, "\n");
  fprintf(ofp, "Alignments Done:    %16.0f\n", Alignments_Done);
  fprintf(ofp, "\n");

  if (DoHistogram) {
    print_histogram(ofp);
  }
}



/*
 * main
 *   controls flow of program
 *   Parameters: argc, argv
 *   Error codes:
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *ofp;			/* the OutputFile file pointer */
  FILE *emfp;			/* the ExportMatrixFile file pointer */
  FILE *fqij; 			/* the Qij file */
  int qargc;			/* args from the OP line in .cs file */
  char **qargv;
  char *blimps_dir;		/* BLIMPS_DIR environment variable */
  int i;

  /* setup version info */
  version_strings("BLIMPS (BLocks IMProved Searcher)",
		  VERSION,
		  "",
		  VERSION_DATE,
		  "(C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center\n\n");

  /* read comand line parameters */
  /* NOTE:!!! Must decide if parameters or config file takes precedence */
  /*          will only use config file to start with, so the only arg */
  /*          should be the config file */

  signal(SIGABRT, ABRT_signal_handler);
#ifdef MALLOC_DEBUG		/* sun specific?  At least not on DECs. */
  malloc_debug(1);		/* needed to raise the error in free(), also */
				/* gives better error messages */
#endif

  /* print the version info to stdout */
  print_version(stdout);
  ErrorLevelReport = PROGRAM_ERR_LVL;     /* Most errors are suppressed */

  /* check that the correct number of argments are given */
  if (argc != 2) {
    fprintf(stderr, "Usage: %s config_file\n", argv[0]);
    exit(1);
  }

  /* read the configuration file, assuming it is arg 1 for now */
  /* NOTE: No errors will be placed in the error file until read_config_file */
  read_config_file(argv[1]);

  /*  See if the BLIMPS_DIR environment variable has been set */
  blimps_dir = getenv("BLIMPS_DIR");

  /* initialize the memory routines */
  init_reclaim_space(blimps_reclaim_space); 

  /* initialize the list data structures used for scores, blocks, */
  /* matrices, and sequences */
  initialize_lists();

  /* load the frequencies for converting blocks to matrices */
  /* see if the frequency file has not been specified */
  if (number_of_files(FREQUENCY_FILE) <= 0) {
    /* get a sequence file and find out the type */
    /* open the default file */
    if (blimps_dir != NULL) sprintf(Buffer, "%s/docs/", blimps_dir);
    else Buffer[0] = '\0';
    /* When searching a block vs a DNA database, use codon frequency instead
       of amino acid frequency because most of translated seq is not coding */
    if( (SearchType == SEARCH_TYPE_MATRIX) && 
        (get_sequence_db_seq_type() == NA_SEQ) )
    {
      strcat(Buffer, LOCAL_CODON_FREQUENCY_FILE);
    }
    else {
      strcat(Buffer, LOCAL_AMINO_FREQUENCY_FILE);
    }
  }
  else {
    /* open the listed frequency file name */
    strcpy(Buffer, get_current_file_name(FREQUENCY_FILE));
  }
  
  sprintf(ErrorBuffer, "Using frequencies from %s.\n", Buffer);
  ErrorReport(INFO_ERR_LVL);
  /*   Creates global array frequency[]  */
  if (! load_frequencies(Buffer)) {
    sprintf(ErrorBuffer, "Error loading frequencies.\n");
    ErrorReport(SERIOUS_ERR_LVL);
  }

  /*  Load the substitution probability matrix for conversion method 3 */
  if (BlockToMatrixConversionMethod >= 3)
  {
     Qij = NULL;
     if (blimps_dir != NULL) sprintf(Buffer, "%s/docs/", blimps_dir);
     else Buffer[0] = '\0';
     strcat(Buffer, LOCAL_QIJ_FILE);
     RTot = LOCAL_QIJ_RTOT;
    /*     Get the arguments from the "OP alts:" line if there is one */
    qargc = -1;
    if (! get_option_args("alts", & qargc, & qargv)) {
      sprintf(ErrorBuffer,
	      "Using default.qij\n");
      ErrorReport(WARNING_ERR_LVL);
    }
    else
    {
       if (qargc > 0)
       {
          RTot = atof(qargv[0]);
          if (qargc > 1)  strcpy(Buffer, qargv[1]);
       }
    }

    if ((fqij = fopen(Buffer, "r")) == NULL) {
      sprintf(ErrorBuffer,
	      "Cannot open 'alts' file \"%s\".  Exiting...\n", Buffer);
      ErrorReport(FATAL_ERR_LVL);
    }
    
    Qij = load_qij(fqij);
    fclose(fqij);
    sprintf(ErrorBuffer,
	  "Using pseudo-count parameters %f and %s.\n", RTot, Buffer);
    ErrorReport(INFO_ERR_LVL);
  }   /*   end of qij file stuff */


  /* initialize translation codes */
  if ((0>GeneticCodeInitializer) ||
      (GeneticCodeInitializer>=NUMBER_OF_GENETIC_CODES)) {
    sprintf(ErrorBuffer,
	    "Unknown genetic code %d.  Setting to Standard code (0).",
	    GeneticCodeInitializer);
    ErrorReport(WARNING_ERR_LVL);
    GeneticCodeInitializer = 0;
  }
  sprintf(ErrorBuffer,
	  "Using genetic code %d; %s.\n", GeneticCodeInitializer,
	  gcodes[GeneticCodeInitializer].name);
  ErrorReport(INFO_ERR_LVL);
  init_gcode(&gcodes[GeneticCodeInitializer], gcode, revgcode);
  
  /* open the output file for writing */
  if (OutputFile[0] != '\0') {
    /* open the output file for reading */
    ofp = fopen(OutputFile, "w");

    if (ofp == NULL) {
      sprintf(ErrorBuffer, 
	      "Unable to open output file \"%s\" for writing, aborting.",
	      OutputFile);
      ErrorReport(FATAL_ERR_LVL);
    }
  }
  else {
    ofp = stdout;
  }
  

  /* open the export file for writing */
  if (ExportMatrixFile[0] != '\0') {
    /* open the output file for reading */
    emfp = fopen(ExportMatrixFile, "w");

    if (emfp == NULL) {
      sprintf(ErrorBuffer, 
	      "Unable to open output file \"%s\" for writing.", 
	      ExportMatrixFile);
      ErrorReport(SERIOUS_ERR_LVL);
      sprintf(ErrorBuffer, 
	      "Not outputing the matrix output.\n");
      ErrorReport(SERIOUS_ERR_LVL);
      emfp = NULL;
    }
  }
  else {
    emfp = NULL;
  }

  
  /*
   * read through the blocks and sequences 
   */
  switch (SearchType) {
  case SEARCH_TYPE_BLOCK :
    if (SiteSpecificScoringMatrixType == SSSM_BLOCK) {
      sequence_vs_blocks(emfp);
    }
    else if (SiteSpecificScoringMatrixType == SSSM_PRECOMP_MAT) {
      sequence_vs_matrices(emfp);
    }
    break;
  case SEARCH_TYPE_MATRIX :
    if (SiteSpecificScoringMatrixType == SSSM_BLOCK) {
      block_vs_sequences(emfp);
    }
    else if (SiteSpecificScoringMatrixType == SSSM_PRECOMP_MAT) {
      matrix_vs_sequences(emfp);
    }
    break;
  case SEARCH_TYPE_UNKNOWN :
    if (SiteSpecificScoringMatrixType == SSSM_BLOCK) {
      blocks_vs_sequences(emfp); /* note plural blocks */
    }
    else if (SiteSpecificScoringMatrixType == SSSM_PRECOMP_MAT) {
      matrices_vs_sequences(emfp); /* note plural matrices */
    }
    break;
  default:
    /* BIG ERROR, should never get here.  Memory corrupted */
    sprintf(ErrorBuffer, 
	    "main(): SearchType variable corrupted, possible memory problems.");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "        Should never have reached this part of the program.");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "        The rest of the run may be invalid.");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer, 
	    "        Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.\n");
    ErrorReport(PROGRAM_ERR_LVL);
    SearchType = SEARCH_TYPE_UNKNOWN;
    blocks_vs_sequences(); /* note plural blocks */
    break;
  }


  /* print out header information */

  /* print the version info */
  print_version(ofp);


  switch (SearchType) {
  case SEARCH_TYPE_BLOCK :
    if (sequence != NULL) {
      fprintf(ofp, "\n");
      fprintf(ofp, "Probe Sequence: %s %s\n", 
             sequence->name, sequence->info);
      fprintf(ofp, "\n");
      if (sequence->type == NA_SEQ) {
	fprintf(ofp, "Probe Size: %d Base Pairs\n", sequence->length);
      }
      else {
	fprintf(ofp, "Probe Size: %d Amino Acids\n", sequence->length);
      }
      fprintf(ofp, "\n");
    }
    else {
      fprintf(ofp, "\n");
      fprintf(ofp, "Probe Sequence: NO SEQUENCE\n");
      fprintf(ofp, "\n");
      fprintf(ofp, "Probe Size: UNKNOWN\n");
      fprintf(ofp, "\n");
    }

    fprintf(ofp, "Probe File: %s\n", get_file_name(0, SEQUENCE_FILES));
    fprintf(ofp, "\n");
    if (SiteSpecificScoringMatrixType == SSSM_BLOCK) {
      fprintf(ofp, "Target File (s) : %s\n", get_file_name(0, BLOCK_FILES));
      for(i=1; i &  for LINUX users.
 Changes since version 3.2.5:
  5/22/99 Only translate query sequence once in sequence_vs_blocks()
  2/23/99 Changed sequence_vs_blocks() to use read_a_block_faster() which
	  ignores clusters & assumes sequence weights are in the block.
  2/ 3/99 Clean up sequence_vs_blocks()
 Changes since version 3.2.4:
 12/12/98 Process StrandsToSearch == -1 
          Used default.amino.frq instead of default.codon.frq for
          DNA seq vs blocks.
 Changes since version 3.1.4:
 5/13/98  Adjust block vs sequence search output for longer seq names.
 Changes since version 3.1:
 1/30/97  Changed use of default qij matrix error from SERIOUS to WARNING.
 1/20/97  Fixed bug in calls to get_file_name() when multiple files
 Changes since version 3.0.0:
 4/22/96  Added SequenceType global variable.
 4/11/96  Changed blocks_to_sequences() to call output_matrix_s(matrix,
          FLOAT_OUTPUT) instead of output_matrix(matrix). This is a bad
          kludge to print a matrix in floating point format by using an
	  "unknown" search type combination of BL with SQ.    JGH
 4/ 3/96  Changed to assume all conversion types >= 3 require loading a
	  Qij file.  JGH
*/
 data structures used for scores, blocks, */
  /* matrices, and sequences */
  initialize_lists();

  /* load the frequencies for converting blocks to matrices */
  /* see if the frequency file has not been specified */
  if (number_of_files(FREQUENCY_FILE) <= 0) {
    /* get a sequence file and find out the type */
blimps-3.9/blimps/blk2DR.c000064400001460000012000000042550774312247700157030ustar00jorjastaff00000400000027/* COPYRIGHT 2000 by the Fred Hutchinson Cancer Research Center
    blk2DR.c  	Makes list of sequences in blocks for expasy (DR format)
           blk2DR 
	   Creates file named .DR
--------------------------------------------------------------------
 3/28/00 J. Henikoff
====================================================================*/

#define BLNORM_C_
#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#include 

void output_DR();

/*=======================================================================*/

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *bfp, *ofp;
  Block *block;
  char bdbname[MAXNAME], prevfam[MAXNAME];
  char outname[MAXNAME];

/* ------------1st arg = blocks database -------------------------------*/
   if (argc > 1)
      strcpy(bdbname, argv[1]);
   else
   {
      printf("\nEnter name of blocks database: ");
      gets(bdbname);
   }
   if ( (bfp=fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbname);
      exit(-1);
   }

/*-----------------------------------------------------------------*/
   strcpy(outname, bdbname);
   strcat(outname, ".DR");
   if ( (ofp=fopen(outname, "w")) == NULL)
   {
         printf("\nCannot open file %s\n", outname);
         exit(-1);
   }

  prevfam[0] = '\0';
  while ((block = read_a_block(bfp)) != NULL)
  {
     if (strcmp(prevfam, block->family) != 0)  /* just process 1st block */
     {
        output_DR(block, ofp);
        strcpy(prevfam, block->family);
     }
  }
   
  fclose(bfp);
  fclose(ofp);

  exit(0);

}  /* end of main */
/*===================================================================
===================================================================*/
void output_DR(block, ofp)
Block *block;
FILE *ofp;
{
   int s;
   char ctemp[MAXNAME], *ptr;

   fprintf(ofp, "DR   BLOCKS;%s;%s\n", block->family, block->de);
   for (s=0; s< block->num_sequences; s++)
   {
         strcpy(ctemp, block->sequences[s].name);
         ptr = strtok(ctemp, "|");
         while (ptr != NULL)
	 {	
            fprintf(ofp, "%s\n", ptr);
            ptr = strtok(NULL, "|");
         }
   }

}  /* end of output_DR  */
blimps-3.9/blimps/blk2GC.c000064400001460000012000000036610774312247700156670ustar00jorjastaff00000400000027/* COPYRIGHT 2000 by the Fred Hutchinson Cancer Research Center
    blk2GC.c  	Makes list of sequences in blocks for GeneCard
           blk2GC 
	   Output to stdout
	Requires blimps libraries
--------------------------------------------------------------------
 4/ 4/00 J. Henikoff
====================================================================*/

#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#include 

void output_GC();

/*=======================================================================*/

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *bfp;
  Block *block;
  char bdbname[MAXNAME], prevfam[MAXNAME];

/* ------------1st arg = blocks database -------------------------------*/
   if (argc > 1)
      strcpy(bdbname, argv[1]);
   else
   {
      printf("\nEnter name of blocks database: ");
      gets(bdbname);
   }
   if ( (bfp=fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbname);
      exit(-1);
   }

/*-----------------------------------------------------------------*/
  prevfam[0] = '\0';
  while ((block = read_a_block(bfp)) != NULL)
  {
     if (strcmp(prevfam, block->family) != 0)  /* just process 1st block */
     {
        output_GC(block);
        strcpy(prevfam, block->family);
     }
  }
   
  fclose(bfp);

  exit(0);

}  /* end of main */
/*===================================================================
	Prints one line for each part of each sequence name
===================================================================*/
void output_GC(block)
Block *block;
{
   int s;
   char ctemp[MAXNAME], *ptr;

   for (s=0; s< block->num_sequences; s++)
   {
         strcpy(ctemp, block->sequences[s].name);
         ptr = strtok(ctemp, "|");
         while (ptr != NULL)
	 {	
            printf("%s | %s, %s;\n", ptr, block->family, block->de);
            ptr = strtok(NULL, "|");
         }
   }

}  /* end of output_DR  */
blimps-3.9/blimps/blk2lis.c000064400001460000012000000037730774312247700161710ustar00jorjastaff00000400000027/* COPYRIGHT 2000 by the Fred Hutchinson Cancer Research Center
    blk2lis.c  	Makes lists of sequences in blocks
           blk2lis 
	   Creates files named AC.lsb
--------------------------------------------------------------------
 3/28/00 J. Henikoff
====================================================================*/

#define BLNORM_C_
#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#include 

void output_lis();

/*=======================================================================*/

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *bfp;
  Block *block;
  char bdbname[MAXNAME], prevfam[MAXNAME];;

/* ------------1st arg = blocks database -------------------------------*/
   if (argc > 1)
      strcpy(bdbname, argv[1]);
   else
   {
      printf("\nEnter name of blocks database: ");
      gets(bdbname);
   }
   if ( (bfp=fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbname);
      exit(-1);
   }

/*-----------------------------------------------------------------*/

  prevfam[0] = '\0';
  while ((block = read_a_block(bfp)) != NULL)
  {
     if (strcmp(prevfam, block->family) != 0)  /* just process 1st block */
     {
        output_lis(block);
        strcpy(prevfam, block->family);
     }
  }
   
  fclose(bfp);
  exit(0);

}  /* end of main */
/*===================================================================
===================================================================*/
void output_lis(block)
Block *block;
{
   FILE *ofp;
   char outname[MAXNAME];
   int s;

   strcpy(outname, block->family);
   strcat(outname, ".lsb");
   if ( (ofp=fopen(outname, "w")) == NULL)
   {
         printf("\nCannot open file %s\n", outname);
         exit(-1);
   }
   else
   {
      fprintf(ofp, ">%s\n", block->family);
      fprintf(ofp, "pros/\n");
      for (s=0; s< block->num_sequences; s++)
         fprintf(ofp, "%s\tBLOCK\n", block->sequences[s].name);
      fclose(ofp);
   }

}  /* end of output_lis  */
blimps-3.9/blimps/blk2mot.c000064400001460000012000000266301054326020000161510ustar00jorjastaff00000400000027/*        blk2mot.c
   Reads a file of sequences (fasta format) & a file of blocks made
   from those sequences, and makes a .mot file readable by motomat:

      blk2mot   
		 is just used to count #of sequences

   Use to make a .mot file from Gibbs blocks, etc.
------------------------------------------------------------------------
10/20/95  J. Henikoff
11/14/95  Get MOTIFJ=[] info. off the Title line if there is one in 
          There is no Title line in  if it came from Gibbs
11/15/95  Treat hybrid as if from motif.
 1/ 3/96  Fix bug with significance level (could be > # seqs!)
 6/20/99  Sequence names can be 18 long instead of 10.
12/23/06  Sequence names can be 20 long instead of 18.
========================================================================*/

#define BLK2MOT_C_
#define EXTERN
#define MAXNAME 80	/* Maximum file name length */
#define MAXWIDTH 60     /* Max block width */

/*  Motomat significance level from Blocks 6.2: x = #sequences   */
#define signif(x) (int) ((double) 0.5 * x + 3.09)

#include 

struct motif_info {
   int Version, RunType, Signif, Dups, Distance, NumSeqs, Total_Motifs, Gibbs;
   int Motif;
   char Title[MAXLINE];
};

int getseqs();
void getblks();
void parse_BL();
void write_motifs();

/*-------------Global variables------------------------------------------*/
int Len[MAXSEQS];		/*  sequence lengths */
char *Seq[MAXSEQS];		/* sequences */
char Seqname[MAXSEQS][SNAMELEN];

/*=======================================================================*/
void main(argc, argv)
     int argc;
     char *argv[];
{
   FILE *fmot, *fblk, *fseq;
   Block *block;
   struct motif_struct *motif;
   struct motif_info *info;
   char *ptr, seqfile[FNAMELEN], blkfile[FNAMELEN],  motfile[FNAMELEN];
   char line[MAXLINE];

   if (argc <= 3)
   {
      printf("BLK2MOT: Copyright 1995 by Fred Hutchinson Cancer");
      printf(" Research Center\n");
      printf("USAGE:  blk2mot   \n");
      printf("         = input file of protein sequences\n");
      printf("         = input file of blocks from sequences\n");
      printf("         = output file for motomat\n");
   }
   info = (struct motif_info *) malloc(sizeof(struct motif_info));
   info->Version = VERSION;
/*----------------1st arg = sequence file --------------------------*/
   if (argc > 1)
      strcpy(seqfile, argv[1]);
   else
   {
      printf("\nEnter name of file containing sequences: ");
      gets(seqfile);
   }
   if ( (fseq=fopen(seqfile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", seqfile);
      exit(-1);
   }
   info->NumSeqs = getseqs(fseq);
   fclose(fseq);
   if (info->NumSeqs < 1 )
   {
      printf("\nNo sequences found in file %s\n", seqfile);
      exit(-1);
   }

/* ------------2nd arg = blocks database ---------------------*/
   if (argc > 2)
      strcpy(blkfile, argv[2]);
   else
   {
      printf("\nEnter name of blocks file: ");
      gets(blkfile);
   }
   if ( (fblk=fopen(blkfile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", blkfile);
      exit(-1);
   }
   /*  Quickly figure out how many blocks are in it & allocate space */
   /*  Pick up any title, too  */
   info->Total_Motifs = 0; info->Title[0] = '\0';
   while (!feof(fblk) && fgets(line, MAXLINE, fblk) != NULL)
   {
      if (line[0] == '>') strcpy(info->Title, line);
      if (strncmp(line, "BL   ", 5) == 0) info->Total_Motifs++;
   }
   rewind(fblk);
/*   info->Title[100] = '\0';
*/
   if (info->Total_Motifs < 1)
   {
      printf("\nNo blocks found in file %s\n", blkfile);
      exit(-1);
   }
   motif = (struct motif_struct *)
     malloc(info->Total_Motifs * sizeof(struct motif_struct));
   getblks(fblk, info, motif);
   fclose(fblk);

/* ------------3rd arg = new .mot file ---------------------*/
   if (argc > 3)
      strcpy(motfile, argv[3]);
   else
   {
      printf("\nEnter name of new motomat file: ");
      gets(motfile);
   }
   if ( (fmot=fopen(motfile, "wb")) == NULL)
   {
      printf("\nCannot open file %s\n", motfile);
      exit(-1);
   }
   write_motifs(fmot, info, motif);
   fclose(fmot);
   exit(0);
}   /* end of main */

/*======================================================================
       Read all sequences in file, fasta format assumed
	Updates global variables NumSeqs, Seqname[], Seq[], Len[]
========================================================================*/
int getseqs(fp)
FILE *fp;
{
   int ns, itemp, i, j;
   char line[MAXLINE], *ptr;

   ns = -1;
   
   while(!feof(fp) && fgets(line, MAXLINE, fp) != NULL)
   {
	if (line[0] == '>')
	{
	   ns++;
	   ptr = strtok(line+1, " \t\r\n");
	   if ((int) strlen(ptr) > SNAMELEN - 1) ptr[SNAMELEN - 1] = '\0';
	   strcpy(Seqname[ns], ptr);
	   Seq[ns] = (char *) malloc(MAX_LENGTH * sizeof(char));
	   if (Seq[ns] == NULL)
	   {
		printf("Couldn't allocate Seq[%d]\n", ns);
		exit(-1);
	   }
	   Len[ns] = j = 0; Seq[ns][0] = '\0';
        }
        else if (Seq[ns] != NULL && Len[ns] < MAX_LENGTH + (int) strlen(line) )
        {
	   for (i=0; i < (int) strlen(line); i++)
           {
              if (isalpha(line[i]))   /*  assuming all is okay here !! */
              {
  	  	   Seq[ns][j++] = line[i];
		   Len[ns] += 1;
              }
           }
           Seq[ns][j] = '\0';
	}
   }

   return(ns + 1);
}  /*  end of getseqs */
/*========================================================================
             Read the blocks & make motifs
==========================================================================*/
void getblks(fblk, info, motif)
FILE *fblk;
struct motif_info *info;
struct motif_struct *motif;
{
   Block *block;
   int nmot, sb, ss, i;
   char *ptr, *bltemp, ctemp[MAXLINE];

   /*---Take Signif, Dups & Distance parameters off the Title, or
        off first block that has them, or else
        use defaults after all the blocks are read in ---------*/
   info->Signif = info->Dups = info->Distance = -1;
   info->RunType = 3;
   info->Gibbs = info->Motif = NO;
   bltemp = strstr(info->Title, "MOTIFJ=[");
   if (bltemp != NULL)
   {
      strcpy(ctemp, bltemp);
      ptr = strtok(ctemp, "[");
      ptr = strtok(NULL, ",");
      info->RunType = atoi(ptr);
      ptr = strtok(NULL, ",");
      info->Signif = atoi(ptr);
      ptr = strtok(NULL, ",");
      info->Dups = atoi(ptr);
      ptr = strtok(NULL, "]");
      info->Distance = atoi(ptr);
   }
   nmot = 0;
   while ((block = read_a_block(fblk)) != NULL &&
           nmot < info->Total_Motifs)
   {
      motif[nmot].domain = block->width;  		/* width= */
      motif[nmot].freq = block->num_sequences;		/* seqs= */
      parse_BL(block, info, &motif[nmot]);
      for (sb=0; sb < block->num_sequences; sb++)
      {
         /*      Match names to determine sequence number    */
         ss = 0;
	 while (ss < info->NumSeqs && 
            strcmp(Seqname[ss], block->sequences[sb].name) != 0)
                ss++;
         motif[nmot].seq_no[sb] = ss;
         motif[nmot].pos[sb] = block->sequences[sb].position;
      }
      nmot++;
      free_block(block);
   }
   /*-------Use defaults if didn't find any of this stuff on the blocks */
   if (info->Signif < 0 || (info->Gibbs && !info->Motif))
       info->Signif = signif(info->NumSeqs);
   if (info->Signif > info->NumSeqs) info->Signif = info->NumSeqs;
   if (info->Dups < 0) info->Dups = 0;
   if (info->Distance < 0 || (info->Gibbs && !info->Motif)) info->Distance = 0;

}   /* end of getmots */
/*========================================================================
       Get info. off the BL line:
	Some is there for most blocks (width=, seqs=) &
	some is only added by mot2blk (dups=, score=, etc.)
BL   *** gibbs=[7,0,0] width=5 seqs=9 dups=0 freq=9 mots=1 score=0 d1=0 d2=4
BL   LNC motif=[47,0,17] width=14 seqs=92 dups=0 freq=74 mots=2 score=1062 d1=12 d2=1
==========================================================================*/
void parse_BL(block, info, motif)
Block *block;
struct motif_info *info;
struct motif_struct *motif;
{
   char *ptr, *bltemp, ctemp[MAXLINE];

   /*  protomat aa numbers are one less than blimps numbers */
   /*   block->motif is empty for Gibbs blocks */
   if (strlen(block->motif) == 3)
   {
      motif->aa1 = (unsigned char) aa_atob[ block->motif[0] ] - 1;
      if (motif->aa1 > 20) motif->aa1 = 20;
      motif->aa2 = (unsigned char) aa_atob[ block->motif[1] ] - 1;
      if (motif->aa2 > 20) motif->aa2 = 20;
      motif->aa3 = (unsigned char) aa_atob[ block->motif[2] ] - 1;
      if (motif->aa3 > 20) motif->aa3 = 20;
   }
   else motif->aa1 = motif->aa2 = motif->aa3 = (unsigned char) 20;

   bltemp = strstr(block->bl, "motif=[");
   if (bltemp != NULL)
   {
      info->Motif = YES;
      strcpy(ctemp, bltemp);
      ptr = strtok(ctemp, "[");
      ptr = strtok(NULL, ",");
      info->Signif = atoi(ptr);
      ptr = strtok(NULL, ",");
      info->Dups = atoi(ptr);
      ptr = strtok(NULL, "]");
      info->Distance = atoi(ptr);
   }

   bltemp = strstr(block->bl, "gibbs");
   if (bltemp != NULL)
   {
      info->Gibbs = YES; 
      if (!info->Motif) info->RunType = 8;	/* tell motomat it's Gibbs */
   }

   bltemp = strstr(block->bl, "freq=");
   if (bltemp != NULL)
   {
      strcpy(ctemp, bltemp);
      ptr = strtok(ctemp, "="); ptr = strtok(NULL, " \t\r\n");
      motif->freq = atoi(ptr);
   }
   else motif->freq = 0;

   bltemp = strstr(block->bl, "dups=");
   if (bltemp != NULL)
   {
      strcpy(ctemp, bltemp);
      ptr = strtok(ctemp, "="); ptr = strtok(NULL, " \t\r\n");
      motif->dups = atoi(ptr);
   }
   else motif->dups = 0;

   bltemp = strstr(block->bl, "mots=");
   if (bltemp != NULL)
   {
      strcpy(ctemp, bltemp);
      ptr = strtok(ctemp, "="); ptr = strtok(NULL, " \t\r\n");
      motif->mots = atoi(ptr);
   }
   else motif->mots = 1;

   bltemp = strstr(block->bl, "score=");
   if (bltemp != NULL)
   {
      strcpy(ctemp, bltemp);
      ptr = strtok(ctemp, "="); ptr = strtok(NULL, " \t\r\n");
      motif->score = atoi(ptr);
   }
   else motif->score = 0;

   bltemp = strstr(block->bl, "d1=");
   if (bltemp != NULL)
   {
      strcpy(ctemp, bltemp);
      ptr = strtok(ctemp, "="); ptr = strtok(NULL, " \t\r\n");
      motif->distance1 = atoi(ptr);
   }
   else motif->distance1 = 0;

   bltemp = strstr(block->bl, "d2=");
   if (bltemp != NULL)
   {
      strcpy(ctemp, bltemp);
      ptr = strtok(ctemp, "="); ptr = strtok(NULL, " \t\r\n");
      motif->distance2 = atoi(ptr);
   }
   else motif->distance2 = motif->domain - 1;

}  /*  end of parse_BL  */
/*========================================================================
       Write an output file for motomat
==========================================================================*/
void write_motifs(mot, info, motif)
FILE *mot;
struct motif_info *info;
struct motif_struct *motif;
{
  int i, j;

  fwrite(&info->Version, sizeof(int), 1, mot);
  fwrite(&info->RunType, sizeof(int), 1, mot);
  fwrite(&info->Signif, sizeof(int), 1, mot);
  fwrite(&info->Dups, sizeof(int), 1, mot);
  fwrite(&info->Distance, sizeof(int), 1, mot);
  fwrite(&info->NumSeqs, sizeof(int), 1, mot);
  fwrite(&info->Total_Motifs, sizeof(int), 1, mot);
  fwrite(Len, sizeof(int), info->NumSeqs, mot);
  fwrite(Seqname, SNAMELEN*sizeof(char), info->NumSeqs, mot);
  for (i=0; iNumSeqs; i++)
     for (j=0; jTotal_Motifs, mot);
  fwrite(&info->Title, strlen(info->Title)*sizeof(char), 1, mot);

}   /* end of write_motifs  */
 lengths */
char *Seq[MAXSEQS];		/* sequences */
char Seqname[MAXSEQS][SNAMELEN];

/*===================blimps-3.9/blimps/blk2pssm.c000064400001460000012000000247570774312247700163710ustar00jorjastaff00000400000027/*  blk2pssm.c	Convert a block to PSSM format
      Requires blimps 3.2.6+ routines for proper calculation of BZX

	blk2pssm    []
		pssm_format = B for blimps, M for mast, G for Gribskov,
			P for psi-blast
		pssm_type = block_to_matrix() conversion type:
		2	odds ratios, sum to 100 in each position
		3-6 are log odds with position-based pseudo counts:
		3	pseudo-counts, log-odds, nats, positive (blimps default)
		4	pseudo-counts, log-odds, bits
		5	pseudo-counts, log-odds, 1/2 bits
		6	pseudo-counts, log-odds, 1/3 bits (cobbler default)
		9	pseudo-counts nearly zero, log-odds, nats, positive
		10	3 but just odds ratios
		20	3 but just (counts+pseudos)/(totcount+totpseudo)
		21	just counts/totcount
		30	average score
		40	SIFT; Pauline's pseudos, (counts+pseudos)/(totc+totp)
		For backward compatibility:
		 without  gives:
		B => 6
		M => 6
		G => 30
		P => 20
           
--------------------------------------------------------------------
 10/ 5/96 J. Henikoff
 10/14/96 Leave out stop codon column for mast.
  2/22/99 Updated for blimps 3.2.6
  5/25/99 Call frq_qij() to load Qij & frequency.
  7/ 3/99 output_gribskov(), output_psi_blast()
 12/29/00 Separate pssm_format from pssm_type
  9/ 9/02 Don't treat null type as invalid
  8/27/03 Fix types to match block_to_matrix() types
>>>types 10,20,21,30 aren't working<<<
====================================================================*/

#define BLK2PSSM_C_
#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#include 

/*
extern struct float_qij *Qij;
extern double frequency[MATRIX_AA_WIDTH];
*/

void output_mast_matrix();
void output_gribskov();
void output_psi_blast();

/*=======================================================================*/
/*
 * main
 *   controls flow of program
 *   Parameters: argc, argv
 *   Error codes:
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *bfp, *ofp, *fp;
  Block *block;
  Matrix *matrix, *logodds;
  char bdbname[MAXNAME], conname[MAXNAME];
  char ctemp[10];
  int format, type, itemp;

  ErrorLevelReport = 5;			/* No blimps errors reported */

   if (argc < 4)
   {
      printf("BLK2PSSM: Copyright 1996-2003 Fred Hutchinson Cancer Research");
      printf(" Center\n");
      printf("USAGE:  blk2pssm    []\n");
      printf("         = B BLIMPS|M MAST|G Gribskov|P Psi-Blast\n");
      printf("         = 3,6,20,21\n");
   }

/* ------------1st arg = blocks database -------------------------------*/
   if (argc > 1)
      strcpy(bdbname, argv[1]);
   else
   {
      printf("\nEnter name of BLOCKS input file: ");
      gets(bdbname);
   }
   if ( (bfp=fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbname);
      exit(-1);
   }
/* ------------2nd arg = PSSM file -----------------------*/
   if (argc > 2)
      strcpy(conname, argv[2]);
   else
   {
      printf("\nEnter name of PSSM output file: ");
      gets(conname);
   }
   if ( (ofp=fopen(conname, "w")) == NULL)
   {
      printf("\nCannot open file %s\n", conname);
      exit(-1);
   }

/*--------------3rd arg = PSSM format-------------------------*/
/* blimps=0, mast=1, gribs=2, psi=3 */
   format = 0; type = 6;
   if (argc > 3) {  strcpy(ctemp, argv[3]);  }
   else
   {
      printf("\nEnter PSSM format type (B=blimps, M=mast, G=Gribskov, P=Psi-Blast) [B]:  ");
      gets(ctemp);
   }
   if (strlen(ctemp) && (ctemp[0] == 'm' || ctemp[0] == 'M'))
   {       format = 1; type = 6;  }
   else 
   {
      if (strlen(ctemp) && (ctemp[0] == 'g' || ctemp[0] == 'G'))
      {  format = 2; type = 10;  }
      else  
      {
         if (strlen(ctemp) && (ctemp[0] == 'p' || ctemp[0] == 'P'))
         {  format = 3; type = 20;   }
      }
    }

/*--------------4th arg = PSSM type -----------------------------*/
   if (argc > 4)
   {
      itemp = atoi(argv[4]);
      if ((itemp > 2 && itemp < 7) || itemp == 9 || itemp == 10 ||
	   itemp == 20 || itemp == 21 || itemp == 30 || itemp == 40) 
      {    
         type = itemp;  
         printf("Using type %d\n", type); 
      }
      else
      { printf("%s Invalid type %d, using type %d\n", argv[4], itemp, type); }
   }
   
/*-----------------------------------------------------------------*/
   /* Sets global variables Qij, frequency[], RTot  */
   /* Always reads default.amino.frq & default.qij & sets RTot = 5 */
   frq_qij();
 
   if (type == 9) RTot = 1.0;		/* see narrow.c */

/*-----------------------------------------------------------------*/
     /*   should write the alphabet once per family */
  if (format == 1) fprintf(ofp, "ALPHABET= ARNDCQEGHILKMFPSTWYVBZX\n");
  while ((block = read_a_block(bfp)) != NULL)
  {
      matrix = block_to_matrix(block, type);
      switch (format)
      {
         case 0:    /* Blocks format */
            output_matrix_s(matrix, ofp, FLOAT_OUTPUT); 
            break;
         case 1:    /* Mast format  */
            output_mast_matrix(matrix, ofp);
            break;
         case 2:
            output_gribskov(matrix, ofp);
            break;
         case 3:
            /* to match cobbler seq */
            logodds = block_to_matrix(block, 6);
            output_psi_blast(matrix, logodds, ofp);
	    free_matrix(logodds);
            break;
         default:
            break;
      }
      free_matrix(matrix);
      free_block(block);
  }
   
  fclose(bfp); fclose(ofp);
  exit(0);

}  /* end of main */
/*=======================================================================
    0- 1A 2R 3N 4D 5C 6Q 7E 8G 9H 10I 11L 12K 13M 14F 15P 16S 17T 18W 19Y
   20V 21B 22Z 23X 24* 25J,O,U 
========================================================================*/
void output_mast_matrix(matrix, ofp)
Matrix *matrix;
FILE *ofp;
{
   int pos, aa;

   fprintf(ofp, "log-odds matrix: alength= 23 w= %d\n", matrix->width);
   for (pos=0; pos < matrix->width; pos++)
   {
      /*  Force U == X */
      matrix->weights[25][pos] = matrix->weights[23][pos];
      for (aa=1; aa <= 23; aa++)
      {
         fprintf(ofp, "% 6.3f ", matrix->weights[aa][pos]);
      }
      fprintf(ofp, "\n");
   }

}  /* end of output_mast_matrix */
/*=======================================================================
	Compute X for each position as average score over entire matrix
	(instead of just over the position). Compute -* as min over
	entire matrix.
>>>>> Have to read in the aa frequencies first <<<<<<<
========================================================================*/
void compute_X(matrix)
Matrix *matrix;
{
   int pos, aa;
   double dmean, dmin;

   dmean = 0.0;
   dmin = 9999.99;

   for (pos=0; pos < matrix->width; pos++)
   {
      for (aa=1; aa <=20; aa++)
      {
/*         dmean += freqs[aa] * matrix->weights[aa][pos];    */
         if (matrix->weights[aa][pos] < dmin) dmin = matrix->weights[aa][pos];
      }
   }
   dmean /= (double) matrix->width;
   for (pos=0; pos < matrix->width; pos++)
   {
      matrix->weights[23][pos] = dmean;			/*   X   */
      matrix->weights[25][pos] = dmean;			/* JOU   */
      matrix->weights[0][pos] = dmin;			/*   -   */
      matrix->weights[24][pos] = dmin;			/*   *   */
   }
} /* end of compute_X */
/*=======================================================================
    0- 1A 2R 3N 4D 5C 6Q 7E 8G 9H 10I 11L 12K 13M 14F 15P 16S 17T 18W 19Y
   20V 21B 22Z 23X 24* 25J,O,U 

PSI-BLAST checkpoint file is supposed to contain the target frequencies
so the values for each column should sum to 1:
	(counts + pseudo-counts) / (total counts)
But the sequence values are taken from a logodds matrix so they should
match the cobbler sequence.
========================================================================*/
void output_psi_blast(matrix, logodds, ofp)
Matrix *matrix, *logodds;
FILE *ofp;
{
   int pos, aa, maxaa;
   long ltemp;
   double dtemp, maxscore;
   char c;

   ltemp = (long) matrix->width;
   fwrite(<emp, sizeof(long), 1, ofp);

   /*  Need to write out the sequence next; pick highest scoring
	amino acid in each column of the logodds matrix */
   for (pos=0; pos < logodds->width; pos++)
   {
      maxaa = -9999; maxscore = -9999.;
      for (aa=1; aa <= 20; aa++)
      {
         if (logodds->weights[aa][pos] > maxscore)
         {   maxaa = aa; maxscore = logodds->weights[aa][pos];  }
      }
      c = aa_btoa[maxaa];
      fwrite(&c, sizeof(char), 1, ofp);
   }

   for (pos=0; pos < logodds->width; pos++)
   {
/*		dsum is always 1.0
      dsum = 0.0;
      for (aa=1; aa <= 20; aa++)
      {
         dsum += matrix->weights[aa][pos];
      }
*/

      for (aa=1; aa <= 20; aa++)
      {
/*
         dtemp = matrix->weights[aa][pos]/dsum;
printf("%f ", dtemp);
*/
         dtemp = matrix->weights[aa][pos];
         fwrite(&dtemp, sizeof(double), 1, ofp);
      }
/*
printf("\n");
*/
   }

}  /* end of output_psi_blast */
/*=======================================================================
    0- 1A 2R 3N 4D 5C 6Q 7E 8G 9H 10I 11L 12K 13M 14F 15P 16S 17T 18W 19Y
   20V 21B 22Z 23X 24* 25J,O,U 

   Do all the entries in a Gribskov profile have to be positive integers?
   They are here; odds ratios normalized to add to 100 in each position.
========================================================================*/
void output_gribskov(matrix, ofp)
Matrix *matrix;
FILE *ofp;
{
   int pos, aa, maxaa, itemp;
   double dmin, dsum, maxscore;

   fprintf(ofp, "(Peptide) Length: %d\n", matrix->width);
   fprintf(ofp, "COBBLER Profile for %s %s\n", matrix->number, matrix->de);
   fprintf(ofp, "Cons");
   for (aa=1; aa <= 20; aa++) fprintf(ofp, "      %c", aa_btoa[aa]);
   fprintf(ofp, "\n");

   dmin = 9999.;
   for (pos=0; pos < matrix->width; pos++)
   {
      for (aa=1; aa <= 20; aa++)
      {
         if (matrix->weights[aa][pos] < dmin)
         {  dmin = matrix->weights[aa][pos];  }
      }
   }
printf("dmin=%f\n", dmin);

   /*  Need to write out the sequence next; pick highest scoring
	amino acid in each column */
   for (pos=0; pos < matrix->width; pos++)
   {
      dsum = 0.0;
      maxaa = -9999; maxscore = -9999.;
      for (aa=1; aa <= 20; aa++)
      {
         dsum += matrix->weights[aa][pos];
         if (matrix->weights[aa][pos] > maxscore)
         {   maxaa = aa; maxscore = matrix->weights[aa][pos];  }
      }
      fprintf(ofp, "%c    ", aa_btoa[maxaa]);

      for (aa=1; aa <= 20; aa++)
      {
/*
         itemp = round( 10. * (matrix->weights[aa][pos] - dmin) );
*/
         itemp = round( 100. * matrix->weights[aa][pos] / dsum );
         fprintf(ofp, "%6d ", itemp);
      }
      fprintf(ofp, "\n");
   }

}  /* end of output_gribskov */
*matrix, *logoddsblimps-3.9/blimps/blk2slx.c000064400001460000012000000041731054326024200161640ustar00jorjastaff00000400000027/*    blk2slx.c Converts a block to Sean Eddy's slx format 
           blk2slx  
--------------------------------------------------------------------
 10/10/94 J. Henikoff
 12/23/06 Longer sequence name
====================================================================*/

#define BLK2SLX_C_
#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#include 

/*
 * Local variables and data structures
 */
void output_slx();
/*=======================================================================*/
/*
 * main
 *   controls flow of program
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *bfp, *ofp;
  Block *block;
  char bdbname[MAXNAME], conname[MAXNAME];

/* ------------1st arg = blocks database -------------------------------*/
   if (argc > 1)
      strcpy(bdbname, argv[1]);
   else
   {
      printf("\nEnter name of blocks database: ");
      gets(bdbname);
   }
   if ( (bfp=fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbname);
      exit(-1);
   }
/* ------------2nd arg = slx blocks database ---------------------*/
   if (argc > 2)
      strcpy(conname, argv[2]);
   else
   {
      printf("\nEnter name of new slx database: ");
      gets(conname);
   }
   if ( (ofp=fopen(conname, "w")) == NULL)
   {
      printf("\nCannot open file %s\n", conname);
      exit(-1);
   }

/*-----------------------------------------------------------------*/

  while ((block = read_a_block(bfp)) != NULL)
  {
     output_slx(block, ofp);
  }
   
  fclose(bfp); fclose(ofp);
  exit(0);

}  /* end of main */
/*===================================================================
     slx format is sequence name, space, segment
====================================================================*/
void output_slx(block, ofp)
Block *block;
FILE *ofp;
{
   int seq, pos;
   for (seq=0; seq < block->num_sequences; seq++)
   {
      fprintf(ofp, "%-20s ", block->sequences[seq].name);
      for (pos=0; pos < block->width; pos++)
         fprintf(ofp, "%c", aa_btoa[ block->residues[seq][pos] ]);
      fprintf(ofp, "\n");
   }
}  /* end of output_slx */
blimps-3.9/blimps/blk_to_PSSM.c000064400001460000012000000352400774312247700167350ustar00jorjastaff00000400000027/*    This program will read all blocks in the input file and write
      out the PSSM of each.

      Aug 20, 96' - blimps 3.1 defines matrix->weights as double (was int)
                    matrix->weights values are rounded before printing.

      Mar 21. 97' - changed passed arguments interface and added option
                    for specifying aa frequencies file.
                    replaced fprintf_matrix procedure with slightly
                    modified (some debugs) from BASE_PRIDE v03.

      Mar 23      - introduced sequence type (a or nuc) option. switched to
                    output_matrix_st from output_matrix.

      Mar 24      - added output_mast_matrix_st and option for it.

      Mar 28      - made fprint_matrix1 (from fprint_matrix), uses alphabet variable.
====================================================================*/

#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#define YES 1
#define NO 0

#define AA_ALPHABET_FULL "ARNDCQEGHILKMFPSTWYVBZX"
#define AA_ALPHABET_SHRT "ARNDCQEGHILKMFPSTWYVX"

#define NT_ALPHABET_FULL "ABCDGHKMNRSTUVWY"
#define NT_ALPHABET_SHRT "ACGTN"

/* # of positions (4 chars each) per line */
#define WWW_MATRIX_PRINT_WIDTH 165
#define SHL_MATRIX_PRINT_WIDTH 18

#define INP_DFLT_FNAME "stdin"
#define INP_DFLT        stdin

#define OUT_DFLT_FNAME "stdout"
#define OUT_DFLT        stdout

#define AA_FREQUENCY_FNAME_DFLT "default.amino.frq"
                                 /* file name of aa frequencies for
                                    load_frequencies procedure */

#define OUTPUT_FORMAT_DFLT 'G'     /* default output format 
                                      (G : generic format) */

#define OUTPUT_FORMAT_TYPES " G g B b M m " 


#define ALPHABET_TYPE_DFLT "FULL" /* default alphabet type */

#define ALPHABET_TYPES " F f FULL full S s SHORT short " /* each type must be flanked by blanks ! */

#define SEQS_TYPE_DFLT 'A'      /* default sequences type */

#define SEQS_TYPES " A a N n "  

#define PSSM_TYPE_DFLT 2        /* default block to matrix conversion method
                                   2 : use seq weights and odds-ratio*/

#define PSSM_TYPES " 2 3 5 6 10 20 30 " /* each type must be flanked by blanks ! */

#define PSSM_DEFS {"","","odds ratios normalized to 100","pseudos, log odds, nats","","pseudos, log odds, half bits","pseudos, log odds, third bits","","","","pseudos, odds ratios, nats","","","","","","","","","","just counts+pseudo counts","","","","","","","","","","average score"}

#define USAGE "%s [blocks-input_file_name [output_file_name]] [-Ppssm_type] [-Faa_frequency_file] [-Ooutput_format] [-Ssequences_type] [-Aalphabet_type]\n\n"

#define GET_HELP "((input now expected from screen; CTRL-C to quit))\n\n"

#define DEFAULTS "Defaults: in-\"%s\" out-\"%s\" pssm_type-\"%d\" aa_frequency-\"%s\" output_format-\"%c\" sequences_type-\"%c\" alphabet_type\"%s\"\n\n"

#define COMMENTS "Comments: \"-\" instead of a input/output file name => stdin/stdout\n          The order of the arguments is not important but the\n          first name is for the input file and the second for the output.\n      output_format = G: generic\n                      B: BLIMPS input\n                      M: MAST input\n     sequences_type = A: amino acids for protein sequences\n                      N: nucleotides  for DNA or RNA sequences\n      alphabet_type = F/FULL including degenerate codes\n                       aa: %s\n                       nt: %s\n                      S/SHORT only specific or unknown aa and DNA nucleotides\n                       aa: %s\n                       nt: %s\n          pssm_type = 2 odds ratios normalized to 100\n                      3 pseudos, log odds, nats\n                      5 pseudos, log odds, half bits\n                      6 pseudos, log odds, third bits\n                     10 pseudos, odds ratios, nats\n                     20 just counts+pseudo counts\n                     30 average score\n\n"

#include "blocksprogs.h"

/*
 * Local variables and data structures
 */

void    fprint_matrix1() ;
void    output_mast_matrix_st() ;
void    getargs() ;

Boolean WWW_FLAG = YES ;


/*=======================================================================*/
/*
 * main
 *   controls flow of program
 *   Parameters: argc, argv
 *   Error codes:
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE  *bfp=INP_DFLT, *outf=OUT_DFLT ;
  FILE  *fqij;
  char  bdbname[MAXNAME]=INP_DFLT_FNAME, outfname[MAXNAME]=OUT_DFLT_FNAME ;
  char  frqname[MAXNAME]="", qijname[MAXNAME]="";
  char  *pssm_defs[]=PSSM_DEFS ;
  char  seqs_type = SEQS_TYPE_DFLT, output_format = OUTPUT_FORMAT_DFLT ;
  char  alphabet_type[MAXNAME] = ALPHABET_TYPE_DFLT ;
  char  *blimps_dir, tmp[MAXNAME], *alphabet, *aa_alphabet, *nt_alphabet ;
  Block *block;
  Matrix *matrix ;
  int   pssm_type = PSSM_TYPE_DFLT, out_style=INT_OUTPUT; /*also possible FLOAT_OUTPUT*/
  int i1 ;

  blimps_dir = getenv("BLIMPS_DIR");

/* Amino acid frequency */
  if (blimps_dir != NULL) 
       sprintf(frqname, "%s/docs/%s", blimps_dir, "default.amino.frq");
  else sprintf(frqname, "%s", AA_FREQUENCY_FNAME_DFLT) ;

  if (argc == 1) /* show usage and what defaults are used */
     {
     fprintf(stderr, USAGE, argv[0]) ;
     fprintf(stderr, DEFAULTS, bdbname, outfname, pssm_type
                             , frqname, output_format, seqs_type
                             , alphabet_type) ;
     fprintf(stderr, COMMENTS, AA_ALPHABET_FULL, NT_ALPHABET_FULL, 
                               AA_ALPHABET_SHRT, NT_ALPHABET_SHRT) ;
     fprintf(stderr, GET_HELP) ;
     }
  else
     getargs(argc,argv,&bfp,&outf,bdbname,outfname,&pssm_type,
             frqname,&output_format,&seqs_type,alphabet_type) ;

/* check arguments */

  sprintf (tmp, " %d ", pssm_type) ;
  if (strstr(PSSM_TYPES, tmp) == NULL) 
     {
     fprintf(stderr, "Warning ! Unspecified pssm type (%d) requested.\nUsing default pssm type (%d).\n\n",
             pssm_type, PSSM_TYPE_DFLT) ;
     pssm_type = PSSM_TYPE_DFLT ;
     }

  if (strchr(OUTPUT_FORMAT_TYPES, output_format) == NULL) 
     {
     fprintf(stderr, "Warning ! Unknown output format (%c) requested.\nUsing default sequences type (%c).\n\n",
             output_format, OUTPUT_FORMAT_DFLT) ;
     output_format = OUTPUT_FORMAT_DFLT ;
     }

  sprintf (tmp, " %s ", alphabet_type) ;
  if (strstr(ALPHABET_TYPES, tmp) == NULL) 
     {
     fprintf(stderr, "Warning ! Unspecified alphabet type (%s) requested.\nUsing default pssm type (%s).\n\n",
             alphabet_type, ALPHABET_TYPE_DFLT) ;
     strcpy(alphabet_type,ALPHABET_TYPE_DFLT) ;
     }

  if (strcmp(alphabet_type,"S") !=0 && strcmp(alphabet_type,"SHORT") !=0 &&
      strcmp(alphabet_type,"s") !=0 && strcmp(alphabet_type,"short") !=0) 
     {
     aa_alphabet = AA_ALPHABET_FULL ;
     nt_alphabet = NT_ALPHABET_FULL ;
     }
  else
     {
     aa_alphabet = AA_ALPHABET_SHRT ;
     nt_alphabet = NT_ALPHABET_SHRT ;
     }

  if (strchr(SEQS_TYPES, seqs_type) == NULL) 
     {
     fprintf(stderr, "Warning ! Unspecified sequences type (%c) requested.\nUsing default sequences type (%c).\n\n",
             seqs_type, SEQS_TYPE_DFLT) ;
     seqs_type = SEQS_TYPE_DFLT ;
     }
  switch (toupper(seqs_type))
     {
     case 'A' :
        seqs_type = AA_SEQ ;
        alphabet = aa_alphabet ;
        break ;
     case 'N' :
        seqs_type = NA_SEQ ;
        alphabet = nt_alphabet ;
        break ;
     default : /* this shouldn't happen (but so does shit) */
        fprintf(stderr, "Using mino acids sequence type.\n") ;
        seqs_type = AA_SEQ ;
        alphabet = aa_alphabet ;
     }


/* open files */
/* Input */
  if (strcmp(bdbname,INP_DFLT_FNAME) !=0 && (bfp=fopen(bdbname, "r")) == NULL)
     {
     fprintf(stderr, "Cannot open input file %s\n", 
             bdbname);
     exit(-1);
     }

/* output */
  if (strcmp(outfname,OUT_DFLT_FNAME) !=0 && (outf=fopen(outfname, "w")) == NULL)
     {
     fprintf(stderr, "Cannot open output file %s\n", 
             outfname);
     exit(-1);
     }

/* qij */
  if (blimps_dir != NULL) sprintf(qijname, "%s/docs/", blimps_dir);

  if (pssm_type == 30) strcat(qijname, "default.iij"); /*average score*/
  else                 strcat(qijname, "default.qij");

  Qij = NULL;
  if ( (fqij=fopen(qijname, "r")) != NULL)
     { Qij = load_qij(fqij); fclose(fqij); }
  RTot = LOCAL_QIJ_RTOT;


  ErrorLevelReport = WARNING_ERR_LVL; /* report all errors */

                   /* load the frequencies for converting blocks to matrices */
  load_frequencies(frqname) ;

/* print parameters used */
  fprintf(outf, "residue frequencies: %s\n", frqname) ;
  fprintf(outf, "PSSM calculation: %s\n\n", pssm_defs[pssm_type]) ;

  while ((block = read_a_block(bfp)) != NULL)
     {
     matrix = block_to_matrix(block,pssm_type) ;

     switch (toupper(output_format))
	{
        case 'G' : 
          fprint_matrix1(matrix,outf,alphabet) ;
          break ;
        case 'B' :
           output_matrix_st(matrix,outf,out_style,seqs_type) ;
           break ;
        case 'M' :
           output_mast_matrix_st(matrix,outf,alphabet) ;
           break ;
	default :
           fprintf(stderr, 
               "Warning unrecognized outout format option - \"%c\".\n", 
               output_format);
           fprint_matrix1(matrix,outf,alphabet) ;
	}

     free_matrix(matrix) ;
     free_block(block) ;
     }

  fclose(bfp);
  exit(0);

}  /* end of main */

/*
 * fprint_matrix1
 *
 *  Prints a Matrix data structure to a file in a generic format. 
 *  adapted from fprint_matrix
 *
 *   Parameters: 
 *     Matrix *matrix:   the matrix to print
 *     FILE   *omfp:     the output matrix file pointer
 *     char   *alphabet: the printed matrix residues and their order
 *   Error Codes: none
 *
 */

void fprint_matrix1(matrix,omfp,alphabet)
     Matrix *matrix;
     FILE *omfp;
     char *alphabet ;
{
  int  pos, low, high, matrix_print_width ;
  char *ptr ;


  if (WWW_FLAG)
     matrix_print_width = WWW_MATRIX_PRINT_WIDTH ;
  else
     matrix_print_width = SHL_MATRIX_PRINT_WIDTH ;

  high = matrix_print_width;
  for (low=0; 
       lowwidth; 
       low = (high+=matrix_print_width) - matrix_print_width) {

  fprintf(omfp,"\n");

  fprintf(omfp,"%s\n", matrix->number);

  if (matrix->width > 99) {
    fprintf(omfp,"  |");
    for (pos=low; poswidth; pos++) {
      if (pos+1 > 99) {
	fprintf(omfp,"% 4d", (pos+1-(((pos+1)/1000)*1000)) / 100);
      }
      else {
	fprintf(omfp,"    ");
      }
    }
  fprintf(omfp,"\n");
  }

  if (matrix->width > 9) {
    fprintf(omfp,"  |");
    for (pos=low; poswidth; pos++) {
      if (pos+1 > 9) {
	fprintf(omfp,"% 4d", (pos+1-(((pos+1)/100)*100)) / 10);
      }
      else {
	fprintf(omfp,"    ");
      }
    }
  fprintf(omfp,"\n");
  }
  
  fprintf(omfp,"  |");
  for (pos=low; poswidth; pos++) {
    fprintf(omfp,"%4d", ((pos-((pos/10)*10))+1)%10);
  }
  
  fprintf(omfp,"\n");
  fprintf(omfp,"--+");
  for (pos=low; poswidth; pos++) {
    fprintf(omfp,"----");
  }

  fprintf(omfp,"\n");

  for (ptr=alphabet; *ptr != '\0'; ptr++)
      {
      fprintf(omfp,"%c |", *ptr);
      for (pos=low; poswidth; pos++) 
          {
          fprintf(omfp,"% 4d", 
                  round(matrix->weights[aa_atob[*ptr]][pos]));
          }
      fprintf(omfp,"\n");
      }

  }

}

/*****************************************************************************
 * get input and output file names and other program parameters.
 *
 * All parameters, except explicit input and output file names, 
 * should be preceded by a "-".
 * A sole "-" (implicitly) specifies a default for a file name.
 * The first explicit or implicit file name will be assigned to the input file
 * and the second to the output file.
 *****************************************************************************/

void getargs(argc,argv,inpf,outf,inpfname,outfname,pssm_type,frqname,
             output_format,seqs_type,alphabet_type)

int    argc;
int    *pssm_type;
char   *argv[];
char   inpfname[], outfname[], frqname[], *output_format ;
char   *seqs_type, alphabet_type[] ;
FILE   **inpf, **outf;

{
   int i1 ;
   int fnames=0 ;
   char *chr_ptr ;

   for(i1=1; i1width);
 
   for (pos=0; pos < matrix->width; pos++)
       {
       for (ptr=alphabet; *ptr != '\0'; ptr++)
           {
           fprintf(outf, "% 6.3f ", 
                   matrix->weights[aa_atob[*ptr]][pos]);
           }
       fprintf(outf, "\n");
       }

}  /* end of output_mast_matrix_st */
E], *alphabet, *aa_alphabet, *nt_alphabet ;
  Block *block;
  Matrix *matrix ;
  int   pssm_type = PSSM_TYPE_DFLT, out_style=INT_OUTPUT; /*also possible FLOAT_OUTPUT*/
  int i1 ;

  blimps_dir = getenv("BLIMPS_DIR");

/* Amino acid frequency */
  if (blimps_dir != NULL) 
       sprintf(frqname, "%s/docs/%s", blimps_dir, "default.amino.frq");
  else sblimps-3.9/blimps/blklis.c000064400001460000012000000031721032252775000160660ustar00jorjastaff00000400000027/* 
	blklis.c:	Read block & make list of sequences for uextract
		blklis  
*/
#define EXTERN

#include "blocksprogs.h"

/*---------------------- Global variables ----------------------------*/
char Version[12] = " 8/24/99.1";		/* Version date */

/*=======================================================================*/
/*
 * main
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE  *fin, *fout;
  char infile[80], outfile[80], ac[30], id[80], *ptr;
  int s;
  Block *block;

  ErrorLevelReport = 2;		/* suppress BLIMPS errors */

   printf("\nblklis: (C) Copyright 1999");
   printf(" Fred Hutchinson Cancer Research Center\n");

   /*  open files */
   if (argc > 1)
      strcpy(infile, argv[1]);
   else
   {
      printf("\nEnter name of file of blocks: ");
      gets(infile);
   }
   if ( (fin=fopen(infile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", infile);
      exit(-1);
   }
   if (argc > 2)
      strcpy(outfile, argv[2]);
   else
   {
      printf("\nEnter name of output file: ");
      gets(outfile);
   }
   if ( (fout=fopen(outfile, "w+")) == NULL)
   {
      printf("\nCannot open file %s\n", outfile);
      exit(-1);
   }

  /*  Process first block only */
  block = read_a_block(fin);
  if (block != NULL)
  {
     strcpy(ac, block->number); ac[7] = '\0';
     strcpy(id, block->id); ptr = strtok(id, ";");
     fprintf(fout, ">%s ;%s;%s; ; $\n", 
	ac, id, block->de);
     fprintf(fout, "pros/\n");
     for (s=0; snum_sequences; s++)
	fprintf(fout, "%s\n", block->sequences[s].name);
  }

  fclose(fin); fclose(fout);

  exit(0);
} /*  end of main */
blimps-3.9/blimps/blkprob.c000064400001460000012000003207761054326033600162540ustar00jorjastaff00000400000027/*=======================================================================
  (C) Copyright 1992-2003, Fred Hutchinson Cancer Research Center
	blkprob.c  USE:  blkprob nhits search_output blocks_db [-stats]
		   OR:   blkprob blimps.cs [-mast|-rank -H n -E n -C n -sum|-gff -stats -S stp-file] 
	    eg:  blkprob 10 sample.hom blocks.dat -stats
       There are three arguments:
	  1. Maximum number of hits to report
	  2. Name of output file from a BLIMPS blocks search.
	  3. Name of blocks database searched (optional, use a nonsense
	     name to omit, eg "none").
	  4. Optionally -stats => statistics written to files blksort.dat &
	     blksort.rep (repeats)
       Tries to read files in the current directory, or in first DB directory
	if input file is a blimps.cs file:
	  1. blkprob.stp:  documentation to print out; or prints.stp
	  2. blksort.stn:  percentiles for true negative blimps scores
	  3. repeats.dat:  number of repeats according to Prosite
	  4. blksort.bias: list of blocks with biased composition

     Assumed format of input file (output of a blimps search):
       [nl]Probe Sequence:...
       [nl][n]]Target Block File:...
       [nl][nl]
       [nl][block name][sp][block #][sp][ID & DE for 60][score for 5]...etc.
       Results start on 7th line.
       Block name is in columns 1-7.
       Description is in columns 15-73.
       Score is in columns 75-79.
       Frame is in columns 80-83.
       Offset in sequence is in columns 84-89.
       Alignment to block is in columns 90-.

--------------------------------------------------------------------------
  7/8/92   J. Henikoff --- major revision of blksort.c
 12/16/98 1. Introduced hit structure.
  1/20/99 1. Added cumprob()
  3/11/99 1. 
  3/25/99 1. Don't apply cut-off to repeats.
          2. Look for blkprob.stp in first database directory
  5/14/99 1. Modified for read_results() for revised blimps 3.2.6 output.
  5/21/99 1. Check for negative NBlock, NAlign (blimps problem?)
	     Option for GFF output.
  5/25/99 1. Fixed bug in init_hits() if blimps output only has one group
  5/26/99 1. Problem in pvale_mast() fixed?; still a problem in flagging
		repeats (see assemble_hits around line 1368)
  6/12/99 1. Sequence name up to 18 chars in align_blocks()
  6/15/99 1. Memory problem in init_hits()
  6/17/99 1. Don't report repeats or other alignments if Evalue <
		CutoffRepeat
  6/17/99 2. Don't divide NAlign by 2 for DNA.
  6/29/99 1. Made -mast default, added -rank. 
	     Added hit # to end of GFF & made GFF tab-delimited.
  7/ 4/99 1. Recognize Blimps version 3.3+
  7/22/99 1. Changed type of NAlign from long long to double (for DECs)
  7/31/99 1. Don't print overlapping repeat & "other" hits
	     Fix block maps.
  8/26/99 1. More changes for DEC systems. Divide NAlign by 2 for DNA if
		results are reported for both strands.
 12/ 9/99 1. Fix memory leaks
 12/15/99 1. Accomodate ACs between 7 and 10 characters
  1/ 2/00 1. Fix output format problem
  5/21/00 1. Fix output format problem with longer ACs; remove anchor evalue
  8/21/02 1. Use sprintf() instead of kr_itoa()
  8/21/03 1. New input parameter for CutoffScore = min anchor block score
  8/22/03 1. New -H option for header (default = blkprob.stp)
 12/23/06.1. Longer sequence names
==========================================================================*/

#define EXTERN			/* Required to use blimps routines */
#include 
#include 

#define NSCORE 9000		/* Maximum # of scores in .hom file */
#define MAXHIT 25		/* Default # hits to report */
#define CUTSCORE 1001		/* Min normalized anchor block score */
#define SEEK_SET 0		/* needed for UNIX fseek routine */
#define MINPAT 1000		/* Minimum blimps score for a hit */
#define MAXMAP 60		/* Maximum map width in columns */
#define MAXMAPLINE 600		/* MAXLINE in protomat.h is only 480 */
#define MAXTILES 620		/* Max. # of lines in blksort.stn */
#define MAXGROUP 2000		/* Max. # lines in repeats.dat file */
#define MAXBIAS 1000		/* Max. # lines in blksort.bias file */
#define MAXSEQ 20		/* Max. #chars in sequence name */
#define MAX_WIDTH 60		/* Max. width of block */
#define MAX_REPEAT 400		/* Max. #aas between repeats */
#define PROTEIN 1
#define DNA 3
/*		cumprob() stuff   */
#define MAXPROB 0.0005		/* upper tail prob */
#define MAXSCORE 10000
#define MAXCOL 100		/* Max matrix width */
struct score_struct {
	double ways, prob;
};

struct hom {			/* search results structure */
   char ac[MAXAC+1];		/* block name, eg. BL00094A */
   char fam[MAXAC+1];		/* family name, eg. BL00094 */
   int min_rank;		/* minimum rank for this group of blocks */
   int rank;			/* rank of this result in search */
   int frame;			/* frame of alignment */
   int strength;		/* block strengh */
   int score;			/* normalized blimps score */
   double cumprob;		/* cumprob of raw score */
   double minprob;		/* min cumprob */
   long offset;			/* offset of alignment */
   int width;			/* width of block */
   char title[25];		/* block description */
   char aa[MAX_WIDTH];	   	/* alignment to block */
   int hit_flag;		/* in assembled hit */
   int repeat_flag;		/* allowed repeat for hit */
   int other_flag;		/* other non-overlapping alignment */
   int map_flag;		/* used by map_blocks() */
				/* 0=>not mapped, 1=>mapped */
   struct blocks_info *binfo;	/* blocks info if in hit */
};

/*	Contains all the info needed to produce all the different reports */
/*  The rank_ values are for the block with the min rank (old blksort);
    the prob_ values are for the block with min cumprob    */
struct hit {
   char fam[MAXAC+1];			/* family name part of AC */
   char de[MAXLINE];
   int strand;
   int min_res, max_res;		/* indices into results array */
   int maxrep;				/* max # repeats for this ac */
   double mast_pvalue;			/* pvalue based on mast alg */
   int prob_res;			/* min cumprob block's results index */
   double prob_min;			/* min cumprob  */
   int rank_res;			/* results index for min rank block */
   int rank_min;			/* min rank for blocks in hit */
   double rank_ptile;      		/* ptile for lowest rank */
   double rank_pvalue;     		/* pvalue based on ranks */
   double evalue;			/* for sorting */
   int nblock;				/* # blocks in group */
   int nblkhit;				/* # blocks in hit */
   struct blocks_info *prob;		/* pointer to min cumprob block*/
   struct blocks_info *rank;		/* pointer to min rank block */
   struct blocks_info *binfo;
};
struct blocks_info {			/* block information needed for a hit */
   char ac[MAXAC+1];         		/* accession number */
   int nseq, width, strength;		/* #seqs, width, strength */
   int minprev, maxprev;		/* distances from prev block */
   int bias;				/* flag if block is biased */
   int hit_flag;			/* flag if block is included in hit */
   int query_res;			/* index into Results[] for query */
   int nrep;				/* number of repeats for block */
   char closest_name[SNAMELEN];		/* name of seq closest to query */
   long closest_offset;			/* offset of seq closest to query */
   char closest_aa[MAX_WIDTH];		/* aas for seq closest to query */
   struct blocks_info *next;
};
struct blocks_list {			/* a full set of blocks */
   char fam[MAXAC+1];			/* family part of AC  */
   Block *block;
   Matrix *pssm;
   struct blocks_info *binfo;
   struct blocks_list *next;
};


struct files_list {
   FILE *fdat;
   char datname[FNAMELEN];
   char prevfam[MAXAC+1];		/* family name part of AC ??? */
   long prevdat;
   struct files_list *next;
};

/*---- Functions in blkprob.c -----*/
int read_config();
void print_blurb();
int get_info();

void open_dbs();
void close_dbs();
struct files_list *make_flist();

void insert_flist();
int read_tiles();			/* read percentiles file */
int read_repeats();			/* read repeats.dat */
int read_bias();			/* read blksort.bias */
void read_results();

int init_hits();
void init_binfo();
struct blocks_list *read_fam();
int group_results();
int assemble_hits();
int assemble_hits_rank();
int print_hits();
void map_blocks();
void align_blocks();

int get_repeats();
double get_ptile();
void check_overlap();
double hypergeo();
int cumprob();
void pvalues();
double pvalue_rank();
double pvalue_mast();
double qfast();
int distance_okay();
long prev_dist();
int distance();
long compute_loc();
void closest_seq();
void consensus();
/*		sorting routines   */
int strandcmp();		
int framecmp();		
int mincmp();	
int tempcmp();
int dtempcmp();
int stempcmp();
int stempcmp2();
int hitcmp();
int hitrank();
int hitfam();
int hitprob();
int hitprank();
int hitmpv();
int hiteval();
/*		blocks_list routines, should be put in a library */
struct blocks_list *make_blist();
void insert_blist();
void free_blist();
/*		blocks_info routines, should be put in a library */
struct blocks_info *make_binfo();
void insert_binfo();
void free_binfo();

/*-------Functions in protomat.c --------*/
struct split_name *split_names();
/*  void kr_itoa(); */

/*------------Global variables -------------*/
int NRead;
int NCumprob;
char Version[12] = "12/23/06.1";/* Version number */
int BlimpsVer;			/* Blimps version */
char Query[SNAMELEN];		/* Query sequence name */
char Qfilename[FNAMELEN];	/* Query file */
unsigned long QLen;		/* Query length */
int NBlock;			/* # blocks searched */
double NAlign;			/* # alignments done */
double Strands;			/* # of strands reported */
double CutoffRepeat;		/* Single block hit cuttoff */
double CutoffExp;		/* Cutoff evalue */
int CutoffScore;		/* Min anchor block score */
int SeqType;			/* =1 if amino acid, =3 if nucleotide */
int MaxHit;			/* # hits to report */
int MaxHits;			/* Max size of hits array */
int Ntiles;			/* # of percentiles read in */
float Tiles[MAXTILES];		/* %-tiles values for scores 1000-1620 */
int Stats;			/* statistics flag */
int Summary;			/* summary output only flag */
int GFF;			/* GFF output flag */
int Mast;			/* use Mast-style evalues */
char HomName[FNAMELEN];		/* Search file name for stats file */
double CumProb[MAXSCORE];	/* Score distribution */
char StpFile[80];		/* Name of header file */

struct working {
  char ac[MAXAC+1];
  int num;
} Repeats[MAXGROUP], Bias[MAXBIAS];	/* Working area */
int NRepeat;			/* # of repeat values read in */
int MaxRepeat;			/* max # of repeats in any group */
int NBias;			/* # of bias values read in */

int Config_Flag;		/* 1st arg is blimps config file */
char DatDir[FNAMELEN];		/* Directory of database files */

struct hom *Results;		/* Blimps search results */
int NResult;

/*======================================================================*/
int main(argc, argv)
int argc;
char *argv[];
{
   FILE *fhom, *fcf;
   char homfile[FNAMELEN], datfile[FNAMELEN], ctemp[FNAMELEN];
   char db[FNAMELEN];
   int i, ngrp, ndb, nhom, nhit;
   struct split_name *datsplit;
   struct files_list *flist, *newdat;
   struct hit *hits;

   ErrorLevelReport = 4;			/* Blimps error level */
   printf("\nBLKPROB Version %s\n", Version);
   if (argc < 2)
   {
      printf("COPYRIGHT 1992-8 Fred Hutchinson Cancer Research Center\n");
      printf("USAGE: blkprob    [-H n -E n -C n -mast|-rank -sum|-gff -stats]\n");
      printf("           = number of hits to report, use 0 for default\n");
      printf("     = blimps search output file\n");
      printf("     = blocks database searched by blimps\n");
      printf("OR:    blkprob \n");
      printf("     = name of blimps configuration file\n");
      printf("Other options\n");
      printf("    -H n            maximum number of hits to report\n");
      printf("    -E n            cutoff expected value for anchor blocks\n");
      printf("    -C n            min cutoff raw score for anchor blocks\n");
      printf("    -mast           order results by MAST-type e-values\n");
      printf("    -rank           order results by RANK-statistic e-values\n");
      printf("    -sum            output summary only (one line per hit)\n");
      printf("    -gff		  Sanger Center's GFF output\n");
      printf("    -stats          produces .dat statistics file\n");
      printf("    -S filename     header file (default=blkprob.stp)\n");
   }
   Config_Flag = NO;
   fcf = NULL;
   MaxHit = 0;

   /*-----------arg 1: # hits to report or config file---------------------*/
   ctemp[0] = '\0';
   flist = make_flist();
   ndb = 0;
   if (argc > 1) strcpy(ctemp, argv[1]);
   else
   {
      printf("\nEnter number of hits to report or ");
      printf("blimps configuration file name [%d]: ", MaxHit);
      gets(ctemp);
   }
   if (!strlen(ctemp)) strcpy(ctemp, "0");
   for (i=0; i 0) strcpy(datfile, flist->next->datname);
         }
    }   /* end of read parameters from blimps config file */
    else
    {   /* parameters are on the command line */
          MaxHit = atoi(ctemp);

         /*------------- arg 2:  .hom file -------------------------------*/
         if (argc > 2)
            strcpy(homfile, argv[2]);
         else
         {
            printf("\nEnter name of file containing blocks search results: ");
            gets(homfile);
         }
         /*------------- arg 3:  blocks database file -----------------------*/
         db[0] = '\0';
         if (argc > 3)
            strcpy(datfile, argv[3]);
         else
         {
            printf("\nEnter name of blocks database searched: ");
            gets(datfile);
         }
         if (strlen(datfile))
         {
            newdat = make_flist();
            strcpy(newdat->datname, datfile);
            insert_flist(flist, newdat);
            ndb++;
         }

    }  /* end of non-config file input */

    /*------------- Check for other options----------------------------*/
    Stats = Summary = GFF = NO;
    Mast = YES;
    CutoffExp = 1.0;		/* default expected value is 1 per search*/
    CutoffScore = CUTSCORE;
    StpFile[0] = '\0';
    for (i=2; i i)
                 {
			CutoffExp = atof(argv[i+1]);
                        if (CutoffExp < 0.0) CutoffExp = 1.0;
                        if (CutoffExp > 100.0) CutoffExp = 100.0;
                 }
                 else if (strncasecmp(argv[i], "-H", 2) == 0 && argc > i)
                      {
			MaxHit = atoi(argv[i+1]);
                        if (MaxHit < 0) MaxHit = 0;
                      }
                 else if (strncasecmp(argv[i], "-C", 2) == 0 && argc > i)
                      {
			CutoffScore = atoi(argv[i+1]);
                        if (CutoffScore < 0) CutoffScore = 0;
                      }
                 else if (strncasecmp(argv[i], "-S", 2) == 0 && argc > i)
                      {
                        strcpy(StpFile, argv[i+1]);
                      }
    }
    if (Summary && GFF) Summary = NO;

   /*  Get the directory of the first datbase file */
   datsplit = split_names(datfile);
   strncpy(DatDir, datfile, datsplit->dir_len);
   DatDir[datsplit->dir_len] = '\0';
   
   /*-------------------------------------------------------------------*/
   /*-----------------Open the search results --------------------------*/
   if ( (fhom=fopen(homfile, "r")) == NULL)
   {
      printf("\nBLKPROB: Cannot open file blimps file %s\n", homfile);
      exit(-1);
   }
   nhom = get_info(fhom, homfile);    /* returns # lines in blimps file */

   /*--- Set MaxHit based on sequence length & type to report at least
	  1 hit per 1000kb of DNA sequence ---*/
   if (MaxHit <= 0)
   {
      if (SeqType == DNA)
      {
         MaxHit = (int) QLen/1000 + 1;
         if (MaxHit < MAXHIT) MaxHit = MAXHIT;
      }
      else  MaxHit = MAXHIT;
   }
   MaxHits = MaxHit;

   /*---------------Open the blocks database files---------------------*/
   open_dbs(flist);

   /*---------------------------------------------------------------------*/
   if (!GFF) print_blurb(ndb);
   printf("\nQuery=%s\nSize=%ld ", Qfilename, QLen);
   if (SeqType == PROTEIN) printf("Amino Acids\n");
   else if (SeqType == DNA) printf("Base Pairs\n");
   if (NBlock > 0) printf("Blocks Searched=%d\n", NBlock); 
   if (NBlock < 1)
   {
      printf("Blocks searched is negative, cannot use for statistics.\n");
      NBlock = 1;
   }
   if (NAlign > 0.0) printf("Alignments Done=%16.0f\n", NAlign); 
   if (NAlign < 1.0)
   {
      printf("Alignments done is negative, cannot use for statistics.\n");
      NAlign = 1.0;
   }
   printf("Cutoff combined expected value for hits=%3.0f\n", CutoffExp);
   printf("Cutoff block expected value for repeats/other=%3.0f\n", 
	   CutoffRepeat);

   /*---------------------------------------------------------------------*/
   frq_qij();			/* load the default PSSM-making files */
   Ntiles = read_tiles();
   NRepeat = read_repeats();
   NBias = read_bias();

   Results = (struct hom *) malloc(nhom * sizeof(struct hom));
   if (Results == NULL)
   {  printf("\nResults: OUT OF MEMORY\n\n"); exit(-1); }
   read_results(fhom);
   fclose(fhom);
   
   ngrp = group_results();
   /*  MaxHits is a crude way to limit memory use, should really
	allocate ngrp hits  */
   MaxHits  = ngrp;
   if (MaxHits > MaxHit) MaxHits = 2*MaxHit; /* extra slots for equal scores */
   hits = (struct hit *) malloc((MaxHits+1) * sizeof(struct hit));
   if (hits == NULL)
   {  printf("\nhits: OUT OF MEMORY\n\n"); exit(-1); }
   /*  Retrieve blocks, compute individual block probabilities, closest seq */
   nhit = init_hits( hits);
   NAlign /= Strands;

/*
printf("NResult=%d ngrp=%d nhit=%d\n\n", NResult, ngrp, nhit);
*/
   if (nhit < 1)
   { printf("No hits found\n"); exit(-1);   }

NRead = NCumprob = 0;
   if (flist->next != NULL) init_binfo(flist, nhit, hits);
/*
printf("NRead=%d NCumprob=%d\n", NRead, NCumprob);
*/
   close_dbs(flist);

   /* Piece together compatible blocks from potential hits & compute hit prob*/
   assemble_hits(nhit, hits);

   pvalues(nhit, hits);

   printf("\n%d possible hits reported\n", print_hits(nhit, hits) );

   exit(0);
}  /*  end of main */
/*============================================================================
  Read a blimps config file:  OU=blimps output file, DB=blocks db(s) searched
  How to override default MaxHit from here - NU ?
=============================================================================*/
int read_config(fcf, homfile, flist)
FILE *fcf;
char homfile[FNAMELEN];
struct files_list *flist;
{
   char line[MAXLINE], keyword[20], *ptr;
   int ndb;
   struct files_list *newdat;

   ndb = 0;
   homfile[0] = '\0';
   /*   Read until end of file or until "//" line is reached   */
   while ( !feof(fcf) && fgets(line, MAXLINE, fcf) != NULL &&
           (strncmp(line, "//", 2)) )
   {
      ptr = strtok(line, " \t\r\n");
      if (ptr != NULL && ptr[0] != ';')
      {
         strcpy(keyword,ptr);
         ptr = strtok(NULL, " \t\r\n;");
         if (ptr != NULL)
         {
            if (strncasecmp(keyword, "OU", 2) == 0)
            {
               strcpy(homfile, ptr);
            }
            else if (strncasecmp(keyword, "DB", 2) == 0)
            {
               newdat = make_flist();
               strcpy(newdat->datname, ptr);
               insert_flist(flist, newdat);
               ndb++;
            }
         }   /* end of if ptr */
      }  /* end of if ptr */
   }  /* end of fcf */

   return (ndb);
}  /* end of read_config */
/*======================================================================*/
void print_blurb(ndb)
int ndb;
{
   FILE *fstp;
   char fname[FNAMELEN], line[MAXLINE];

   
   /*  First, look for a user file */
   if ((fstp=fopen(StpFile, "r")) == NULL)
   {
      /* If only one database, look for blkprob.stp first in its directory,
      then in the current directory, otherwise look in the current
      directory only */
      if (ndb == 1)
      {   sprintf(fname, "%sblkprob.stp", DatDir); }
      else
      {   strcpy(fname, "blkprob.stp");  }
      if ((fstp=fopen(fname, "r")) == NULL)
      {
         if (ndb == 1)
         {
            strcpy(fname, "blkprob.stp");
            fstp=fopen(fname, "r");
         }
      }
   }

   if (fstp == NULL)
   {
      printf("\n========================================");
      printf("=======================================");
      printf("\nHere are your search results from the BLOCKS searcher.");
      printf("\n========================================");
      printf("=======================================");
      printf("\n");
   }
   else
   {
      while (!feof(fstp) && fgets(line, MAXLINE, fstp) != NULL)
         printf("%s", line);
      fclose(fstp);
   }

}  /* end of print_blurb */
/*=====================================================================
     Set global variables from the preface of the blimps results file
=========================================================================*/
int get_info(fhom, homfile)
FILE *fhom;
char homfile[FNAMELEN];
{
   char line[MAXLINE], db[FNAMELEN];
   char *ptr, *ptr1;
   int i, j, nrec, done;
   long fpos;
   struct split_name *homsplit;

   homsplit = split_names(homfile);
   strncpy(HomName, homfile + homsplit->dir_len, homsplit->name_len);
   HomName[homsplit->name_len] = '\0';
   db[0] = Qfilename[0] = Query[0] = '\0';
   NBlock = 0; QLen = (unsigned long) 0;
   NAlign = 0.0;
   SeqType = PROTEIN;		/* amino acid is default type */
   BlimpsVer = 326;		/* Blimps format changed with 3.2.6 */
   done = NO;
   while (!done &&
	  !feof(fhom) && fgets(line,MAXLINE,fhom) != NULL)
   {
      if (strstr(line, "Version 3.2.5")) BlimpsVer = 325;
      if (strstr(line, "Version 3.2.4")) BlimpsVer = 325;
      if (strstr(line, "Version 3.2.3")) BlimpsVer = 325;
      if (strlen(line) > SNAMELEN && strstr(line, "Probe Sequence:") != NULL)
      {   /*  "Probe Sequence: query  Probe Size: length" */
         ptr = strstr(line, "Probe Sequence:");
         /* Copy up to SNAMELEN characters to Query name */
         j = strlen(ptr); if (j > FNAMELEN) j = FNAMELEN;
	 strncpy(Qfilename, ptr+16, j); Qfilename[j] = '\0';

         /*  Get rid of tabs, etc. put first SNAMELEN chars in Query */
         if (Qfilename[0] == '>') i = 1; else i = 0;
         j = 0;
         for (i=0; i SNAMELEN && strstr(line, "Size") != NULL)
      {   /* Probe Size: length Amino Acids */
         ptr = strstr(line, ":"); 
         if (ptr != NULL)
         {
            if (strstr(ptr, "Base Pair") != NULL) SeqType = DNA;
            ptr1 = strtok(ptr, " ");
            if (ptr1 != NULL)
            {
               ptr1 = strtok(NULL, " \n\r");
               if (ptr1 != NULL) QLen = atol(ptr1);
            }
         }
      } 
      else if (strlen(line) > SNAMELEN && strstr(line, "Target") != NULL)
      {   /* Target File (s): database */
/*	 strcpy(db, &line[20]); db[strlen(db)-1] = '\0'; */
         ptr = strstr(line, ":"); 
         if (ptr != NULL)
         {
            ptr1 = strtok(ptr, " ");
            if (ptr1 != NULL)
            {
               ptr1 = strtok(NULL, " \n\r");
               if (ptr1 != NULL) strcpy(db, ptr1);
            }
         }
      }
      else if (strlen(line) > SNAMELEN && strstr(line, "Records") != NULL)
      {  /* Records Searched: nblock */
         ptr = strstr(line, ":");
         if (ptr != NULL)
         {
            ptr1 = strtok(ptr, " ");
            if (ptr1 != NULL)
            {
               ptr1 = strtok(NULL, " \n\r");
               if (ptr1 != NULL) NBlock = atoi(ptr1);
            }
         }
      }
      else if (strlen(line) > SNAMELEN && strstr(line, "Alignments") != NULL)
      {  /* Alignments Done: nalign */
         ptr = strstr(line, ":");
         if (ptr != NULL)
         {
            ptr1 = strtok(ptr, " ");
            if (ptr1 != NULL)
            {
               ptr1 = strtok(NULL, " \n\r");
               if (ptr1 != NULL) NAlign = atof(ptr1);
            }
         }
         done=YES;
      }
      else if (strncmp(line, "AC#", 3) == 0) done=YES;
   }

   /*  Don't report any single block hits for which the highest-scoring block's
       cumprob (position p-value) is surely a chance hit */
/*
   CutoffRepeat = 1.0;
   if (NAlign > 0)
   {
      CutoffRepeat = 1.0/ (double) NAlign;
      if (SeqType == DNA) {  CutoffRepeat = 2.0 / NAlign; }
      else                {  CutoffRepeat = 1.0 / NAlign; }
   }
*/
   CutoffRepeat = CutoffExp;
   if (SeqType == DNA)
   {
      CutoffRepeat *= 2.0;
   }
   Strands = 1.0;		/* Changed later if 2nd detected */

   fpos = ftell(fhom);
   nrec = 0;
   while (!feof(fhom) && fgets(line,MAXLINE,fhom) != NULL) nrec++;
   /*  Reposition file to start of results for read_results()  */
   fseek(fhom, fpos, SEEK_SET);

   return(nrec);

}   /*  end of get_info */
/*========================================================================
     Open all the files in the list of blocks databases searched
==========================================================================*/
void open_dbs(flist)
struct files_list *flist;
{
   struct files_list *fcur;

   fcur = flist->next;
   while (fcur != NULL)
   {
      if ( (fcur->fdat=fopen(fcur->datname, "r")) == NULL)
      {
         printf("\nBLKPROB: Cannot open blocks file %s", fcur->datname);
      }
      else
      {
         fcur->prevdat = ftell(fcur->fdat);
         printf("Database=%s\n", fcur->datname); 
      }
      fcur = fcur->next;
   }
}   /*  end of open_dbs */
/*========================================================================
     Close all the files in the list of blocks databases searched
==========================================================================*/
void close_dbs(flist)
struct files_list *flist;
{
   struct files_list *fcur;

   fcur = flist->next;
   while (fcur != NULL)
   {
      if (fcur->fdat != NULL) fclose(fcur->fdat);
      fcur = fcur->next;
   }
}   /* end of close_dbs */
/*======================================================================*/
int read_tiles()
{
   int ntiles, score, i;
   float tile;
   FILE *fstn;
   char fname[FNAMELEN], line[MAXLINE];

   ntiles = 0;

   /*   Look in current directory first */
   fstn=fopen("blksort.stn", "r");
   if (fstn == NULL)
   {
      sprintf(fname, "%sblksort.stn", DatDir);
      fstn=fopen(fname, "r");
   }

   if (fstn != NULL)
   {
      while (ntiles < MAXTILES && 
             !feof(fstn) && fgets(line, MAXLINE, fstn) != NULL)
      {
         if (line[0] != '>' && line[0] != '#')
         {
            sscanf(line, "%d %f", &score, &tile);
            for (i=ntiles; i<=(score-1000) ;i++)
               Tiles[i] = tile;
            ntiles = i;
         }
      }
      fclose(fstn);
   }

   return(ntiles);
}  /*  end of read_tiles */
/*======================================================================*/
int read_repeats()
{
   int nrep;
   FILE *frep;
   char line[MAXLINE], fname[FNAMELEN];

   nrep = 0;
   MaxRepeat = 0;

   /*   Look in current directory first */
   frep=fopen("repeats.dat", "r");
   if (frep == NULL)
   {
      sprintf(fname, "%srepeats.dat", DatDir);
      frep=fopen(fname, "r");
   }

   if (frep != NULL)
   {
      while (nrep < MAXGROUP && 
             !feof(frep) && fgets(line, MAXLINE, frep) != NULL)
      {
         if (line[0] != '>' && line[0] != '#')
         {
            sscanf(line, "%s %d", Repeats[nrep].ac, &Repeats[nrep].num);
            if (Repeats[nrep].num < 0) Repeats[nrep].num = 0;
            if (Repeats[nrep].num > MaxRepeat) MaxRepeat = Repeats[nrep].num;
            nrep++;
         }
      }
   }
   return(nrep);
}  /* end of read_repeats */
/*======================================================================*/
int read_bias()
{
   int nbias;
   FILE *fbias;
   char line[MAXLINE], fname[FNAMELEN];

   nbias = 0;

   /*   Look in current directory first */
   fbias = fopen("blksort.bias", "r");
   if (fbias == NULL)
   {
      sprintf(fname, "%sblksort.bias", DatDir);
      fbias = fopen(fname, "r");
   }

   if (fbias != NULL)
   {
      while (nbias < MAXBIAS && 
             !feof(fbias) && fgets(line, MAXLINE, fbias) != NULL)
      {
         if (line[0] != '>' && line[0] != '#')
         {
            sscanf(line, "%s %d", Bias[nbias].ac, &Bias[nbias].num);
            if (Bias[nbias].num < 1) Bias[nbias].num = 1;
            nbias++;
         }
      }
   }
   return(nbias);
}  /* end of read_bias */
/*=======================================================================
	Read the blimps results into memory; assumes fixed format
        Groups results by AC within each frame but doesn't determine
	 which blocks for an AC constitute a valid hit.
        Puts search results into global array Results[], sets NResult
=========================================================================*/
void read_results(fhom)
FILE *fhom;
{
   int i, done, title_len;
   int ac_pos, title_pos, str_pos, score_pos, frame_pos, off_pos, aa_pos;
   char line[MAXLINE], ctemp[8], save_ac[MAXAC+1];

   if (BlimpsVer >= 326)
   {
      ac_pos=0; title_pos=12; str_pos=66; score_pos=73; frame_pos=80; 
      off_pos=82; aa_pos=90; title_len=25;
   }
   else		/* Blimps version 3.2.5 and earlier */
   {
      ac_pos=0; title_pos=14; str_pos=63; score_pos=70; frame_pos=77; 
      off_pos=79; aa_pos=87; title_len=25;
   }
   NResult = 0;
   while (!feof(fhom) && fgets(line,MAXLINE,fhom) != NULL)
   {
      if (strlen(line) > aa_pos && NResult < NSCORE)
      {
	 save_ac[0]= '\0';
	 strncpy(save_ac, &line[ac_pos], MAXAC); save_ac[MAXAC] = '\0';
         for (i=MAXAC; i >= MINAC; i--)
            if (save_ac[i] == ' ') save_ac[i] = '\0';
	 strcpy(Results[NResult].ac, save_ac);
         i = strlen(save_ac); done = NO;
         while (!done && i >= MINAC)
         {
            if (isalpha(save_ac[i])){ save_ac[i] = '\0'; done=YES; }
            else  { i--;  }
         }
	 strcpy(Results[NResult].fam, save_ac);

	 Results[NResult].rank = Results[NResult].min_rank = NResult + 1;
	 Results[NResult].title[0] = '\0';
	 strncpy(Results[NResult].title, &line[title_pos], title_len);
	 Results[NResult].title[title_len - 1] = '\0';
         strncpy(ctemp, &line[str_pos], 6); ctemp[6] = '\0';
         Results[NResult].strength = atoi(ctemp);
	 strncpy(ctemp, &line[score_pos], 6); ctemp[6] = '\0';
	 Results[NResult].score = atoi(ctemp);
	 strncpy(ctemp, &line[frame_pos], 2); ctemp[2] = '\0';
	 Results[NResult].frame = atoi(ctemp);
	 strncpy(ctemp, &line[off_pos], 7); ctemp[7] = '\0';
	 Results[NResult].offset = atol(ctemp);
	 Results[NResult].width = 0; i=aa_pos;
	 while (line[i++] != '\n') Results[NResult].width += 1;
	 if (Results[NResult].width > MAX_WIDTH)
		Results[NResult].width=MAX_WIDTH;
	 strncpy(Results[NResult].aa, &line[aa_pos], Results[NResult].width);
	 Results[NResult].aa[Results[NResult].width] = '\0';
         /*    Initialize fields that will be used later */
         Results[NResult].hit_flag = NO;
         Results[NResult].repeat_flag = NO;
         Results[NResult].other_flag = NO;
         Results[NResult].map_flag = NO;
         /*   For sorting purposes, make this max instead of min value */
         Results[NResult].cumprob = Results[NResult].minprob = 1.0;
         Results[NResult].binfo = NULL;
	 NResult++;
      }
   }
}  /* end of read_results */

/*========================================================================
	Group results into strand,ac pairs; each group has unique min_rank
==========================================================================*/
int group_results()
{
   int i, j, ngrp, strand, save_strand, save_rank, min_rank;
   char save_fam[MAXAC+1];

   /*----------Sort by strand and block name-----------*/
   qsort(Results, NResult, sizeof(struct hom), strandcmp);

   /*--------Group the results & determine minimum rank -----------*/
   ngrp = 0;
   strcpy(save_fam, Results[0].fam); save_rank = 0;
   if (Results[0].frame < 0) save_strand = -1;
   else                   save_strand = 1;
   min_rank = Results[0].rank;
   for (i=1; i save_rank)
	   for (j=save_rank; j save_rank)
   {
       for (j=save_rank; j 1000 or
      if nhit == MaxHit, unless current score == last score --------------*/
   nhit = -1;			/* first hit is # 0 */
   save_rank = 0;		/* each strand,ac pair has unique min_rank */
   last_strand = 0;
   done = NO;
   ires = 0;
   while (!done && nhit < MaxHits && ires < NResult)
   {
      if (Results[ires].min_rank != save_rank)
      {
         /*  See if the previous hit is the last one   */
         if ( nhit >= 0 && Results[ hits[nhit].rank_res ].score < CutoffScore)
         {  done = YES; }

         else if ( nhit >=1 && nhit == MaxHit &&
 Results[ hits[nhit].rank_res ].score < Results[ hits[nhit-1].rank_res ].score)
         {  done = YES; }

         if (!done)
         {
            nhit++;
            save_rank = Results[ires].min_rank;
            strcpy(hits[nhit].fam, Results[ires].fam); 
            if (Results[ires].frame < 0) hits[nhit].strand = -1;
            else                         hits[nhit].strand = 1;
            if (last_strand == 0) last_strand = hits[nhit].strand;
            else if (Strands == 1.0 &&
                     last_strand != 0 && last_strand != hits[nhit].strand)
                 { Strands = 2.0; }

            hits[nhit].min_res = hits[nhit].max_res = ires;
            hits[nhit].rank_min = save_rank;

            hits[nhit].prob_res = hits[nhit].rank_res = 0;
            hits[nhit].rank_ptile = hits[nhit].evalue = 0.0;
            hits[nhit].rank_pvalue = hits[nhit].mast_pvalue = 0.0;
            hits[nhit].prob_min = 0.0;
            hits[nhit].nblock = hits[nhit].nblkhit = 0;

            /* Later hits will be sorted by probs, but will always
               get from hits[] to Results[] via these indices  */
            hits[nhit].rank = hits[nhit].binfo = hits[nhit].prob = NULL;

            if (Results[ires].rank == save_rank)
            {
               hits[nhit].rank_res = ires;
               hits[nhit].rank_ptile = get_ptile(Results[ires].score);
            }
        
            /* Check whether this ac allows repeats */
            hits[nhit].maxrep = get_repeats(hits[nhit].fam); 

         }   /* end of !done */
      }  /* end of new hit */
      else		/* same hit */
      {
            hits[nhit].max_res = ires;
            if (Results[ires].rank == save_rank)
            {
               hits[nhit].rank_res = ires;
               hits[nhit].rank_ptile = get_ptile(Results[ires].score);
            }
      }   /* end of same hit */
      ires++;
   }   /* end of first pass through Results for ac data */

   /*   Problem if only one result, nhit++ never gets incremented */
/*
   if (nhit == 0 && hits[nhit].rank_res >= 0) nhit++;
*/

   return(nhit+1);
}  /* end of init_hits */

/*=====================================================================
   Put block information in hits[].binfo
   hit -> Results[min_res] to Results[max_res] = all results for AC
   hit -> binfos = all database blocks for AC
   binfo -> Results[query] = highest-scoring result for block
   binfo -> Results[repeats] = lower-scoring results for block
	"score" is either Results[].rank or Results[].cumprob
======================================================================*/
void init_binfo(flist, nhit, hits)
struct files_list *flist;
int nhit;
struct hit *hits;
{
   struct blocks_list *blist, *bcur, *bprev;
   struct blocks_info *binfo;
   int ihit, ires, raw;
   double dtemp, minprob, maxraw;

   /*  More efficient to sort by family first   */
   qsort(hits, nhit, sizeof(struct hit), hitfam);

   for (ihit=0; ihitblock->de);
         hits[ihit].binfo = make_binfo(bcur->block);
         bcur->binfo = hits[ihit].binfo;
         hits[ihit].nblock = 1;
         bcur = bcur->next;
         while (bcur != NULL)
         {
               binfo = make_binfo(bcur->block);
               insert_binfo(binfo, hits[ihit].binfo);
               hits[ihit].nblock += 1;
               bcur->binfo = binfo;
               bcur = bcur->next;
         }

         /*  Go through Results[] for this hit & calc minprob    */
         maxraw = 0;
         minprob = 99.0;
         bprev = NULL;
         for (ires = hits[ihit].min_res; ires <= hits[ihit].max_res; ires++)
         {
            /*  Set bcur to the db block for this Results[]   */
            if (bprev != NULL &&
                   strcmp(Results[ires].ac, bprev->block->number) == 0)
            { bcur = bprev;  }
            else
            {
               bcur = blist; 
/*
printf("%d:%s vs %d:%s\n", strlen(Results[ires].ac), Results[ires].ac,
                           strlen(bcur->block->number), bcur->block->number);
*/
               while (bcur != NULL &&
                   strcmp(Results[ires].ac, bcur->block->number) != 0)
               { bcur = bcur->next; }
            }

            if (bcur != NULL && bcur->block != NULL &&
                   strcmp(Results[ires].ac, bcur->block->number) == 0)
            {
                /*  bcur is now the block that corresponds to Results[ires]
                       & bcur->binfo points to the hit->binfo record for it */
                /*  Get cumprob for Results[ires]  */
                if (bcur != bprev)
                {
                   /*  Creates global array CumProb[]  */
                   maxraw = cumprob(bcur->pssm);
NCumprob++;
                   bprev = bcur;
                }
                dtemp = (double) Results[ires].score;
                dtemp *= (double) bcur->block->percentile;
                raw = round(dtemp/1000.0);
                if (raw < 0) raw = 0;
                if (raw > maxraw) raw = maxraw;
                Results[ires].cumprob = CumProb[raw];

                if (Results[ires].rank == hits[ihit].rank_min)
                {
                      hits[ihit].rank = bcur->binfo;
                }

                /*  Could be more than one Results[] with this ac
                    want to link binfo to the first one; Results[]
			is sorted by rank within block name  */
                if (bcur->binfo->query_res < 0)
                {
                      bcur->binfo->query_res = ires;

                      if (Results[ires].cumprob < minprob)
                      {
                          minprob = Results[ires].cumprob;
                          hits[ihit].prob = bcur->binfo;
                          hits[ihit].prob_res = ires;
                          hits[ihit].prob_min = minprob;
                      }

		      /*  calc closest seq & put in bcur->binfo */
                      /*  Would rather do this in assemble_hits(), but
                          no longer have the blocks to for closest_seq() */
                      closest_seq(bcur);
                }  /*  end of query_res */
            }  /* end of bcur->binfo for this ires */
         }  /*  end of Results[ires] for hit */

         /* Go through Results[] again & set minprob for all   */
         for (ires = hits[ihit].min_res; ires <= hits[ihit].max_res; ires++)
         { 
		Results[ires].minprob = minprob;
         }  /*  end of ires  */

         /*   Done with blocks & pssms now */
         free_blist(blist);
      }  /* end of blist for hit */
   }  /* end of ihit */

}   /* end of init_binfo */

/*=========================================================================
	Look up number of repeats for ac     
==========================================================================*/
int get_repeats(fam)
char *fam;
{
   int j;

   j = 0;
   /*   Assumes repeats.dat is sorted by ac     */
   while (j < NRepeat && strcmp(Repeats[j].ac, fam) <= 0) j++;
   if (j > 0 && strcmp(Repeats[j-1].ac, fam) == 0)
	return(Repeats[j-1].num);
   else return(0);
} /* end of get_repeats  */

/*=======================================================================
      Find hits among results: anchor block must score above cutoff;
	other blocks must be in order and distanced appropriately
      Compute pvalue elsewhere: old, resort hit results by rank
				mast, just need the cumprobs
========================================================================*/
int assemble_hits_rank(nhit, hits)
int nhit;
struct hit *hits;
{
   struct blocks_info *binfo;
   struct temp *temp;
   int i, t, ihit, min, nres;

   /*  sort by min_rank */
   qsort(hits, nhit, sizeof(struct hit), hitrank);

   for (ihit = 0; ihit < nhit; ihit++)
   {
      min = hits[ihit].min_res;
      nres = hits[ihit].max_res - min + 1;
      /*------ Sort this group of hits by rank now --------------*/
      temp = (struct temp *) malloc((nres) * sizeof(struct temp));
      if (temp == NULL) 
      { printf("assemble_hits(): OUT OF MEMORY\n\n"); exit(-1); }

      for (i=0; iac) != 0)
                binfo = binfo->next;
         /*  Because of the sort, first matching binfo == anchor */
	 if (binfo != NULL && !binfo->hit_flag &&
             (i==0 || distance_okay(Results[t].offset, hits[ihit].binfo, binfo)) )
	 {
            hits[ihit].nblkhit += 1;
            Results[t].hit_flag = YES;
            Results[t].binfo = binfo;
            binfo->hit_flag = YES;
            binfo->query_res = t;
         }
      }  /* end of temp[i]  */
      free(temp);
   }  /* end of a hit */

   return(nhit);
}  /* end of assemble_hits_rank */
/*=======================================================================
      Find hits among results: anchor block must score above cutoff;
	other blocks must be in order and distanced appropriately
      Compute pvalue elsewhere: old, resort hit results by rank
				mast, just need the cumprobs
========================================================================*/
int assemble_hits(nhit, hits)
int nhit;
struct hit *hits;
{
   struct blocks_info *binfo;
   struct dtemp *dtemp;
   int i, t, ihit, min, nres;

   /*  sort by min cumprob, strand, block AC    */
   qsort(hits, nhit, sizeof(struct hit), hitprob);

   for (ihit = 0; ihit < nhit; ihit++)
   {
      min = hits[ihit].min_res;
      nres = hits[ihit].max_res - min + 1;
      /*------ Sort this group of hits by cumprob now --------------*/
      dtemp = (struct dtemp *) malloc((nres) * sizeof(struct dtemp));
      if (dtemp == NULL) 
      { printf("assemble_hits(): OUT OF MEMORY\n\n"); exit(-1); }

      for (i=0; iac) != 0)
                binfo = binfo->next;

         /*  Because of the sort, first matching binfo == anchor */
	 if (binfo != NULL)
         {
            if ( !binfo->hit_flag &&
                (i==0 ||
                 distance_okay(Results[t].offset, hits[ihit].binfo, binfo) ) )
	    {		/* this result is in the hit */
               hits[ihit].nblkhit += 1;
               Results[t].hit_flag = YES;
               Results[t].binfo = binfo;
               binfo->hit_flag = YES;
               binfo->query_res = t;
            }
         }  /* end of if binfo != NULL  */  
      }  /* end of dtemp[i]  */

      /*  All blocks in hit have now been flagged. Flag remaining
		non-overlapping blocks */
      /*  Sets Results[].other_flag == YES if doesn't overlap  */
      check_overlap(nres, dtemp);
      for (i=0; i ac) != 0)
                binfo = binfo->next;

	    if (binfo != NULL)
            {
                if (binfo->hit_flag && binfo->nrep < hits[ihit].maxrep)
               {
                  binfo->nrep += 1;
                  Results[t].repeat_flag = YES;
                  Results[t].other_flag = NO;
                  Results[t].binfo = binfo;
               }
            }
         }
      }  /* end of dtemp[i]  */
      free(dtemp);
   }  /* end of a hit */

   return(nhit);
}  /* end of assemble_hits */

/*===================================================================
	Read through the list of databases looking for ac &
	return a list of blocks & pssms. Assumes each db is
        ordered by family name.
======================================================================*/
struct blocks_list *read_fam(flist, fam)
struct files_list *flist;
char *fam;
{
   struct blocks_list *new_list;
   struct files_list *fcur;
   Block *block;
   int famlen, len, found, done;

   new_list = make_blist();
   strcpy(new_list->fam, fam);

   famlen = strlen(fam);

   found = 0; done = NO;
   fcur = flist->next;
   while (!found && fcur != NULL)
   {
      /*  Check to see whether the previous fam for this file was
	beyond the current fam; assumes all fdats are sorted by fam */
      if (strlen(fcur->prevfam) < famlen) len = strlen(fcur->prevfam);
      else len = famlen;
      if (len < MINAC ||
          strncasecmp(fam, fcur->prevfam, len) <= 0)     /* beyond fam */
      {
         rewind(fcur->fdat);
         fcur->prevfam[0] = '\0';
         fcur->prevdat = ftell(fcur->fdat);
      }
      else
      { fseek(fcur->fdat, fcur->prevdat, SEEK_SET);   }  /* backup */

      if ( (found = read_to_block(fcur->fdat, fam)) )
      {
         strcpy(fcur->prevfam, fam);
         fcur->prevdat = ftell(fcur->fdat);
      }
      else  
      {  
         rewind(fcur->fdat);
         fcur->prevfam[0] = '\0';
         fcur->prevdat = ftell(fcur->fdat);
         fcur = fcur->next;
      }
   }  /* end of while !found */

   if (found)
   {
      while (!done && (block = read_a_block_faster(fcur->fdat)) != NULL)
      {
NRead++;
/*printf("%d %s\n", NRead, block->number); */
         if (strlen(block->number) < famlen) len = strlen(block->number);
         else                                len = famlen;

         if (strncasecmp(block->number, fam, len) == 0)
         {
	   insert_blist(new_list, block);
           fcur->prevdat = ftell(fcur->fdat);
         }
         else 
         { 
            if (strncasecmp(block->number, fam, len) > 0)
            {
               done = YES;
            }
            free_block(block);
         }
      }    /* end of read_a_block(fcur->fdat) */

      return(new_list);
   }   /* end of if found  */

   else { free_blist(new_list); return(NULL);  }

}  /* end of read_fam */

/*=======================================================================
      compute pvalues for hits
========================================================================*/
void pvalues(nhit, hits)
int nhit;
struct hit *hits;
{
   int ihit;

/*
   double dalign;
   if (SeqType == DNA) {  dalign = NAlign / 2.0; }
   else                {  dalign = NAlign; }
*/

   for (ihit=0; ihit< nhit; ihit++)
   {
      if (hits[ihit].nblkhit > 1)
         hits[ihit].rank_pvalue = pvalue_rank(&hits[ihit]);
      else
         hits[ihit].rank_pvalue = 1.0;

      hits[ihit].mast_pvalue = pvalue_mast(&hits[ihit]);

      /*   Assign an evalue to each hit */
      if (Mast)
      {   hits[ihit].evalue = (double) NBlock * hits[ihit].mast_pvalue; }
      else
      {
         hits[ihit].evalue = NAlign * hits[ihit].prob_min;

/*  This isn't really valid ....
         if (hits[ihit].nblkhit == 1)
         {   hits[ihit].evalue = NAlign * hits[ihit].prob_min;  }
         else
         {   hits[ihit].evalue = (double) NBlock * hits[ihit].rank_pvalue; }
*/
      }
   }
}    /* end of pvalues */
/*=======================================================================
      Print hits
========================================================================*/
int print_hits(nhit, hits)
int nhit;
struct hit *hits;
{
   FILE *fstats;
   int i, ihit, qres, goodhit, frame;
   long locfirst, loclast;
   char pline[MAXLINE];
   struct blocks_info *binfo;

   strcpy(pline, "blksort.dat");
   if (Stats) fstats = fopen(pline, "a");
   else       fstats = NULL;

/*
   double dalign;
   if (SeqType == DNA) {  dalign = NAlign / 2.0; }
   else                {  dalign = NAlign; }
*/


   /*   Sort hits by evalue, strand, ac  */
   qsort(hits, nhit, sizeof(struct hit), hiteval);

   if (!GFF)
   {
      /*   List of scores  */
   printf("==============================================================================\n");
      if (Mast)
      {
         printf("                                                             Combined\n");
         printf("Family                                       Strand  Blocks   E-value\n");
      }
      else
      {
         printf("                                                           Rank\n");
         printf("Family                                       Strand  Blocks   P-value\n");
      }
   }

   goodhit = 0;
   for (ihit=0; ihit< nhit; ihit++)
   {
     if (hits[ihit].evalue <= CutoffExp)
     {
         if (!GFF)
         {
            strcpy(pline, hits[ihit].de);
            if (strlen(pline) > 35) pline[35] = '\0';
            else
            {
               for (i=strlen(pline); i<35; i++) pline[i] = ' ';
               pline[35] = '\0';
            }
            printf("%-10s %s  % 2d  %2d of %-2d", 
                hits[ihit].fam, pline, hits[ihit].strand,
                hits[ihit].nblkhit, hits[ihit].nblock);
            if (Mast) { printf(" %8.2g\n", hits[ihit].evalue); }
            else 
            {
               if (hits[ihit].nblkhit > 1)
               {  printf(" %8.2g\n", hits[ihit].rank_pvalue); }
               else { printf("\n"); }
            }
         }
         goodhit++;
         /*   summary statistics */
         if (fstats != NULL)
         {
            fprintf(fstats, "%d %s %s %d %d %g %g %g %g\n",
             goodhit, Query, hits[ihit].fam, 
             hits[ihit].nblock, hits[ihit].nblkhit,
             hits[ihit].prob_min, hits[ihit].rank_pvalue,
             hits[ihit].mast_pvalue, hits[ihit].evalue);
         }
     }  /* end of goodhit */
   } /* end of ihit */
   if (fstats != NULL) fclose(fstats);
   if (Summary) return(goodhit);
 		
   /*    more detailed output */
   printf("\n==============================================================================\n");
   goodhit = 0;
   for (ihit=0; ihit< nhit; ihit++)
   {
     if (hits[ihit].evalue <= CutoffExp)
     {
       if (!GFF)
       {
         printf(">%s %d/%d blocks Combined E-value=%8.2g: %s\n", 
             hits[ihit].fam,
             hits[ihit].nblkhit, hits[ihit].nblock,
             hits[ihit].evalue,
             hits[ihit].de);
         printf("Block    Frame    Location");
         if (SeqType == DNA) printf(" (bp)      Block E-value\n");
         else                printf(" (aa)      Block E-value\n");
      }
      
      /*  Individual blocks in the hit */
      binfo = hits[ihit].binfo;
      while (binfo != NULL)
      {
         if (binfo->hit_flag)
         {
            qres = binfo->query_res;
            locfirst = compute_loc(Results[qres].frame, Results[qres].offset+1);
	    loclast = compute_loc(Results[qres].frame, 
              Results[qres].offset + Results[qres].width);
            if (!GFF)
            {
               printf("%-10s % 1d     %6ld-%-6ld        %8.2g",
                  binfo->ac, Results[qres].frame, 
                  locfirst, loclast,
                  Results[qres].cumprob * NAlign);
               if (binfo->bias) printf("       **biased**\n");
               else             printf("\n");
            }
            else		/* GFF format */
            {
               /* locfirst & loclast are bp locations */
               /* aa locations are Results[qres].offset+1,
                                   Results[qres].offset + Results[qres].width*/
               printf("%s\tBLOCKS\tsimilarity\t%ld\t%ld\t%8.2g ",
		Query, locfirst, loclast,
                Results[qres].cumprob * NAlign);
               frame = Results[qres].frame;
               if (frame < 0) 
               {   
                  frame = 0-frame; 
                  printf("-\t%d\t", frame);
               }
               else
               {  printf("+\t%d\t", frame); }
               printf("%s ", binfo->ac);
               if (binfo->bias) printf(" **biased** ");
               printf("(hit) %s\t\"%d\"\n", hits[ihit].de, goodhit+1);
            }
         }  /*  end of binfo->hit_flag  for a block in the hit */
         binfo = binfo->next;
      }  /* end of binfo for a block in the family */

      /*   Detailed info for repeats */
      if (hits[ihit].maxrep > 0)
      {
         if (!GFF) printf("Up to %d repeats expected:\n", hits[ihit].maxrep);
         for (qres=hits[ihit].min_res; qres <= hits[ihit].max_res; qres++)
         {
            if (Results[qres].repeat_flag)
            {
               locfirst = compute_loc(Results[qres].frame, 
		 Results[qres].offset+1);
	       loclast = compute_loc(Results[qres].frame, 
                 Results[qres].offset + Results[qres].width);
               if (!GFF)
               {
                  printf("%-10s % 1d     %6ld-%-6ld        %8.2g\n",
                     Results[qres].ac, Results[qres].frame, 
                     locfirst, loclast,
                     Results[qres].cumprob * NAlign);
               }
               else		/* GFF format */
               {
                  printf("%s BLOCKS similarity %ld %ld %8.2g ",
		   Query, Results[qres].offset+1,
                   Results[qres].offset + Results[qres].width,
                   Results[qres].cumprob * NAlign);
                  frame = Results[qres].frame;
                  if (frame < 0) 
                  {   
                     frame = 0-frame; 
                     printf("- %d ", frame);
                  }
                  else
                  {  printf("+ %d ", frame); }
                  printf("%s ", Results[qres].ac);
                  if (Results[qres].binfo->bias) printf(" **biased** ");
                  printf("(repeat) %s\n", hits[ihit].de);
               }
            }  /*  end of repeat for family */
         }  /* end of Result[] for family */
      }  /* end of if family has repeats */

      /*   Detailed info for other reported alignments */
      if (!GFF) printf("Other reported alignments:\n");
      for (qres=hits[ihit].min_res; qres <= hits[ihit].max_res; qres++)
      {
/*
            if (!Results[qres].hit_flag && !Results[qres].repeat_flag &&
                Results[qres].cumprob * NAlign <= CutoffRepeat)
*/
            if (Results[qres].other_flag)
            {
               locfirst = compute_loc(Results[qres].frame, 
		 Results[qres].offset+1);
	       loclast = compute_loc(Results[qres].frame, 
                 Results[qres].offset + Results[qres].width);
               if (!GFF)
               {
                  printf("%-10s % 1d     %6ld-%-6ld        %8.2g\n",
                     Results[qres].ac, Results[qres].frame, 
                     locfirst, loclast,
                     Results[qres].cumprob * NAlign);
               }
               else		/* GFF format */
               {
                  printf("%s BLOCKS similarity %ld %ld %8.2g ",
		   Query, Results[qres].offset+1,
                   Results[qres].offset + Results[qres].width,
                   Results[qres].cumprob * NAlign);
                  frame = Results[qres].frame;
                  if (frame < 0) 
                  {   
                     frame = 0-frame; 
                     printf("- %d ", frame);
                  }
                  else
                  {  printf("+ %d ", frame); }
                  printf("%s ", Results[qres].ac);
/*	No binfo for these
                  if (Results[qres].binfo->bias) printf(" **biased** ");
*/
                  printf("(other) %s\n", hits[ihit].de);
               }
            } 
      }  /* end of Result[] for family */

      if (!GFF)
      {
         if (hits[ihit].nblock > 1) map_blocks(&hits[ihit]);
         align_blocks(&hits[ihit]);

         printf("\n------------------------------------------------------------------------------\n");
      }

      goodhit++;
    }  /* end of goodhit */

   } /* end of ihit */

   return(goodhit);
}   /* end of print_hits  */
/*====================================================================
    Map a path of blocks
    The mapping is done in three phases:
    1. The blocks in the database are mapped from the 1st position of
       the first block to the last position of the last block. This
       range divided by MAXMAP (number of columns for the map to occupy
       when printed) determines the scale of the map.
    2. The blocks in the query sequence that are consistent with the
       database are mapped to the same scale as the database blocks.
       The two maps are aligned on the highest scoring block (anchor).
       The query map may occupy more than MAXMAP columns and may have
       to be truncated or compressed. A maximum of MAXLINE characters
       are mapped before compression.
    3. The blocks in the query sequence that are not consistent with the
       database are mapped to the same scale. Since these blocks may
       overlap one another, they may take more than one line. Each line
       is aligned with the left end of the map in 2.
=======================================================================*/
void map_blocks(hit)
struct hit *hit;
{
   int maxdist, i, imin, imax, pos, maxspot, qres, famlen;
   int maxseq, spot, qspot, t, done, qleft, qright;
   double scale;
   struct blocks_info *block, *anchor;
   char dbline[MAXMAPLINE], qline[MAXMAPLINE], pline[MAXMAPLINE];

   famlen = strlen(hit->fam);		/* length of family name */
   maxdist = 0;
   anchor = hit->prob;
   /*--- Determine the scale for the database blocks (# aas per space) ---*/
   block = hit->binfo;
   while (block != NULL)
   {
      /*------ Don't map distance before the first block --------------*/
      if (block != hit->binfo)
         maxdist += block->maxprev;  /* distance from previous block */
      maxdist += block->width;    /* width of this block */
      block = block->next;
   }
   scale = (double) maxdist/MAXMAP;       /* max of 60 spaces per line */
   printf("\n                         |---%5d amino acids---|",
          (int) ((double) 0.5+(scale*25.0)) );

   /*---  1. Now map the database blocks ------------------------------*/
   for (spot=0; spotbinfo;
   while (block != NULL)
   {
      if (block != hit->binfo)
      {
         imin = (int) ((double) 0.5+block->minprev/scale);
         imax = (int) ((double) 0.5+(block->maxprev-block->minprev)/scale);
         for (i=spot; i < spot+imin; i++) dbline[i] = ':';
         spot += imin;
         for (i=spot; i < spot+imax; i++) dbline[i] = '.';
         spot += imax;
      }
      imin = (int) ((double) 0.5+block->width/scale);
      if (imin < 1) imin = 1;
      for (i=spot; i < spot+imin; i++) strncpy(dbline+i, block->ac+famlen, 1);
      spot += imin;
      if (block==anchor) maxspot=spot;
      block = block->next;
   }
   dbline[spot] = '\0';
   printf("\n%20s ", hit->fam);
   printf("%s", dbline);

   /*---- 2. Now map the query sequence if there is one ----------------*/
   /*---Line up the highest scoring query block with the database ----*/
   /*---   Determine qspot = print position for beginning of anchor
           block in query . Line it up with maxspot = print position
           for beginning of anchor block in database line.--- */
   spot=qspot=0;
   pos=0;
   block = hit->binfo;
   while (block != NULL)
   {
      if (block->hit_flag)
      {
         qres = block->query_res;
	 imin = (int) ((double) 0.5+(Results[qres].offset-pos)/scale);
         if (imin >= 0)   /* skip over blocks in wrong order */
         {
	    if (spot+imin > MAXMAPLINE && spot+1 < MAXMAPLINE)
               qline[spot++] = '<';
            else
            {
	       for (i=spot; iwidth/scale);
	    if (imin < 1) imin = 1;
            if (spot+imin < MAXMAPLINE)
            {
	       for (i=spot; iac+famlen, 1);
	       spot += imin;
            }
	    pos = Results[qres].offset + block->width;
	    if (block == anchor) qspot = spot;
         }
      }
      block = block->next;
   }
   qline[spot] = '\0';

   /*------ If the query starts in the after the map, have to
            print some spaces first --------*/
   printf("\n%20s ", Query);
   if (qspot <= maxspot)
   {
       qleft = 0;
       for (i=qspot; i 0 && (pline[0] == '.' || pline[0] == ':')) pline[0] = '<';
   if (qright != strlen(qline)) pline[strlen(pline)-1] = '>';

   printf("%s", pline);

   /*---------3. Now map the repeats wrt consistent hits ---------------*/
   done = NO; 
   while (!done)
   {
      done=YES; spot = 0;
      pos = (int) qleft * scale;   /* offset of first qline with anchor */
      for (i=0; imin_res; t <= hit->max_res; t++)
         if (!Results[t].map_flag && 
             Results[t].repeat_flag)
         {
            imin = (int) ((double) 0.5+(Results[t].offset-pos)/scale);
            if (imin >=0)
            {
               if (spot+imin < MAXMAPLINE) 
               {
                  spot += imin;
                  imin = (int) ((double) 0.5+Results[t].width/scale);
                  if (imin < 1) imin = 1;
                  if (spot+imin < MAXMAPLINE)
                  {
                     for (i=spot; i maxseq) 
         {
            if (qline[maxseq-1] == ' ') qline[maxseq-1] = '>'; 
            qline[maxseq] = '\0';
         }
         printf("%s", qline);
      }
   }

   /*--------4. Now map the inconsistent hom hits wrt consistent ones--*/
   done = NO; 
   while (!done)
   {
      done=YES; spot = 0;
      pos = (int) qleft * scale;   /* offset of first qline with anchor */
      for (i=0; imin_res; t <= hit->max_res; t++)
         if (!Results[t].hit_flag && !Results[t].map_flag &&
              Results[t].other_flag)
         {
            imin = (int) ((double) 0.5+(Results[t].offset-pos)/scale);
            if (imin >=0)
            {
               if (spot+imin < MAXMAPLINE) 
               {
                  spot += imin;
                  imin = (int) ((double) 0.5+Results[t].width/scale);
                  if (imin < 1) imin = 1;
                  if (spot+imin < MAXMAPLINE)
                  {
                     for (i=spot; i maxseq) 
         {
            if (qline[maxseq-1] == ' ') qline[maxseq-1] = '>'; 
            qline[maxseq] = '\0';
         }
         printf("%s", qline);
      }
   }

   printf("\n");

}  /* end of map_blocks */

/*========================================================================
	Align the query sequence with the sequence closest to it in
	each block for which it has a hit.
	blkline[] = distances, datline[] = database segment, barline[] = marks,
	homline[] = query segment, repline[] = repeats.
=========================================================================*/
void align_blocks(hit)
struct hit *hit;
{
   struct blocks_info *block;
   int i, t, savspot, repspot, spot, bspot, datmin, datmax, homdist;
   int first, famlen;
   char datline[MAXLINE], homline[MAXLINE], blkline[MAXLINE];
   char barline[MAXLINE], repline[MAXLINE], saveac[MAXAC+1];
   char ctemp[10];

   famlen = strlen(hit->fam);		/*  length of family name */
   for (i=0; ibinfo;
   while (block != NULL)
   {
      if (block->hit_flag)
      {
	 datmin += block->minprev;
	 datmax += block->maxprev;
         homdist = Results[ block->query_res ].offset - homdist;

	 /*--- 28 spaces for name & offset on datline & homline;
	       30 spaces for distance info on blkline ----*/
	 bspot = block->width;
	 if (bspot < 30) bspot = 30;

         /*    Check to see whether this block will fit on the current line */
         /* bspot could be 55, +28 = 83   */
	 if ((spot + bspot + 28) > 83)
         {
	    homline[spot]= datline[spot]= blkline[spot]= barline[spot]= '\0';
            repline[spot] = '\0';
	    printf("\n%s", blkline);
            printf("\n%s", datline); printf("\n%s", barline);
	    printf("\n%s\n", homline);
            for (i=0; i 0) spot += 3;   }
         strncpy(blkline+spot, block->ac, strlen(block->ac));
         strncpy(datline+spot, block->closest_name, strlen(block->closest_name));
         strncpy(homline+spot, Query, strlen(Query));
	 spot+=19;		/* seq name + 1 */

	 blkline[spot] = saveac[famlen];		/* from block A-Z */
	 strncpy(blkline+spot+1, "<->", 3);
	 blkline[spot+4] = block->ac[famlen];		/* to block A-Z  */
	 /* offset starts at 1 in */
         sprintf(ctemp, "%ld", block->closest_offset);
	 strncpy(datline+spot, ctemp, strlen(ctemp));
         sprintf(ctemp, "%ld", Results[ block->query_res ].offset + 1);
	 strncpy(homline+spot, ctemp, strlen(ctemp));
         /* save location in case there are repeats */
         savspot = spot;
	 spot+=8;		/* offset + 1 */

	 bspot = spot;
	 strncpy(blkline+bspot, "(", 1); bspot++;
/*	 kr_itoa(datmin, ctemp, 10); */
         sprintf(ctemp, "%d", datmin);
	 strncpy(blkline+bspot, ctemp, strlen(ctemp));
	 bspot += strlen(ctemp);
	 strncpy(blkline+bspot, ",", 1); bspot++;
/*	 kr_itoa(datmax, ctemp, 10); */
         sprintf(ctemp, "%d", datmax);
	 strncpy(blkline+bspot, ctemp, strlen(ctemp));
	 bspot += strlen(ctemp);
	 strncpy(blkline+bspot, ")", 1); bspot++;
	 strncpy(blkline+bspot, ":", 1); bspot++;
/*	 kr_itoa(homdist, ctemp, 10); */
         sprintf(ctemp, "%d", homdist);
	 strncpy(blkline+bspot, ctemp, strlen(ctemp));
	 bspot += strlen(ctemp);

	 for (i=0; iwidth; i++)
         {
            strncpy(datline+spot, block->closest_aa+i, 1);
	    strncpy(homline+spot, Results[ block->query_res].aa+i, 1);
            if (strncmp(datline+spot, homline+spot, 1) == 0)
                barline[spot] = '|';
	    spot++;
         }
         /*-------  Block may be narrower than offset heading.. */
         if (spot < bspot) spot = bspot;

         /*   Now look for repeats & print them */
         first = YES;
         for (t=hit->min_res; t<= hit->max_res; t++)
         {
            if (strcmp(block->ac, Results[t].ac) == 0 &&
                (Results[t].repeat_flag || Results[t].other_flag) )
            {
               if (first)  /* have to print out everything else first */
               {
	    homline[spot]= datline[spot]= blkline[spot]= barline[spot]= '\0';
	          printf("\n%s", blkline);
                  printf("\n%s", datline); printf("\n%s", barline);
	          printf("\n%s\n", homline);
                  for (i=0; iwidth;
               repline[repspot] = '\0';
               printf("%s\n", repline);
            }
         }     /*  end of for t */
	 datmin = datmax = 0;
	 homdist = Results[ block->query_res ].offset + block->width;
	 strcpy(saveac, block->ac);
      }   /*  end of block is in the hit */
      else
      {		/*  block not in query sequence */
	 datmin += block->minprev + block->width;
	 datmax += block->maxprev + block->width;
      }
      block = block->next;
   }  /*  end of block */

   if (spot > 0)
   {
   homline[spot] = datline[spot] = blkline[spot] = barline[spot] = '\0';
   printf("\n%s", blkline);
   printf("\n%s", datline); printf("\n%s", barline);
   printf("\n%s\n", homline);
   }
}  /* end of align_blocks */
/*=======================================================================
	This is the old pvalue based on ranks; it assumes all blocks
	in the databases searched have been ordered by the query
	sequence. Ignores repeated scores.
>>>>change this so it doesn't re-assemble the hits, just uses the
Results[].hit_flag & ancho info; maybe hit_flag should even be
ordinal with anchor=1, 1st supporting=2, etc.
==========================================================================*/
double pvalue_rank(hit)
struct hit *hit;
{
   struct temp *temp;
   int i, qnblock, mblock, t, min, nres, lastrank, ntemp;
   double n, r, p, prob;

   min = hit->min_res;
   nres = hit->max_res - min + 1;

   /*-------Assuming blimps is run with repeats -------------*/
/*   qnblock *= SeqType*QLen;  */
   qnblock = hit->nblock * QLen;

   /*------ Sort this group of hits by rank --------------*/
   temp = (struct temp *) malloc((hit->nblkhit) * sizeof(struct temp));
   if (temp == NULL)
   {
      printf("\npvalue_rank(): OUT OF MEMORY\n\n"); exit(-1);
   }
   ntemp = 0;
   for (i=0; inblkhit && Results[i+min].hit_flag)
      {
         temp[ntemp].value = Results[i+min].rank;
         temp[ntemp].index = i+min;
         ntemp++;
      }
   }
   qsort(temp, hit->nblkhit, sizeof(struct temp), tempcmp);

   /*----------- Piece together a set of compatible hits, highest
       rank first and compute probability of multiple blocks ----------*/
   prob = 1.0;
   mblock = 0;  	/* number of blocks in the map */
   lastrank = 0;	/* rank of previous block in the map */
   for (i=0; inblkhit; i++)
   {
      t = temp[i].index;
      /*--- Compute probability -----*/
      if (i>0 && NBlock > 0 && QLen > 0)
      {
         mblock++;     /* number of supporting blocks so far */
         /* compute prob a block of this family could rank this high*/
         /* Call the blocks in the group "red". Compute prob. that
            this red block had this rank using sampling without
            replacement. At this point are assuming:
              Total #blocks = #db blocks-rank of last red block drawn
              Total #reds = #blocks in family - #reds drawn so far
              Total blocks drawn = rank of this red - rank of last red
              Want Prob. one of blocks drawn is red.   */
/*               n = (double) SeqType*QLen*NBlock-lastrank; */
         n = (double) QLen*NBlock-lastrank;
         r = (double) temp[i].value-lastrank;
         p = (double) qnblock-mblock;
        /*      Avoid going beyond max. hypergeo value  */
         if (p * r >= n - p + 1) r = (double) ((int) (n - p + 1) / p);

         prob *= hypergeo(n, r, p, 1.0);

         /* compute prob this block is this far from the anchor block */
         /* QLen may be in protein or dna units, distance is always
            in protein units so multiply by SeqType to convert it to
            correct units. Min dist = -1; Max dist = distance() */
  prob *= (double) SeqType*(distance(hit->rank, Results[t].binfo) + 1) / QLen;
      }

      lastrank = temp[i].value;
   }  /*  end of for i = min to max for hit */
 
   if (prob > 1.0) prob = 1.0;
   if (prob < 0.0) prob = 0.0;

   return(prob);
}  /*  end of pvalue_rank */
/*=======================================================================
	This is the pvalue used by mast, but modified to only count
	the blocks in the hit (ignores other blocks for the family)
==========================================================================*/
double pvalue_mast(hit)
struct hit *hit;
{
   int ires;
   double pvalue, nalign, result;

   pvalue = 1.0;
   for (ires = hit->min_res; ires <= hit->max_res; ires++)
   {
      if (Results[ires].hit_flag) 
      {
         nalign = (double) QLen + (double) Results[ires].width - 1.0;
         /* cumprob is the mast position p-value */
         pvalue *= Results[ires].cumprob;
         /* This is the mast sequence p-value  */
         pvalue *= nalign;
      }
   }
/*>>>>> For large queries, pvalue can be > 1 <<<<<<<<*/
   if (pvalue > 1.0) pvalue = 1.0;
   if (pvalue < 0.0) pvalue = 0.0;

   /*  For true mast, give qfast hit->nblock, not hit->nblkhit; the
	blocks not in the hit are assumed to have p = 1.0   */
   if (hit->nblkhit > 1) {   result = qfast(hit->nblkhit, pvalue);  }
   else                  {   result = pvalue;   }

/*    This is the e-value
   return( (double) NBlock * result );
*/
   /* This is the mast combined p-value */
   return(result);
}  /*  end of pvalue_mast */
/*=======================================================================*/
double get_ptile(score)
int score;
{
   int i;
   double ptile;

   ptile = 0.0;
   if (Ntiles > 0)
   {
      i = score - 1000;
      if (i < 0) i = 0;
      else if (i > Ntiles-1) i = Ntiles-1;
           { ptile = Tiles[i]; }
   }
   return(ptile);
}  /* end of get_ptile */
/*=======================================================================
	Checks Results[ires] vs Results[min] - Results[max]
	dtemp is sorted by cumprob.
========================================================================*/
void check_overlap(nres, dtemp)
int nres;
struct dtemp *dtemp;
{
   int i, j, ires, jres, over;
   long iright, jright, ileft, jleft;

   for (i=0; i < nres; i++)
   {
      ires = dtemp[i].index;
      if (!Results[ires].hit_flag &&
          Results[ires].cumprob * NAlign <= CutoffRepeat)
      {
         over = NO;
         for (j=i+1; j < nres; j++)
         {
            jres = dtemp[j].index;
            if (Results[jres].hit_flag || Results[jres].other_flag)
            {
		ileft = Results[ires].offset;
		jleft = Results[jres].offset;
		iright = Results[ires].offset + Results[ires].width;
		jright = Results[jres].offset + Results[jres].width;
                if (iright > jleft || jright > ileft) over = YES;
            }
         }
         if (!over) Results[ires].other_flag = YES;
      }
   }

}  /* end of check_overlap */
/*===================================================================
    Compute probability from hypergeometric distribution:
    Assume there are n objects, p of one kind and n-p of another.
    Then when r objects are selected at random from among the n
    objects, the prob. that k of the r are of type p is:
  
      ( p )  ( n-p )        p!               (n-p)!
      ( k )  ( r-k )       ----- * -----------------------
                          k!(p-k)!  (r-k)!( (n-p)-(r-k) )!
    -----------------  =  ---------------------------------
         ( n )                       n!
         ( r )                   ----------
                                  r!(n-r)!

       p!         r!          (n-p)!         (n-r)!
  =  -------- * --------  * ----------  * -----------------
     k!(p-k)!    (r-k)!         n!         ( (n-r)-(p-k) )!

  Which can be simplified to a product of these expressions:
   1.  k terms:
       p*(p-1)*(p-2)*...(p-k+1) / k!
   2.  k terms:
       r*(r-1)*(r-2)*...(r-k+1)
   3.  p terms:
       1/(n*(n-1)*(n-2)*...(n-p+1))
   4.  p-k terms:
       (n-r)*(n-r-1)*....(n-r-(p-k)+1)
      
=====================================================================*/
double hypergeo(n, r, p, k)
double n, r, p, k;
{
   double prob, i;

   prob = 1.0;
   if (r > 0.)
   {
   for (i=0.0; inseq for more flexibility.
    fblock should be a list of all possible blocks, starting with
	the leftmost; nblock is one of these to be fitted in.
=====================================================================*/
int distance_okay(offset, fblock, nblock)
long offset;
struct blocks_info *fblock, *nblock;
{
   struct blocks_info *block, *lblock, *rblock;
   long mindist, maxdist;

   lblock = rblock = NULL;
   block = fblock;
   while (block != NULL && rblock == NULL)
   {
      if (block->hit_flag)	/* this block already in hit */
      {
	 if (strcmp(block->ac, nblock->ac) < 0)
	    lblock = block;	/* closest block on the left */
	 else if (strcmp(block->ac, nblock->ac) > 0 && rblock == NULL)
	    rblock = block;	/* closest block on the right */
      }
      block = block->next;
   }
   /*---------  Check the distance to the left --------------------*/
   if (lblock != NULL)
   {
      mindist = maxdist = Results[lblock->query_res].offset + (long) lblock->width;
      block = lblock->next;
      while (block != NULL && block != nblock)
      {
	 if (strcmp(block->ac, nblock->ac) < 0)
         {
            mindist += block->width;
	    maxdist += prev_dist(block) + block->width;
         }
	 block = block->next;
      }
      if (mindist-1 > offset) return(NO); /* allow overlap of 1 */
      if (maxdist + prev_dist(nblock) < offset) return(NO);
   }
   /*----------Check the distance to the right ---------------------*/
   if (rblock != NULL)
   {
      mindist = maxdist = offset + (long) nblock->width;
      block = nblock->next;
      while (block != NULL && block != rblock)
      {
	 if (strcmp(block->ac, rblock->ac) < 0)
         {
            mindist += block->width;
	    maxdist += prev_dist(block) + block->width;
         }
	 block = block->next;
      }
      if (mindist-1 > Results[rblock->query_res].offset) return(NO);
      if (maxdist + prev_dist(rblock) < Results[rblock->query_res].offset)
	 return(NO);
   }
   return(YES);
}  /*  end of distance_okay */
/*===================================================================
    Compute maximum distance preceding a block
    Twice as much distance allowed for DNA
>>> Should do something when minprev == maxprev == 0, especially
    if there are only a few sequences (eg BL00904)
=====================================================================*/
long prev_dist(block)
struct blocks_info *block;
{
   long dist;

/*
   dist = (long) block->minprev + block->maxprev;
*/
   if (SeqType == DNA) dist = (long) 4 * block->maxprev;
   else                dist = (long) 2 * block->maxprev;
   if (dist < 1) dist = 1;
   return(dist);
}  /* end of prev_dist */
/*===================================================================
     Compute maximum allowable distance between two blocks
====================================================================*/
int distance(fromblock, toblock)
struct blocks_info *fromblock, *toblock;
{
    long dist, maxdist;
    struct blocks_info *block, *lblock, *rblock;
  
    if (fromblock == NULL || toblock == NULL) return(-1);

    if (strcmp(fromblock->ac, toblock->ac) < 0)
    { lblock=fromblock; rblock=toblock;
      maxdist = QLen-(Results[fromblock->query_res].offset+fromblock->width);
    }
    else
    { lblock=toblock; rblock=fromblock;
      maxdist = Results[fromblock->query_res].offset;
    }
    if (SeqType*maxdist > QLen) maxdist = (int) QLen/SeqType;

    dist = 0;
    block=lblock->next;
    while (block != NULL && block != rblock)
    {
       dist += prev_dist(block) + block->width;
       block = block->next;
    }
    dist += prev_dist(rblock);
    /*  Don't want possible distance to be larger than possible
        sequence positions! */
    if (dist > maxdist) dist = maxdist;
    return(dist);
}  /* end of distance */
/*======================================================================
   Find the sequence closest to the last sequence in the block
      based on the number of identities
   block is blist->block; query is results[ blist->binfo->query_res ]
   compare aa_btoa[ blist->block->sequences[s].sequence[i] ]
   with    results[ blist->binfo->query_res ].aa[i], i = 1,blist->block->width
======================================================================*/
void closest_seq(blist)
struct blocks_list *blist;
{
   Block *block;
   int npair, s1, i;
   int aaint, qres, maxscore, maxs1;
   struct pair *pairs;
/*SGI   delete above declaration of pairs and use fixed below */
/*SGI   struct pair pairs[MAXSEQS*(MAXSEQS-1)/2];  */

   block = blist->block;
   qres = blist->binfo->query_res;

   npair = block->num_sequences;
/*SGI  delete malloc() and free(pairs) and used fixed allocation */
   pairs = (struct pair *) malloc(npair * sizeof(struct pair));
   if (pairs == NULL)
   {
      printf("\nclosest_seq: Unable to allocate pair structure!\n");
      exit(-1);
   }

   /*    Compute scores for all possible pairs of sequences            */
   for (s1=0; s1num_sequences; s1++) 
   {
      pairs[s1].score = 0;
      for (i=0; i< block->width; i++)
      {
         aaint = aa_atob[ Results[qres].aa[i] ];
	 /* s1 is the block seq & is all caps, but s2 is the query
	    seq & it may have lower case chars in it */
	 if (aaint == block->sequences[s1].sequence[i])
		   pairs[s1].score += 1;
      }
   }  /* end of s1 */
   maxs1 = -1; maxscore = -1;
   for (s1=0; s1 < block->num_sequences; s1++)
      if (pairs[s1].score > maxscore)
      {
	 maxscore = pairs[s1].score;
	 maxs1 = s1;
      }

/*SGI   delete free(pairs) and use fixed allocation  */
      free(pairs);

      /*    Store the closest aa now; fix consensus here?  */
      strcpy(blist->binfo->closest_name, block->sequences[maxs1].name);
      blist->binfo->closest_offset = block->sequences[maxs1].position;
      for (i=0; i < block->width; i++)
	blist->binfo->closest_aa[i] = aa_btoa[ block->sequences[maxs1].sequence[i] ];
      blist->binfo->closest_aa[block->width] = '\0';
}  /*  end of closest_seq */
/*======================================================================
    If the search was of a matrix database, the sequence segment will be
    all lower case. Change any residue that matches any sequence in the
    block to upper case. The block segments are all upper case.
========================================================================*/
void consensus(res, block)
int res;
Block *block;
{
   int s1, i, aaint;
   char aatemp[2];

   /*  res is the query sequence  */
   for (s1=0; s1 < block->num_sequences; s1++)
      for (i=0; i < block->width; i++)
      {
         aaint = aa_atob[ Results[res].aa[i]  ];
         if (aaint == block->sequences[s1].sequence[i] )
         {
            strncpy(aatemp, Results[res].aa+i, 1);
            if (aatemp[0] >= 97 && aatemp[0] <= 122)
            {
               aatemp[0] -= 32;
               strncpy(Results[res].aa+i, aatemp, 1);
            }
         }
      }

}  /* end of consensus */
/*======================================================================*/
/*  Sort by strand (sign of frame) and block name */
int strandcmp(t1, t2)
struct hom *t1, *t2;
{
   int strand1, strand2;

   strand1=strand2=1;
   if (t1->frame < 0) strand1=-1; if (t2->frame < 0) strand2=-1;
   if (strand1 != strand2)  return(strand1 - strand2);
   else return (strcmp(t1->ac, t2->ac));
}  /* end of strandcmp */
/*======================================================================*/
/*  Sort by frame and block name */
int framecmp(t1, t2)
struct hom *t1, *t2;
{
   if (t1->frame != t2->frame)  return(t1->frame - t2->frame);
   else return (strcmp(t1->ac, t2->ac));
}  /* end of framecmp */
/*======================================================================*/
/*   Sort by min_rank, strand (sign of frame), block name & rank */
int mincmp(t1, t2)
struct hom *t1, *t2;
{
   int strand1, strand2;

   strand1=strand2=1;
   if (t1->frame < 0) strand1=-1; if (t2->frame < 0) strand2=-1;
   if (t1->min_rank != t2->min_rank) return(t1->min_rank - t2->min_rank);
   else if (strand1 != strand2) return(strand1 - strand2);
   else if (strcmp(t1->ac, t2->ac) != 0) return(strcmp(t1->ac, t2->ac));
   else return(t1->rank - t2->rank);
}  /* end of mincmp */
/*========================================================================*/
/*  Sort temp structure by value field */
int tempcmp(t1, t2)
struct temp *t1, *t2;
{
   return(t1->value - t2->value);
}
/*========================================================================*/
/*  Sort dtemp structure by value field, with index as tie breaker */
int dtempcmp(t1, t2)
struct dtemp *t1, *t2;
{
   double diff;

   diff = t1->value - t2->value;
   if (diff > 0.0 )     return(1);
   else if (diff < 0.0) return(-1);

   diff = t1->index - t2->index;
   if (diff > 0.0 )     return(1);
   else if (diff < 0.0) return(-1);
   else                 return(0);
}
/*========================================================================*/
/*  Sort hits by family */
int hitfam(t1, t2)
struct hit *t1, *t2;
{
   return (strcmp(t1->fam, t2->fam));
}  /* end of hitfam */
/*======================================================================*/
/*  Sort by rank_min, strand (sign of frame) and block name */
int hitrank(t1, t2)
struct hit *t1, *t2;
{
   if (t1->rank_min != t2->rank_min) return(t1->rank_min - t2->rank_min);
   else if (t1->strand != t2->strand)  return(t1->strand - t2->strand);
   else return (strcmp(t1->fam, t2->fam));
}  /* end of hitrank */
/*========================================================================*/
/*  Sort hit structure by min cumprob. strand & ac */
int hitprob(t1, t2)
struct hit *t1, *t2;
{
   double diff;

   /*   Ascending min cumprob; smaller first   */
   diff = t1->prob_min - t2->prob_min;
   if (diff < 0.0 )      {   return(-1);  }
   else
   {    
     if (diff > 0.0)  {   return(1);   }
     else 
     {
        if (t1->strand != t2->strand) {return(t1->strand - t2->strand);}
        else {return (strcmp(t1->fam, t2->fam));}
     }
   }
}  /*  end of hitprob */
/*========================================================================*/
/*  Sort hit structure by evalue, strand & ac */
int hiteval(t1, t2)
struct hit *t1, *t2;
{
   double diff;

   /*   Ascending evalue; smaller first   */
   diff = t1->evalue - t2->evalue;
   if (diff < 0.0 )      {   return(-1);  }
   else
   {    
     if (diff > 0.0)  {   return(1);   }
     else 
     {
        if (t1->strand != t2->strand) {return(t1->strand - t2->strand);}
        else {return (strcmp(t1->fam, t2->fam));}
     }
   }
}  /*  end of hiteval */
/*========================================================================*/
/*  Sort hit structure by rank pvalue, min cumprob. strand & ac */
int hitprank(t1, t2)
struct hit *t1, *t2;
{
   double diff;

   diff = t1->rank_pvalue - t2->rank_pvalue;
   if (diff < 0.0 )      {   return(-1);  }
   else
   {    
     if (diff > 0.0)  {   return(1);   }
     else 
     {

        diff = t1->prob_min - t2->prob_min;
        if (diff < 0.0 )      {   return(-1);  }
        else
        {    
          if (diff > 0.0)  {   return(1);   }
          else 
          {
             if (t1->strand != t2->strand) {return(t1->strand - t2->strand);}
             else {return (strcmp(t1->fam, t2->fam));}
          }
        }
     }
   }
}  /*  end of hitprank */
/*========================================================================*/
/*  Sort hit structure by mast pvalue. strand & ac */
int hitmpv(t1, t2)
struct hit *t1, *t2;
{
   double diff;

   /*   Ascending; smaller first   */
   diff = t1->mast_pvalue - t2->mast_pvalue;
   if (diff < 0.0 )      {   return(-1);  }
   else
   {    
     if (diff > 0.0)  {   return(1);   }
     else 
     {
        if (t1->strand != t2->strand) {return(t1->strand - t2->strand);}
        else {return (strcmp(t1->fam, t2->fam));}
     }
   }
}  /*  end of hitmpv */
/*========================================================================*/
/*  Sort hit structure by rank pvalue, rank ptile (D) & min rank */
int hitcmp(t1, t2)
struct hit *t1, *t2;
{
   double diff;

   /*   Ascending pvalue; smaller first   */
   diff = t1->rank_pvalue - t2->rank_pvalue;
   if (diff < 0.0 ) {   return(-1);  }
   else
   {    
        if (diff > 0.0)  {   return(1);   }
        else 
        {
           /* Descending ptile; larger first */
           diff = t1->rank_ptile - t2->rank_ptile;
           if (diff < 0.0) {   return(1);   }
           else
           {
                if (diff > 0.0) {   return(-1);   }
                 /* Ascending rank; smaller first */
                else             {   return(t1->rank_min - t2->rank_min);   }
           }
        }
   }
} /*  end of hitcmp */
/*=========================================================================
       frame  1:1 => bp 1,     2:1 => 2,         3:1 => 3
           bp = frame + 3 * offset
       frame -1:1 => bp QLen, -2:1 => QLen - 1, -3:l => QLen - 2 
           bp = frame + (QLen + 1) - 3 * offset
=========================================================================*/
long compute_loc(frame, offset)
int frame;
int offset;
{
   long loc;

   loc = (offset - 1) * SeqType;
   if (frame < 0) loc = (QLen + 1) - loc;
   loc += frame;
   if (frame == 0) loc++;	/* Blimps frame = 0 for protein */
   return(loc);
}   /* end of compute_loc */
/*==========================================================================
      First entry in the list is not used
============================================================================*/
struct files_list *make_flist()
{
   struct files_list *new;

   new = (struct files_list *) malloc(sizeof(struct files_list));
   new->fdat = NULL;
   new->datname[0] = '\0';
   new->prevfam[0] = '\0';
   new->prevdat = (long) 0;
   return(new);
}  /*   end of make_flist()   */
/*==========================================================================*/
void insert_flist(flist, new)
struct files_list *flist, *new;
{
   struct files_list *fcur;

   fcur = flist;
   while (fcur->next != NULL)
      fcur = fcur->next;
   fcur->next = new;
}   /* end of insert_flist  */
/*=======================================================================
	Compute cumulative prob dist for a matrix = cumprob[x] =
		prob(score >= x)
	Return cumprob[score]
        Assumes global array frequency[]
========================================================================*/
int cumprob(matrix)
Matrix *matrix;
{
  struct score_struct scores[2][MAXSCORE], *last, *this;
  struct score_struct ends[MAXSCORE], middle[MAXSCORE];
  int col, aa, minvalue, maxvalue, minscore, maxscore, mincol, maxcol;
  int x, minfirst, minlast, itemp;
  double cum, dtemp, probwt[MAXCOL];

  minscore = maxscore = 0;
  maxvalue = -1;		/* assumes no negative scores */
  minvalue = 9999;
  probwt[0] = 20.0;

  /*  This method only works for integer weights; round as papssm does */
  for (col = 0; col < matrix->width; col++)
     for (aa=1; aa <= 20; aa++)
     {
         itemp = round(matrix->weights[aa][col]);
         matrix->weights[aa][col] = (double) itemp;
     }

  for (col = 0; col < matrix->width; col++)
  {
     /*  Intialize probability weights with powers of 20 */
     if (col > 0) probwt[col] = probwt[col - 1] * 20.0;
     mincol = 9999; maxcol = -1;
     for (aa = 1; aa <= 20; aa++)
     {
        if (matrix->weights[aa][col] > maxvalue)
            maxvalue = matrix->weights[aa][col];
	if (matrix->weights[aa][col] < minvalue)
	    minvalue = matrix->weights[aa][col];
        if (matrix->weights[aa][col] > maxcol)
            maxcol = matrix->weights[aa][col];
	if (matrix->weights[aa][col] < mincol)
	    mincol = matrix->weights[aa][col];
     }
     maxscore += maxcol;
     minscore += mincol;
     if (col == 0) minfirst = mincol;
     if (col == (matrix->width - 1) ) minlast = mincol;
   }
   /*    Probability weights: weights applied to probs depending
         on how many columns of the block are aligned, the
         full alignment width gets about 19/21 = .905, alignments
         off either end of the sequence get the remainder */
   dtemp = probwt[matrix->width - 1] * 21.0 - 40.0;
   cum = 0.0;
   for (col = 0; col < matrix->width; col++)
   {
      probwt[col] = probwt[col] * 19.0 / dtemp;
      cum += probwt[col];
      if (col < matrix->width - 1) cum += probwt[col];
   }
   /* ---- Min. score could be just first or last column ----*/
   if (minfirst < minscore) minscore = minfirst;
   if (minlast < minscore)  minscore = minlast;

/*
   printf("%s: minscore=%d maxscore=%d\n",
	   matrix->number, minscore, maxscore);
*/

   if (maxscore > MAXSCORE) 
   { 
      printf("maxscore is too big, increase MAXSCORE from %d\n", maxscore);
      maxscore = MAXSCORE - 1;
   }
   /*-----------------------------------------------------------------*/
   last = scores[0]; this = scores[1];
   for (x = minvalue; x <= maxscore; x++)
   {  last[x].ways = last[x].prob = this[x].ways = this[x].prob = 0.0; 
      ends[x].ways = ends[x].prob = middle[x].ways = middle[x].prob = 0.0; }

   /*---------Initialize from first column -------------------------------*/
   col = 0;
   for (aa=1; aa <= 20; aa++)
   {
      x = matrix->weights[aa][col];
      last[x].ways += 1.0;
      last[x].prob += frequency[aa];   
   }

   /*---- Now enumerate all possible scores, expanding one column
          at a time ----------*/
   for (col=1; col < matrix->width; col++)
   {
      /*--------- Save the alignments hanging off the left end ------*/
      /*    There are currently col+1 columns of the block aligned  */
      for (x=minvalue; x <= maxscore; x++)
      {
            ends[x].ways += last[x].ways;
            ends[x].prob += last[x].prob * probwt[col - 1];
      }
      for (aa=1; aa <= 20; aa++)
      {
         for (x=minvalue; x <= maxscore; x++)
         {
            if (last[x].ways > 0)
            {
               itemp = x +  (int) matrix->weights[aa][col];
               this[itemp].ways += last[x].ways;
               this[itemp].prob += last[x].prob * frequency[aa];
            }
         } /* end of score x */
      }  /* end of aa */
      /*---------   Switch the arrays ------------------------------*/
      if (this == scores[1])
      {  last = scores[1]; this = scores[0]; }
      else
      {  last = scores[0]; this = scores[1]; }
      for (x = minvalue; x <= maxscore; x++)
      {  this[x].ways = this[x].prob = 0.0;  }
   }  /* end of col */

   /*-------- last now has the final counts of all combinations
      of column scores for full blocks, and ends has the counts
      for alignments off the left end. Still have to get counts
      for alignments off the right end and need two arrays to do
      it. So have to keep last results in another array--------*/
   for (x=minvalue; x <= maxscore; x++)
   {
	middle[x].ways = last[x].ways;
	middle[x].prob = last[x].prob * probwt[matrix->width - 1];
	last[x].ways = last[x].prob = 0.0;
   }

   /*-------- Get the alignments hanging off the right end -------*/
   /*    Initialize with last column   */
   col = matrix->width - 1;
   for (aa=1; aa <= 20; aa++)
   {
      x = matrix->weights[aa][col];
      last[x].ways += 1.0;
      last[x].prob += frequency[aa];   
   }
   for (col = matrix->width - 2; col >= 1; col--)
   {
      /*--------- Save the gapped alignments off the right end ------*/
      /*  There are currently length-col columns of the block aligned */
      for (x=minvalue; x <= maxscore; x++)
      {
            ends[x].ways += last[x].ways;
            ends[x].prob += last[x].prob * probwt[matrix->width - col - 2];
      }
      for (aa=1; aa <= 20; aa++)
      {
         for (x=minvalue; x <= maxscore; x++)
         {
            if (last[x].ways > 0)
            {
               itemp = x + (int) matrix->weights[aa][col];
               this[itemp].ways += last[x].ways;
               this[itemp].prob += last[x].prob * frequency[aa];
            }
         } /* end of score x */
      }  /* end of aa */
      /*---------   Switch the arrays ------------------------------*/
      if (this == scores[1])
      {  last = scores[1]; this = scores[0]; }
      else
      {  last = scores[0]; this = scores[1]; }
      for (x = minvalue; x <= maxscore; x++)
      {  this[x].ways = this[x].prob = 0.0;  }
   }  /* end of column */
   /*--------- Save the gapped alignments off the right end ------*/
   /*  Need to get the length - 1 counts from the right   */
   for (x=minvalue; x <= maxscore; x++)
   {
         ends[x].ways += last[x].ways;
         ends[x].prob += last[x].prob * probwt[matrix->width - 2];
   } 

   /*--------CumProb[x] has sum from x to maxscore of prob[x]; this
	is the prob(score >= x) -------------------------------------*/
   cum = 0.0;
   for (x = maxscore; x >= minvalue; x--)
   {
      if (middle[x].ways > 0.0 || ends[x].ways > 0.0)
      {
         cum += (middle[x].prob + ends[x].prob);
      }
      CumProb[x] = cum;
   }
   return(maxscore);

}  /* end of cumprob */
/*=======================================================================
     Routines for a list of blocks
	First item in list contains first block
========================================================================*/
struct blocks_list *make_blist()
{
   struct blocks_list *new;
   
   new = (struct blocks_list *) malloc (sizeof(struct blocks_list));
   new->fam[0] = '\0';
   new->block = NULL;
   new->pssm = NULL;
   new->binfo = NULL;
   new->next = NULL;

   return(new);
}  /* end of make_blist */

void insert_blist(blist, block)
struct blocks_list *blist;
Block *block;
{
   struct blocks_list *cur;

   /*--- Insert a new record for the current block at the end of the list ---*/
   /*    or in the first record if it's empty  */
   cur = blist;
   while (cur->next != NULL) cur = cur->next;

   if (cur->block != NULL)
   { cur->next = make_blist(); cur = cur->next; }

   strcpy(cur->fam, block->family);
   cur->block = block;
   cur->pssm = block_to_matrix(block, 3);

}  /* end of insert_blist */

void free_blist(blist)
struct blocks_list *blist;
{
   struct blocks_list *cur, *last;

   cur = last = blist;
   while (cur->next != NULL)
   {
      last = cur;  cur = cur->next;
   }
   if (cur != blist)
   {
      if (cur->block != NULL) free_block(cur->block);
      if (cur->pssm != NULL) free_matrix(cur->pssm);
/*	don't do this; binfos are still in use!
      if (cur->binfo != NULL) free_binfo(cur->binfo);
*/
      free(cur);
      last->next = NULL;
      free_blist(last);
   }
   else free(blist);

}  /* end of free_blist */
/*=======================================================================
     Routines for a list of blocks
	First item in list contains first block
========================================================================*/
struct blocks_info *make_binfo(block)
Block *block;
{
   struct blocks_info *new;
   int i;
   
   new = (struct blocks_info *) malloc (sizeof(struct blocks_info));
   new->ac[0] = '\0';
   new->nseq = new->width = new->strength = new->minprev = new->maxprev = 0;
   new->bias = NO;
   new->query_res = -1;
   new->hit_flag = NO;
   new->nrep = 0;
   new->closest_offset = (long) 0;
   new->closest_name[0] = '\0';
   new->closest_aa[0] = '\0';
   new->next = NULL;

   if (block != NULL)
   {
      strcpy(new->ac, block->number);
      new->nseq = block->num_sequences;
      new->width = block->width;
      new->strength = block->strength;
      new->minprev = block->min_prev;
      new->maxprev = block->max_prev;
      /*------------------ Now check for bias --------------------*/
      i = 0;
      while (i < NBias)
      {
         if (strcmp(Bias[i].ac, new->ac) == 0)
         {   new->bias = YES; i = NBias;   }
         else {   i++;  }
      }
   }

   return(new);
}  /* end of make_binfo */

void insert_binfo(binfo, list)
struct blocks_info *binfo, *list;
{
   struct blocks_info *cur;

   /*--- Insert a new record at the end of the list ---*/
   cur = list;
   while (cur->next != NULL) cur = cur->next;
   cur->next = binfo;

}  /* end of insert_binfo */

void free_binfo(binfo)
struct blocks_info *binfo;
{
   struct blocks_info *cur, *last;

   cur = last = binfo;
   while (cur->next != NULL)
   {
      last = cur;  cur = cur->next;
   }
   if (cur != binfo)
   {
      free(cur);
      last->next = NULL;
      free_binfo(last);
   }
   else free(binfo);

}  /* end of free_binfo */
/*=======================================================================
   From: Timothy L. Bailey & Michael Gribskov, "Combining evidence
	 using p-values:...", CABIOS (1998) 14.1:48-54, Fig. 3
========================================================================*/
double qfast(n, p)
int n;
double p;
{
   int i;
   double x, t, q;

   if (p <= 0.0) return(0.0);
   if (n <= 1) return(p);

   x = -log(p);
   t = q = p;
   for (i=1; i" or "#MAP#" input files
          Longer sequence names (10->18)
 12/23/06 Longer sequence names (18->20)
 */

#include 
#include "blockmap.h"

/* The character used to represent non-block bases. */
#define C_BASE '-'

/* The maximum length of each line to read in. */
#define LINEBUF_LEN 160

/* Program name for the helptext */
char *program ;

/*
 * Scale control variables.
 * SCALE_CONSTANT means that 1 square = o_scale_val bases.
 * SCALE_MAX means that the scale is such that the longest sequence is
 *   o_scale_val squares, and all other sequences are proportional.
 * SCALE_FLUSH means that the scale is such that each sequence is o_scale_val
 *   squares.
 */
enum {SCALE_CONSTANT, SCALE_MAX, SCALE_FLUSH};
int o_scale = SCALE_CONSTANT;
int o_scale_val = 10;

/* We did nothing - why run the program? (A warning flag) */
int o_did_nothing = 1;

/* Name of a single block family (BLxxxxx) */
const char *one_family = 0;

#ifdef INCLUDE_REOUTPUT_STUFF
/*
 * Take the data we get from the input files and reoutput into a file with
 * the same format.
 */ 
int o_reoutput = 0;
#endif

/*
 * Level 0 = no output
 * Level 1 = errors only
 * Level 2 = quiet
 * Level 3 = normal
 * Level 4 = verbose
 * Level 5 = debug
 * Level 6 = verbose debug (!)
 */
int o_output_level = 3;

/* Full debug mode. Exactly the same as o_output_level = 5. */
int o_full_debug = 0;

/* Input files (up to 16, for no particular reason). */
char *o_input_filenames[16];
int o_num_input_files = 0;

/* The output file - defaults to stdout. */
char *o_output_filename = "-";

/* Currently unused option. */
int o_bare_output = 0;

/* Function to determine whether a particular message is OK to show. */
int mlevel(int req)
{
  return (o_output_level >= req || o_full_debug);
}

/* Text for the -h (help) option. */

#define HELPTEXT \
"This program takes block map data and generates a graphical map of the\n"\
"sequences.\n\n"\
"Usage: %s [infiles] [options]\n"\
"Example: %s blocks.mapdata -v2 -o blocks.maps -m80\n\n"\
"Arguments to options should be '-o[argument]' or '-o [argument]'.\n"\
"Use '-' to stand for standard input/output.\n"\
"Default output is to the screen.\n\n"\
"Available options:\n"\
" Option          Effect\n"\
" -[cfm] number   Use scale mode [constant/full/maximum]\n"\
"                 Constant: Each character is  amino acids.\n"\
"                 Full: Each sequence is  characters long.\n"\
"                 Maximum: The longest sequence in each family is \n"\
"                 characters long, the rest are to scale.\n"\
"                 The default is -c10 (each character is 10 amino acids).\n"\
" -h              Get this help screen.\n"\
" -i filename     Add an input file(s) (this is not needed if input files\n"\
"                 are placed before the options). Seperate multiple filenames\n"\
"                 with spaces.\n"\
" -o filename     Set the output filename. The input filename is substituted\n"\
"                 for '*' within , so '*.vis' is '.vis'.\n"\
"                 You must use single quotes around  if it contains\n"\
"                 '*'.\n"\
" -v number       Set verbosity level, 0-5. 0 = no messages, 1 = errors only,\n"\
"                 2 = quiet, 3 = normal (default), 4 = verbose, 5 = debug.\n"\
" -a BLxxxxx      Do only a single block family.\n"

/* A simple function to put the help text on the screen. */
void do_help(void)
{

  fprintf(stderr, HELPTEXT, program, program) ;

}

/* 
 * Process an option.
 *
 * This function should use the option and return 1 if arguments are
 * possible but not neccessary, 2 if arguments are impossble, and 0 if 
 * arguments are needed.
 */
int arg_start(char c)
{
  switch (c)
  {
  case 'd':
    o_full_debug = 1;
    if (mlevel(5)) 
      fprintf(stderr, "Debug messages on.\n");
    return 2;

  case 'b':
    o_bare_output = 1;
    if (mlevel(4))
      fprintf(stderr, "Output is in bare format.\n");
    return 2;

#ifdef INCLUDE_REOUTPUT_STUFF
  case 'r':
    o_reoutput = 1;
    if (mlevel(4))
      fprintf(stderr, "Data will be reoutput to .reout files.\n");
    return 2;
#endif

  case 'c':
    o_scale = SCALE_CONSTANT;
    return 0;

  case 'm':
    o_scale = SCALE_MAX;
    return 0;

  case 'f':
    o_scale = SCALE_FLUSH;
    return 0;

  case 'i':
  case 'o':
  case 'v':
  case 'a':
    return 0;

  case 'h':
  case '?':
    do_help();
    o_did_nothing = 0;
    return 2;

  default:
    if (mlevel(2))
      fprintf(stderr, "Warning: unrecognized option '-%c'.\n", c);
    return 1;
  }
}

/*
 * Take an argument to an option.
 *
 * This returns the same values as arg_start(c), above, to indicate whether
 * more arguments are wanted.
 */
int arg_input(char c, char *s)
{
  switch (c)
  {
  case 'c':
  case 'm':
  case 'f':
    o_scale_val = atoi(s);
    if (mlevel(4))
      fprintf(stderr, "Scale type is %c, scale value is %i.\n", c, o_scale_val);
    return 2;

  case 'i':
    o_input_filenames[o_num_input_files++] = s;
    if (mlevel(4))
      fprintf(stderr, "Input file %i is '%s'.\n", o_num_input_files, s);
    o_did_nothing = 0;
    return o_num_input_files >= 16 ? 2 : 1;

  case 'o':
    o_output_filename = s;
    if (mlevel(4))
      fprintf(stderr, "Output file is '%s'.\n", s);
    return 2;

  case 'v':
    o_output_level = atoi(s);
    if (mlevel(6))
      fprintf(stderr, "Verbosity level is %i.\n", o_output_level);
    return 2;

  case 'a':
    one_family = s; /* This is NOT a copy, beware */
    return 2;
  }
  return 2;
}

/*
 * Use the command-line arguments to set options.
 * Each option must have an entry in arg_start(c), above.
 * Arguments taking options must have an entry in arg_input(c, s), above.
 *
 * No input files is probably a condition that should give a warning.
 */
void read_args(int argc, char *argv[])
{
  int n;
  char c = 'i';
  int used = 1;

  /* Check each argument */
  for (n = 1; n < argc; n++)
  {
    /* '-' is special; anything else starting with '-' is an option. */
    if ((argv[n][0] == '-' || argv[n][0] == '+') && argv[n][1])
    {
      /* Warn about options that need arguments but didn't get any. */
      if (!used)
	if (mlevel(3))
	  fprintf(stderr, "Warning: option '-%c' not used.\n", c);

      /* arg_start(c) and arg_input(c,s) expect lower case. */
      c = tolower(argv[n][1]);

      /* Argumentless options take effect now. */
      used = arg_start(c);
      
      /* There could be an argument passed in the same string (eg -v2). */
      if (argv[n][2])
      {
	/* If an argument is wanted, use it. */
	if (used < 2)
	  used = arg_input(c, argv[n] + 2);
	/* Otherwise, warn. The used == 2 is for decoration; used <= 2. */
	else if (mlevel(2) && used == 2)
	{
	  fprintf(stderr, "Warning: option '-%c' has an attached argument (ignored).\n", c);
	  used = 3;
	}
      }
    }
    /* If it's not an option, it's an argument. */
    else
    {
      /* If an argument is wanted, use it. */
      if (used < 2)
	used = arg_input(c, argv[n]);
      /* Otherwise, warn. Used will be 3 if the user has already been warned. */
      else if (mlevel(2) && used == 2)
      {
	fprintf(stderr, "Warning: option '-%c' has too many arguments (ignored).\n", c);
	used = 3;
      }
    }
  }

  /* Warn if the last option expected arguments and got none. */
  if (!used)
    if (mlevel(3))
      fprintf(stderr, "Warning: option '-%c' not used.\n", c);
}

/* A pointer to some malloc()'d memory. */
blocks_map *current_map;

/* Three file pointers, see how they run */
FILE *in_file;
FILE *out_file;
FILE *reout_file;

/* A buffer for the most recently read input line. */
char buffer[LINEBUF_LEN];

/* fgets() might work, but it has some unwanted behavior. */
void read_line(char *s)
{
  int i;
  int c;
  
  /* In debug mode, it's good to know what's expected. */
  if (mlevel(6))
    fprintf(stderr, "Reading line: %s\n", s);

  /* Get characters one at a time. */
  for (i = 0; i < LINEBUF_LEN-1; i++)
  {
    c = fgetc(in_file);

    /* EOF or newline is *not* put in the buffer. */
    if (c == EOF || c == '\n')
      break;

    buffer[i] = c;
  }

  /* Always zero-terminate. */
  buffer[i] = 0;

  /* In debug mode, tell the user what we read. */
  if (mlevel(6))
    fprintf(stderr, "# %s\n", buffer);
}

int maps_processed;

/*
 * Takes the file pointed to by FILE *in_file and reads the data into
 * blocks_map *current_map (a pointer to dynamically allocated memory).
 */
void read_blocks_map(void)
{
  int i1, i2;
  sequence_map *current_seq;
  block_pos *current_block;
  char junk[LINEBUF_LEN];

  /* More debug messages. */
  if (mlevel(5))
    fprintf(stderr, "Reading one family...\n");

  /* Allocate space for the blocks_map structure (remember to dealloc) */
  current_map = (blocks_map *)malloc(sizeof(blocks_map));
  
  /* Read the structure from the file */

  /* End-of-file check */
  if (feof(in_file))
  {
    /* Always clean up memory. */
    free((void *)current_map);

    /* This tells read_file we barfed. */
    current_map = 0;

    /* Tell the user what's going on. Perhaps change to mlevel(4)? */
    if (mlevel(5))
      fprintf(stderr, "End of input file reached.\n");
    return;
  }

  /* Find the family information, and discard any junk lines before that. */
  do 
  {
    read_line("blocks_map");
    
    /* If mlevel(6), we printed this in the read_line() function. */
    if (mlevel(5) && !mlevel(6) && buffer[0])
      fprintf(stderr, "# %s\n", buffer);

    /* End-of-file check, like above */
    if (feof(in_file))
    {
      free((void *)current_map);
      current_map = 0;
      if (mlevel(5))
        fprintf(stderr, "End of input file reached.\n");
      return;
    }
  } while (strncmp(buffer, ">", 1) != 0 &&
           strncasecmp(buffer, "#MAP#", 5) != 0);
/*
  } while ((sscanf(buffer, "%s %s %d %d %d %s", junk, current_map->block_family, 
 		 ¤t_map->tot_num_blocks, ¤t_map->num_seqs, 
		 ¤t_map->max_seq_len, current_map->id) < 6) );
*/
  if (strncmp(buffer, ">", 1) == 0)
        sscanf(buffer, ">%s %d %d %d %s", current_map->block_family, 
 		 ¤t_map->tot_num_blocks, ¤t_map->num_seqs, 
		 ¤t_map->max_seq_len, current_map->id);
/*
  if (strncasecmp(buffer, "#MAP#", 5) == 0)
*/
  else
        sscanf(buffer, "%s %s %d %d %d %s", junk, current_map->block_family, 
 		 ¤t_map->tot_num_blocks, ¤t_map->num_seqs, 
		 ¤t_map->max_seq_len, current_map->id);

  /* Allocate space for the sequence_map structures (remember to dealloc) */
  current_map->seq_map = (sequence_map *)malloc(sizeof(sequence_map) * 
						current_map->num_seqs);

  /* Description line. */
  read_line("description");
  strcpy(current_map->description, buffer);

  /* End-of-file check, like above (we'll be doing this often) */
  if (feof(in_file))
  {
    free((void *)current_map->seq_map);
    free((void *)current_map);
    current_map = 0;
    if (mlevel(1))
      fprintf(stderr, "Error: premature end of input file.\n");
    return;
  }

  /* Multiple sequence_map structures. */
  for (i1 = 0; i1 < current_map->num_seqs; i1++)
  {
    /* A pointer, for easy reference. */
    current_seq = current_map->seq_map + i1;
    
    /* Line with sequence_map information. */
    read_line("sequence_map");
    sscanf(buffer, "%s %d %d", current_seq->seq_name, ¤t_seq->seq_len,
	   ¤t_seq->num_blocks);

    /* End-of-file check, again. */
    if (feof(in_file))
    {
      for (i2 = 0; i2 < i1; i2++)
	free((void *)current_map->seq_map[i2].blocks);
      free((void *)current_map->seq_map);
      free((void *)current_map);
      current_map = 0;
      if (mlevel(1))
        fprintf(stderr, "Error: premature end of input file.\n");
      return;
    }

    /* Allocate space for the block_pos structures (remember to dealloc) */
    current_seq->blocks = (block_pos *)malloc(sizeof(block_pos) *
					      current_seq->num_blocks);

    /* Multiple block_pos structures */
    for (i2 = 0; i2 < current_seq->num_blocks; i2++)
    {
      /* Another handy pointer. */
      current_block = current_seq->blocks + i2;
      
      /* Line with block_pos information */
      read_line("block_pos");
      sscanf(buffer, "%c %d %d", ¤t_block->code, ¤t_block->start,
	     ¤t_block->end);

      /* End-of-file check */
      if (feof(in_file))
      {
        for (i2 = 0; i2 <= i1; i2++)
 	  free((void *)current_map->seq_map[i2].blocks);
        free((void *)current_map->seq_map);
        free((void *)current_map);
        current_map = 0;
        if (mlevel(1))
          fprintf(stderr, "Error: premature end of input file.\n");
        return;
      }
    }
  }

  /* End-of-family marker. If this is wrong, we screwed up somewhere. */
  read_line("marker");
  if (strcmp(buffer, "//") != 0)
  {
    /*
     * This is very important. Freeing everything and aborting would be
     * smart right now, but we don't. Hopefully, the next family will be
     * parsed correctly.
     */
    if (mlevel(1))
      fprintf(stderr, "Error: bad data read.\n");
    return;
  }

  maps_processed++;
}

/* Ignore this. */
#ifdef INCLUDE_REOUTPUT_STUFF
void write_a_map(void)
{
  int i1, i2 ;
  blocks_map *map = current_map;

  /* Marker, so other programs can tell this is the start of the data. */
  fprintf(reout_file, "#MAP# ") ;

  /* The blocks_map information. */
  fprintf(reout_file, "%s %d %d %d %s\n%s\n", map->block_family, 
	  map->tot_num_blocks, map->num_seqs, map->max_seq_len, 
	  map->id, map->description);

  /* For each sequence... */
  for(i1=0; i1num_seqs; i1++)
  {
    /* ...print the name, (possibly fake) length, number of blocks... */
    fprintf(reout_file, "%s %d %d\n",
	    map->seq_map[i1].seq_name, map->seq_map[i1].seq_len,
	    map->seq_map[i1].num_blocks) ;

    /* ...and all the block information, just like makeblockmap does. */
    for(i2=0; i2seq_map[i1].num_blocks; i2++)
      fprintf(reout_file, "%c %d %d\n", map->seq_map[i1].blocks[i2].code,
	      map->seq_map[i1].blocks[i2].start,
              map->seq_map[i1].blocks[i2].end) ;
  }

  /* Print an end-of-family marker to keep everyone in synch. */
  fprintf(reout_file, "//\n\n") ;

  /* I have no idea what this does, I copied it from makeblockmap.c */
  fflush(reout_file) ;
}
#endif

/* Free all the memory allocated in read_blocks_map. This is very important. */
void dealloc_blocks_map(void)
{
  int i1, i2;

  /* Deallocate the blocks in each sequence_map */
  for (i1 = 0; i1 < current_map->num_seqs; i1++)
  {
    free((void *)current_map->seq_map[i1].blocks);
  }

  /* Deallocate the sequence_maps */
  free((void *)current_map->seq_map);

  /* Deallocate the blocks_map */
  free((void *)current_map);

  /* Mark the blocks_map as gone */
  current_map = 0;
}

/* Two variables which I was too lazy to pass to each function. */
int length;
int maxlength;

/* Convert an amino acid position to a square position. */
int aa_to_square(int aa)
{
  switch (o_scale)
  {
  case SCALE_CONSTANT:
    return (aa + o_scale_val/2) / o_scale_val;
  case SCALE_MAX:
    return (aa * o_scale_val + maxlength/2) / maxlength;
  case SCALE_FLUSH:
    return (aa * o_scale_val + length/2) / length;
  }
}

/* Determine the size of the average square, rounded up. */
int square_size(int n)
{
  switch (o_scale)
  {
  case SCALE_CONSTANT:
    return o_scale_val * n;
  case SCALE_MAX:
    return (n * maxlength + (o_scale_val - 1)) / o_scale_val;
  case SCALE_FLUSH:
    return (n * length + (o_scale_val - 1)) / o_scale_val;
  }
}

/* Take a sequence_map and sort the blocks by position. */
void sort_sequence_map(sequence_map *seq)
{
  int i1;
  int i2;
  int t;

  /* Do a bubble sort (aaarrrggghhh!) */
  for (i1 = 0; i1 < seq->num_blocks - 1; i1++)
  {
    for (i2 = i1 + 1; i2 < seq->num_blocks; i2++)
    {
      /* Wrong order, reverse */
      if (seq->blocks[i1].start > seq->blocks[i2].start)
      {
	t = seq->blocks[i1].start;
	seq->blocks[i1].start = seq->blocks[i2].start;
	seq->blocks[i2].start = t;

	t = seq->blocks[i1].end;
	seq->blocks[i1].end = seq->blocks[i2].end;
	seq->blocks[i2].end = t;

	t = seq->blocks[i1].code;
	seq->blocks[i1].code = seq->blocks[i2].code;
	seq->blocks[i2].code = t;
      }
    }
  }
}

/*
 * I _know_ there's a stdio.h function that does this...
 */
void rep_char(char c, int n)
{
  while (n-- > 0) fputc(c, out_file);
}

/* 
 * Does the dirty work. Enjoy.
 *
 * 'Never use comments. If it was hard to write, it should be hard
 * to understand.'
 */
void make_graph(sequence_map *seq)
{
  int i1, i2, n;
  
  /* Store length where other functions can get to it. */
  length = seq->seq_len;

  /* Sort the blocks by starting positions */
  sort_sequence_map(seq);

  /* Print the name and (probably fudged) length. */
  fprintf(out_file, "%-20s (%4d) ", seq->seq_name, length);

  /* Print the empty space before each block, and the blocks. */
  for (i1 = 0; i1 < seq->num_blocks; i1++)
  {
    n = aa_to_square(min(seq->blocks[i1].end, seq->seq_len) - 
		     max(seq->blocks[i1].start, 1) + 1);
    if (n <= 0) n = 1;

    if (i1 == 0)
      rep_char(C_BASE, aa_to_square(max(seq->blocks[i1].start, 1) - 1));
    else
      rep_char(C_BASE, aa_to_square(seq->blocks[i1].start - 
				    seq->blocks[i1 - 1].end - 1));

    rep_char(seq->blocks[i1].code, n);
  }

  /* Print any last empty space */
  rep_char(C_BASE, aa_to_square(seq->seq_len - 
				seq->blocks[seq->num_blocks-1].end));

  /* Add a scale bar, in flush mode */
  if (o_scale == SCALE_FLUSH)
    fprintf(out_file, " [---- %d aa]", square_size(4));

  /* Add a return */
  fprintf(out_file, "\n");
}

/* Draw all the sequences in a blocks_map. */
void graph_all(void)
{
  int i;

  /* Print the sequence information. */
  fprintf(out_file, "%s: %s\n",
	  current_map->block_family, current_map->description);
  fprintf(out_file, "%d distinct blocks in %d sequences\n", 
	  current_map->tot_num_blocks, current_map->num_seqs);

  /* Store maxlength where other functions can get it. */
  maxlength = current_map->max_seq_len;

  /* Graph each sequence. */
  for (i = 0; i < current_map->num_seqs; i++)
  {
    make_graph(current_map->seq_map + i);
  }

  /* Draw a scale bar */
  if (o_scale != SCALE_FLUSH)
  {
    fprintf(out_file, "%20s---- %d amino acids\n\n", "", square_size(4));
  }
}

/* 
 * Open all the neccessary files, read and graph all the sequences,
 * and close the file again. This is the meat of the program.
 */
void read_file(char *ifilename, char *ofilename)
{
  char rofilename[80];

  maps_processed = 0;

#ifdef INCLUDE_REOUTPUT_STUFF
  /* Find the reoutput file name, but special case for ifilename == "-" */
  if (o_reoutput)
  {
    if (ifilename[0] == '-')
      sprintf(rofilename, "stdio.reout");
    else
      sprintf(rofilename, "%s.reout", ifilename);
  }
#endif

  if (mlevel(5)) 
    fprintf(stderr, "Opening '%s' for read.\n", ifilename);

  /* Open the input file, but special-case for "-" == stdio. */
  if (ifilename[0] == '-')
    in_file = stdin;
  else
    in_file = fopen(ifilename, "rb");

  /* Check for failure to open. */
  if (!in_file)
  {
    /* This is a very important error message. */
    if (mlevel(1))
      fprintf(stderr, "Error: cannot open input file '%s'.\n", ifilename);
    
    /* Abort! Abort! */
    return;
  }

  if (mlevel(5)) 
    fprintf(stderr, "Opening '%s' for write.\n", ofilename);

  /* Open the output file, special-casing again. */
  if (ofilename[0] == '-')
    out_file = stdout;
  else
    out_file = fopen(ofilename, "wb");

  /* Check for failure to open again. */
  if (!out_file)
  {
    if (ifilename[0] != '-')
      fclose(in_file);
    if (mlevel(1))
      fprintf(stderr, "Error: cannot open output file '%s'.\n", ofilename);
    return;
  }

#ifdef INCLUDE_REOUTPUT_STUFF
  /* The reoutput file is simpler to open. */
  if (o_reoutput)
    reout_file = fopen(rofilename, "wb");

  /* Only check for failure if the reoutput file is needed. */
  if (o_reoutput && !reout_file)
  {
    if (ifilename[0] != '-')
      fclose(in_file);
    if (ofilename[0] != '-')
      fclose(out_file);
    if (mlevel(1))
      fprintf(stderr, "Error: cannot open reoutput file '%s'.\n", rofilename);
    return;
  }
#endif

  /* We stop when we reach end-of-file. */
  while (1)
  {
    /* Read a family. */
    read_blocks_map();

    /* End-of-file signal is !current_map */
    if (!current_map) break;

#ifdef INCLUDE_REOUTPUT_STUFF
    /* Reoutput the data, if neccessary. */
    if (o_reoutput)
      write_a_map();
#endif

    if (!one_family || strcmp(current_map->block_family, one_family) == 0)
    {
        /* Draw the graph. */
        graph_all();
    }
    else
        maps_processed--;

    /* Always clean up (memory) after yourself. */
    dealloc_blocks_map();
  }

  /* Close the input file, except stdio. */
  if (ifilename[0] != '-')
    fclose(in_file);

  /* Flush output (?) */
  fflush(out_file);

  /* Close the output file, except stdio. */
  if (ofilename[0] != '-')
    fclose(out_file);

#ifdef INCLUDE_REOUTPUT_STUFF
  /* Close the reoutput file, if neccessary. */
  if (o_reoutput)
    fclose(reout_file);
#endif

  if (maps_processed)
  {
/*		Don't want any messages !
    if (mlevel(3))
      fprintf(stderr, "%d families successfully processed.\n", maps_processed);
*/
  }
  else
  {
    if (mlevel(1))
      if (one_family)
        fprintf(stderr, "Error: Family '%s' not found in file '%s'\n.",
                one_family, ifilename);
      else
        fprintf(stderr, "Error: no usable data in file '%s'.\n", ifilename);
  }

/*
  if (mlevel(3))
    if (ofilename[0] == '-')
      fprintf(stderr, "Output sent to stdout.\n");
    else
      fprintf(stderr, "Output placed in file '%s'.\n", ofilename);
*/
}

/*
 * Get the arguments from the command line, then process
 * each input file. The only actual work done here is interpreting
 * '*' in the output filename.
 */
void main(int argc, char *argv[])
{
  int i1, i2, i3, i4;
  char out_filename[80];

  program = argv[0] ;

  /* Read the arguments. */
  read_args(argc, argv);

  /* Process each input file. */
  for (i1 = 0; i1 < o_num_input_files; i1++)
  {
    /* It's always nice to know what's going on. */
    if (mlevel(4))
      fprintf(stderr, "Processing file '%s'.\n", o_input_filenames[i1]);

    /* We copy the output filename to a buffer by hand... */
    for (i2 = i3 = 0; o_output_filename[i2]; i2++)
    {
      /* Because '*' within the output filename stands for the input filename. */
      if (o_output_filename[i2] == '*')
	for (i4 = 0; o_input_filenames[i1][i4]; i4++)
	  out_filename[i3++] = o_input_filenames[i1][i4];
      else
	out_filename[i3++] = o_output_filename[i2];
    }

    /* Always zero-terminate strings. */
    out_filename[i3++] = 0;
	  
    /* Process the file. */
    read_file(o_input_filenames[i1], out_filename); 
  }

  /* Warn of lack of purpose */
  if (o_did_nothing && mlevel(2) && argc > 1)
    fprintf(stderr, "Warning: no input files.\n");

  /* No arguments? Give the user some help (and skip the warning above) */
  if (argc == 1)
    do_help();
}

g everything and aborting would be
     * smart right now, but we don't. Hopefully, the next family will be
     * parsed correctly.
     */
    if (mlevel(1))
      fprintf(stderr, "Error: bad data read.\n");
    return;
  }

  maps_processed++;
}

/* Ignore this. */
#ifdef INCLUDE_REOUTPUT_STUFF
void write_a_map(void)
{
  int i1, i2 blimps-3.9/blimps/blocks.c000064400001460000012000001126211054325674600160740ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */

/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* blocks.c: basic block operations on the Blocks data type */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

/*	system headers not in global.h */
/*	blimps library headers */
#include 
#include 
#include 

/*
 * Exported variables and data structures
 */

/*
 * Local variables and data structures
 */

#define BLOCK_SEQUENCE_INCREASE_SIZE 20 /* default number of sequences to */
				   /* allocate if the number of sequences */
				   /* in the block is not specified */
#define BLOCK_CLUSTER_INCREASE_SIZE 2 /* default number of sequences to */
				   /* allocate if the number of sequences */
				   /* in the block is not specified */


#define DEFAULT_BLOCK_SEQUENCE_WEIGHT 0.0 /* the default weight of each */
					  /* sequence if there is no weight */
					  /* defined in the block */

/*
 * Function definitions
 */

/* 
 * Block file related functions
 *
 *   Block *read_a_block ()
 *   Boolean read_block_header(bfp, block)
 *   int read_block_body(bfp, block)
 *   int next_cluster(bfp, block, num_clusters_seen, num_sequences_seen)
 *   void resize_block_sequences(block)
 *   void resize_block_clusters(block)
 *   void free_block(block)
 *
 */

/*
static Boolean read_block_header();
static void read_block_body();
static void next_cluster();
static void resize_block_sequences();
static void resize_block_clusters();
*/

/*
 * read_a_block
 *   reads a block from the data base and returns a pointer to the new
 *   block data structure
 *   Parameters:  
 *     FILE *bfp: the file pointer the the blocks database/file
 *   Error codes: NULL if a block was not read
 */

static int BlockBufLength;
static char *BlockBuffer;

Block *read_a_block (bfp)
     FILE *bfp;			/* block file pointer */
{
  Block *new_block;


  /* get the block file pointer */
/*  bfp = get_file(BLOCK_FILES);*/
  if (bfp == NULL) {
    /* no more data to read into blocks */
    new_block = NULL;
    return new_block;
  }

  /* allocate space for a new block */
  CheckMem(
	   new_block = (Block *) malloc(sizeof(Block))
	   );

  /* set the max sizes of the clusters and sequences */
  new_block->max_clusters = 0;
  new_block->max_sequences = 0;
  new_block->undefined = 0;
  new_block->undefined_dbl = 0.0;
  new_block->undefined_ptr = NULL;

  /* read header */
  if (read_block_header(bfp, new_block) == FALSE) {
    free(new_block);
    return NULL;
  }

  /* setup to handle extra wide blocks */
  if (new_block->width + 30 < EXTRA_LARGE_BUFF) {
    BlockBufLength = EXTRA_LARGE_BUFF;
    BlockBuffer = Buffer;
  }
  else {
    BlockBufLength = new_block->width + 30;
    CheckMem(
	     BlockBuffer = malloc(sizeof(char)*BlockBufLength)
	     );
  }

  /* read body */
  read_block_body(bfp, new_block); 

  /* free the block buffer if it was malloc'd */
  if (BlockBuffer != Buffer) {
    free(BlockBuffer);
  }

  /* return block */
  return new_block;
}


/*
 * read_block_header
 *   Reads the header information for the block.
 ID   ; BLOCK
 AC   ;
 DE   
 BL   

 *   Parameters:
 *     FILE *bfp:    the block file pointer. 
 *     Block *block: the block to put the data in.
 *   Error Codes: FALSE if the block could not be read, TRUE otherwise
 */

Boolean read_block_header(bfp, block)
     FILE *bfp;
     Block *block;
{
  char *buf2, *buf3;
  Boolean bflag;			/* found a real block */
  Boolean idflag, acflag, deflag, blflag;
  int i, done;

  bflag = idflag = acflag = deflag = blflag = FALSE;

  block->bl[0] = '\0';	/* make sure the BL string is empty */
  block->motif[0] = '\0';	/* make sure the motif string is empty */
  block->width = 0; /* make sure the width is small */
  block->percentile = 0;	
  block->strength = 0;	
  block->max_sequences = 0;	
  block->num_sequences = 0;	
  block->max_clusters = 0;	
  block->num_clusters = 0;	
  block->min_prev = block->max_prev = 0;

  /* scan for first ID, AC, DE, BL */
  fgets(Buffer, LARGE_BUFF_LENGTH, bfp);

  /*  need to check further, can be fooled (see mablock)  */
  while (  (strncmp(Buffer, "ID   ", 5)) != 0 &&
           (strncmp(Buffer, "AC   ", 5)) != 0 &&
           (strncmp(Buffer, "DE   ", 5)) != 0 &&
           (strncmp(Buffer, "BL   ", 5)) != 0 
	 && !feof(bfp) ) { 
    fgets(Buffer, LARGE_BUFF_LENGTH, bfp);
  }

  /* if we reached the end of the file, then there was no block */
  if (feof(bfp)) { return FALSE; }

  /* read ID if it exists */
  if ( strncmp(Buffer, "ID   ", 5) == 0) 
  {
     if (Buffer[5] != ' ')
     {
       if (strstr(Buffer, "; MATRIX") == NULL)
       {
          idflag = bflag = TRUE;
          buf2 = &Buffer[2];		/* Eat the ID at the beginining */
          buf2 = eat_whitespace(buf2); /* a pointer to the string after ID */
          remove_trailing_whitespace(buf2); 
          strncpy(block->id, buf2, SMALL_BUFF_LENGTH);
       }
       else    /*  this looks like a pssm */
       {
          sprintf(ErrorBuffer, "MATRIX on ID line; not a BLOCK");
          ErrorReport(SERIOUS_ERR_LVL);
          return(bflag);
       }
     }
     else 
     { /* invalid ID field, raise error */
       strcpy(block->id, "none; BLOCK");
       sprintf(ErrorBuffer, "Error in block file format.  Invalid ID line:");
       ErrorReport(WARNING_ERR_LVL);
       sprintf(ErrorBuffer, "%s\n", Buffer);
       ErrorReport(WARNING_ERR_LVL);
     }

     fgets(Buffer, LARGE_BUFF_LENGTH, bfp);	/* read the next line */
     while (strncmp(Buffer, "CC   ", 5) == 0)	/* skip over comment lines */
     { fgets(Buffer, LARGE_BUFF_LENGTH, bfp); }
  }
  else 
  { /* no valid ID field, raise error */
    strcpy(block->id, "none; BLOCK");
    sprintf(ErrorBuffer, "Error in block file format.  No ID line.\n");
    ErrorReport(WARNING_ERR_LVL);
  }

  /* read AC if it exists */
  if ( strncmp(Buffer, "AC   ", 5) == 0)
  {
     if (Buffer[5] != ' ')
     {
       acflag = bflag = TRUE;
       buf2 = &Buffer[2];		/* Eat the AC at the beginining */
       buf2 = eat_whitespace(buf2); /* get a pointer to the string after AC */
       remove_trailing_whitespace(buf2); /* remove the \n */
       strncpy(block->ac, buf2, SMALL_BUFF_LENGTH);
       buf2 = get_token(buf2);	/* get the number */
       if (buf2[strlen(buf2)-1] == ';') 
       {
         buf2[strlen(buf2)-1] = '\0';      /* remove the ';'*/
       }
       strncpy(block->number, buf2, SMALL_BUFF_LENGTH);
       strcpy(block->family, block->number);
       i = strlen(block->family); 
       if (i > MAXAC) { block->family[MAXAC] = '\0'; i = MAXAC; }
       done = FALSE;
       while (!done && i >= MINAC)
       {
          if (isalpha(block->family[i])){ block->family[i] = '\0'; done=TRUE; }
          else  { i--;  }
       }
       /* ; distance from previous block=(min,max) */
       strcpy(Buffer, block->ac);		/* Buffer's been destroyed */
       buf3 = strstr(Buffer, "block=(");
       if (buf3!=NULL) 
       {
         sscanf(buf3, "block=(%d,%d);", &(block->min_prev), &(block->max_prev));
       }
     }
     else
     {
       strcpy(block->ac, "none; distance from previous block=( , )");
       block->number[0] = '\0';	/* make sure string is empty */
       block->family[0] = '\0';	/* make sure string is empty */
       sprintf(ErrorBuffer, "Error in block file format.  Invalid AC line:");
       ErrorReport(WARNING_ERR_LVL);
       sprintf(ErrorBuffer, "%s\n", Buffer);
       ErrorReport(WARNING_ERR_LVL);
     }
     fgets(Buffer, LARGE_BUFF_LENGTH, bfp);	/* read the next line */
     while (strncmp(Buffer, "CC   ", 5) == 0)	/* skip over comment lines */
     { fgets(Buffer, LARGE_BUFF_LENGTH, bfp); }
  }
  else { /* no AC field, raise error */
    strcpy(block->ac, "none; distance from previous block=( , )");
    block->number[0] = '\0';	/* make sure string is empty */
    sprintf(ErrorBuffer, "Error in block file format.  No AC line.\n");
    ErrorReport(WARNING_ERR_LVL);
  }

  /* read DE if it exists */
  /* Be more strict about accepting DE to start a block if haven't seen
	ID or AC line yet */
  if (strncmp(Buffer, "DE   ", 5) == 0)
  {
     if ( Buffer[5] != ' ' || idflag || acflag ) 
     {
       deflag = bflag = TRUE;
       buf2 = &Buffer[2];		/* Eat the DE at the beginining */
       buf2 = eat_whitespace(buf2); /* get a pointer to the string after DE */
       remove_trailing_whitespace(buf2); /* remove the \n  */
       strncpy(block->de, buf2, SMALL_BUFF_LENGTH);
     }
     else 
     {
       strcpy(block->de, "none");
       sprintf(ErrorBuffer, "Error in block file format.  Invalid DE line:");
       ErrorReport(WARNING_ERR_LVL);
       sprintf(ErrorBuffer, "%s\n", Buffer);
       ErrorReport(WARNING_ERR_LVL);
     }
     fgets(Buffer, LARGE_BUFF_LENGTH, bfp);	/* read the next line */
     while (strncmp(Buffer, "CC   ", 5) == 0)	/* skip over comment lines */
     { fgets(Buffer, LARGE_BUFF_LENGTH, bfp); }
  }
  else
  {
    strcpy(block->de, "none");
    sprintf(ErrorBuffer, "Error in block file format.  No DE line.\n");
    ErrorReport(WARNING_ERR_LVL);
  }
  
  /* read BL if it does not exist raise an error */
  /* Blocks from MEME have only BL line, no ID|AC|DE   */
  /* Be more strict about accepting BL to start a block if haven't seen
	ID or AC line yet */
  if (strncmp(Buffer, "BL   ", 5) == 0)
  {
     if ( Buffer[5] != ' ' || idflag || acflag )
     {
       blflag = bflag = TRUE;
       buf2 = &Buffer[2];		/* Eat the BL at the beginining */
       buf2 = eat_whitespace(buf2); /* get a pointer to the string after BL */
       remove_trailing_whitespace(buf2); /* remove the \n  */
       strncpy(block->bl, buf2, SMALL_BUFF_LENGTH);
    
       /* scan and process the BL line */
       /* find the motif */
       buf3 = strstr(Buffer, "motif");
       if (buf3!=NULL) 
       {
         buf3 -= 4;		/* move back to the motif type */
         sscanf(buf3, "%s", block->motif);
       }

       /* find the width */
       buf3 = strstr(Buffer, "width=");
       if (buf3!=NULL) 
       { sscanf(buf3, "width=%d;", &(block->width)); }
       else 
       {
         /* report an error, it is serious if the width is not set */
         sprintf(ErrorBuffer, "No width field for block %s", block->number);
         ErrorReport(SERIOUS_ERR_LVL);
         sprintf(ErrorBuffer, "Setting width to zero\n");
         ErrorReport(SERIOUS_ERR_LVL);
         block->width = 0;
       }

       /* find the seqs */
       buf3 = strstr(Buffer, "seqs=");
       if (buf3!=NULL) 
       {
         sscanf(buf3, "seqs=%d", &(block->num_sequences));
         if (block->num_sequences < 0) { block->num_sequences = 0; }
       }
    
       /* find the 99.5% */
       buf3 = strstr(Buffer, "99.5%=");
       if (buf3!=NULL) { sscanf(buf3, "99.5%%=%d;", &(block->percentile)); }

       /* find the strength */
       buf3 = strstr(Buffer, "strength=");
       if (buf3!=NULL) { sscanf(buf3, "strength=%d", &(block->strength)); }

     }  /* end of valid BL */
     else 
     { 
       sprintf(ErrorBuffer, "Error in block file format.  Invalid BL line:");
       ErrorReport(SERIOUS_ERR_LVL);
       sprintf(ErrorBuffer, "%s\n", Buffer);
       ErrorReport(SERIOUS_ERR_LVL);
     }
   }    /* end of "BL   " */
   else
   {
       sprintf(ErrorBuffer, "Error in block file format.  No BL line.\n");
       ErrorReport(SERIOUS_ERR_LVL);
   }

  return(bflag);
}  /* end of read_block_header  */


/*
 * read_block_body
 *   Reads the body information of the block.
 *   Parameters:
 *     FILE *bfp:    the block file pointer. 
 *     Block *block: the block to put the data in.
 *   Error Codes:
 *   Programming note: I'm trying to malloc as large of chunks as
 *     possible hoping that there will be a slight speed increase in
 *     the program due to locality of reference (less page swapping).
 */

void read_block_body(bfp, block)
     FILE *bfp;
     Block *block;
{
  int i;
  
  Sequence *sequence_pointer;
  Residue  *residue_pointer;
  
  if (block->num_sequences <= 0) {
    block->max_sequences = BLOCK_SEQUENCE_INCREASE_SIZE;
  }
  else {
    block->max_sequences = block->num_sequences;
  }

  /* allocate space for all the Sequences of the block sequence array */
  CheckMem(
	   sequence_pointer = (Sequence *) calloc(block->max_sequences,
						  sizeof(Sequence))
	   );

  /* initialize the block sequences array */
  block->sequences = sequence_pointer;
  /* allocate space for all residues */
  CheckMem(
	   residue_pointer = (Residue *) calloc(block->width *
						block->max_sequences,
						sizeof(Residue))
	   );

  /* initialize the residues 2-d array */
  CheckMem(
	   block->residues = 
	   (Residue **) calloc(block->max_sequences,
			       sizeof(Residue *))
	   );

/* testing: */ /*
  for(i=0; i<(block->width *block->max_sequences); i++) {
    residue_pointer[i] = i;
  }
*/

  /* initialize sequences and residues */
  for(i=0; imax_sequences; i++) {
    sequence_pointer[i].length = block->width;
    sequence_pointer[i].sequence = 
      &(residue_pointer[i * block->width]);
    block->residues[i] = &(residue_pointer[i * block->width]);
  }


/* testing: */ /*
  for(i=0;imax_sequences;i++) {
    printf("%d\t",block->sequences[i].sequence[0]);
  }
  printf("\n");
*/

  /* read the clusters */
  /* num clusters seen = 0, num seqs seen = 0 */
  next_cluster(bfp, block, 0, 0); 
}  /* end of read_block_body */


/*
 * next_cluster
 *   next_cluster reads in the next set of sequences for a cluster.
 *   When the end of block, "//", is seen the space for the clusters
 *   is allocated.  This procedure calls itself recursively so when
 *   the memory is allocated all of the clusters have been seen and
 *   the data is stored within each clusters procedure.
 *   Parameters:
 *     FILE *bfp: the block file pointer
 *     Block *block: the block of the clusters.  Where the sequences are.
 *     int num_clusters_seen: the number of clusters seen so far
 *     int num_sequences_seen: the number of sequences seen so far
 *   Precondition: There is no space allocated for the clusters.  Attempts
 *                 to access will result in ambiguous behavior
 *   Postcondition: The space for has been allocated.  The clusters after
 *                  the current number seen are correctly set up.
 *   Error Codes:
 */

void next_cluster(bfp, block, num_clusters_seen, num_sequences_seen)
     FILE *bfp;
     Block *block;
     int num_clusters_seen;
     int num_sequences_seen;
{
  int i, eob;
  int low_sequence;
  int return_value;

  char *buf, *name_buf;

  low_sequence = num_sequences_seen;	/* this clusters starting Sequence */
  eob = FALSE;		/*  end of block flag */
  fgets(BlockBuffer, BlockBufLength, bfp); /* read a line */
  if (feof(bfp)) eob = TRUE;
  if (BlockBuffer[0] == '/' && BlockBuffer[1] == '/') eob = TRUE;

  /* while not a blank line and not the end of the block read the sequences */
  /* also be sure not at next block (ID   ) or end of file */
  while (!blank_line(BlockBuffer) && !eob)
  {
    /* get the name, getting early for use in error reporting if needed */
    name_buf = get_token(BlockBuffer);
  
    /* it is a sequence, so make sure there is enough space for the sequence */
    if (block->max_sequences < num_sequences_seen +1) { /* indexing starts */
  	    /* at 1 for block->max_sequences and 0 for num_sequences_seen  */
      /* more sequences than space */

      /* announce error */
      sprintf(ErrorBuffer, 
	      "No space allocated for sequence %s in block %s.",
	      name_buf, block->number);
      ErrorReport(INFO_ERR_LVL);
      sprintf(ErrorBuffer,
	      "Allocating more space\n");
      ErrorReport(INFO_ERR_LVL);
      
      /* get more space */
      resize_block_sequences(block);
    }

    /* enter the sequence name into the data struct */
    strncpy(block->sequences[num_sequences_seen].name, name_buf, SMALL_BUFF_LENGTH);

    buf = get_token(NULL);		/* eat the "(" or "(#)" */
    if (buf != NULL && buf[1] != '\0') {
      /* this is mainly the old style format */
      sscanf(buf, "(%d)", &(block->sequences[num_sequences_seen].position));
    }
    else {     
      buf = get_token(NULL);		/* get the part with the position */
      if (buf != NULL)
      {  sscanf(buf, "%d)", &(block->sequences[num_sequences_seen].position));}
    }
    
    buf = get_token(NULL);		/* skip over position to the seq. */
    

    /* read the sequence from the string into the Sequence */

    return_value = read_sequence(&(block->sequences[num_sequences_seen]), 
				 AA_SEQ, 0, buf); 
				/* the Sequence, sequence type, starting */
				/* position, string with the sequence */
    /* check to see if there was an error */
    
    if (return_value < 0) {
      /* Error, more residues in the sequence than expected */
      sprintf(ErrorBuffer, "Error reading sequence %s in block %s,", 
	      block->sequences[num_sequences_seen].name,
	      block->number);
      ErrorReport(WARNING_ERR_LVL);
      sprintf(ErrorBuffer, 
	      "%d more residues in the sequence than the expected %d.",
	      - return_value,
	      block->sequences[num_sequences_seen].length);
      ErrorReport(WARNING_ERR_LVL);
      /*  reset the lengths & reread the sequence */
      block->width -= return_value;
      block->sequences[num_sequences_seen].length -= return_value;
      resize_block_sequences(block);
      sprintf(ErrorBuffer, 
	      "Resetting block width to %d.\n",
	      block->sequences[num_sequences_seen].length);
      ErrorReport(WARNING_ERR_LVL);
      return_value = read_sequence(&(block->sequences[num_sequences_seen]), 
				 AA_SEQ, 0, buf); 
    }
    else if (return_value < block->sequences[num_sequences_seen].length) {
      /* Error, not enough residues for the sequence, filling with blanks */
      sprintf(ErrorBuffer, "Error reading sequence %s in block %s,", 
	      block->sequences[num_sequences_seen].name,
	      block->number);
      ErrorReport(WARNING_ERR_LVL);
      sprintf(ErrorBuffer, 
	      "not enough residues to fill the sequence.");
      ErrorReport(WARNING_ERR_LVL);
      sprintf(ErrorBuffer, 
	      "Filling the rest of the sequence with blanks.\n");
      ErrorReport(WARNING_ERR_LVL);

      /* filling with blanks */
      if (block->sequences[num_sequences_seen].type == AA_SEQ) {
	for(i=return_value;isequences[num_sequences_seen].length;i++) {
	  block->sequences[num_sequences_seen].sequence[i] = aa_atob['-'];
	}
      }
      else if (block->sequences[num_sequences_seen].type == NA_SEQ) {
	for(i=return_value;isequences[num_sequences_seen].length;i++) {
	  block->sequences[num_sequences_seen].sequence[i] = nt_atob['-'];
	}
      }
      else {
	sprintf(ErrorBuffer, 
		"next_cluster(): Unknown sequence type, assuming an amino acid sequence.\n");
	ErrorReport(PROGRAM_ERR_LVL);
	for(i=return_value;isequences[num_sequences_seen].length;i++) {
	  block->sequences[num_sequences_seen].sequence[i] = aa_atob['-'];
	}
      }
    }
    else if (return_value > block->sequences[num_sequences_seen].length) {
      /* BIG Error, an undocumented return value from read_sequence */
      sprintf(ErrorBuffer, 
	      "next_cluster(): Error reading sequence %s in block %s,", 
	      block->sequences[num_sequences_seen].name,
	      block->number);
      ErrorReport(PROGRAM_ERR_LVL);
      sprintf(ErrorBuffer, 
	      "                Undocumented return value, %d, from read_sequence().\n",
	      return_value);
      ErrorReport(PROGRAM_ERR_LVL);
    } /* else, ret_value == seq.length, OK */

    /* if there is a sequence weight, read it */
    buf = get_token(NULL);
    if (buf != NULL) {
      /* there is a weight */
      sscanf(buf, "%lg", &block->sequences[num_sequences_seen].weight);
    }
    else {
      /* there was no weight */
      block->sequences[num_sequences_seen].weight = 
	DEFAULT_BLOCK_SEQUENCE_WEIGHT;
    }
    
    /* update sequence count */
    num_sequences_seen++;

    /* get the next line */
    fgets(BlockBuffer, BlockBufLength, bfp);	
    if (feof(bfp)) eob = TRUE;
    if (BlockBuffer[0] == '/' && BlockBuffer[1] == '/') eob = TRUE;
    /*  Assumes no extra sequence will be named "ID     " !!!  */
    if (num_sequences_seen >= block->num_sequences &&
        strncmp(BlockBuffer, "ID   ", 5) != 0)
    {
       eob = TRUE;
       /*  should also backup bfp one record; see ftell()/fseek()  */
    }
  } /* end of while */

  /* if at the end of block: */
  if (eob) { 

    block->num_clusters = num_clusters_seen + 1; /* reached end saw this one */
    block->max_clusters = block->num_clusters;  

    /* allocate space for all the clusters */
    CheckMem(
	     block->clusters = (Cluster *) calloc(block->max_clusters,
						  sizeof(Cluster))
	     );


    /* report size difference */
    if (block->num_sequences != num_sequences_seen) {
      sprintf(ErrorBuffer, 
	      "Number of sequences in block %s read from file as %d but is %d\n",
	      block->number,
	      block->num_sequences,
	      num_sequences_seen);
      ErrorReport(INFO_ERR_LVL);
      block->num_sequences = num_sequences_seen;
    }

  }
  else {
    /* read in the next cluster */
    next_cluster(bfp, block, num_clusters_seen+1, num_sequences_seen);
  }

  /* assign the sequences to the cluster, space has now been allocated */
  block->clusters[num_clusters_seen].num_sequences = 
    num_sequences_seen-low_sequence;
  
  block->clusters[num_clusters_seen].sequences = 
    &(block->sequences[low_sequence]);
}  /*  end of next_cluster */


/* 
 * resize_block_sequences
 *   Increases the memory for the storage of the sequences of a block.
 *   Parameter:
 *     Block *block: the block to resize
 *   Error codes: none
 */

void resize_block_sequences(block)
     Block *block;
{
  int i, j, s;
  void *tmp_ptr;		/* don't want to ruin pointer in case there */
				/* is a repeated realloc call */

  /* announce info */
  sprintf(ErrorBuffer, 
	  "Allocating more space for sequences in block %s.\n",
	  block->number);
  ErrorReport(INFO_ERR_LVL);

  
  /* get more space */
  block->max_sequences += BLOCK_SEQUENCE_INCREASE_SIZE;
  
  CheckMem(
	   tmp_ptr = 
	   (Sequence *) realloc(block->sequences,
				sizeof(Sequence) *
				block->max_sequences)
	   );
  block->sequences = (Sequence *) tmp_ptr;
  
  CheckMem(
	   tmp_ptr = 
	   (Residue *) realloc(block->sequences[0].sequence,
			       sizeof(Residue) *
			       block->width *
			       block->max_sequences)
	   );
  block->sequences[0].sequence = (Residue *) tmp_ptr;

  CheckMem(
	   tmp_ptr = 
	   (Residue **) realloc(block->residues,
				sizeof(Residue *) *
				block->max_sequences)
	   );
  block->residues = (Residue **) tmp_ptr;
  
  /* re-initialize sequences and residues, same data, just different place */
  for(i=0; imax_sequences; i++) {
    block->sequences[i].length = block->width;
    block->sequences[i].sequence = 
      &(block->sequences[0].sequence[i * block->width]);
    block->residues[i] = 
      &(block->sequences[0].sequence[i * block->width]);
  }
  /*  Need to re-initialize clusters; point to first seq,
      assumes sequences are in cluster order  */
  s = 0;	/* sequence number */
  for (j=0; jnum_clusters; j++)
  {
      block->clusters[j].sequences = &(block->sequences[s]);
      for (i=0; iclusters[j].num_sequences; i++)
              s++;
  }

}


/* 
 * resize_block_clusters
 *   Increases the memory for the storage of the clusters of a block.
 *   Parameter:
 *     Block *block: the block to resize
 *   Error codes: none
 */

void resize_block_clusters(block)
     Block *block;
{
  Cluster *tmp_ptr;		/* don't want to ruin pointer in case there */
				/* is a repeated realloc call */

  /* announce info */
  sprintf(ErrorBuffer, 
	  "Allocating more space for clusters in block %s.\n",
	  block->number);
  ErrorReport(INFO_ERR_LVL);

  
  block->max_clusters += BLOCK_CLUSTER_INCREASE_SIZE;

  CheckMem(
	   tmp_ptr = (Cluster *) realloc(block->clusters,
					 block->max_clusters *
					 sizeof(Cluster))
	   );
  block->clusters = tmp_ptr;
}


/* 
 * free_block
 *   Frees the block and the sub elements.
 *   Parameters: 
 *     Score *score: the score to free
 *   Return code: none
 *   Error code: none
 */

void free_block(block) 
     Block *block;
{
  free(block->residues);
  free(block->clusters);
  free(block->sequences[0].sequence);
  free(block->sequences);
  free(block);
}


/*
 * block_comparison
 *   Compares two blocks.   It compares by the value in the id
 *   field if it exists.
 *   Parameters:
 *     BlockListEntry a, b: the entries to compare
 *   Return codes:  a return value < 0 if a < b, a return value = 0 if a == b,
 *                  and a return value > 0 if a > b
 *   Error codes: none
 */

int block_comparison(a, b)
     Block *a, *b;
{
  char *sa, *sb;

  if (a->id != NULL) {    
    sa = a->id;
  }
  else {
    if (b->id != NULL) {  
      return -1;		/* NULL < something */
    }
    else {
      return 0;			/* NULL = NULL */
    }
  }
  
  if (b->id != NULL) {    
    sb = b->id;
  }
  else {
    return 1;			/* something > NULL */
  }

  return (int) (strcmp(sa, sb));
}



/*
 * Block printing.
 */

/*
 * print_block
 *   Prints a block data structure.  Primarily for debugging purposes.
 *   Parameters: 
 *     Block *block:  the block to print
 *   Error Codes: none
 */

void print_block(block)
     Block *block;
{
  int i,j,k;

  printf("--- block ---\n");
  printf("ID\t%s\n", block->id);
  printf("AC\t%s\n", block->ac);
  printf("DE\t%s\n", block->de);
  printf("BL\t%s\n", block->bl);
  printf("motif:\t%s\n", block->motif);
  printf("width=%d; 99.5%%=%d; strength=%d;\n", 
	 block->width,
	 block->percentile,
	 block->strength);
  printf("num sequences: %d\tnum clusters: %d\n",
	 block->num_sequences,
	 block->num_clusters);

  /* print clusters */
  for (i=0; inum_clusters; i++) {
    for (j=0; jclusters[i].num_sequences; j++) {
/*      print_sequence(&(block->clusters[i].sequences[j])); */
      printf("%s \t( %d:%d, ", 
	     block->clusters[i].sequences[j].name,
	     block->clusters[i].sequences[j].position,
	     block->clusters[i].sequences[j].length);
      if (block->clusters[i].sequences[j].type == AA_SEQ) {
	printf("AA) \t");
	for(k=0; kclusters[i].sequences[j].length; k++) {
	  printf("%c", aa_btoa[block->clusters[i].sequences[j].sequence[k]]);
	}
      }
      else if (block->clusters[i].sequences[j].type == NA_SEQ) {
	printf("NA) \t");
	for(k=0; kclusters[i].sequences[j].length; k++) {
	  printf("%c", nt_btoa[block->clusters[i].sequences[j].sequence[k]]);
	}
      }    
      else {
	printf("??) \t");
	for(k=0; kclusters[i].sequences[j].length; k++) {
	  printf("%c", aa_btoa[block->clusters[i].sequences[j].sequence[k]]);
	}
      }
      printf("\n");
    } /* end of cluster */
    printf("\n");
  }  

  /* print sequences */
  printf("--- ----- ---\n");
  
}


/*
 * ouput_block
 *   Outputs a block data structure to the given file. 
 *   Parameters: 
 *     Block *block:  the block to print
 *     FILE  *obfp:   the ouput block file pointer
 *   Error Codes: none
 */

void output_block(block, obfp)
     Block *block;
     FILE *obfp;
{
  output_block_s(block, obfp, INT_OUTPUT);
}


/*
 * ouput_block_s
 *   Outputs a block data structure to the given file with the 
 *   specified style of data.
 *   Parameters: 
 *     Block *block:  the block to print
 *     FILE  *obfp:   the ouput block file pointer
 *     int    style:   the kind of output (INT_OUTPUT, FLOAT_OUTPUT)
 *   Error Codes: none
 */

void output_block_s(block, obfp, style)
     Block *block;
     FILE *obfp;
     int style;
{
  int i,j,k, offset, lenb, iend, ic;
  char *ptr, bltemp[132];

  if (!((style == INT_OUTPUT) || (style == FLOAT_OUTPUT))) {
    sprintf(ErrorBuffer, 
	    "Unknown output type: %d, using integer output\n", style);
    ErrorReport(WARNING_ERR_LVL);
    output_block_s(block, obfp, INT_OUTPUT);
    return;
  }

  fprintf(obfp, "ID   %s\n", block->id);
  fprintf(obfp, "AC   %s\n", block->ac);
  fprintf(obfp, "DE   %s\n", block->de);

  /*  Edit BL line: update or add width, seqs, 99.5, strength
      BL    ECA motif; width=40; seqs=34; 99.5%=1833; strength=1412 */
/*  This may wipe out some other stuff on the BL line
  sprintf(block->bl, "%s motif; width=%d; seqs=%d; 99.5%%=%d; strength=%d ",
      block->motif, block->width, block->num_sequences,
      block->percentile, block->strength);
*/
  /*  Rewrite everything after width= if it is found, else append */
  lenb = strlen(block->bl);
  ptr = strstr(block->bl, "width=");
  if (ptr!=NULL) 
  {
     strcpy(bltemp, block->bl);
     block->bl[0] = '\0';
     offset = lenb - strlen(ptr);
     strncat(block->bl, bltemp, offset);	/* preserve first part */
     block->bl[offset] = '\0';
  }
  sprintf(bltemp, " width=%d; seqs=%d; 99.5%%=%d; strength=%d ",
      block->width, block->num_sequences,
      block->percentile, block->strength);
  strcat(block->bl, bltemp);
  fprintf(obfp, "BL   %s", block->bl);

  /* print clusters */
  for (i=0; inum_clusters; i++) {
    fprintf(obfp, "\n");
    for (j=0; jclusters[i].num_sequences; j++) {
      strcpy(bltemp, block->clusters[i].sequences[j].name);
      if (strlen(bltemp) > 20)   /* look for nearest | */
      {
         iend = ic = 20;
         while (ic > 0)
         {
            if (bltemp[ic] == '|') { iend = ic; break; }
            ic--;
         }
         bltemp[iend] = '\0';
      }
      /*  right-justify is %20.20s */
      fprintf(obfp, "%-20s (%4d) ", 
              bltemp,
	      block->clusters[i].sequences[j].position);
      for(k=0; kclusters[i].sequences[j].length; k++) {
	fprintf(obfp, "%c", 
		aa_btoa[block->clusters[i].sequences[j].sequence[k]]);
      }
      if (style == INT_OUTPUT) {
	fprintf(obfp, " %3d\n", 
		(int) round(block->clusters[i].sequences[j].weight));
      }
      else { /* FLOAT_OUTPUT -- only two options allowed with beginning if */
	fprintf(obfp, " %f\n", 
		(double) block->clusters[i].sequences[j].weight);
      }
    } /* end of cluster */
  }  
  /* end of the block */
  fprintf(obfp, "//\n");
  fflush(obfp);
}




/*
 *  new_block(#columns, #rows)
 *     Create a block structure
 */


Block *new_block(ncols, nrows)
int ncols, nrows;
{
   Block *new;
   Residue *residue_pointer;
   int i;

   /* allocate space for a new block */
   CheckMem(
	   new = (Block *) malloc(sizeof(Block))
	   );

   /*  Initialize  */
   new->max_sequences = new->num_sequences = nrows;
   new->width = ncols;
   new->id[0] = new->ac[0] = new->de[0] = '\0'; 
   strcpy(new->id, "id");
   strcpy(new->ac, "ac");
   strcpy(new->de, "de");
   sprintf(new->bl, " ; width=%d; seqs=%d; ", ncols, nrows);
   new->number[0] = new->family[0] = new->motif[0] = '\0';
   new->percentile = new->strength = new->undefined = 0;
   new->undefined_dbl = 0.0;
   new->undefined_ptr = NULL;

   /*  Allocate space for a single "cluster"  */
   new->max_clusters = new->num_clusters = 1;
   CheckMem(
	     new->clusters = (Cluster *) calloc(new->max_clusters,
						  sizeof(Cluster))
	     );


   new->clusters[0].num_sequences = nrows;

  /* allocate space for all the Sequences of the block sequence array */
  CheckMem(
	   new->sequences = (Sequence *) calloc(new->max_sequences,
						  sizeof(Sequence))
	   );

  new->clusters[0].sequences = &(new->sequences[0]);

  /* allocate space for all residues */
  CheckMem(
	   residue_pointer = (Residue *) calloc(new->width *
						new->max_sequences,
						sizeof(Residue))
	   );

  /* initialize the residues 2-d array */
  CheckMem(
	   new->residues = 
	   (Residue **) calloc(new->max_sequences, sizeof(Residue *))
	   );

  /* initialize sequences and residues */
  for(i=0; imax_sequences; i++) {
    new->sequences[i].weight = 1.0;
    new->sequences[i].length = new->width;
    new->sequences[i].sequence = &(residue_pointer[i * new->width]);
    new->residues[i] = new->sequences[i].sequence;
  }

   /* return block */
   return new;
}  /*  end of new_block */

/*
 * read_to_block
 *   positions file at AC
 *   assumes AC is 7 chars; assumes bfp is sorted by AC
 *   Parameters:  
 *     FILE *bfp: the file pointer the the blocks database/file
 *     char *ac:  AC of the block to fine
 *   
 */

Boolean read_to_block(bfp, ac)
     FILE *bfp;			/* block file pointer */
     char *ac;
{
  long idpos;

  idpos = -1;
  while (!(feof(bfp)) && fgets(Buffer, LARGE_BUFF_LENGTH, bfp) != NULL)
  {
     if (strncmp(Buffer, "ID   ", 5) == 0) { idpos = ftell(bfp); }
     else
     {
        if (strncmp(Buffer, "AC   ", 5) == 0) 
        {
           if (strncmp(Buffer+5, ac, 7) > 0)  /* beyond AC */
           {   return(FALSE);  }
           else if (strncmp(Buffer+5, ac, 7) == 0)
           {
              fseek(bfp, idpos, 0);	/* back up to start of block */
              return(TRUE);
           }
        }
     }
  }
  return(FALSE);
}  /*  end of read_to_block  */

/*
 * read_a_block_faster
 *   reads a block from the data base and returns a pointer to the new
 *   block data structure
 *   Parameters:  
 *     FILE *bfp: the file pointer the the blocks database/file
 *   Error codes: NULL if a block was not read
>>>>>still only about 20% faster <<<<<
 */

Block *read_a_block_faster(bfp)
     FILE *bfp;			/* block file pointer */
{
  Block *new_block;
  Residue  *residue_pointer;
  char ctemp[80], ctemp2[20];
  int iseq, pos, eob;

  if (bfp == NULL) { return(NULL); }

  /* allocate space for a new block */
  CheckMem( new_block = (Block *) malloc(sizeof(Block)) );
  new_block->undefined = 0;
  new_block->undefined_dbl = 0.0;
  new_block->undefined_ptr = NULL;

  /* read header */
  if (read_block_header(bfp, new_block) == FALSE) {
    free(new_block);
    return(NULL);
  }

  /* This routine assumes num_sequences is set & correct  */
  if (new_block->num_sequences <= 0)
  {
    read_block_body(bfp, new_block);
    return(new_block);
  }
  
  new_block->max_sequences = new_block->num_sequences;
  /* allocate space for all the Sequences of the block sequence array */
  CheckMem(
	   new_block->sequences = (Sequence *) calloc(new_block->max_sequences,
						  sizeof(Sequence))
	   );

  /* allocate space for all residues */
  CheckMem(
	   residue_pointer = (Residue *) calloc(new_block->width *
						new_block->max_sequences,
						sizeof(Residue))
	   );

   /* initialize the residues 2-d array */
   CheckMem(
	   new_block->residues = 
	   (Residue **) calloc(new_block->max_sequences,
			       sizeof(Residue *))
	   );

   /* initialize sequences and residues */
   for(iseq=0; iseqmax_sequences; iseq++) {
      new_block->sequences[iseq].length = new_block->width;
      new_block->sequences[iseq].max_length = new_block->width;
      new_block->sequences[iseq].sequence = 
        &(residue_pointer[iseq * new_block->width]);
      new_block->residues[iseq] = &(residue_pointer[iseq * new_block->width]);
    }

    /* allocate space for one cluster */
    new_block->num_clusters = new_block->max_clusters = 1;
    CheckMem(
	     new_block->clusters = (Cluster *) calloc(new_block->max_clusters,
						  sizeof(Cluster))
	     );
   new_block->clusters[0].num_sequences = new_block->num_sequences;
   new_block->clusters[0].sequences = &(new_block->sequences[0]);

  /*  Now get the sequences  */
  eob = FALSE;		/*  end of block flag */
  iseq = 0;
  while (!eob && !(feof(bfp)) && fgets(Buffer, LARGE_BUFF_LENGTH, bfp) != NULL)
  {
     if ( (strncmp(Buffer, "//", 2) == 0)    ||
          (strncmp(Buffer, "ID   ", 5) == 0)    )
                eob = TRUE;
     /*  see if this looks like a sequence line:
         name(offset)sequenceweight  */
     if (iseq < new_block->max_sequences &&
         strlen(Buffer) > 5 && strstr(Buffer, "(") != NULL)
     {
        sscanf(Buffer, "%s (%d) %s %s",
           &(new_block->sequences[iseq].name),
           &(new_block->sequences[iseq].position),
           &ctemp,
           &ctemp2  );

        new_block->sequences[iseq].weight = atof(ctemp2);
        if ( (int) strlen(ctemp) != new_block->width)
        {
          sprintf(ErrorBuffer, "Error in block %s: seq %s\n",
           new_block->number, new_block->sequences[iseq].name);
          ErrorReport(WARNING_ERR_LVL);
        }
        for (pos=0; pos < new_block->width; pos++)
           new_block->sequences[iseq].sequence[pos] = aa_atob[ ctemp[pos] ];
        strcpy(new_block->sequences[iseq].info, new_block->sequences[iseq].name);
        iseq++;
     }
  }
  return(new_block);
}  /* end of read_a_block_faster */



/* Change log information follows. */
/*
  Changes since version 3.8:
12/23/06 output_block() increase sequences->name from 18 to 20
  Changes since version 3.6:
 4/15/04 Fix abort in next_cluster() if reading incomplete blocks.
  Changes since version 3.4:
12/23/00 BlockBufLength starts at EXTRA_LARGE_BUFF
  Changes since version 3.3.2:
 2/23/00  output_block() Be sure seq name is < 18 chars
12/17/99  undefined_dbl and family fields added.
  Changes since version 3.2.5:
 5/11/99  Changed read_block_header() to do a better job of recognizing
	  whether the input contains a block.
 2/22/99  Added read_a_block_faster() & read_to_block()
 2/11/99  read_block_header(): get block->min_prev & block->max_prev
 1/28/99  output_block(): sequence name field increased from 10 to 18
  Changes since version 3.2.2:
 1/29/98  Removed all static declarations.
          Re-set cluster pointers in resize_block_sequences()
12/30/97  Changed read_block_header() to do a better job of recognizing
	  whether the input contains a block.
  Changes since version 3.2.1:
 7/10/97  Changed next_cluster() to recover from missing width on BL line.
 7/ 7/97  Modified output_block_s() to rebuild BL line.
  Changes since version 3.2:
 4/16/97  Removed static declaration from resize_block_sequences()
  Changes since version 3.1:
 2/14/97  Added new_block().
          Allow CC comment lines between header lines before BL line.
  Changes since version 3.0.0:
 4/15/96  Fix bug in read_a_block()/next_cluster() if block doesn't end with //.
*/
RR_LVL);
    output_block_s(block, obfp, INT_OUTPUT);
    return;
  }

  fprintf(obfp, "ID   %s\n", block->id);blimps-3.9/blimps/blocks_search.c000064400001460000012000000506741013365042700174170ustar00jorjastaff00000400000027/*      blocks_search.c             WWW Blocks Searcher
   Copyright 1994-2003 Fred Hutchinson Cancer Research Center

   Developed from the query.c program in the httpd distribution
   WARNING! Location specific variables: look for fhcrc
   WARNING! This is not a very robust piece of code.  If the data in the 
            entry.val field overflows the allowed space it will be truncated
	    by the following entry and have the following entry.name appended 
	    to the truncation.
	    Because of this the sequence needs to be the last entry in the
	    html form because there is no entry following it to truncate 
	    the sequence data. */
/*-----------------------------------------------------------------------
   1994     Written by Bill Alford.
   5/02/95  Modified chmod calls to give proper permissions to log files. 
	    Wouldn't compile: had to remove calls to "remove_trailing_
	    whitespace(); also a problem with Buffer[], changed to buf[] JGH
   5/ 6/95  Modified .cs file to search mats.dat instead of blocks.dat
   7/11/95  Added "umask 006" to prevent general read on wwwuser files
	    Added more "chmod"s for .cs, seq, .out
   7/19/95  Changed the error message when the page is not accessed by a post.
            Netscape does this sometimes when backing up to a page.
   9/ 5/95  Changed blimps search to search a blocks db using pseudo-counts.
	    Added option to search the Prints database in blocks format.
   9/23/95  Fixed problem introduced 9/5 with blimps options.
   9/25/95  Changed log file entry to indicate blocks or prints
  12/ 2/95  Changed SMALL_BUFF_LENGTH to LARGE_BUFF_LENGTH everywhere
	    blksort_output, etc. was getting corrupted ...
  12/ 3/95  Changed to look for environment variables BLOCKS_HOME &
            BLOCKS_EMAIL before using values here.
   5/22/96  Don't require results type to be specified - defaults to blksort
   5/25/96  Mail_Flag => both blocks & prints are searched now
   7/26/96  Changed blosum62.qij to default.qij
   8/26/96  Changed to search blocks.dat with CO 3 like makecs does.
  10/ 3/96  Changed blksort to read blimps cs file like dosearch.sh does.
   2/21/97  Changed to check for btest execution.
   3/17/97  Added "DB prints.noBL" to default (blocks) .cs file
   4/ 2/97  Moved blocks.dat,etc to data-blocks/
	    Dropped title from form, just let them dump the whole sequence
	    in any format into the form - write_sequence().
  11/15/97  Moved home directory definitions to homedir.h
   6/24/98  Use Mail instead of sendmail to setup email stuff (mailprog)
   7/ 7/98  Added Prodom database.
  10/ 8/98  Added Domo database.
  10/24/98  Added Pfam database.
  11/21/98  Remove all hard-coded directory names, assume execution is
	    from ~/bin
   3/12/99  Execute bin/blkprob -mast instead of bin/blksort 
   3/13/99  Expect parameter for blkprob
   3/24/99  Just search data-blplus/blocks.dat
   3/26/99  Detect & parse GET submissions. Output parameter for blkprob.
   4/ 4/99  Look for title for GET submissions.
   4/11/99  Changed from htmlize-blksort to htmlize-blkprob
   5/ 3/99  Don't require title with GET submissions.
   6/ 6/00  Changes for Blimps 3.4
   9/ 7/02  Don't write to log file (will still create log directory)
   5/ 3/03  Fundamental change to processing: Create .cs, .seq and .csh files;
		queue .csh and terminate if Mail_Flag; else execute .csh
   5/ 5/03  Stopped all logging (use the www log)
   3/ 2/04  Limit query sequence to 5000 chars (write_sequence()).
===========================================================================*/
#include 
#include 
#include 
#include  
#include 	/* for execlp */

typedef struct {
    char *name;
    char *val;
} entry;

/* from util.c */
char *makeword(char *line, char stop);
char *fmakeword(FILE *f, char stop, int *len);
char x2c(char *what);
void unescape_url(char *url);
void plustospace(char *str);
 
entry entries[10000];
 

/*  Assumes execution is from ~/bin directory */
#define HOME   ".."
#define BIN_SUBDIR   "."
#define DOCS_SUBDIR   "../docs"
#define TMP_SUBDIR   "../tmp"
#define LOG_SUBDIR   "../log"
#define BLOCKS_SUBDIR "../data-blocks"
#define PRINTS_SUBDIR "../data-prints"
#define PRODOM_SUBDIR "../data-prodom"
#define DOMO_SUBDIR "../data-domo"
#define PFAM_SUBDIR "../data-pfam"
#define PLUS_SUBDIR "../data-blplus"
#define MINUS_SUBDIR "../data-blplus-minus"
#define BLOCKS_EMAIL "blocks@fhcrc.org"
#define BTEST_EMAIL "btest@fhcrc.org"

char Expect[10], Output[10];				/* blksort parameters*/
char blimps[LARGE_BUFF_LENGTH];
char blksort[LARGE_BUFF_LENGTH];
char blkprob[LARGE_BUFF_LENGTH];
char mailprog[LARGE_BUFF_LENGTH];
char seq_file[LARGE_BUFF_LENGTH];
char cs_file[LARGE_BUFF_LENGTH];
char csh_file[LARGE_BUFF_LENGTH];
char log_dir[LARGE_BUFF_LENGTH];
char log_file[LARGE_BUFF_LENGTH];
char blimps_output[LARGE_BUFF_LENGTH];
char blksort_output[LARGE_BUFF_LENGTH];
char html_output[LARGE_BUFF_LENGTH];
char database[LARGE_BUFF_LENGTH];		/* database of blocks */
char printsbase[LARGE_BUFF_LENGTH];		/* Prints blocks db */
char plusbase[LARGE_BUFF_LENGTH];		/* Blocks+ blocks db */
char minusbase[LARGE_BUFF_LENGTH];		/* Blocks+ blocks db -biased */
char qij[LARGE_BUFF_LENGTH];			/* for pseudo counts */
char frq[LARGE_BUFF_LENGTH];			/* for amino counts */
char tmp_dir[LARGE_BUFF_LENGTH];
char mail_file[LARGE_BUFF_LENGTH];
char email_addr[LARGE_BUFF_LENGTH];
char buf[LARGE_BUFF_LENGTH];

int pid;

entry *Sequence_Ptr;
entry *Title_Ptr;
entry *Address_Ptr;

Boolean Blimps_Flag = FALSE;
Boolean Blksort_Flag = FALSE;
Boolean Blkprob_Flag = FALSE;
Boolean Mail_Flag = FALSE;
Boolean Prints_Flag = FALSE;
Boolean Prodom_Flag = FALSE;
Boolean Domo_Flag = FALSE;
Boolean Pfam_Flag = FALSE;
Boolean Minus_Flag = FALSE;
Boolean Post = FALSE;
 
/*
FILE *jgh;
*/

void read_startup_info()
{
  int i;
  char *script, *ptr;
  FILE *logdate, *curr_year_month;

  script = getenv("SCRIPT_NAME");

  ptr = getenv("BLOCKS_EMAIL");
  if (ptr != NULL) sprintf(email_addr, "%s", ptr);
  else             sprintf(email_addr, "%s", BLOCKS_EMAIL);

/*fprintf(jgh, "%s %s\n", ptr, email_addr);
*/

  pid = getpid();
  curr_year_month = popen("date '+\%y\%m'", "r");
  logdate = popen("date \"+\%y\%m\%d\"", "r");

  sprintf(blimps, "%s/blimps", BIN_SUBDIR);
  sprintf(blksort, "%s/blksort", BIN_SUBDIR);
  sprintf(blkprob, "%s/blkprob", BIN_SUBDIR);
/*
  sprintf(mailprog, "%s/Mail", BIN_SUBDIR);
*/
  sprintf(mailprog, "/usr/bin/mailx");
  sprintf(database, "%s/blocks.dat", BLOCKS_SUBDIR);
  sprintf(printsbase, "%s/prints.dat", PRINTS_SUBDIR);
  sprintf(plusbase, "%s/blocks.dat", PLUS_SUBDIR);
  sprintf(minusbase, "%s/blocks.dat", MINUS_SUBDIR);
  sprintf(qij, "%s/default.qij", DOCS_SUBDIR);
  sprintf(frq, "%s/default.amino.frq", DOCS_SUBDIR);
  sprintf(seq_file, "%s/%d.seq", TMP_SUBDIR, pid);
  sprintf(cs_file, "%s/%d.cs", TMP_SUBDIR, pid);
  sprintf(csh_file, "%s/%d.csh", TMP_SUBDIR, pid);
  fgets(buf, LARGE_BUFF_LENGTH, curr_year_month);
  remove_trailing_whitespace(buf);
  sprintf(log_dir, "%s/%s", LOG_SUBDIR, buf);
  fgets(buf, LARGE_BUFF_LENGTH, logdate);
  remove_trailing_whitespace(buf);
  sprintf(log_file, "%s/%s", log_dir, buf);
  sprintf(mail_file, "%s/%d.mail", TMP_SUBDIR, pid);
  sprintf(tmp_dir, "%s", TMP_SUBDIR);
  sprintf(blimps_output, "%s/%d.out", TMP_SUBDIR, pid);
  sprintf(blksort_output, "%s/%d.blk", TMP_SUBDIR, pid);
  sprintf(html_output, "%s/%d.html", TMP_SUBDIR, pid);

  pclose(curr_year_month);
  pclose(logdate);
}   /*  end of read_startup_info */


/*==================================================================
    Read the blocks_search.html form & parse the output.
    Also write the options to mail_file

	Form				Mail
	database=plus | minus | prints	#DB PLUS | MINUS | PRINTS
	ty=auto | AA | DNA		#TY AUTO | AA | DNA 
	st=0 | 1 | -1			#ST BOTH | FORWARD | REVERSE
	ge=0 to 16			#GE 0 to 16
	ou=all | sum | gff | old | raw	#OU ALL | SUM | GFF | OLD | RAW
					#FO TEXT | HTML
	ex=n				#EX n
	sequence=			#SQ
	
====================================================================*/
int parse_and_cs_setup()
{
/*
+Parsing and .cs setup
parse the input
  before start
    write the .cs error level
  while parsing
    write blimps flags to the .cs file
    set the email flag if there is an address, remember which entry it is in.
    set the pointer to the search title if it exists
    set the pointer to the sequence 
    set blimps and/or blksort output flags
  at end
    write the sequence and database names (need to read the database name 
      from somewhere rather than having it hard coded!).
    write the .cs terminator
*/
  int i, num_entries=0;
  char *query_string;
  FILE *csfp, *mailfp;
  int cl;
  char strands[80], gecode[80], histo[80], type[80];	/* Blimps parameters */

  strcpy(strands, "2");			/* Default blimps parameters */
  strcpy(type, "auto");
  strcpy(gecode, "0");
  strcpy(histo, "No");
  strcpy(Expect, "2");
  strcpy(Output, "-all");
  Blkprob_Flag = TRUE;
  Blimps_Flag = Blksort_Flag = FALSE;

  /* parse the query string into individual entries */
  /*  For Post, QUERY_STRING is null and CONTENT_LENGTH and
       CONTENT_TYPE are defined; input is from stdin */
  if (Post)
  {
     cl = atoi(getenv("CONTENT_LENGTH"));
     for(num_entries=0; cl && (!feof(stdin)); num_entries++) 
     {
       entries[num_entries].val = fmakeword(stdin,'&', &cl);
     }
   }   /* end of POST */

  /*  For Get, QUERY_STRING is defined and CONTENT_LENGTH and
       CONTENT_TYPE are null */
   else   /*  database=blocks-db&st=2&sequence=...   */
   {
      query_string = getenv("QUERY_STRING");
      cl = strlen(query_string);
      num_entries = 0;
      for (num_entries=0; query_string[0]; num_entries++)
      {
         entries[num_entries].val = makeword(query_string, '&');
      }
   }  /* end of GET */

   Sequence_Ptr = Title_Ptr = Address_Ptr = NULL;
   for (i=0; i< num_entries; i++)
   {
      plustospace(entries[i].val);
      unescape_url(entries[i].val);
      entries[i].name = makeword(entries[i].val,'=');

/*
fprintf(jgh, "%s %s\n", entries[i].name, entries[i].val);
*/

      if (!strncmp(entries[i].name, "sequence", 8)) 
      { Sequence_Ptr = &entries[i]; }
      else if (!strncmp(entries[i].name, "title", 5)) 
      { Title_Ptr = &entries[i]; }
      else if (!strncmp(entries[i].name, "address", 7)) 
      {
        Address_Ptr = &entries[i];
        if (strlen(entries[i].val) > 0) { Mail_Flag = TRUE; }
/*
fprintf(jgh,"Address_Ptr->val=%s\n", Address_Ptr->val);
*/
      }
      else if (!strncmp(entries[i].name, "database", 8)) 
      {
        if (!strncmp(entries[i].val, "prints", 9))
        { Prints_Flag = TRUE; }
        if (!strncmp(entries[i].val, "minus", 9))
        { Minus_Flag = TRUE; }
        else if (!strncmp(entries[i].val, "prodom", 9))
        { Prodom_Flag = TRUE; }
        else if (!strncmp(entries[i].val, "domo", 9))
        { Domo_Flag = TRUE; }
        else if (!strncmp(entries[i].val, "pfam", 9))
        { Pfam_Flag = TRUE; }
      }
      else if (!strncmp(entries[i].name, "bias", 4)) 
      { strcpy(Minus_Flag, entries[i].val); }
      else if (!strncmp(entries[i].name, "ty", 2)) 
      { strcpy(type, entries[i].val); }
      else if (!strncmp(entries[i].name, "st", 2)) 
      { strcpy(strands, entries[i].val); }
      else if (!strncmp(entries[i].name, "ge", 2)) 
      { strcpy(gecode, entries[i].val); }
      else if (!strncmp(entries[i].name, "hi", 2)) 
      { strcpy(histo, entries[i].val); }
      else if (!strncmp(entries[i].name, "ex", 2)) 
      { strcpy(Expect, entries[i].val); }
      else if (!strncmp(entries[i].name, "ou", 2)) 
      { 
         if (strcmp(entries[i].val, "old") == 0)
         { Blkprob_Flag = FALSE; Blksort_Flag = TRUE; }
         else if (strcmp(entries[i].val, "raw") == 0)
         { Blimps_Flag = TRUE; }
         else if (strcmp(entries[i].val, "sum") == 0)
         { strcpy(Output, "-sum"); }
         else if (strcmp(entries[i].val, "gff") == 0)
         { strcpy(Output, "-gff"); }
      }
  }  /* end of for i */


  /*----------------------------------------------------------------------*/
  /* Always create the cs file */
/*
ERror_level		2			-- only WARNINGs and higher
SQuence			$1.seq			-- the query sequence
DBase			mats.dat		-- the BLOCKS database
OUtput_file		$1.out			-- the output file
TYpe						-- force sequence type
STrands_to_search	2			-- if DNA, search both strands
FRequency file		../docs/default.amino.frq
REpeats_allowed		yes			-- repeats are allowed
NUmber_to_report	0			-- have blimps judge
COnversion_method	3			-- the conversion method
*/
  csfp = fopen(cs_file, "w");

  fprintf(csfp, "ERror_level          2\n");
  if (Prints_Flag) {fprintf(csfp, "DBase                %s\n", printsbase);}
  else if (Minus_Flag) {fprintf(csfp, "DBase                %s\n", minusbase);}
  else
  {
     fprintf(csfp, "DBase                %s\n", plusbase);
  }
  fprintf(csfp, "SQuence              %s\n", seq_file);
  fprintf(csfp, "OUtput_file          %s\n", blimps_output);
  fprintf(csfp, "TYpe                 %s\n", type);
  fprintf(csfp, "STrands_to_search    %s\n", strands);
  fprintf(csfp, "FRequency            %s\n", frq);
  fprintf(csfp, "GEnetic_code         %s\n", gecode);
  fprintf(csfp, "HIstogram            %s\n", histo);
  fprintf(csfp, "REpeats_allowed      yes\n");
  if (!Blksort_Flag) fprintf(csfp, "SV                   yes\n");
  fprintf(csfp, "NUmber_to_report     0\n");
  fprintf(csfp, "COnversion_method    3\n");
  fprintf(csfp, "OP alts: 5.0 %s :alts\n", qij);   /* pseudo counts */

  sprintf(buf, "chmod -f 660 %s", cs_file);	/* no general read */
  fclose(csfp);
  /* end of cs_file */

  return num_entries;
} /*  end of parse_and_cs_setup */


/*=========================================================================*/
void write_csh()
{
   FILE *cshp;

   cshp = fopen(csh_file, "w");

   fprintf(cshp, "\#\!/bin/csh\n");
   fprintf(cshp, "unalias mv\n");
   fprintf(cshp, "%s %s >& /dev/null\n", blimps, cs_file);
   if (Title_Ptr != NULL)
   {  sprintf(buf, "%s Block Search Results", Title_Ptr->val);   }
   else
   {  sprintf(buf, "Block Search Results");   }
   if (Blimps_Flag) 
   {		/* blimps output only */
       fprintf(cshp, "%s/htmlize-blimps.pl %s >& %s\n",
		 BIN_SUBDIR, blimps_output, html_output);
       if (Mail_Flag)
       {
          fprintf(cshp, "%s -r %s -s \"%s\" %s < %s\n",
              mailprog, email_addr, buf, Address_Ptr->val, blimps_output);
       }
   }
   else if (Blkprob_Flag) 
   {
       fprintf(cshp, "%s %s -mast -E %s %s >& %s\n", 
		blkprob, cs_file, Expect, Output, blksort_output);
       fprintf(cshp, "%s/htmlize-blkprob.pl %s >& %s\n",
                BIN_SUBDIR, blksort_output, html_output);
       if (Mail_Flag)
       {
          fprintf(cshp, "%s -r %s -s \"%s\" %s < %s\n",
              mailprog, email_addr, buf, Address_Ptr->val, blksort_output);
       }
   }
   else if (Blksort_Flag) 
   {
       fprintf(cshp, "%s %s >& %s\n", blksort, cs_file, blksort_output);
       fprintf(cshp, "%s/htmlize-blksort.pl %s >& %s\n",
               BIN_SUBDIR, blksort_output, html_output);
       if (Mail_Flag)
       {
          fprintf(cshp, "%s -r %s -s \"%s\" %s < %s\n",
              mailprog, email_addr, buf, Address_Ptr->val, blksort_output);
       }
   }
   fprintf(cshp, "exit\(0\)\n");
   fclose(cshp);
   sprintf(buf, "chmod a+x %s", csh_file);
   system(buf);

} /* end of write_csh

/*=========================================================================*/
void write_sequence()
{
  FILE *sfp;
  Boolean loop = TRUE;
  int tot, sum;

  if (Sequence_Ptr->val[0] == NULL) {
    printf("
      Search Error
      \n");
    printf("You need to enter a sequence to search with.
      \n");
    exit(0);
  }

  tot = strlen(Sequence_Ptr->val);
  if (tot > 5000)
  {
    printf("
      Search Error
      \n");
    printf("Your sequence has more than 5000 characters.
      \n");
    printf("Please break it into smaller pieces for searching.
      \n");
    exit(0);
  }

  sfp = fopen(seq_file, "w");
  /* Use title line for GET access, but should try to determine
                 if Sequence_Ptr->val includes a title first...  */
  if (!Post)
  {
     if (Title_Ptr != NULL)
     {  fprintf(sfp, ">%s\n", Title_Ptr->val);   }
     else
     {  fprintf(sfp, ">Unknown\n");   }
  }

  sum=0;

/*>>>>>		Why chop it up into 80 character lines? */
  while (sum < tot) {
    strncpy(buf, &Sequence_Ptr->val[sum], 80);
    sum = sum + strlen(buf);
/*    fprintf(sfp, "%s\n", buf); */
    fprintf(sfp, "%s", buf);
  }

  fprintf(sfp, "\n");
  fclose(sfp);
  sprintf(buf, "chmod -f 660 %s", seq_file);

}  /* end of write_sequence */


 

/*
+Run search
-
if submitted in the background, check the load level before running
  if have waited for more than half an hour?, then submit.
run blimps and keep track of where the output goes

if needed run blksort with the output of blimps 
-
*/
void run_search()
{
  FILE *dfp;
  char datein[LARGE_BUFF_LENGTH];
  char dateout[LARGE_BUFF_LENGTH];
  char db[10];
  
  dfp = popen("date", "r");
  remove_trailing_whitespace(fgets(datein, LARGE_BUFF_LENGTH, dfp));
  pclose(dfp);

  /*  Do the blimps search */
  sprintf(buf, "%s %s > /dev/null 2>&1", blimps, cs_file);
  if (system(buf) && !Mail_Flag)
  {
      printf("
      Blimps Error
      \n");
      printf("An error occured during the search:
      \n%s\n", buf);
      exit(0);
  }
  
  /* Post-process the blimps results */
  if (Blkprob_Flag) 
  {
    sprintf(buf, "%s %s -mast -E %s %s > %s 2>&1", 
		blkprob, cs_file, Expect, Output, blksort_output);
    if (system(buf) && !Mail_Flag)
    {
	printf("
      Blkprob Error
      \n");
        printf("An error occured during the search:
      \n%s\n", buf);
	exit(0);
    }
  }
  else if (Blksort_Flag) 
  {
    sprintf(buf, "%s %s > %s 2>&1", blksort, cs_file, blksort_output);
    if (system(buf) && !Mail_Flag)
    {
	printf("
      Blksort Error
      \n");
        printf("An error occured during the search:
      \n%s\n", buf);
	exit(0);
    }
  }

  dfp = popen("date", "r");
  remove_trailing_whitespace(fgets(dateout, LARGE_BUFF_LENGTH, dfp));
  pclose(dfp);

}  /*  end of run_search */


/*====================================================================
     Output is piped through the htmlize routines & then
     printed to stdout
======================================================================*/
void display_output()
{
  FILE *fp;

  if (Blimps_Flag) {		/* blimps output only */
    sprintf(buf, "%s/htmlize-blimps.pl %s", BIN_SUBDIR, blimps_output);
  }
  else if (Blkprob_Flag) {	/* new blkprob output  */
    sprintf(buf, "%s/htmlize-blkprob.pl %s", BIN_SUBDIR, blksort_output);
  }
  else if (Blksort_Flag) {	/* old blksort output */
    sprintf(buf, "%s/htmlize-blksort.pl %s", BIN_SUBDIR, blksort_output);
  }

  if (!(fp = popen(buf, "r"))) {
    printf("Error opening pipe\n");
  }

  while (!feof(fp) &&
	 fgets(buf, LARGE_BUFF_LENGTH, fp) != NULL) {
    printf(buf);
  }
  
  pclose(fp);

}  /* end of display_output */
/*====================================================================
     printed to stdout
======================================================================*/
void display_html()
{
  FILE *fp;

  if (!(fp = fopen(html_output, "r"))) {
    printf("blocks_search: Error opening %s\n", html_output);
  }

  while (!feof(fp) &&
	 fgets(buf, LARGE_BUFF_LENGTH, fp) != NULL) {
    printf(buf);
  }
  
  fclose(fp);

}  /* end of display_html */


/*=======================================================================*/
void main(int argc, char *argv[]) {


/*
jgh = fopen("jorja.out", "w");
*/

  printf("Content-type: text/html\n\n\n");
  printf("
      Blocks Search Results
      \n");

  if (strcmp(getenv("REQUEST_METHOD"),"POST") == 0 &&
      strcmp(getenv("CONTENT_TYPE"),"application/x-www-form-urlencoded") == 0)
	Post = TRUE;
  else  Post = FALSE;

  /*    Set file permissions to "rw-rw----"     */
  system("umask 006");

  read_startup_info();

  /*   Creates mail_file or cs_file */
  parse_and_cs_setup();

  /*   Creates seq_file  */
  write_sequence();

  /*  Creates csh_file */
  write_csh();

  printf("You can check this URL within 4 hours for \n");
  printf("your results.
      \n", pid);
/*
  printf("your results.
      \n", pid);
*/
  if (Mail_Flag)
  {
     printf("Your results will also be emailed to %s
      \n",
	Address_Ptr->val);
     printf("Queuing %d...", pid);
     sprintf(buf, "%s/add_queue_entry.pl BLOCKS_queue %s", 
       BIN_SUBDIR, csh_file);
     system(buf);
  }
  else
  {
/*
     printf("Searching...\n");
     fflush(stdout);
*/

     sprintf(buf, "%s", csh_file);
     system(buf);

     display_html();
/*
     run_search();
     display_output();
*/
  }



/*
  fclose(jgh);
*/
  exit(0);
}  /* end of main */
RUE; }
        if (!strncmp(entries[i].val, "minus", 9))
        { Mblimps-3.9/blimps/blpssm.c000064400001460000012000002041650774312247700161250ustar00jorjastaff00000400000027/*    blpssm.c  Make various pssms from blocks
         blpssm  

	 must contain:
	BL	blocks database to make PSSMs from (input)
	EX	PSSM database output file
	OU      observed frequencies output file
	FR	frequency file
        GR	substitution matrix for Gribskov ratios
	GQ	qij matrix for Gribskov
	DI	Dirichlet mixtures file for pseudo counts
  	AL	R qij matrix file for Altschul pseudo counts (AL = RC + AQ)
	AQ	qij matrix file for Altschul pseudo counts
	RC	R => tot. # pseudos = R * #residues 
	BC	B = total number of pseudos in a column
	ST	min max qij   Multiple entries for Steve's method
	CL	substitution matrix file for pseudo counts
	GI	make simple background pseudo counts like Gibbs does
        LO	use natural log scores (DI, CL or GI only)
	BR	get counts using Bill Bruno's method instead of seq wts
	HY	hybrid counts; nseq from Bruno, counts from seq wts
	HC	% hybrid counts; nseq from % clumping, counts from seq wts
	NN	YES => set all real counts to zero
	PA	min_score  pattern_output_file
	FP	Output matrix in floating point format

	If DI or CL, must have FR
	If just FR, makes usual PATMAT PSSM
>>> should change struct dirichlet to use struct diri in blimps convert.h <<<
--------------------------------------------------------------------
 6/30/94 J. Henikoff 
 7/ 2/94 Added log option for make_diri()
 7/ 4/94 Changed log calculations to make a positive PSSM by
         subtracting the min. log value for the entire matrix
         from every entry in the matrix, rather than doing each
         position separately.
 7/ 7/94 Changed load_subst() to make matrix non-neg. if nec.
         Added make_clav()  CL option
 7/11/94 Added make_gribs() GR option
 8/10/94 Added make_gibbs()  GI option, simple pseudo counts like Gibbs
         Cleaned up code
         Changed from 0,AASALL to 1,AAS for all but make_gribs()
 8/18/94 Added load_qij()
 8/29/94 Added make_gribq() GQ option - doesn't work, scaling problem
 8/31/94 Added counts_bruno() BR option.
 9/ 4/94 Multiply final matrices to give score range b/w 0 and 99 (final).
 9/ 7/94 Make sure multiplying by a number >= 1.0.
 9/15/94 Added counts_hybrid() HY option.
	 Added counts_clumps() HC option.
 9/26/94 Added Steve's elaboration of Altschul's method
10/31/94 Changed make_matrix() to add seqs= to matrix->ma if not in block
-------------------Added to /howard/local/bin----------------------------
12/ 7/94 Also outputs the observed frequencies, with pseudo counts.
 1/16/95 Changed pseudo-count count from sqrt(n) to 1/n for GI & AL
 1/18/95 Changed pseudo-count count from 1/n to column entropy for GI & AL,
         added compute_entropy()
	 Changed pseudo-count count from entropy to #residues for GI & AL,
         added count_residues()
 1/28/95 Modified Steve's method; use a different substitution matrix
         for every column of a block, not just for every block.
	 Added ratio_counts(), make_steves()
 1/30/95 Fixed problem with too many FILEs in make_steves(). 
	 NOTE: This routine is currently very inefficient, reads qij
         file over for each column!
 2/ 8/95 Changed pseudo_count count from #residues to RTot * # residues for
	 GI, AL, ST
 2/ 8/95 Changed pseudo_alts() to use unweighted counts for pseudo
         counts (not sequence-weighted). Counts are still seq-wted
	 Modified struct working, counts(), pseudo_alts().
 2/15/95 Changed pseudo_alts() back to use weighted counts.
 2/19/95 Made RTot a parameter on the AL option
 2/19/95 Added bruno_rind() & changed counts_bruno() to use Bruno's
         new rind program.
 2/26/95 Initialized col stuff in counts_bruno().
 3/20/95 Changed default RTOT from 1.0 to 5.0; applies to make_gibbs() also.
 3/30/95 Changed make_gibbs() back to use sqrt(N).
         Changed make_gribs() to rescale between 0 and 99; added positive_matrix()
 4/ 6/95 Added free_block() & also freed other data structures.
 4/ 8/95 Changed all counting routines so B->D, Z->E and only the 20
         real aas are counted. Therefore, column counts may not add to
	 the number of sequences if a column contains "-" or "X".
 4/12/95 Changed Gribskov to score B,Z,X,- & * like the other methods.
 5/28/95 Added PA option, PA lines to PSSM
 6/29/95 Write PA lines to a separate file
 7/ 7/95 Fixed problem in add_patterns() when only one pattern.
 7/12/95 Fixed problem in make_col() initialization.
 8/30/95 Added AQ, RC, BC and NN parameters (AL = RC + AQ)
	 Added BTot variable = total # pseudos in a column
 9/11/95 Changed GQ, make_gribq() to use log-odds 
10/ 2/95 Changed strnicmp() to strncasecmp()
 4/24/96 Initialized matrix->patterns in make_matrix() - caused abort with
	 prints.cf input file.
 7/ 4/96 Updated Bruno counts for new version of rind program.
 9/19/96 Added option for floating point output (FP, FloatPt);
	 matrices aren't re-scaled at all in this case.
 11/25/97 Increased MAXWIDTH from 60 to 200 for Bork's groups
  5/26/00 Modified to use BLIMPS libraries; MAXWIDTH to 400
 12/23/00 MAXWIDTH replaced by EXTRA_LARGE_BUFF, MAXNSEQ to 1000
====================================================================*/

#define BLPSSM_C_
#define EXTERN

#include 
#include 

#define FNAMELEN 80
#define AAS 21
#define AASALL 26
/* 0- 1A 2R 3N 4D 5C 6Q 7E 8G 9H 10I 11L 12K 13M 14F 15P 16S 17T 18W 19Y
   20V 21B 22Z 23X 24* 25J,O,U */
#define MAXCOMP 40			/* Max. # of Dirichlet components */
#define MAXNSEQ 1000			/* Max. # seqs in a block */
#define MAXMAT 10			/* Max. #matrices for Steve's method*/
#define PATCUT 90			/* Default pattern cutoff score */
#define RTOT 5.0			/* Total #pseudos in col  = RTOT * R*/
#define BTOT 25.0			/* Total # pseudos in col */
#define PI 3.141592654
/*   INDEX & INDEXCOL compute the sequential indices for the lower half of an
     nxn symmetric matrix given row & column coordinates.  Lower half has
     n(n-1)/2 entries; col=0,n-2 and row=col+1,n-1; col has n-col-1 rows.
     Index runs from 0 to n(n-1)/2 - 1 down columns with
     (index=0)==(col=0,row=1) and (index=n(n-1)/2-1)==(col=n-2,row=n-1).  */
#define INDEXCOL(n, col)    ( col*n - (col*(col+1))/2 )
#define INDEX(n, col, row)  ( col*n - (col*(col+3))/2 - 1 + row )

struct dirichlet {	/* Dirichlet mixture information */
   int ncomp;		/* number of components */
   double q[MAXCOMP];
   double altot[MAXCOMP];
   double alpha[MAXCOMP][AAS];
};

struct clump_work {
   int cluster[MAXNSEQ], ncluster[MAXNSEQ], nclus[MAXNSEQ];
};

struct working {	/* Working information for one column */
   double cnt[AASALL];		/* Sequence-weighted counts */
   double totcnt;
   double raw[AASALL];		/* unweighted counts */
   double totraw;
   double probn[MAXCOMP];
   double probj[MAXCOMP];
   double reg[AASALL];		/*  pseudo counts */
   double totreg;
};

struct work_pssm {		/* Working PSSM area */
   double value[EXTRA_LARGE_BUFF][AASALL];
   double sum[EXTRA_LARGE_BUFF];
};

struct steve {
   double nmin, nmax;		/* min & max diag/off-diag ratio for col */
   char qijname[FNAMELEN];
};

int read_cf();
void load_subst();
struct dirichlet *load_diric();
double nrgamma();
double addlogs();
struct working *make_col();
struct work_pssm *make_pssm();
Matrix *make_matrix();
Matrix *make_diri();
Matrix *make_grib();
Matrix *make_gribq();
Matrix *make_clav();
Matrix *make_alts();
Matrix *make_patmat();
Matrix *make_gibbs();
Matrix *make_steves();
FILE *steves_qij();
void counts();
void counts_hybrid();
void counts_clumps();
int clump_seqs();
void pseudo_diric();
void pseudo_clav();
void pseudo_alts();
void pseudo_gibbs();
double compute_entropy();
int count_residues();
double ratio_counts();
void fillin();
void final();
void compute_BZX();
void positive_matrix();
void add_patterns();
/*     Bill Bruno's rind program   */
struct work_pssm *bruno_rind();
void counts_bruno();

/*-------------global variables ----------------------------------------*/
FILE *Fbl, *Fex, *Fou, *Ffr, *Fal, *Fdi, *Fcl, *Fgr, *Fgq;  /* files */
FILE *Fpa;
int LogScores;				/* take natural log of scores */
struct steve *Steve[MAXMAT];			/* Steve's parameters */
int BrunoCounts;			/* use Bill Bruno's counts */
int HybridCounts;			/* use hybrid counts */
int ClumpCounts;			/* use hybrid clump counts */
int NoCounts;				/* don't use actual counts */
int FloatPt;				/* floating point output */
int ClumpTot;				/* # of clumps in block */
int PatternCutoff;			/* pattern cutoff score */
double RTot;				/* B_c = RTot * # residues */
double BTot;				/* B_c = BTot = Total pseudos */
/*    Dirichlet stuff */
double LCof = 2.50662827465;	/* sqrt(2*PI)  */
double Cof[6] = {76.18009173, -86.50532033, 24.01409822, -1.231739516,
                  0.120858003e-2, -0.536382e-5};
double Log2;
/*     Bruno stuff */
/*   blimps[aa] == bruno[ Bruno_Order[aa] ]     */
int Bruno_Order[AASALL] = {1, 21, 5, 4, 7, 14, 8, 9, 10, 23, 12, 11, 13,
        3, 23, 15, 6, 2, 16, 17, 23, 20, 18, 23, 19, 22};

/*=====================================================================
 * main
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
   FILE *cfp;
   Block *block;
   int type;
   char cfname[FNAMELEN];
   double freqs[AASALL], subst[AASALL][AASALL];
   struct float_qij *qij;
   struct dirichlet *diric;
   Matrix *matrix, *obs_freqs;

   Log2 = log(2.0);
/* ------------1st arg = configuration file ----------------------------*/
   if (argc > 1)
      strcpy(cfname, argv[1]);
   else
   {
      printf("\nEnter name of configuration file: ");
      gets(cfname);
   }
   if ( (cfp=fopen(cfname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", cfname);
      exit(-1);
   }
   type = read_cf(cfp);
   if (type <= 0)
   {
      printf("\nConfiguration file errors\n");
      exit(-1);
   }
   else
   {
      switch(type)
      {
         case 1:
            printf("Using PATMAT algorithm...\n");
            break;
        case 2:		/* Gribskov profile */
           printf("Using Gribskov algorithm...\n");
           break;
        case 3:		/* Altschul's pseudo-counts */
           printf("Using Altschul's pseudo-counts...\n");
           break;
        case 4:		/* Claverie's pseudo-counts */
	   printf("Using Claverie pseudo-counts...\n");
           break;
        case 5:		/* Dirichlet pseudo-counts */
           printf("Using Dirichlet pseudo-counts\n");
           break;
        case 6:		/* simple background pseudo-counts */
           printf("Using background pseudo-counts (like Gibbs)\n");
           break;
        case 7:		/* Gribskov profile with qij */
           printf("Using Gribskov algorithm with qij...\n");
           break;
 	case 8:		/* Steve's method */
	   printf("Using Steve's method...\n");
	   printf("WARNING: Parameters are not checked for validity!\n");
           break;
        default:
           break;
      }
   }

/*----------------------------------------------------------------------*/
  if (Ffr != NULL) load_frequencies(Ffr, freqs);
  if (type == 2) load_subst(Fgr, subst);
  if (type == 3) qij = load_qij(Fal);
  if (type == 4) load_subst(Fcl, subst);
  if (type == 5) diric = load_diric(Fdi);
  if (type == 7) qij = load_qij(Fgq);

  while ((block = read_a_block(Fbl)) != NULL)
  {
     normalize(block);
     if (ClumpCounts) ClumpTot = clump_seqs(block);
     if (Fou != NULL) obs_freqs = make_matrix(block);
     switch (type)
     {
        case 1:		/* Patmat odds ratios */
           matrix = make_patmat(block, freqs, obs_freqs);
           break;
        case 2:		/* Gribskov profile */
           matrix = make_grib(block, subst, obs_freqs);
           break;
        case 3:		/* Altschul's pseudo-counts */
           matrix = make_alts(block, freqs, qij, obs_freqs); 
           break;
        case 4:		/* Claverie's pseudo-counts */
           matrix = make_clav(block, freqs, subst, obs_freqs);
           break;
        case 5:		/* Dirichlet pseudo-counts */
           matrix = make_diri(block, freqs, diric, obs_freqs);
           break;
        case 6:		/* simple background pseudo-counts */
           matrix = make_gibbs(block, freqs, obs_freqs);
           break;
        case 7:		/* Gribskov profile with qij */
           matrix = make_gribq(block, qij, obs_freqs);
           break;
	case 8:		/* Steve's method */
	   matrix = make_steves(block, freqs, obs_freqs);
	   break;
        default:
           break;
     }
     if (matrix != NULL)
     {
        if (!FloatPt) output_matrix(matrix, Fex);
        else          output_matrix_s(matrix, Fex, 1); /* FLOAT_OUTPUT == 1 */
        if (PatternCutoff && Fpa != NULL)  add_patterns(matrix, Fpa);
        free_matrix(matrix);
     }
     if (obs_freqs != NULL)
     {
        output_matrix(obs_freqs, Fou);
        free_matrix(obs_freqs);
     }
     free_block(block);
  }
   
  fclose(Fbl); fclose(Fex);
  if (Fpa != NULL) fclose(Fpa);
  if (Fou != NULL) fclose(Fou);
  exit(0);

}  /* end of main */
/*=======================================================================*/
int read_cf(cfp)
FILE *cfp;
{
   int type, gibbs, nsteve;
   char line[MAXLINE], keyword[20], *ptr;
   char blname[FNAMELEN], exname[FNAMELEN], frname[FNAMELEN];
   char alname[FNAMELEN], diname[FNAMELEN], clname[FNAMELEN];
   char grname[FNAMELEN], gqname[FNAMELEN], ouname[FNAMELEN];
   char paname[FNAMELEN];

   type = 0;
   gibbs = FALSE;
   Fbl = Fex = Fpa = Fou = Ffr = Fal = Fdi = Fcl = Fgr = Fgq = NULL;
   for (nsteve = 0; nsteve < MAXMAT; nsteve++) Steve[nsteve] = NULL;
   nsteve = 0;
   BTot = RTot = -1;
   LogScores = BrunoCounts = HybridCounts = ClumpCounts = NoCounts = FALSE;
   FloatPt = FALSE;
   PatternCutoff = 0;
   while (!feof(cfp) && fgets(line, MAXLINE, cfp) != NULL)
   {
      ptr = strtok(line, " \t\r\n");
      if (ptr != NULL && ptr[0] != ';')
      {
         strcpy(keyword,ptr);
         ptr = strtok(NULL, " \t\r\n;");
         if (ptr != NULL)
         {
            if (strncasecmp(keyword, "BL", 2) == 0)
            {
               strcpy(blname, ptr);
               if ( (Fbl = fopen(blname, "r")) == NULL)
                  printf("\nCannot open BL file %s\n", blname);
            }
            else if (strncasecmp(keyword, "EX", 2) == 0)
            {
               strcpy(exname, ptr);
               if ( (Fex = fopen(exname, "w")) == NULL)
                  printf("\nCannot open EX file %s\n", exname);
            }
            else if (strncasecmp(keyword, "OU", 2) == 0)
            {
               strcpy(ouname, ptr);
               if ( (Fou = fopen(ouname, "w")) == NULL)
                  printf("\nCannot open OU file %s\n", ouname);
            }
            else if (strncasecmp(keyword, "FR", 2) == 0)
            {
               strcpy(frname, ptr);
               if ( (Ffr = fopen(frname, "r")) == NULL)
                  printf("\nCannot open FR file %s\n", frname);
            }
            else if (strncasecmp(keyword, "AL", 2) == 0)
            {
               RTot = atof(ptr);
	       if (RTot < 0.0) RTot = RTOT;
	       ptr = strtok(NULL, " \t\r\n");
               strcpy(alname, ptr);
               if ( (Fal = fopen(alname, "r")) == NULL)
                  printf("\nCannot open AL file %s\n", alname);
            }
            else if (strncasecmp(keyword, "RC", 2) == 0)
            {
               RTot = atof(ptr);
	       if (RTot < 0.0) RTot = RTOT;
            }
            else if (strncasecmp(keyword, "BC", 2) == 0)
            {
               BTot = atof(ptr);
	       if (BTot < 0.0) BTot = BTOT;
            }
            else if (strncasecmp(keyword, "AQ", 2) == 0)
            {
               strcpy(alname, ptr);
               if ( (Fal = fopen(alname, "r")) == NULL)
                  printf("\nCannot open AQ file %s\n", alname);
            }
            else if (strncasecmp(keyword, "ST", 2) == 0)
            {
               if (Steve[nsteve] == NULL)
	   Steve[nsteve] = (struct steve *) malloc(sizeof(struct steve));
	       if (Steve[nsteve] == NULL)
               {
                   printf("\nread_cf: OUT OF MEMORY\n");
                   exit(-1);
               }
               Steve[nsteve]->nmin = atof(ptr);
               ptr = strtok(NULL, " \t\r\n");
               Steve[nsteve]->nmax = atof(ptr);
               ptr = strtok(NULL, " \t\r\n");
	       strcpy(Steve[nsteve]->qijname, ptr);
               nsteve++;
            }
            else if (strncasecmp(keyword, "GR", 2) == 0)
            {
               strcpy(grname, ptr);
               if ( (Fgr = fopen(grname, "r")) == NULL)
                  printf("\nCannot open GR file %s\n", grname);
            }
            else if (strncasecmp(keyword, "GQ", 2) == 0)
            {
               strcpy(gqname, ptr);
               if ( (Fgq = fopen(gqname, "r")) == NULL)
                  printf("\nCannot open GQ file %s\n", gqname);
            }
            else if (strncasecmp(keyword, "DI", 2) == 0)
            {
               strcpy(diname, ptr);
               if ( (Fdi = fopen(diname, "r")) == NULL)
                  printf("\nCannot open DI file %s\n", diname);
            }
            else if (strncasecmp(keyword, "CL", 2) == 0)
            {
               strcpy(clname, ptr);
               if ( (Fcl = fopen(clname, "r")) == NULL)
                  printf("\nCannot open CL file %s\n", clname);
            }
            else if (strncasecmp(keyword, "LO", 2) == 0)
            {
                if (ptr[0] == 'y' || ptr[0] == 'Y' ||
                    ptr[0] == 't' || ptr[0] == 'T')
		LogScores = TRUE;
            }
            else if (strncasecmp(keyword, "BR", 2) == 0)
            {
                if (ptr[0] == 'y' || ptr[0] == 'Y' ||
                    ptr[0] == 't' || ptr[0] == 'T')
		BrunoCounts = TRUE;
            }
            else if (strncasecmp(keyword, "HY", 2) == 0)
            {
                if (ptr[0] == 'y' || ptr[0] == 'Y' ||
                    ptr[0] == 't' || ptr[0] == 'T')
		HybridCounts = TRUE;
            }
            else if (strncasecmp(keyword, "NN", 2) == 0)
            {
                if (ptr[0] == 'y' || ptr[0] == 'Y' ||
                    ptr[0] == 't' || ptr[0] == 'T')
		NoCounts = TRUE;
            }
            else if (strncasecmp(keyword, "FP", 2) == 0)
            {
                if (ptr[0] == 'y' || ptr[0] == 'Y' ||
                    ptr[0] == 't' || ptr[0] == 'T')
		FloatPt = TRUE;
            }
            else if (strncasecmp(keyword, "HC", 2) == 0)
            {
		ClumpCounts = atoi(ptr);
		if (ClumpCounts < 0 || ClumpCounts > 100) ClumpCounts = 0;
            }
            else if (strncasecmp(keyword, "GI", 2) == 0)
            {
               gibbs = TRUE;
            }
            else if (strncasecmp(keyword, "PA", 2) == 0)
            {
		PatternCutoff = atoi(ptr);
		if (PatternCutoff < 0 || PatternCutoff > 100)
			 PatternCutoff = PATCUT;
	        ptr = strtok(NULL, " \t\r\n");
                strcpy(paname, ptr);
                if ( (Fpa = fopen(paname, "w")) == NULL)
                  printf("\nCannot open PA file %s\n", paname);
            }
         }   /* end of if ptr */
      }  /* end of if ptr */
   }  /* end of cfp */
   /*   Set PSSM type:  1 is Patmat (FR)
                        2 is Gribskov (GR)
                        3 is Altschul pseudo counts (FR & AL)
                        4 is Claverie pseudo counts (FR & CL)     
                        5 is Dirichlet pseudo counts (FR & DI) 
                        6 is Gibbs pseudo counts (FR) 
			7 is Gribskov with qij (GQ)
			8 is Steve's (ST)
   */
   /*    Can only have one type of total pseudo counts */
   if (RTot > 0 && BTot > 0)  BTot = -1;
   type = 0;
   /* If only have FR; PSSM type = 1 */
   if (Ffr != NULL && Fdi == NULL && Fal == NULL && Fcl == NULL && 
       Fgr == NULL && Fgq == NULL)
       type = 1;
   /*  Steve's method is type 8 */
   if (Ffr != NULL && Steve[0] != NULL && nsteve >= 1)
   {
      type = 8;
      if (Fdi != NULL) fclose(Fdi);
      if (Fcl != NULL) fclose(Fcl);
      if (Fal != NULL) fclose(Fal);
      if (Fgr != NULL) fclose(Fgr);
   }
   /* If have GR, ignore DI and FR and CL; PSSM type = 2 */
   if (Fgr != NULL)
   {
      type = 2;
      if (Fdi != NULL) fclose(Fdi);
      if (Fcl != NULL) fclose(Fcl);
      if (Fal != NULL) fclose(Fal);
      if (Ffr != NULL) fclose(Ffr);
   }
   /* If have GQ,  PSSM type = 7 */
   if (Fgq != NULL)
   {
      type = 7;
      if (Fdi != NULL) fclose(Fdi);
      if (Fcl != NULL) fclose(Fcl);
      if (Fal != NULL) fclose(Fal);
      if (Ffr != NULL) fclose(Ffr);
   }
   /* If have AL, ignore DI and FR and CL; PSSM type = 3 */
   if (Fal != NULL && Ffr != NULL)
   {
      type = 3;
      if (Fdi != NULL) fclose(Fdi);
      if (Fcl != NULL) fclose(Fcl);
      if (Fgr != NULL) fclose(Fgr);
   }
   /* If have CL, ignore the rest */
   if (Fcl != NULL && Ffr != NULL)
   {
      type = 4;
      if (Fal != NULL) fclose(Fal);
      if (Fdi != NULL) fclose(Fdi);
      if (Fgr != NULL) fclose(Fgr);
   }
   /* If have DI, ignore the rest */
   if (Fdi != NULL && Ffr != NULL)
   {
      type = 5;
      if (Fal != NULL) fclose(Fal);
      if (Fcl != NULL) fclose(Fcl);
      if (Fgr != NULL) fclose(Fgr);
   }
   /*  If have FR and GI, type = 6 */
   if (type == 1 && gibbs) type = 6;

   if (type == 0)
      printf("\nNo valid PSSM type specified\n");
   /* Must always have BL and EX */
   if (Fbl == NULL)
   {
      printf("\nMissing BL (input block) file\n");
      type = 0;
   }
   if (Fex == NULL)
   {
      printf("\nMissing EX (output PSSM) file\n");
      type = 0;
   }

   return(type);
}  /* end of read_cf */
/*======================================================================
=======================================================================*/
FILE *steves_qij(col)
struct working *col;
{
   FILE *fst;
   int i;
   char fname[FNAMELEN];
   double ratio;

   ratio = ratio_counts(col);
   fst = NULL;
   fname[0] = '\0';
   i = 0;
   while (!strlen(fname) && Steve[i] != NULL && i < MAXMAT)
   {
      if (ratio >= Steve[i]->nmin &&
          ratio < Steve[i]->nmax)
             strcpy(fname, Steve[i]->qijname);
      i++;
   }
   if ( (fst=fopen(fname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", fname);
      exit(-1);
   }

   return(fst);
}  /* end of steves_qij */
/*======================================================================
   Dirichlet input file order (0-19) is  ARNDCQEGHILKMFPSTWYV
   Blimps order (0-24) is               -ARNDCQEGHILKMFPSTWYVBZX*
   Store Dirichlet alphas in positions 1-20 to match blimps
=======================================================================*/
struct dirichlet *load_diric(fin)
FILE *fin;
{
   int aa, numc, type;
   char line[MAXLINE], *ptr;
   struct dirichlet *diric;

   diric = (struct dirichlet *) malloc(sizeof(struct dirichlet));
   if (diric == NULL)
   {
      printf("\nOUT OF MEMORY\n");
      exit(-1);
   }
   numc = 0;
   while (numc < MAXCOMP && !feof(fin) && fgets(line, MAXLINE, fin) != NULL)
   {
      type = 0;
      if (strstr(line, "Mixture=") != NULL) type = 1;
      if (strstr(line, "Alpha=") != NULL)  type = 2;
      if (type > 0)
      {
         ptr = strtok(line, "="); ptr = strtok(NULL, "\t\n\r ");
         switch (type)
         {
	    case 1:
               diric->q[numc] = atof(ptr);
               break;
            case 2:
               diric->altot[numc] = atof(ptr);
               aa = 1;
               while (aa < AAS && ptr != NULL)
               {
                  ptr = strtok(NULL, "\t\n\r ");
                  diric->alpha[numc][aa++] = atof(ptr);
               }
               numc++;
               break;
            default:
               break;
         }
      }
   }  /* end of while */
   diric->ncomp = numc;

   fclose(fin);
   return(diric);
}   /* end of load_diric */
/*===================================================================
    Returns log of gamma using Lanczos' approximation.
    Taken from "Numerical Recipes in C".
    NOTE:  Alternative to Sun's lgamma() function

    gamma(x) = integral(0,infinity) y^(x-1) * e^(-y) dy
      gamma(0.5) = sqrt(pi)
      gamma(1) = gamma(2) = 1
      gamma(x) = (x-1) * gamma(x-1), x > 2
      If x is an integer, gamma(x) = (x-1)!
      gamma(1-x) = (pi * x)/{gamma(1+x) * sine(pi * x)}
===================================================================*/
double nrgamma(x)
double x;
{
   double xx, dtemp, dtemp2, lg, g;
   int j;

   if (x <= 0.0) lg = 0.0;
   else if (x < 1.0)   		/*  use the reflection formula */
   {
     dtemp = PI * (1.0 - x);
     dtemp2 = sin(dtemp);
     lg = log(dtemp) - nrgamma(2.0 - x) - log(dtemp2);
   }
   else
   {

      xx = x - 1.0;
      dtemp = xx + 5.5;
      dtemp -= (xx + 0.5) * log(dtemp);
      dtemp2 = 1.0;
      for (j=0; j <= 5; j++)
      {
          xx += 1.0;
          dtemp2 += Cof[j] / xx;
      }
      lg = -dtemp + log(LCof * dtemp2);
      if (lg <= 50) g = exp(lg);		/* overflows quickly */
      else g = 1e50;
   }

   return(lg);
}  /* end of nrgamma */
/*======================================================================*/
Matrix *make_patmat(block, freqs, obs_freqs)
Block *block;
double *freqs;
Matrix *obs_freqs;
{
   double dtemp, sum, temp[AASALL];
   int pos, aa;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *bruno;

   col = make_col();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;

   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);

      sum = 0.0;
      for (aa=1; aa < AAS; aa++)
      {
         if (obs_freqs != NULL)
         {
	    dtemp = 100. * col->cnt[aa] / col->totcnt;
	    obs_freqs->weights[aa][pos] = round(dtemp);
         }
          if (freqs[aa] > 0.0)
             temp[aa] = col->cnt[aa] / freqs[aa];
          else temp[aa] = 0.0;
          sum += temp[aa];
      }
      for (aa=1; aa < AAS; aa++)
      {
         dtemp = 99.0 * temp[aa] / sum;
         matrix->weights[aa][pos] = round(dtemp);
      }
      compute_BZX(freqs, matrix, pos);
   }  /*  end of for pos */

   free(col);
   if (bruno != NULL) free(bruno);
   return(matrix);

}  /* end of make_patmat */

/*==========================================================================
NOTE:  This is essentially the same as make_gribs() in convert.c
     Uses Gribskov's method 
     Assumes a non-negative substition matrix (min. value = 0)
     Sets 20 aas plus B and Z from the matrix; X, etc to zero = min. value
     Index for B is 21, for Z is 22
===========================================================================*/
Matrix *make_grib(block, subst, obs_freqs)
Block *block;
double subst[AASALL][AASALL];
Matrix *obs_freqs;
{
   double dtemp, sum, temp[AASALL];
   int pos, aa, aa1;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *bruno;

   col = make_col();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;

   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);

      sum = 0.0;
      for (aa=0; aa <= 22; aa++)
      {
         if (obs_freqs != NULL)
         {
	    dtemp = 100. * col->cnt[aa] / col->totcnt;
	    obs_freqs->weights[aa][pos] = round(dtemp);
         }
         temp[aa] = 0.0;
         for (aa1=1; aa1 <= 22 ; aa1++)
         {
            temp[aa] += col->cnt[aa1] * subst[aa][aa1];
         }
         temp[aa] /= col->totcnt;
         sum += temp[aa];
      }
      for (aa=1; aa <= 22; aa++)
      {
         dtemp = temp[aa];
         matrix->weights[aa][pos] = round(dtemp);
      }
      /*  Set X, * and - to zero */
      matrix->weights[0][pos] = matrix->weights[23][pos] = 0;
      matrix->weights[24][pos] = matrix->weights[25][pos] = 0;
   }  /*  end of for pos */

   free(col);
   if (bruno != NULL) free(bruno);
   /*  scale final matrix to lie between 0 and 99 */
   positive_matrix(block, matrix);
   return(matrix);
}   /*  end of make_grib */
/*==========================================================================
     Uses Gribskov's method with log(qij/pipj) instead of sij
     NOTE: no BZX values
===========================================================================*/
Matrix *make_gribq(block, qij, obs_freqs)
Block *block;
struct float_qij *qij;
Matrix *obs_freqs;
{
   double dtemp, sum, temp[AASALL];
   int pos, aa, aa1, minval;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *bruno;

   col = make_col();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;

   minval = 99999;			/* min. val in matrix  */
   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);

      sum = 0.0;
      for (aa=1; aa <= 20; aa++)
      {
         if (obs_freqs != NULL)
         {
	    dtemp = 100. * col->cnt[aa] / col->totcnt;
	    obs_freqs->weights[aa][pos] = round(dtemp);
         }
         temp[aa] = 0.0;
         for (aa1=1; aa1 <= 20 ; aa1++)
         {
            dtemp = qij->value[aa][aa1] / (qij->marg[aa] * qij->marg[aa1]);
            dtemp = log(dtemp) / log(2.0);	/* sij scaled in bits */
            temp[aa] += col->cnt[aa1] * dtemp;
         }
         temp[aa] /= col->totcnt;
         sum += temp[aa];
      }
      for (aa=1; aa <= 20; aa++)
      {
         dtemp = 100.0 * temp[aa];	/* beef up weights for scaling */
         matrix->weights[aa][pos] = round(dtemp);  /* weights are ints */
	 if (matrix->weights[aa][pos] < minval)
		minval = matrix->weights[aa][pos];
      }
   }  /*  end of for pos */

   /*  Set B, Z, X, * and - to min. value */
   for (pos = 0; pos < block->width; pos++)
   {
      matrix->weights[0][pos] = matrix->weights[23][pos] = minval;
      matrix->weights[24][pos] = matrix->weights[25][pos] = minval;
      matrix->weights[21][pos] = matrix->weights[22][pos] = minval;
   }

   free(col);
   if (bruno != NULL) free(bruno);
   /*  scale final matrix to lie between 0 and 99 */
   positive_matrix(block, matrix);
   return(matrix);
}   /*  end of make_gribq */
/*==========================================================================
     Uses Altschul's method of getting pseudo-counts with a qij matrix,
===========================================================================*/
Matrix *make_alts(block, freqs, qij, obs_freqs)
Block *block;
double *freqs;
struct float_qij *qij;
Matrix *obs_freqs;
{
   double epsilon;
   int pos;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *pssm, *bruno;

   col = make_col();
   pssm = make_pssm();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;

   /*--------------  Do one position at a time -------------------*/
   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);
/*      epsilon = sqrt(col->totcnt); 
      epsilon = 1.0 / col->totcnt;
      epsilon += compute_entropy(col); 
*/
      /*    epsilon = total number of pseudo counts in the column   */
      if (RTot >= 0.0) epsilon = (double) RTot * count_residues(col);
      else if (BTot >= 0.0) epsilon = BTot;
      else epsilon = sqrt(col->totcnt);

      /*---------- get the pseudo counts -------------------------------*/
      pseudo_alts(col, qij, epsilon);

      /*---------   Fill in the matrix entries --------------------*/
      fillin(pos, freqs, col, pssm, obs_freqs);

   }  /*  end of for pos */
   /*------ Now make the final scores; make log scores non-neg    */
   /*       by subtracting the min. value for all positions ----- */
   final(block, freqs, pssm, matrix);

   free(col);
   free(pssm);
   if (bruno != NULL) free(bruno);
   return(matrix);
}  /* end of make_alts */
/*==========================================================================
     Uses Steve's modification of
         Altschul's method of getting pseudo-counts with a qij matrix,
         different matrix for each column.
===========================================================================*/
Matrix *make_steves(block, freqs, obs_freqs)
Block *block;
double *freqs;
Matrix *obs_freqs;
{
   double epsilon;
   int pos;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *pssm, *bruno;
   struct float_qij *qij;
   FILE *fin;

   col = make_col();
   pssm = make_pssm();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;
   qij = NULL;
   fin = NULL;

   /*--------------  Do one position at a time -------------------*/
   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);
      if (RTot >= 0.0) epsilon = (double) RTot * count_residues(col);
      else if (BTot >= 0.0) epsilon = BTot;
      else epsilon = sqrt(col->totcnt);
      if (qij != NULL) free(qij);
      fin = steves_qij(col);
      qij = load_qij(fin);
      fclose(fin);

      /*---------- get the pseudo counts -------------------------------*/
      pseudo_alts(col, qij, epsilon);

      /*---------   Fill in the matrix entries --------------------*/
      fillin(pos, freqs, col, pssm, obs_freqs);

   }  /*  end of for pos */
   /*------ Now make the final scores; make log scores non-neg    */
   /*       by subtracting the min. value for all positions ----- */
   final(block, freqs, pssm, matrix);

   free(col);
   free(pssm);
   if (bruno != NULL) free(bruno);
   return(matrix);
}  /* end of make_steves */
/*==========================================================================
     Uses Claverie's method of getting pseudo-counts with a subst. matrix,
     not Gribskov's method
===========================================================================*/
Matrix *make_clav(block, freqs, subst, obs_freqs)
Block *block;
double *freqs;
double subst[AASALL][AASALL];
Matrix *obs_freqs;
{
   double epsilon, maxsubst, minfreq;
   int pos, aa, row;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *pssm, *bruno;

   col = make_col();
   pssm = make_pssm();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;

   /*-----------------  Get the scaling value ------------------*/
   maxsubst = -999.9; minfreq = 999.9;
   for (row = 1; row < AAS; row++)
   {
      if (freqs[row] < minfreq && freqs[row] > 0.0)
           minfreq = freqs[row];
      for (aa = row; aa < AAS; aa++)
         if (subst[row][aa] > maxsubst) maxsubst = subst[row][aa];
   }

   /*--------------  Do one position at a time -------------------*/
   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);
      epsilon = (minfreq * sqrt(col->totcnt)) / maxsubst;

      /*---------- get the pseudo counts -------------------------------*/
      pseudo_clav(col, subst, epsilon);

      /*---------   Fill in the matrix entries --------------------*/
      fillin(pos, freqs, col, pssm, obs_freqs);

   }  /*  end of for pos */
   /*------ Now make the final scores; make log scores non-neg    */
   /*       by subtracting the min. value for all positions ----- */
   final(block, freqs, pssm, matrix);

   free(col);
   free(pssm);
   if (bruno != NULL) free(bruno);
   return(matrix);
} /* end of make_clav */
/*==========================================================================
     Uses simple background frequencies to make pseudo counts,
     b[aa] = sqrt(#seqs) * freq[aa]
     After Chip Lawrence's Gibbs sampling paper
===========================================================================*/
Matrix *make_gibbs(block, freqs, obs_freqs)
Block *block;
double *freqs;
Matrix *obs_freqs;
{
   double epsilon;
   int pos;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *pssm, *bruno;

   col = make_col();
   pssm = make_pssm();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;

   /*--------------  Do one position at a time -------------------*/
   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);
/*
      epsilon = 1.0 / (double) block->num_sequences;
      epsilon += compute_entropy(col);
      epsilon = (double) RTot * count_residues(col);
*/
      if (RTot >= 0.0) epsilon = (double) RTot * count_residues(col);
      else if (BTot >= 0.0) epsilon = BTot;
      else epsilon = sqrt( (double) block->num_sequences); 

      /*---------- get the pseudo counts -------------------------------*/
      pseudo_gibbs(col, freqs, epsilon);

      /*---------   Fill in the matrix entries --------------------*/
      fillin(pos, freqs, col, pssm, obs_freqs);

   }  /*  end of for pos */
   /*------ Now make the final scores; make log scores non-neg    */
   /*       by subtracting the min. value for all positions ----- */
   final(block, freqs, pssm, matrix);

   free(col);
   free(pssm);
   if (bruno != NULL) free(bruno);
   return(matrix);
} /* end of make_gibbs */
/*======================================================================*/
Matrix *make_diri(block, freqs, diric, obs_freqs)
Block *block;
double *freqs;
struct dirichlet *diric;
Matrix *obs_freqs;
{
   int pos;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *pssm, *bruno;

   col = make_col();
   pssm = make_pssm();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;

   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);

      /*--------  get the Dirichlet mixture pseudo-counts ---------------*/
      pseudo_diric(col, diric);

/*    printf("\npos=%d\n", pos);
      for (aa = 1; aa < AAS; aa++)
         printf("%c: actual=%f diric=%f diric/Z=%f\n",
              aa_btoa[aa], col->cnt[aa], col->cnt[aa] + col->reg[aa],
              (col->cnt[aa] + col->reg[aa])/(col->totcnt + col->totreg) );
*/
  
      /*---------   Fill in the matrix entries --------------------*/
      fillin(pos, freqs, col, pssm, obs_freqs);
       
   }  /*  end of for pos */
   /*------ Now make the final scores; make log scores non-neg    */
   /*       by subtracting the min. value for all positions ----- */
   final(block, freqs, pssm, matrix);

   free(col);
   free(pssm);
   if (bruno != NULL) free(bruno);
   return(matrix);

}  /* end of make_diri */
/*===============================================================
      Returns log(e^x + e^y)
================================================================*/
double addlogs(lx, ly)
double lx, ly;
{
   if (lx > ly)  return(lx + log(1.0 + exp(ly - lx)));
   else          return(ly + log(1.0 + exp(lx - ly)));
}  /*  end of addlogs */

/*=======================================================================
      Loads scoring matrix.  Assumes alphabet for file is
      listed on first non-blank line following any comment lines starting
      with # or ;.
      Adds min. value to each entry to make matrix non-negative.
=========================================================================*/
void load_subst(fin, subst)
FILE *fin;
double subst[AASALL][AASALL];
{
   char line[MAXLINE], *ptr;
   int alpha[AASALL+10], nrows, ncols, row, col, i;
   double minval;

/*----------Read file until first non-blank, non-comment line -----------*/
      line[0] = '\0';
      while (fgets(line, sizeof(line), fin) != NULL &&
             (!strlen(line) || line[0] == '#' || line[0] == ';'))
	    ;
/*------See if the first line has characters on it ------------*/
      for (col=0; col < 30; col++) alpha[col] = -1;
      if (strstr(line, "A") != NULL)	/* This line has characters */
      {
	 row = 0;	/* # of alphabetic characters on the line */
	 for (i=0; i < (int) strlen(line); i++)
	 {
	    col = aa_atob[line[i]];
	    if (col >= 0 && col < AASALL)
	    {
	       alpha[row] = col;
	       row++;
	    }
	    else if (isalpha(line[i])) row++; /* skip over other alpha */
	 }
      }
/*-------Get the data values now ------------*/
      for (row=0; row 1)
	 {
	    if (alpha[nrows] >= 0 && alpha[nrows] < AASALL)
	    {
	       row = alpha[nrows]; ncols = 0;
	       ptr = strtok(line, " ,\t\n");
	       while (ptr != NULL)
	       {
		  if (strspn(ptr, "+-0123456789") == strlen(ptr))
		  {
		     col = alpha[ncols];
		     if (col >= 0 && col < AASALL)
			subst[row][col] = (double) atoi(ptr);
		     ncols++;
		  }
		  ptr = strtok(NULL, " ,\t\n");
	       }
	    }
	    nrows++;
	 }
      }

/*-------If some entries are still missing, assume symmetry ---------*/
      for (row=0; rowwidth);
   matrix->block = block;
   strcpy(ctemp, block->id);
   strncpy(strstr(ctemp, "BLOCK"), "MATRIX\0", 7);
   strcpy(matrix->id, ctemp);
   strcpy(matrix->ac, block->ac);
   strcpy(matrix->de, block->de);
   strcpy(matrix->ma, block->bl);
   strcpy(matrix->number, block->number);
   strcpy(matrix->motif, block->motif);
   matrix->width = matrix->max_length = block->width;
   matrix->num_sequences = block->num_sequences;
   matrix->percentile = block->percentile;
   matrix->strength = block->strength;
   matrix->patterns = NULL;
   matrix->undefined_ptr = NULL;
   /*  Add seqs= to MA line if not there */
   if (strstr(matrix->ma, "seqs=") == NULL)
   {
	strcpy(ctemp, matrix->ma);
	ptr = strtok(ctemp, "\n\r");
	sprintf(matrix->ma, "%s seqs=%d",
		ptr, matrix->num_sequences);
   }

   return(matrix);
}  /* end of make_matrix */
/*======================================================================*/
void counts(block, col, pos)
Block *block;
struct working *col;
int pos;
{
   int seq, aa;

      col->totcnt = col->totraw = col->totreg = 0.0;
      for (aa = 0; aa < AASALL; aa++) 
      { col->cnt[aa] = col->raw[aa] = col->reg[aa] = 0.0; }

      /*  Only count the real 20 aas, combine B(21) with D & Z(22) with E  */
      for (seq = 0; seq < block->num_sequences; seq++)
      {
         aa = block->residues[seq][pos];
         if (aa == 21) aa = 4;			/* combine B with D */
	 if (aa == 22) aa = 7;			/* combine Z with E */
         if (aa >= 1 && aa < AAS)
         {
            col->cnt[aa] += block->sequences[seq].weight;
            col->totcnt += block->sequences[seq].weight;
	    col->raw[aa] += 1.0;
            col->totraw += 1.0;
         }
         else printf("Uncounted character for %s: %d\n",
              block->number, block->residues[seq][pos]);
      }
}  /* end of counts */
/*======================================================================
    Get col->totcnt from Bruno but col->cnt[aa] from sequence weights
    Each column has a different col->totcnt
======================================================================*/
void counts_hybrid(bruno, block, col, pos)
struct work_pssm *bruno;
Block *block;
struct working *col;
int pos;
{
   int aa;
   double totbruno, factor;

   counts_bruno(bruno, col, pos);
   totbruno = col->totcnt;
   counts(block, col, pos);
   /*   Re-normalize sequence-weighted counts to add to Bruno total */
   factor = totbruno / col->totcnt;
   for (aa = 0; aa < AASALL; aa++) col->cnt[aa] *= factor;
   col->totcnt = totbruno;
}  /* end of counts_hybrid */
/*======================================================================
    Get col->totcnt from # clumps but col->cnt[aa] from sequence weights
    Each column has the same col->totcnt = ClumpsTot
======================================================================*/
void counts_clumps(block, col, pos)
Block *block;
struct working *col;
int pos;
{
   int aa;
   double factor;

   counts(block, col, pos);
   /*   Re-normalize sequence-weighted counts to add to clumps total */
   factor = ClumpTot / col->totcnt;
   for (aa = 0; aa < AASALL; aa++) col->cnt[aa] *= factor;
   col->totcnt = ClumpTot;
}  /* end of counts_clumps */
/*=====================================================================*/
double compute_entropy(col)
struct working *col;
{
   int aa;
   double entropy, dtemp;

   entropy = 0.0;
   for (aa=1; aa < AAS ; aa++)
   {
      dtemp = col->cnt[aa] / col->totcnt;
      if (dtemp > 0.0000) entropy -= dtemp * log(dtemp);
   }
   entropy /= Log2;		/* convert it to bits */
   return(entropy);
}   /* end of compute_entropy */
/*=====================================================================*/
int count_residues(col)
struct working *col;
{
   int aa, nr;

   nr = 0;
   for (aa = 1; aa < AAS; aa++)
      if (col->cnt[aa] > 0.0) nr++;

   return(nr);
}  /*  end of count_residues */
/*=======================================================================
    Count all pairs of amino acids in a column. Return the ratio of
    diagonal counts (identities) to off-diagonal counts.
    Working from the sequence-weighted aa counts in the column,
    not the actual block column.
    The total number of pairwise counts is tot*(tot-1)/2
========================================================================*/
double ratio_counts(col)
struct working *col;
{
   int aa;
   double ndiag, total, ratio;

   total = col->totcnt * (col->totcnt - 1.0) / 2.0;
   ndiag = 0.0;
   for (aa = 1; aa < AAS; aa++)
      if (col->cnt[aa] > 1.0)
         ndiag += col->cnt[aa] * (col->cnt[aa] - 1.0) / 2.0;

   if (ndiag < total) ratio = ndiag/(total - ndiag);
   else               ratio = 10.0;			/* infinity */
   return(ratio);
}  /*  end of ratio_counts */
/*=====================================================================*/
void pseudo_diric(col, diric)
struct working *col;
struct dirichlet *diric;
{
   int j, aa;
   double denom, dtemp;

      /*-----------   compute equation (3), Prob(n|j) ------------  */
      for (j = 0; j < diric->ncomp; j++)
      {
         col->probn[j] = lgamma(col->totcnt + 1.0) + lgamma(diric->altot[j]);
         col->probn[j] -= lgamma(col->totcnt + diric->altot[j]);
         /*   Note range on aa varies; Diric values only for 1-20 */
         for (aa = 1; aa < AAS; aa++)
         {
         /*  ni = cnt[i] */
            if (col->cnt[aa] >= 0.0)
            {
               dtemp = lgamma(col->cnt[aa] + diric->alpha[j][aa]);
               dtemp -= lgamma(col->cnt[aa] + 1.0);
               dtemp -= lgamma(diric->alpha[j][aa]);
               col->probn[j] += dtemp;
            }
         }
      }

      /*------ compute sum qk * p(n|k) using logs & exponents ----------*/
      denom = log(diric->q[0]) + col->probn[0];
      for (j = 1; j < diric->ncomp; j++)
      {
         dtemp = log(diric->q[j]) + col->probn[j];
         denom = addlogs(denom, dtemp);
      }

      /*   compute equation (3), Prob(j|n)  */
      for (j = 0; j < diric->ncomp; j++)
      {
         col->probj[j] = log(diric->q[j]) + col->probn[j] - denom;
/*       printf("j=%d probn[j]=%f probj[j]=%f\n",
             j, exp(col->probn[j]), exp(col->probj[j]));
*/
      }

      /* ----- compute equation (4), ni + bi, bi = Prob(j|n) * alpha[j][i]  */
      for (aa = 1; aa < AAS; aa++)
      {
         for (j = 0; j < diric->ncomp; j++)
            col->reg[aa] += (exp(col->probj[j]) * diric->alpha[j][aa]);
         col->totreg += col->reg[aa];
      }

}  /* end of pseudo_diric */
/*=====================================================================*/
void pseudo_alts(col, qij, epsilon)
struct working *col;
struct float_qij *qij;
double epsilon;
{
   int aa, row;

   /*---------- get the pseudo counts -------------------------------*/
   for (aa=1; aa < AAS; aa++)
   {
      col->reg[aa] = 0.0;
      for (row = 1; row < AAS; row++)
      {
        col->reg[aa] += (col->cnt[row] * qij->value[aa][row] / qij->marg[row]);
/*
        col->reg[aa] += (col->raw[row] * qij->value[aa][row] / qij->marg[row]);
*/
      }
      col->reg[aa] *= epsilon;
/*    col->reg[aa] /= col->totraw;
*/
      col->reg[aa] /= col->totcnt;
      col->totreg += col->reg[aa];
   }
}  /* end of pseudo_alts */
/*=====================================================================*/
void pseudo_clav(col, subst, epsilon)
struct working *col;
double subst[AASALL][AASALL];
double epsilon;
{
   int aa, row;

      /*---------- get the pseudo counts -------------------------------*/
      for (aa=1; aa < AAS; aa++)
      {
         col->reg[aa] = 0.0;
         for (row = 1; row < AAS; row++)
         {
            col->reg[aa] += col->cnt[row] * subst[aa][row];
         }
         col->reg[aa] *= epsilon;
         col->reg[aa] /= col->totcnt;
         col->totreg += col->reg[aa];
      }
}  /* end of pseudo_clav */
/*=====================================================================*/
void pseudo_gibbs(col, freqs, epsilon)
struct working *col;
double *freqs;
double epsilon;
{
   int aa;

   /*---------- get the pseudo counts -------------------------------*/
   col->totreg = 0.0;
   for (aa=1; aa < AAS; aa++)
   {
      col->reg[aa] = epsilon * freqs[aa];
      col->totreg += col->reg[aa];
   }
}  /* end of pseudo_gibbs */
/*=====================================================================*/
void fillin(pos, freqs, col, pssm, obs_freqs)
int pos;
double *freqs;
struct working *col;
struct work_pssm *pssm;
Matrix *obs_freqs;
{
      int aa;
      double dtemp;

      pssm->sum[pos] = 0.0; 
      for (aa=1; aa < AAS; aa++)
      {
         if (NoCounts)
         {
            pssm->value[pos][aa] = col->reg[aa];
            pssm->value[pos][aa] /= col->totreg;
         }
         else
         {
            pssm->value[pos][aa] = col->cnt[aa] + col->reg[aa];
            pssm->value[pos][aa] /= (col->totcnt + col->totreg);
         }
	 if (obs_freqs != NULL)
         {
             dtemp = 100. * pssm->value[pos][aa];
	     obs_freqs->weights[aa][pos] = round(dtemp);
         }
         if (freqs[aa] > 0.0)
             pssm->value[pos][aa] /= freqs[aa];

         if (LogScores && pssm->value[pos][aa] > 0.0)
             pssm->value[pos][aa] = log(pssm->value[pos][aa]);

         pssm->sum[pos] += pssm->value[pos][aa];
      }
}  /* end of fillin */
/*=========================================================================
      Adds negative minval to give all positive matrix,
      then multiplies by 99/maxval to give scores ranging from 0 to99 
===========================================================================*/
void final(block, freqs, pssm, matrix)
Block *block;
double *freqs;
struct work_pssm *pssm;
Matrix *matrix;
{
   int pos, aa;
   double factor, maxval, minval, dtemp;

   minval = 9999.9;
   maxval = -9999.9;
   for (pos = 0; pos < block->width; pos++)
      for (aa=1; aa < AAS; aa++)
      {
         if (pssm->value[pos][aa] < minval) minval = pssm->value[pos][aa];
         if (pssm->value[pos][aa] > maxval) maxval = pssm->value[pos][aa];
      }

   if (minval < 0.0) factor = 99.0 / (maxval - minval);
   else              factor = 99.0 / maxval;
   if (factor < 1.0) factor = 1.0;
   for (pos = 0; pos < block->width; pos++)
   {
      for (aa=1; aa < AAS; aa++)
      {
         if (FloatPt)		/* Just copy pssm to matrix */
         {
            matrix->weights[aa][pos] = pssm->value[pos][aa];
         }
         else			/* Rescale it */
         {
            if (LogScores) 
            {
               if (minval < 0.0)
                  dtemp = factor * (pssm->value[pos][aa] - minval);
               else dtemp = factor * pssm->value[pos][aa];
            }
            else 
            { 
              dtemp = 99.0 * pssm->value[pos][aa] / pssm->sum[pos];
            }
            matrix->weights[aa][pos] = round(dtemp);
         }	/* end of if not floating point */
      }   /* end of aa */
      compute_BZX(freqs, matrix, pos);
   }  /*  end of for pos */
}  /* end of final */
/*=====================================================================*/
void compute_BZX(frequency, matrix, col)
double *frequency;
Matrix *matrix;
int col;
{
  double part_D;		/* the partition of D for B. */
				/* = freq[D] / ( freq[D] + freq[N] ) */
  double part_N;		/* the partition of N for B. */
				/* = freq[N] / ( freq[D] + freq[N] ) */
  double part_E;		/* the partition of E for Z. */
				/* = freq[E] / ( freq[E] + freq[Q] ) */
  double part_Q;		/* the partition of Q for Z. */
				/* = freq[Q] / ( freq[E] + freq[Q] ) */
  /*
   * find the partitions of D, N, E, and Q for B and Z
   */
  part_D = frequency[aa_atob['D']] / 
    ( frequency[aa_atob['D']] + frequency[aa_atob['N']] );
  part_N = frequency[aa_atob['N']] / 
    ( frequency[aa_atob['D']] + frequency[aa_atob['N']] );
  part_E = frequency[aa_atob['E']] / 
    ( frequency[aa_atob['E']] + frequency[aa_atob['Q']] );
  part_Q = frequency[aa_atob['Q']] / 
    ( frequency[aa_atob['E']] + frequency[aa_atob['Q']] );

    /* fill in the matrix for B, Z, X, gap, stop and non */
    matrix->weights[aa_atob['B']][col] = 
      (int) ((part_D * matrix->weights[aa_atob['D']][col] +
	      part_N * matrix->weights[aa_atob['N']][col]) + 0.5);
				/* rounding to ints by adding 0.5 */
    matrix->weights[aa_atob['Z']][col] =
      (int) ((part_E * matrix->weights[aa_atob['E']][col] +
	      part_Q * matrix->weights[aa_atob['Q']][col]) + 0.5);
				/* rounding to ints by adding 0.5 */
    matrix->weights[aa_atob['X']][col] = 
      (int) (frequency[aa_atob['X']] + 0.5);
				/* rounding to ints by adding 0.5 */
    matrix->weights[aa_atob['-']][col] = 
      (int) (frequency[aa_atob['-']] + 0.5);
				/* rounding to ints by adding 0.5 */
    matrix->weights[aa_atob['*']][col] = 
      (int) (frequency[aa_atob['*']] + 0.5);
				/* rounding to ints by adding 0.5 */
}  /* end of compute_BZX */

/*=====================================================================*/
struct work_pssm *make_pssm()
{
   struct work_pssm *pssm;
   int pos, aa;

   pssm = (struct work_pssm *) malloc(sizeof(struct work_pssm));
   if (pssm == NULL)
   {
      printf("make_pssm: OUT OF MEMORY\n");
      exit(-1);
   }
   for (pos = 0; pos < EXTRA_LARGE_BUFF; pos++)
   {
      pssm->sum[pos] = 0.0;
      for (aa=0; aa < AASALL; aa++)
         pssm->value[pos][aa] = 0.0;
   }
   return(pssm);

}  /* end of make_pssm */
/*==================================================================*/
struct working *make_col()
{
   struct working *col;
   int aa;

   col = (struct working *) malloc(sizeof(struct working));
   if (col == NULL)
   {
      printf("make_col:  OUT OF MEMORY\n");
      exit(-1);
   }

   col->totcnt = col->totreg = 0.0;
   for (aa=0; aa < AASALL; aa++)
   {
      col->cnt[aa] = col->reg[aa] = 0.0;
   }

   return(col);
}  /* end of make_col */

/*=======================================================================
    Bill Bruno's character counts:
	creates file "data" with sequences
	executes program "rind" & waits for it to finish
	reads output file "counts" to get counts
     Computes counts for all positions at once
========================================================================*/
struct work_pssm *bruno_rind(block)
Block *block;
{
   struct work_pssm *bruno;
   FILE *fp;
   int seq, pos, baa;
   char line[1000], *ptr;
   double dtemp;

   bruno = make_pssm();
   /*------Turn the block into file "data" for rind --------------*/
   if ( (fp = fopen("data", "w")) == NULL)
   {
       printf("\nbruno_rind(): Cannot open file data\n");
       return(bruno);
   }
   for (seq=0; seq < block->num_sequences; seq++)
   {
      fprintf(fp, "%10s ", block->sequences[seq].name);
      for (pos=0; pos < block->width; pos++)
         fprintf(fp, "%c", aa_btoa[ block->residues[seq][pos] ]);
      fprintf(fp, "\n");
   }
   fclose(fp);
   /*------Execute rind ------------------------------------------*/
   printf("\nExecuting rind ....\n");
   sprintf(line, "rind");
   if (system(line) != 0)
   {
       printf("\nbruno_rind(): Execution of rind failed\n");
       exit(-1);
/*       return(bruno);  */
   }
   /*------Get the counts from "counts"-------------------------*/
   if ( (fp = fopen("counts", "r")) == NULL)
   {
       printf("\nbruno_rind(): Cannot open file counts\n");
       return(bruno);
   }
   pos = baa = -1;
   while (pos < block->width && 
          !feof(fp) && fgets(line, 1000, fp) != NULL)
   {
      if (strstr(line, "position") != NULL)
      {
         pos++; baa = 0;
         bruno->sum[pos] = 0.0;
      }
      else if (pos >= 0 && baa == 0)
      {
         ptr = strtok(line, " \t");
         while (baa < 25 && ptr != NULL)
         {
            dtemp = atof(ptr);
            bruno->value[pos][ Bruno_Order[baa] ] = dtemp;
            bruno->sum[pos] += dtemp;
            baa++;
            ptr = strtok(NULL, "-");
	    ptr = strtok(NULL, " \t");
	    ptr = strtok(NULL, " \t");
         }
      }
   }
   fclose(fp);
   /*--------------------------------------------------------------*/
   return(bruno);
}  /* end of bruno_rind()  */
/*=======================================================================
        Looks up Bruno counts
========================================================================*/
void counts_bruno (bruno, col, pos)
struct work_pssm *bruno;
struct working *col;
int pos;
{ 
   int aa;

   for (aa = 0; aa < AASALL; aa++) 
   { col->cnt[aa] = col->raw[aa] = col->reg[aa] = 0.0; }
   for (aa=1; aa < AAS; aa++)
      col->cnt[aa] = bruno->value[pos][aa];
   col->totcnt = bruno->sum[pos];

} /* end of counts_bruno */

/*======================================================================*/
/*    Cluster sequences in a block based on the number of               */
/*    identities within the block. Sets Block.cluster & Block.ncluster  */
/*      1. Compute number of identities for each possible pair of seqs. */
/*         Results stored in lower half of matrix (pairs).              */
/*      2. Use clustering threshold % of # of AAs in trimmed block.     */
/*      3. Cluster recursively by traversing cols, rows of matrix.      */
/*UNIX NOTE:  Program aborts when running under UNIX at free(pairs),
   so use the fixed size declaration pairs & remove the malloc() &
   free() calls when compiling for UNIX                                 */
/*======================================================================*/
int clump_seqs(block)
Block *block;
{
   int clus, npair, threshold, s1, s2, l1, l2, px, i, i1, i2;
   int minclus, oldclus;
   struct pair *pairs;
   struct clump_work *clumps;
/*UNIX   struct pair pairs[MAXNSEQ*(MAXNSEQ-1)/2];  */

   npair = block->num_sequences * (block->num_sequences - 1) / 2;
   pairs = (struct pair *) malloc (npair * sizeof(struct pair));
   clumps = (struct clump_work *) malloc (sizeof(struct clump_work));
   if (pairs == NULL || clumps == NULL)
   {
      printf("\nclump_seqs: Unable to allocate pair structure!\n");
      exit(-1);
   }
   threshold = (int) (ClumpCounts * (block->width))/100;

/*    Compute scores for all possible pairs of sequences            */
   for (s1=0; s1num_sequences - 1; s1++) /* col = 0, n-2     */
   {
      l1 = 0;
      for (s2=s1+1; s2num_sequences; s2++)	/* row = col+1, n-1 */
      {
	 l2 = 0;
	 px = INDEX(block->num_sequences, s1, s2);
	 pairs[px].score = 0;
	 pairs[px].cluster = -1;
	 for (i=0; i<=block->width; i++)
	 {
	    i1 = l1+i;  i2 = l2+i;
	    if (i1 >= 0 && i1 < block->width &&
		i2 >= 0 && i2 < block->width &&
                block->residues[s1][i1] == block->residues[s2][i2])
		   pairs[px].score += 1;
	 }
      }  /* end of s2 */
   }  /* end of s1 */

/*-------Cluster if score exceeds threshold by scanning cols (s1) */
   for (s1=0; s1num_sequences; s1++)
   {
      clumps->cluster[s1] = -1;	/* clear out old values */
      clumps->ncluster[s1] = 1;
      clumps->nclus[s1] = 0;
   }
   clus = 0;        				/* cluster number */
   for (s1=0; s1num_sequences - 1; s1++) 	/* col = 0, n-2     */
      for (s2=s1+1; s2num_sequences; s2++)	/* row = col+1, n-1 */
      {
	 px = INDEX(block->num_sequences, s1, s2);
	 if (pairs[px].score >= threshold)	/*  cluster this pair */
	 {
	    if (clumps->cluster[s1] < 0)          /* s1 not yet clustered */
	    {
	       if (clumps->cluster[s2] < 0)       /* new cluster */
	       {
		  clumps->cluster[s1] = clus++;
		  clumps->cluster[s2] = clumps->cluster[s1];
	       }
	       else  				/* use s2's cluster  */
		  clumps->cluster[s1] =  clumps->cluster[s2];
	    }
	    /*  use s1's cluster if it has one and s2 doesn't */
	    else if (clumps->cluster[s1] >= 0 && clumps->cluster[s2] < 0)
	       clumps->cluster[s2] = clumps->cluster[s1];
	    /* merge the two clusters into the lower number */
	    else if (clumps->cluster[s1] >= 0 && clumps->cluster[s2] >= 0)
	    {
	       minclus = clumps->cluster[s1]; oldclus = clumps->cluster[s2];
	       if (clumps->cluster[s2] < clumps->cluster[s1])
	       {
		  minclus = clumps->cluster[s2]; oldclus = clumps->cluster[s1];
	       }
	       for (i1=0; i1num_sequences; i1++)
		 if (clumps->cluster[i1] == oldclus)
		     clumps->cluster[i1] = minclus;
	    }
	 }  /* end of if pairs */
      }  /* end of s2 */

   /*---  Set ncluster, get rid of negative cluster numbers --*/
   for (s1=0; s1num_sequences; s1++)
      if (clumps->ncluster[s1] >= 0)  clumps->nclus[clumps->cluster[s1]]++;
   for (s1=0; s1num_sequences; s1++)
   {
      if (clumps->cluster[s1] < 0)
      {
	  clumps->cluster[s1] = clus++;
	  clumps->ncluster[s1] = 1;
      }
      else
	  clumps->ncluster[s1] = clumps->nclus[clumps->cluster[s1]];
   }
   free(pairs);
   return(clus);
}  /*  end of clump_seqs */
/*=========================================================================
    Scales positive matrix to lie between 0 and 99
===========================================================================*/
void positive_matrix(block, matrix)
Block *block;
Matrix *matrix;
{
   int pos, aa;
   double factor, maxval, minval, dtemp;

   minval = 9999.9;
   maxval = -9999.9;
   for (pos = 0; pos < block->width; pos++)
      for (aa=0; aa < AASALL; aa++)
      {
         if (matrix->weights[aa][pos] < minval)
             minval = matrix->weights[aa][pos];
         if (matrix->weights[aa][pos] > maxval)
             maxval = matrix->weights[aa][pos];
      }

   if (minval < 0.0) factor = 99.0 / (maxval - minval);
   else              factor = 99.0 / maxval;
/*   if (factor < 1.0) factor = 1.0;     ????why????? */
   for (pos = 0; pos < block->width; pos++)
   {
      for (aa=0; aa < AASALL; aa++)
      {
            if (minval < 0.0)
               dtemp = factor * (matrix->weights[aa][pos] - minval);
            else dtemp = factor * matrix->weights[aa][pos];
            matrix->weights[aa][pos] = round(dtemp);
      }
   }  /*  end of for pos */
}  /* end of positive_matrix */
/*=====================================================================*/
/*    Find patterns & add them to output file containing the matrix    */
/*    There is at most one pattern per matrix position, and it will    */
/*    have only one non-x position in it. Patterns may be made more    */
/*    general later on                                                 */

void add_patterns(matrix, Fpa)
Matrix *matrix;
FILE *Fpa;
{
   int pos, aa, npos, naa, i;
   int aas[AASALL];
   char pattern[MAXLINE], ctemp[5], *ptr;

   /*    Change MATRIX to PATMAT on id line    */
   strcpy(pattern, matrix->id);
   ptr = strtok(pattern, ";");
   if (ptr != NULL) strcat(pattern, "; PATMAT");
   fprintf(Fpa, "ID   %s\n", pattern);
   fprintf(Fpa, "AC   %s\n", matrix->ac);
   fprintf(Fpa, "DE   %s\n", matrix->de);
   fprintf(Fpa, "PA   %s\n", matrix->ma);
   for (pos = 0; pos < matrix->width; pos++)
   {
      npos = naa = 0;
      pattern[0] = '\0';
      for (aa=1; aa <= 20; aa++)
      {
         if (matrix->weights[aa][pos] >= PatternCutoff)
         {
            aas[naa] = aa;
            naa++;
         }
      }
      if (naa == 1)
      {
         for (i=0; i < pos; i++) strcat(pattern, "x");
         ctemp[0] = aa_btoa[ aas[0] ]; ctemp[1] = '\0';
         strcat(pattern, ctemp);   /* this is i = pos */
         for (i=pos+1; i < matrix->width; i++) strcat(pattern, "x");
         npos++;
      }
      else if (naa > 1)
           {
              for (i=0; i < pos; i++) strcat(pattern, "x");
              strcat(pattern, "[");
              ctemp[1] = '\0';
              for (i=0; i < naa; i++)
              {
                 ctemp[0] = aa_btoa[ aas[i] ];
                 strcat(pattern, ctemp);
              }
              strcat(pattern, "]");
              for (i=pos; i < matrix->width; i++) strcat(pattern, "x");
              npos++;
           }
      if (npos > 0) fprintf(Fpa, "%s\n", pattern);
   }
   fprintf(Fpa, "//\n");
}  /* end of add_patterns */
 = 0.0;
   for (aa=0; aa < AASALL; aa++)
   {
      col->cnt[aa] = col->reg[aa] = 0.0;
   }

   return(col);
}  /* end of make_col */

/*=======================================================================
    Bill Bruno's character counts:
	creates file "data" with sequences
	executes program "rind" & waits for it to finish
	reads output file "counts" to get counts
     Computes counts foblimps-3.9/blimps/blweight.c000064400001460000012000000637141056472630500164300ustar00jorjastaff00000400000027/* Copyright 1994-2000 Fred Hutchinson Cancer Research Center
  blweight.c  Compute Steve's sequence weights for blocks
           blweight    
		type = P  (position-based weights)
		     = V  (Voronoi weights)
		     = A  (Vingron & Argos weights)
                     = Cn (n% clustering)
 		scale = max (max == 100)
			n (sum == number of sequences)
			# (sum == #)
--------------------------------------------------------------------
 2/10/94 J. Henikoff
 2/21/94 Added Voronoi option
 3/ 4/94 Added cluster % option. Position-based columns are normalized.
 5/23/94 Added Vingron & Argos option.
 8/ 6/94 Added option to scale weights to sum to number of sequences
 4/ 5/95 Added call to free_block()
 1/ 6/96 Increased MAXWIDTH from 60 to 100 for Shmuel; still too inflexible.
12/ 5/96 Ignore X instead of treating it like another character in position().
 2/ 2/97 Increased MAXROWS from 400 to 800 to accomodate current blocks.
         Increased MAXWIDTH from 100 to 400 for Shmuel.
 2/ 2/97 Set MAXWIDTH to 1500 for postion-based only; other methods 
         use MAXWIDTH = 100.
 4/22/99 Don't output garbage on block consisting of all Xs.
 6/14/99 Adjustments for longer sequence names
 7/23/99 Added call to srandom() - only used for Voronoi weights
12/13/99 When clumping by percent id, rewrite blocks with clumps indicated.
 3/13/00 Comments
12/23/00 Replaced MAXWIDTH & MAXPWIDTH with EXTRA_LARGE_BUFF (=1000)
12/25/04 Increased MAXROWS from 800 to 1000
12/23/06 Longer sequence names
 1/14/07 Correct number of sequences if necessary in put_block()
============================================================================*/

#define BLWEIGHT_C_
#define EXTERN
#define YES 1
#define NO 0
#define MAXNAME 80	/* Maximum file name length */
#define MAXAA 26	/* Dimension of aa_ arrays */
#define MAXROWS 1000	/* Maximum number of rows (seqs) in a block */
#define MAXINT 32000
/*   Already defined for Solaris
#define RAND_MAX 2147483647		 2^31 - 1
*/
#define NUMOFMUTANTS 10000		/* Voronoi randomizations */
#define ROUND(x) ((x >= 0.0) ? (int) (x+0.5) : (int) (x-0.5))
#define ORD(x) ((int) x - 65)
#define INDEX(n, col, row) (col*n - (col*(col+3))/2 - 1 + row)

#include 
#include 

/*
 * Local variables and data structures
 */

void position();
void voronoi();
void noteaa();				/* used by voronoi() */
void calculate();			/* used by voronoi() */
void adjustweights();			/* used by voronoi() */
Block *cluster();
void argos();
void scale_weights();
void put_block();
int ran0();

struct vor {				/* used by voronoi() */
  int aapresent[EXTRA_LARGE_BUFF][MAXAA];
  int aanumber[EXTRA_LARGE_BUFF];
};

/*	Defined in protomat.h; used by cluster()
struct pair {	
   int score, cluster;
};
*/

/*=======================================================================*/
/*
 * main
 *   controls flow of program
 *   Parameters: argc, argv
 *   Error codes:
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *bfp, *ofp;
  Block *block, *cblock;
  int wtype, clus, stype;
  char bdbname[MAXNAME], conname[MAXNAME], ctemp[10];
  struct timeval tv;

  ErrorLevelReport = 5;			/* don't want to see them */
  /* initialize random number generator */
  gettimeofday(&tv, NULL);
  srandom(tv.tv_sec^tv.tv_usec);

  if (argc < 5)
  {
     printf("BLWEIGHT: Copyright 1994-2000 by the Fred Hutchinson");
     printf(" Cancer Research Center, \n\tSeattle, WA, USA\n");
     printf("Add sequence weights to blocks.\n");
     printf("USAGE: blweight    \n");
     printf("\t=input file of blocks to weight\n");
     printf("\t=output file of weighted blocks\n");
     printf("\t=P (position-based) | V (Voronoi) | \n\t\t");
     printf("A (Vingron & Argos) | Cn (n percent clumping)\n");
     printf("\t=M (max=100) | N (sum=#seqs) | # (sum=#)\n");
  }

/* ------------1st arg = blocks database -------------------------------*/
   if (argc > 1)
      strcpy(bdbname, argv[1]);
   else
   {
      printf("\nEnter name of blocks database: ");
      gets(bdbname);
   }
   if ( (bfp=fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbname);
      exit(-1);
   }
/* ------------2nd arg = weighted blocks database ---------------------*/
   if (argc > 2)
      strcpy(conname, argv[2]);
   else
   {
      printf("\nEnter name of new weighted blocks database: ");
      gets(conname);
   }
   if ( (ofp=fopen(conname, "w")) == NULL)
   {
      printf("\nCannot open file %s\n", conname);
      exit(-1);
   }
/* ------------3rd arg = weighting type -------------------------------*/
   wtype = 0;			/* Position-based is default */
   clus = -1;
   ctemp[0] = '\0';
   if (argc > 3)
      strcpy(ctemp, argv[3]);
   else
   {
      printf("\nEnter weighting scheme (P=position-based, V=Voronoi, ");
      printf("\n A=Vingron & Argos, Cn = n-percent cluster [P]: ");
      gets(ctemp);
   }
   if (strlen(ctemp))
   {
      if (ctemp[0] == 'V' || ctemp[0] == 'v') wtype = 1;
      else if (ctemp[0] == 'A' || ctemp[0] == 'a') wtype = 3;
           else if (ctemp[0] == 'C' || ctemp[0] == 'c')
                {
                   wtype = 2;  clus = atoi(ctemp+1);
                   if (clus < 0) clus = 0;
                   if (clus > 100) clus = 100;
                }
   }
   if (wtype < 0 || wtype > 3) wtype = 0;
   switch (wtype)
   {
        case 0:
  	   printf("blweight: Calculating position-based weights\n");
	   break;
	case 1:
  	   printf("blweight: Calculating Voronoi weights\n");
	   break;
	case 2:
  	   printf("blweight: Calculating %d percent cluster weights\n", clus);
	   break;
	case 3:
  	   printf("blweight: Calculating Vingron & Argos weights\n");
	   break;
	default:
	   break;
   }
   /*---------------------Scale ----------------------------------*/
   stype = 0;
   if (argc > 4)
      strcpy(ctemp, argv[4]);
   else
   {
      printf("\nEnter scale (M=>max=100, N=>sum=#seq, ###=>sum=###) [M]: ");
      gets(ctemp);
   }
   if (strlen(ctemp))
   {
      if (ctemp[0] == 'm' || ctemp[0] == 'M') stype = 0;
      else if (ctemp[0] == 'n' || ctemp[0] == 'N') stype = 1;
           else 
           {
              stype = atoi(ctemp);
              if (stype < 100) stype = 100;
              if (stype > 999) stype = 999;
           }
   }
   switch (stype)
   {
        case 0:
  	   printf("blweight: Integer weights, maximum weight = 100\n");
	   break;
	case 1:
  	   printf("blweight: Decimal weights, sum = number of sequences\n");
	   break;
	default:
  	   printf("blweight: Integer weights, sum = %d\n", stype);
	   break;
   }
   /*-----------------------------------------------------------------*/

  cblock = NULL;
  while ((block = read_a_block(bfp)) != NULL)
  {
     switch (wtype)
     {
        case 0:
  	   position(block);
	   break;
	case 1:
	   voronoi(block);
	   break;
	case 2:
	   cblock = cluster(clus, block);
	   break;
	case 3:
	   argos(block);
	   break;
	default:
	   break;
     }
     if (cblock != NULL)
     {
        scale_weights(cblock, stype);
        put_block(cblock, ofp, stype);
/*		be careful here because cblock is using block's sequences
        free_block(cblock);
*/
     }
     else
     {
        scale_weights(block, stype);
        put_block(block, ofp, stype);
     }
     free_block(block);
  }
   
  fclose(bfp); fclose(ofp);
  exit(0);

}  /* end of main */
/*=======================================================================
      Compute Steve's position-based sequence weights      
	Doesn't count - (0), X (23) or * (24), other chars are 1-22
========================================================================*/
void position(block)
Block *block;
{
   double diffaas[EXTRA_LARGE_BUFF], naas[EXTRA_LARGE_BUFF][MAXAA+1], dtemp;
   int seq, pos, aa, width;

   for (pos = 0; pos < EXTRA_LARGE_BUFF; pos++)
   { 
      diffaas[pos] = 0.0;
      for (aa = 0; aa < MAXAA+1; aa++)
         naas[pos][aa] = (double) 0.0;
   }
  
   width = block->sequences[0].length;
   if (width > EXTRA_LARGE_BUFF)
   {
        width = EXTRA_LARGE_BUFF;
	fprintf(stderr, "ERROR: Block %s is too wide (%d), truncated to %d\n",
		block->number, block->sequences[0].length, width);
   }
   for (pos = 0; pos < width; pos++)
      for (seq = 0; seq < block->num_sequences; seq++)
      {
         if (block->residues[seq][pos] >= 1 &&
             block->residues[seq][pos] <= 22)
         {
            naas[pos][block->residues[seq][pos]] += 1;
         }
         else printf("Residue not counted: %d\n", block->residues[seq][pos]);
      }

   for (pos = 0; pos < width; pos++)
   { 
      for (aa = 1; aa <= 22; aa++)
      {
         if (naas[pos][aa] > 0.0)
         {
            diffaas[pos] += 1;	/* # of different types of aas in pos */
         }
      }
   }

   for (seq = 0; seq < block->num_sequences; seq++)
   {
      block->sequences[seq].weight = 0.0;
      for (pos = 0; pos < width; pos++)
      {
         aa = block->residues[seq][pos];
         dtemp = diffaas[pos] * naas[pos][aa];
         if (dtemp > 0.0)
           block->sequences[seq].weight += 1.0 / dtemp;
      } 
   }
}  /* end of position */
/*=========================================================================
    For each pair of segments in the block, count the number of positions
    that differ.
===========================================================================*/
void argos(block)
Block *block;
{
   int width, pos, seq, seq1, seqs, diff[MAXROWS][MAXROWS];
   double total;

   width = block->sequences[0].length;
   if (width > EXTRA_LARGE_BUFF)
   {
        width = EXTRA_LARGE_BUFF;
	fprintf(stderr, "ERROR: Block %s is too wide (%d), truncated to %d\n",
		block->number, block->sequences[0].length, width);
   }
   seqs = block->num_sequences;
   if (seqs > MAXROWS)
   {
      seqs = MAXROWS;
	fprintf(stderr,"ERROR: Block %s is too deep (%d), truncated to %d sequences\n",
		block->number, block->num_sequences, seqs);
   }
   for (seq = 0; seq < seqs; seq++)
      for (seq1 = 0; seq1 < seqs; seq1++)
         diff[seq][seq1] = 0;
   for (seq = 0; seq < seqs; seq++)
      for (seq1 = 0; seq1 < seqs; seq1++)
         for (pos = 0; pos < width; pos++)
            if (block->residues[seq][pos] !=
                block->residues[seq1][pos])
                    diff[seq][seq1] = diff[seq][seq1] + 1;
 
   total = 0.0;
   for (seq = 0; seq < seqs; seq++)
      block->sequences[seq].weight = 0.0;
   for (seq = 0; seq < seqs; seq++)
      for (seq1 = 0; seq1 < seqs; seq1++)
      {
         block->sequences[seq].weight += (double) diff[seq][seq1];
         total += (double) diff[seq][seq1];
      }
   for (seq = 0; seq < seqs; seq++)
   {
      block->sequences[seq].weight /= total;
   }
   
}   /* end of argos */
/*===================================================================
======================================================================*/
void voronoi(block)
Block *block;
{
  struct vor *v;
  int irow, seqs;
  double owned[MAXROWS];

  v = (struct vor *) malloc(sizeof(struct vor));
  noteaa(block, v);
  seqs = block->num_sequences;
  if (seqs > MAXROWS)
  {
     seqs = MAXROWS;
     fprintf(stderr, "ERROR: Block %s is too deep (%d), truncated to %d sequences\n",
	block->number, block->num_sequences, seqs);
  }
  for (irow = 0; irow < seqs; irow++)
      owned[irow]  =  0.0; /* set # owned to zero */
  calculate(block, v, owned);
  for (irow = 0; irow < seqs; irow++)
     block->sequences[irow].weight = owned[irow];
}  /* end of voronoi */
/*===================================================================
 examine the alignment and store the amino acids that occur at
 each col in the array aapresent. Note how many different aa  
 occur at each col and store in the array aanumber.            
======================================================================*/
void noteaa(block, v)
Block *block;
struct vor *v;
{ /* noteaa */
 int acol, arow;
 int alreadypresent;      /* used to ensure that only one occurrence */
                          /* of each aa goes into aapresent          */
 int aap;                /* used to count in the array aanumber */
 int cols, rows;

 cols = block->sequences[0].length;
 if (cols > EXTRA_LARGE_BUFF)
 {
     cols = EXTRA_LARGE_BUFF;
     fprintf(stderr, "ERROR: Block %s is too wide (%d), truncated to %d\n",
		block->number, block->sequences[0].length, cols);
 }
 rows = block->num_sequences;
 if (rows > MAXROWS)
 {
     rows = MAXROWS;
     fprintf(stderr, "ERROR: Block %s is too deep (%d), truncated to %d sequences\n",
	block->number, block->num_sequences, rows);
 }

 for (acol = 0; acol < cols; acol++) {
  v->aapresent[acol][0] = block->residues[0][acol] ;
  v->aanumber[acol]  =  1;
 }
 for (acol = 0; acol < cols; acol++) {
  for (arow = 1; arow < rows; arow++) {
   alreadypresent  =  NO;
   for (aap = 0; aap < v->aanumber[acol]; aap++)
     if (block->residues[arow][acol] == v->aapresent[acol][aap])
       alreadypresent  =  YES;
   if (!alreadypresent) {
    v->aapresent[acol][v->aanumber[acol]] = block->residues[arow][acol];
    v->aanumber[acol] += 1; /* another aa occurs */
   } /* if */
  } /* for arow */
  v->aapresent[acol][v->aanumber[acol]] = '\0';
 } /* for acol */
}   /* end of noteaa */
/*===================================================================
 for every mutant needed,  generate the mutant, find its distance 
 to the other sequences in the alignment,  keeping short distance
 and the identities of those sequences that lie closest. Then   
 adjust weights.                                               
======================================================================*/
void calculate(block, v, owned)
Block *block;
struct vor *v;
double owned[MAXROWS];
{
 double mutant[EXTRA_LARGE_BUFF][MAXAA];
 int icol, mut, z;
 double total, value, rrand;
 int cols, rows;

 cols = block->sequences[0].length;
 if (cols > EXTRA_LARGE_BUFF)
 {
     cols = EXTRA_LARGE_BUFF;
     fprintf(stderr, "ERROR: Block %s is too wide (%d), truncated to %d\n",
		block->number, block->sequences[0].length, cols);
 }
 rows = block->num_sequences;
 if (rows > MAXROWS)
 {
   rows = MAXROWS;
   fprintf(stderr, "ERROR: Block %s is too deep (%d), truncated to %d rows\n",
		block->number, block->num_sequences, rows);
 }

 total = 0.0;
 for (mut = 0; mut < NUMOFMUTANTS; mut++) {
  for (icol = 0; icol < cols; icol++) { /* make the mutant */
   value = 0;
   for (z = 0; z < v->aanumber[icol]; z++) {
    rrand = (double) ran0() / (RAND_MAX + 1.0);  /* between 0.0 and 1.0 */
    if (rrand != 0.0) value = -log(rrand);
    else value = 0.0;
    mutant[icol][v->aapresent[icol][z]] = value;
    total = total + value;
   }
   for (z = 0; z < v->aanumber[icol]; z++)
    mutant[icol][v->aapresent[icol][z]] =
      mutant[icol][v->aapresent[icol][z]] / total;
  } /* for icol */ /* that finishes making the mutant */
    adjustweights(block, mutant, owned);
 } /* for mut,  i.e. for every mutant needed */
}  /*  end of calculate */
/*===================================================================
======================================================================*/
void adjustweights(block, mutant, owned)
Block *block;
double mutant[EXTRA_LARGE_BUFF][MAXAA], owned[MAXROWS];
{
 double distance, shortdistance;
 int jrow, jcol, rowset[MAXROWS], r;
 int numinset; 			/* number of elements in the set */
 int cols, rows;

 cols = block->sequences[0].length;
 if (cols > EXTRA_LARGE_BUFF)
 {
     cols = EXTRA_LARGE_BUFF;
     fprintf(stderr, "ERROR: Block %s is too wide (%d), truncated to %d\n",
		block->number, block->sequences[0].length, cols);
 }
 rows = block->num_sequences;
 if (rows > MAXROWS)
 {
   rows = MAXROWS;
   fprintf(stderr, "ERROR: Block %s is too deep (%d), truncated to %d rows\n",
		block->number, block->num_sequences, rows);
 }

 shortdistance  =  MAXINT;
 for (r = 0; r < rows; r++) rowset[r] = NO;
 for (jrow = 0; jrow < rows; jrow++) {
  distance  =  0;
  /* identity distances are used */
  for (jcol = 0; jcol < cols; jcol++)
   distance = distance + mutant[jcol][block->residues[jrow][jcol]];
  if (distance <= shortdistance)
  {
   if (distance < shortdistance)
   {
     for (r = 0; r < rows; r++) rowset[r] = NO;
     rowset[jrow]  =  YES;		/* initialize rowset here */
     shortdistance  =  distance;
     numinset  =  1;
   }
   else
   {
     rowset[jrow] = YES;		/* add row to rowset here */
     numinset  =  numinset + 1;
   }
  } /* if distance <= */
 } /* for jrow */ /* found the shortest distance and those rows in the */
                    /* alignment that have that distance. now weights.  */
 /* calculate a single weight */
 for (jrow = 0; jrow < rows; jrow++)
  if (rowset[jrow])
     owned[jrow] += ((double) 1.0 / numinset);
}  /* end of adjustweights */
/*======================================================================*/
/*=================================================================
   From Press, et al, "Numerical Recipes in C", pp.207-208
   Improved random number generator (breaks up sequential correlations)

   Assumes random number generator has been seeded elsewhere (does
   not call srand).
   Assumes caller will divide results by RAND_MAX+1 (so it can be
   used the same as rand()).
========================================================================*/
int ran0()
{
   static int y, v[98];
   static int iff=0;			/* first call flag */
   int j;

   if (iff == 0)	/* fill array on first call */
   {
      iff=1;
      for (j=0; j<=97; j++) v[j] = random();
      y=random();
   }
   j = 1 + 97.0 * y / (RAND_MAX+1.0);
   if (j >=0 && j <= 97)
   {
      y=v[j];
      v[j] = random();
   }
   else y=random();
   return (y);
}  /* end of ran0 */

/*=========================================================================
===========================================================================*/
/*======================================================================*/
/*    Cluster sequences in a block based on the number of               */
/*    identities within the block. Sets Block.cluster & Block.ncluster  */
/*      1. Compute number of identities for each possible pair of seqs. */
/*         Results stored in lower half of matrix (pairs).              */
/*      2. Use clustering threshold % of # of AAs in trimmed block.     */
/*      3. Cluster recursively by traversing cols, rows of matrix.      */
/*   iclus = #clusters, nclus[iclus] = #seqs in cluster,
     icluster[s1] = cluster seq s1 belongs to
========================================================================*/
Block *cluster(clus, block)
int clus;
Block *block;
{
   int iclus, npair, threshold, s1, s2, l1, l2, px, i, i1, i2, first;
   int nclus[MAXROWS], icluster[MAXROWS], minclus, oldclus, width, nseq;
   struct pair *pairs;
   Block *newblock;

   width = block->sequences[0].length;
   nseq = block->num_sequences;
   if (nseq > MAXROWS)
   {
     nseq = MAXROWS;
     fprintf(stderr, "ERROR: Block %s is too deep (%d), truncated to %d nseq\n",
		block->number, block->num_sequences, nseq);
   }
   npair = nseq*(nseq-1)/2;
   pairs = (struct pair *) malloc(npair * sizeof(struct pair));
   threshold = (int) (clus*(width))/100;

   /*    Compute scores for all possible pairs of sequences            */
   for (s1=0; s1= 0 && i1 < width &&
		i2 >= 0 && i2 < width &&
		block->residues[s1][i1] == block->residues[s2][i2])
		   pairs[px].score += 1;
	 }
      }  /* end of s2 */
   }  /* end of s1 */

/*  Print scores */
/*   printf("\nThreshold=%d", threshold);
   for (s2=1; s2= threshold)	/*  cluster this pair */
	 {
	    if (icluster[s1] < 0)          /* s1 not yet clustered */
	    {
	       if (icluster[s2] < 0)       /* new cluster */
	       {
		  icluster[s1] = iclus++;
		  icluster[s2] = icluster[s1];
	       }
	       else  				/* use s2's cluster  */
		  icluster[s1] =  icluster[s2];
	    }
	    /*  use s1's cluster if it has one and s2 doesn't */
	    else if (icluster[s1] >= 0 && icluster[s2] < 0)
	       icluster[s2] = icluster[s1];
	    /* merge the two clusters into the lower number */
	    else if (icluster[s1] >= 0 && icluster[s2] >= 0)
	    {
	       minclus = icluster[s1]; oldclus = icluster[s2];
	       if (icluster[s2] < icluster[s1])
	       {
		  minclus = icluster[s2]; oldclus = icluster[s1];
	       }
	       for (i1=0; i1sequences[s1].weight = (double) 1.0 / nclus[icluster[s1]];
   }
   /*----------- Now reorder the block clusters ----------------------*/
   newblock = new_block(width, nseq);	/* allocates 1 Cluster */
   strcpy(newblock->id, block->id);
   strcpy(newblock->ac, block->ac);
   strcpy(newblock->number, block->number);
   strcpy(newblock->de, block->de);
   strcpy(newblock->bl, block->bl);
   newblock->num_clusters = 0;
   newblock->max_clusters = iclus;
   newblock->clusters = (Cluster *) realloc(newblock->clusters, iclus*sizeof(Cluster));
   s2 = 0; i2 = 0;
   for (i=0; i< iclus; i++)
   {
      if (nclus[i] > 0)  /* merged clumps have no members */
      {
         newblock->num_clusters += 1;
         newblock->clusters[i2].num_sequences = nclus[i];
         first = YES;
         for (s1=0; s1 < nseq; s1++)
         {
            if (icluster[s1] == i)
            {
               newblock->sequences[s2] = block->sequences[s1];
               if (first)	/* first sequence for this clump */
               {
                  newblock->clusters[i2].sequences = &(newblock->sequences[s2]);
                  first = NO;
               }
               s2++;
            }
         }
         i2++;
      }
   }
/*
   for (i=0; inum_sequences; seq++)
   {
      sumweight += block->sequences[seq].weight;
      if (block->sequences[seq].weight > maxweight) 
           maxweight = block->sequences[seq].weight;
      if (block->sequences[seq].weight < minweight) 
           minweight = block->sequences[seq].weight;
   }

   factor = 1.0;
   /*    Force maximum weight to be 100  */
   if (stype == 0 && maxweight > 0.0)
   {  factor = 100. / maxweight;  }
   else if (sumweight > 0.0)
   {
        /*    Force sum of weights to be number of sequences */
        if (stype == 1 && sumweight > 0.0) 
        { factor = (double) block->num_sequences / sumweight; }
        /*    Force sum of weights to be stype */
        else
        {
         if (stype > 1 && sumweight > 0.0) 
         { factor = (double) stype / sumweight; }
        }
   }

   for (seq = 0; seq < block->num_sequences; seq++)
   {
      block->sequences[seq].weight *= factor;
   }
}  /* end of scale_weights */

/*=======================================================================
 * put_block
     Same as blimps output_block(), but outputs weight in floating
     point if stype == 1 => weights sum to # of sequences
 *   Outputs a block data structure to the given file. 
 *   Parameters: 
 *     Block *block:  the block to print
 *     FILE  *obfp:   the ouput block file pointer
 ======================================================================*/

void put_block(block, obfp, stype)
     Block *block;
     FILE *obfp;
     int stype;
{
  int i,j,k, lenb, offset;
  char *ptr, bltemp[132];

  fprintf(obfp, "ID   %s\n", block->id);
  fprintf(obfp, "AC   %s\n", block->ac);
  fprintf(obfp, "DE   %s\n", block->de);
  /* Number of sequences may have changed; need to update block->bl if so */
  /*  Rewrite everything after width= if it is found, else append */
  lenb = strlen(block->bl);
  ptr = strstr(block->bl, "width=");
  if (ptr!=NULL)
  {
     strcpy(bltemp, block->bl);
     block->bl[0] = '\0';
     offset = lenb - strlen(ptr);
     strncat(block->bl, bltemp, offset);        /* preserve first part */
     block->bl[offset] = '\0';
  }
  sprintf(bltemp, " width=%d; seqs=%d; 99.5%%=%d; strength=%d ",
      block->width, block->num_sequences,
      block->percentile, block->strength);
  strcat(block->bl, bltemp);
  fprintf(obfp, "BL   %s", block->bl);

  /* print clusters */
  for (i=0; inum_clusters; i++) {
    fprintf(obfp, "\n");
    for (j=0; jclusters[i].num_sequences; j++) {
      /*  right-justify is %20.20s   */
      fprintf(obfp, "%-20s (%4d) ", 
	      block->clusters[i].sequences[j].name,
	      block->clusters[i].sequences[j].position);
      for(k=0; kclusters[i].sequences[j].length; k++) {
	fprintf(obfp, "%c", 
		aa_btoa[block->clusters[i].sequences[j].sequence[k]]);
      }
      if (stype == 1)
      fprintf(obfp, " %7.3f\n", block->clusters[i].sequences[j].weight);
      else
      fprintf(obfp, " %3d\n", round(block->clusters[i].sequences[j].weight));
    } /* end of cluster */
  }  
  /* end of the block */
  fprintf(obfp, "//\n");
  fflush(obfp);
} /* end of put_block */
istance  =  distance;
     numinset  =  1;
   }
   eblimps-3.9/blimps/cluster.c000064400001460000012000000107360774312247700163050ustar00jorjastaff00000400000027Block *cluster(clus, block)
int clus;
Block *block;
{
   int iclus, npair, threshold, s1, s2, l1, l2, px, i, i1, i2, first;
   int nclus[MAXROWS], icluster[MAXROWS], minclus, oldclus, width, nseq;
   struct pair *pairs;
   Block *newblock;

   width = block->sequences[0].length;
   nseq = block->num_sequences;
   if (nseq > MAXROWS)
   {
     nseq = MAXROWS;
     fprintf(stderr, "ERROR: Block %s is too deep (%d), truncated to %d nseq\n",
		block->number, block->num_sequences, nseq);
   }
   npair = nseq*(nseq-1)/2;
   pairs = (struct pair *) malloc(npair * sizeof(struct pair));
   threshold = (int) (clus*(width))/100;

   /*    Compute scores for all possible pairs of sequences            */
   for (s1=0; s1= 0 && i1 < width &&
		i2 >= 0 && i2 < width &&
		block->residues[s1][i1] == block->residues[s2][i2])
		   pairs[px].score += 1;
	 }
      }  /* end of s2 */
   }  /* end of s1 */

/*  Print scores */
/*   printf("\nThreshold=%d", threshold);
   for (s2=1; s2= threshold)	/*  cluster this pair */
	 {
	    if (icluster[s1] < 0)          /* s1 not yet clustered */
	    {
	       if (icluster[s2] < 0)       /* new cluster */
	       {
		  icluster[s1] = iclus++;
		  icluster[s2] = icluster[s1];
	       }
	       else  				/* use s2's cluster  */
		  icluster[s1] =  icluster[s2];
	    }
	    /*  use s1's cluster if it has one and s2 doesn't */
	    else if (icluster[s1] >= 0 && icluster[s2] < 0)
	       icluster[s2] = icluster[s1];
	    /* merge the two clusters into the lower number */
	    else if (icluster[s1] >= 0 && icluster[s2] >= 0)
	    {
	       minclus = icluster[s1]; oldclus = icluster[s2];
	       if (icluster[s2] < icluster[s1])
	       {
		  minclus = icluster[s2]; oldclus = icluster[s1];
	       }
	       for (i1=0; i1sequences[s1].weight = (double) 1.0 / nclus[icluster[s1]];
   }
   /*----------- Now reorder the block clusters ----------------------*/
   newblock = new_block(width, nseq);	/* allocates 1 Cluster */
   strcpy(newblock->id, block->id);
   strcpy(newblock->ac, block->ac);
   strcpy(newblock->number, block->number);
   strcpy(newblock->de, block->de);
   strcpy(newblock->bl, block->bl);
   newblock->num_clusters = 0;
   newblock->max_clusters = iclus;
   newblock->clusters = (Cluster *) realloc(newblock->clusters, iclus*sizeof(Cluster));
   s2 = 0; i2 = 0;
   for (i=0; i< iclus; i++)
   {
      if (nclus[i] > 0)  /* merged clumps have no members */
      {
         newblock->num_clusters += 1;
         newblock->clusters[i2].num_sequences = nclus[i];
         first = YES;
         for (s1=0; s1 < nseq; s1++)
         {
            if (icluster[s1] == i)
            {
               newblock->sequences[s2] = block->sequences[s1];
               if (first)	/* first sequence for this clump */
               {
                  newblock->clusters[i2].sequences = &(newblock->sequences[s2]);
                  first = NO;
               }
               s2++;
            }
         }
         i2++;
      }
   }
/*
   for (i=0; i
		Required: BL, OU, FR, QM and (PC or SU)
		Optional: (DB or SQ) and MA 
			  
		First determines consensus (TY, make_consensus());
		then sequence in blocks closest to consensus; 
		then embeds consensus in closest sequence (DB), or
		in provided sequence (SQ); also outputs embedded
		PSSM (if MA).
		TY Consensus type:
			1 Percent of weighted counts ( percent_consensus() )
			  Requires PC
			2 Scores with weighted counts ( score_consensus() )
			  Requires SU
			3 Scores with weighted counts + pseudo-counts
				( score_pseudos() )
			  Requires SU, FR & QM
			4 Maximum PSSM residue ( pssm_consensus() )
			  Requires FR & QM
		BL input file of blocks to make consensus from; must
		   contain sequence weights.
		OU output file of consensus blocks, or embedded
		   sequences if DB or SQ is specified.
		PC Percent identity for consensus residue in a position
		   of a block. PC = 0 => use most common residue; PC < 0
		   => use a residue at random. Or use SU instead.
		SU Name of substitution matrix to use to determine
		   consensus residues, instead of using PC. Takes residue
		   with highest pairwise score with other residues in position.
		   Use blosum62.iij, e.g.
		MA Name of PSSM to use when making profile. 
		   This triggers profile output = .prf file in format
		   specified by PF.
		   Use single55.mat for SWAT; single55.psi for PSI.
		   Use single55.mat for PFS (does PFS work?)
		PF format of output PSSM: BLIMPS|SWAT|PSI|PFS=Gribskov
		DB file containing sequences in blocks in BL file.
		   Consensus blocks will be embedded in the
		   first sequence most like the consensus & written
		   to file OU.
		SQ file containing selected query sequence.
		   First family of blocks in BL will be aligned with
		   sequence using a PSSM; then consensus blocks will
		   be embedded at the alignments if all blocks are
		   aligned in the correct order without overlap and
	           written to file OU. Requires FR and QM.
		FR Name of frequency matrix to use to make PSSM for SQ & MA.
		   Also used to make PSSMs for "TY 3" & "TY 4".
		   In summary, used to make all required log-odds PSSMS; 
		   see also QM.
		   Use default.amino.frq, e.g.
		QM Name of qij matrix used for pseudo-counts when making
		   Altschul-type log-odds PSSMs. Used to make PSSM for 
		   aligning blocks with SQ sequence. Also used to make 
		   embedded PSSM when MA is specified. Also used to make
		   PSSM to select consensus residues when "TY 4" is used.
		   Also used to make pseudo-counts for selecting consensus
		   residues when "TY 3" is used.
		   Should separate these options; see also FR.
		   These PSSMs are always 1/3 bit log odds (6).
		   Use default.qij or blosum55.qij e.g.
		TR Trimmed length: length of cobbler sequence before &
		   after start of blocks to include in output sequence
		   (entire sequence is output by default)


>>>>> Problems if: Not same sequences in all blocks, or
 	     blocks not in same order in all blocks, or
	     blocks overlap

--------------------------------------------------------------------
 7/ 7/97 Changed extract_seq() to look for id anywhere on title line.
         Changed score_pseudos() to just use the 20 major aas.
 2/21/98 Added TR option, SHORT_TRIM, etc. to output trimmed sequence.
         Changed MAXWIDTH from 60 to 80.
 6/12/99 Tried to fix problem if lots of sequence left after last block
	 (truncate sequence in extract_seq()). Blimps 3.2.6
 7/ 3/99 Option to output psi-blast checkpoint file; PrfOutType = PRF_PSI
 7/ 5/99 Replaced extract_seq() with read_seq(); reworked embed_consensus()
 7/ 6/99 Reworked query_consensus()
 7/ 8/99 Bug fix
 7/10/99 For pre-selected sequence (SQ), don't count the distance
	 before the first block in the min length; query_consensus()
 7/23/99 Commented out RAND_MAX
 8/ 5/99 Check that embedded sequence/profile doesn't exceed length of
	 chosen sequence.
 8/ 6/99 Handle embedded seqs with blocks out of order; added Version.
 8/19/99 Indicate if DB seq not found; match seqs on any part of name
	 separated by "|"
 9/ 3/99.1 Added BLIMPS output PSSM option (to PF).
           Check that input blocks (BL) have sequence weights &
           run pb_weights if they don't.
12/ 9/99.1 Fix memory leaks
12/17/99.1 Changes for longer AC
12/23/99.1 Print width on pssm->ma for output_matrix()
 3/28/00.1 Revised output text
 3/28/00.2 New ML/LL config file options to output most like/least like seqs
 4/14/00.1 Fix problem with multi-part names in read_seq()
>>>>>>>>>>>>>>>>>>>>Blimps 3.4<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 6/27/00.1 Fix problem not finding LL sequence in read_seq()
>>>>>>>>>>>>>>>>>>>>Blimps 3.5<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 1/16/03.1 Default SU, QM, FR if not specified in config file
====================================================================*/

#define COBBLER_C_
#define EXTERN
#define MAXNAME 80	/* Maximum file name length */
#define MAXAA 25	/* Dimension of aa_ arrays */
#define MAXWIDTH 80	/* Maximum block width */
#define CPROP .25	/* Default Minimum proportion of consensus weight */
#define PRF_SWAT 0	/* swat */
#define PRF_PFS 1	/* profilesearch */
#define PRF_PSI 2	/* psi-blast */
#define PRF_BLI 3	/* blimps format */
/*		Already defined for Solaris  2^31 - 1
#define RAND_MAX 2147483647
*/
#define YES 1
#define NO 0
#define SHORT_TRIM 10	/* Default trimmed length */

#include 
#include 

/*   Blimps routines and data structures   */
extern int ErrorLevelReport;
extern struct float_qij *Qij;
extern double RTot;
extern double frequency[MATRIX_AA_WIDTH];
extern struct float_qij *load_qij();
extern int load_frequencies();
extern Matrix *block_to_matrix();

/*
 * Global variables and data structures
 */

char Version[12] = " 1/16/03.1";	/* Version number */

/*  List of blocks structure:
    First entry has no block, just nblock, nseq, totwidth & minseq,
    other entries in list have pointers to the blocks, minprev & seqprev
*/
struct blocks_list {		/* list of blocks for a family */
   int nblock;				/* number of blocks in family */
   int nseq;				/* number of sequences in blocks */
   int totwidth;			/* total width of blocks in list  */
   int minseq;				/* sequence most like consensus */
   int maxseq;				/* sequence least like consensus */
   int minprev;				/* min distance from previous block*/
   int maxprev;
   int minseqprev;			/* previous distance for minseq */
   int maxseqprev;			/* previous distance for maxseq */
   int query_pos;
   int *consensus;			/* consensus for this block */
   Block *block;
   Matrix *matrix;
   struct blocks_list *next;		/* next block in ABC order */
   struct blocks_list *next_min;		/* next block in minseq order */
};
struct seqseq { int seq; };

struct sorttemp {
   int position;			/* sequence position */
   struct blocks_list *blist;		/* block list */
};

int read_cf();
void process_family();
void make_consensus();
void percent_consensus();
void score_consensus();
void score_pseudos();
void cons_diff();
void closest();
void print_consensus();
void embed_consensus();
Sequence *read_seq();
void query_consensus();
int best_pos();
void pssm_consensus();
void write_cobbler();
void get_seq();

void make_random();
int ran0();

struct blocks_list *make_blist();
void insert_blist();
void free_blist();
void order_seq();
void load_sij();
int sortcmp();

int SeqType;			/*  why??? blimps stuff */
int Type;			/* Consensus type */
int PrfOutType;			/* Output profile type */
int PrfInType;			/* Input profile type */
int ShortTrim, Short;		/* Sequence trimming info */
double CProp;			/* Min weight % for consensus residue */
int Scores[MAXAA][MAXAA];	/*  Scoring matrix */
Matrix *Profile;		/* Baseline PSSM for making a profile */
FILE *Fbl, *Fou, *Fml, *Fll, *Fpr, *Fsq, *Fdb;	/* Config. files */
/*======================================================================
 * main
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *cfp;
  Block *block;
  struct blocks_list *blist;
  char cfname[MAXNAME], save_family[MAXAC+1];
  struct timeval tv;

  ErrorLevelReport = 5;			/* don't want to see them */
  /* initialize random number generator */
  gettimeofday(&tv, NULL);
  srandom(tv.tv_sec^tv.tv_usec);

   if (argc <= 1)
   {
       printf("COBBLER Version %s\n", Version);
       printf("COPYRIGHT 1999 Fred Hutchinson Cancer Research Center\n");
       printf("Make a consensus sequence and PSSM from a family of blocks\n");
       printf("USAGE:  cobbler \n");
   }
/*------------1st arg = configuration file -------------------------------*/
   if (argc > 1)
      strcpy(cfname, argv[1]);
   else
   {
      printf("\nEnter name of configuration file: ");
      gets(cfname);
   }
   if ( (cfp=fopen(cfname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", cfname);
      exit(-1);
   }
   if ( (Type = read_cf(cfp)) < 0)
   {
      printf("Configuration file errors\n");
      exit(-1);
   }

  /*-------------------Read in each family of blocks -------------------*/
  save_family[0] = '\0';
  blist = NULL;
  while ((block = read_a_block(Fbl)) != NULL)
  {
     if (strcmp(save_family, block->family) != 0)
     {  /*  new family */
         process_family(blist, Fou, Fpr); /* process previous family */
         /*   initialize new family */
         strcpy(save_family, block->family);
         if (Fdb == NULL && Fsq == NULL) 
              fprintf(Fou, ">%s %s\n", save_family, block->de); 
         blist = make_blist();			/* header for list */
         insert_blist(blist, block);		/* 1st block in list */
     }
     else      /*  same family */
     {
         insert_blist(blist,block);
     }
  }     /*  end of block */

  /*  process previous family */
  process_family(blist, Fou, Fpr);
  if (cfp != NULL) fclose(cfp); 
  if (Fbl != NULL) fclose(Fbl); 
  if (Fou != NULL) fclose(Fou); 
  if (Fpr != NULL) fclose(Fpr);
  if (Fsq != NULL) fclose(Fsq);

  /*  print out most like/ least like sequences if requested */
  if (Fdb != NULL)
  {
     if (Fml != NULL) 
          get_seq(blist->next->block->family,
                  blist->next->block->sequences[blist->minseq].name, 
                  Fdb, Fml);
     if (Fll != NULL)
          get_seq(blist->next->block->family,
                  blist->next->block->sequences[blist->maxseq].name, 
                  Fdb, Fll);
  }
   
  if (Fml != NULL) fclose(Fml);
  if (Fll != NULL) fclose(Fll);
  if (Fdb != NULL) fclose(Fdb);
  exit(0);

}  /* end of main */
/*=======================================================================*/
int read_cf(cfp)
FILE *cfp;
{
   char line[MAXLINE], keyword[20], *blimps_dir, *ptr;
   char blname[MAXNAME], ouname[MAXNAME], frname[MAXNAME];
   char mlname[MAXNAME], llname[MAXNAME];
   char suname[MAXNAME], qmname[MAXNAME], sqname[MAXNAME];
   char dbname[MAXNAME], maname[MAXNAME], ctemp[MAXNAME];
   int cscores, freqs;
   FILE *fqm, *fsu, *fma;

   blimps_dir = getenv("BLIMPS_DIR");

   CProp = CPROP;
   PrfOutType = PRF_SWAT;
   Type = -1;
   RTot = 5.0;
   Short = NO;
   cscores = freqs = NO;

   Fbl = Fou = Fml = Fll = Fsq = Fdb = fqm = fma = NULL;
   while (!feof(cfp) && fgets(line, MAXLINE, cfp) != NULL)
   {
      ptr = strtok(line, " \t\r\n");
      if (ptr != NULL && ptr[0] != ';')
      {
         strcpy(keyword,ptr);
         ptr = strtok(NULL, " \t\r\n;");
         if (ptr != NULL)
         {
            if (strncasecmp(keyword, "TY", 2) == 0)
            {
               Type = atoi(ptr);
            }
            else if (strncasecmp(keyword, "BL", 2) == 0)
            {
               strcpy(blname, ptr);
               if ( (Fbl = fopen(blname, "r")) == NULL)
                  printf("\nCannot open BL file %s\n", blname);
            }
            else if (strncasecmp(keyword, "OU", 2) == 0)
            {
               strcpy(ouname, ptr);
               if ( (Fou = fopen(ouname, "w")) == NULL)
                  printf("\nCannot open OU file %s\n", ouname);
               else printf("Consensus written to %s\n", ouname);
            }
            else if (strncasecmp(keyword, "ML", 2) == 0)
            {
               strcpy(mlname, ptr);
               if ( (Fml = fopen(mlname, "w")) == NULL)
                  printf("\nCannot open ML file %s\n", mlname);
               else printf("Most like consensus written to %s\n", mlname);
            }
            else if (strncasecmp(keyword, "LL", 2) == 0)
            {
               strcpy(llname, ptr);
               if ( (Fll = fopen(llname, "w")) == NULL)
                  printf("\nCannot open LL file %s\n", llname);
               else printf("Least like consensus written to %s\n", llname);
            }
            else if (strncasecmp(keyword, "SQ", 2) == 0)
            {
               strcpy(sqname, ptr);
               if ( (Fsq = fopen(sqname, "r")) == NULL)
                  printf("\nCannot open SQ file %s\n", sqname);
            }
            else if (strncasecmp(keyword, "DB", 2) == 0)
            {
               strcpy(dbname, ptr);
               if ( (Fdb = fopen(dbname, "r")) == NULL)
                  printf("\nCannot open DB file %s\n", dbname);
            }
            else if (strncasecmp(keyword, "FR", 2) == 0)
            {
               strcpy(frname, ptr);
               if (load_frequencies(frname) < 0)
                  printf("\nCannot open FR file %s\n", frname);
               else freqs = YES;
            }
            else if (strncasecmp(keyword, "PC", 2) == 0)
            {
               CProp = (double) atoi(ptr) / 100.;
               if (CProp > 1.0 || CProp < 0.0) CProp = -1.0;
            }
            else if (strncasecmp(keyword, "SU", 2) == 0)
            {
               strcpy(suname, ptr);
               if ( (fsu = fopen(suname, "r")) == NULL)
                  printf("\nCannot open SU file %s\n", suname);
               else
               {  cscores=YES;  load_sij(fsu, Scores);  fclose(fsu);  }
            }
            else if (strncasecmp(keyword, "MA", 2) == 0)
            {
               strcpy(maname, ptr);
               if ( (fma = fopen(maname, "r")) == NULL)
                  printf("\nCannot open MA file %s\n", maname);
               else
               {   Profile = read_a_matrix(fma);  fclose(fma);  }
            }
            else if (strncasecmp(keyword, "PF", 2) == 0)
            {
               strcpy(ctemp, ptr);
               if (strncasecmp(ctemp, "PSI", 3) == 0) PrfOutType = PRF_PSI;
               else if (strncasecmp(ctemp, "PFS", 3) == 0) PrfOutType = PRF_PFS;
               else if (strncasecmp(ctemp, "BLI", 3) == 0) PrfOutType = PRF_BLI;
            }
            else if (strncasecmp(keyword, "QM", 2) == 0)
            {
               strcpy(qmname, ptr);
               if ( (fqm = fopen(qmname, "r")) == NULL)
                  printf("\nCannot open QM file %s\n", qmname);
               else
               { Qij = load_qij(fqm); RTot = 5.0; fclose(fqm);   }
            }
            else if (strncasecmp(keyword, "TR", 2) == 0)
            {
                 Short = YES;
                 ShortTrim = atoi(ptr);
                 if (ShortTrim < 0) ShortTrim = SHORT_TRIM;
            }
         }   /* end of if ptr */
      }  /* end of if ptr */
   }  /* end of cfp */

   /*   Get some defaults */
   if (blimps_dir != NULL)
   {
      /*  Default SU if not specified to default.iij */
      if (!cscores)
      {
         sprintf(suname, "%s/docs/default.iij", blimps_dir);
         if ( (fsu = fopen(suname, "r")) != NULL)
         {  cscores=YES;  load_sij(fsu, Scores);  fclose(fsu);  }
      }
      /*  Default FR and QM if they weren't specified  */
      /* Sets global variables Qij, frequency[], RTot  */
      /* Always reads default.amino.frq & default.qij & sets RTot = 5 */
      if (!freqs)
      {
         sprintf(frname, "%s/docs/default.amino.frq", blimps_dir);
         if (load_frequencies(frname) >= 0)
          { freqs = YES;  }
      }
      if (Qij == NULL)
      {
         sprintf(qmname, "%s/docs/default.qij", blimps_dir);
         if ( (fqm = fopen(qmname, "r")) != NULL)
         { Qij = load_qij(fqm); RTot = 5.0; fclose(fqm);   }
      }
   }

   if (Profile != NULL)
   {
      strcpy(ctemp, ouname); strcat(ctemp, ".prf");
      if ( (Fpr = fopen(ctemp, "w")) == NULL)
      {
            printf("\nCannot open OU file %s\n", ctemp);
            free_matrix(Profile);
	    Profile = NULL; PrfOutType = -1;
      }
      else printf("Profile written to %s\n", ctemp);
   }
   else { PrfOutType = -1;  }

   /*----------------------------------------------------------------*/
   /*    Figure out the type now   */
   /*  1  Percent
       2  Substitution matrix + counts
       3  Substitution matrix + counts + pseudo-counts
       4  PSSM
   */
   if (Type < 0)		/* TY wasn't specified explicitly */
   {
      if (cscores) Type = 3;
      else if (Qij != NULL && freqs) Type = 4;
      else Type = 1;
   }
   else				/* TY was specified explicitly */
   {
      if (Type == 1)
      {  cscores = NO;  }
      else if (Type == 2)
      {
         if (!cscores)
         {  printf("Missing SU input file name\n"); Type = -1; }
      }
      else if (Type == 3)
      {
         if (!cscores)
         {  printf("Missing SU input file name\n"); Type = -1; }
         if (Qij == NULL || !freqs)
         {  printf("FR and QM required with Type 3\n");  Type = -1; }
      }
      else if (Type == 4)
      {
         if (Qij == NULL || !freqs)
         {  printf("FR and QM required with Type 4\n");  Type = -1; }
      }
   }
   if (Type > 4)
   {  printf("Invalid consensus type: %d\n", Type); Type = -1; }
   if (Fbl == NULL)
   {  printf("Missing BL input file name\n"); Type = -1; }
   if (Fou == NULL)
   {  printf("Missing OU output file name\n"); Type = -1; }
   if (Fdb != NULL && Fsq != NULL)
   {  printf("Cannot specify both DB and SQ\n"); Type = -1; }
   if (Fsq != NULL && (Qij == NULL || !freqs))
   {  printf("FR and QM required with SQ\n");  Type = -1; }
   if (Fpr != NULL && (Qij == NULL || !freqs))
   {  printf("FR and QM required with MA\n");  Type = -1; }
   if (Fml != NULL && Fdb == NULL)
   {  printf("DB required with ML\n");  Type = -1; }
   if (Fll != NULL && Fdb == NULL)
   {  printf("DB required with LL\n");  Type = -1; }
   

   return(Type);
}  /* end of read_cf */
/*=======================================================================
========================================================================*/
void process_family(blist, ofp, pfp)
struct blocks_list *blist;
FILE *ofp, *pfp;
{

  if (blist != NULL && blist->nblock > 0)
  {
      switch (Type)
      {
         case 1:			/* percentage */
		printf("Type 1: Consensus based on percentage: %d\n",
			(int) (100. * CProp) );
		break;
	 case 2:			/* subst. with counts */
		printf("Type 2: Consensus based on substitution matrix");
                printf(" with counts (no pseudo-counts)\n");
		break;
	 case 3:			/*subst with counts + pseudos */
		printf("Type 3: Consensus based on substitution matrix");
		printf(" with counts + pseudo-counts\n");
		break;
	 case 4:			/* PSSM */
		printf("Type 4: Consensus based on PSSM\n");
		break;
	 default:
		break;
     }
     if (Type == 1 && CProp < 0.0)
     {   make_random(blist, ofp);    }
     else
     {
        make_consensus(blist); 
        if (Fdb != NULL)      embed_consensus(blist, ofp, pfp, NULL);
        else if (Fsq != NULL) query_consensus(blist, ofp, pfp);
             else             print_consensus(blist, ofp);
     }

/*
     free_blist(blist);
*/
   }

}   /* end of process_family  */
/*=======================================================================
      Turn a list of blocks into a consensus sequence
      Count the number of positions each sequence in the block differs
      from the consensus. The master sequence order is that in the 
      first block of the family.
========================================================================*/
void make_consensus(blist)
struct blocks_list *blist;
{
   struct blocks_list *bcur;
   Block *block, *first_block;
   struct seqseq *sseq;

   sseq = (struct seqseq *) malloc (blist->nseq * sizeof(struct seqseq));
   first_block = NULL;
   bcur = blist->next;
   while(bcur != NULL && bcur->block != NULL)
   {
      /*  process each block separately  */
      block = bcur->block;

      /*-----  Figure out the consensus segment for this block ------------*/
      /*  (Puts result in bcur->consensus )   */
      switch (Type)
      {
         case 1:			/* percentage */
		percent_consensus(bcur);
		break;
	 case 2:			/* subst. with counts */
		score_consensus(bcur);
		break;
	 case 3:			/*subst with counts + pseudos */
		score_pseudos(bcur);
		break;
	 case 4:			/* PSSM */
		pssm_consensus(bcur);
		break;
	 default:
		break;
      }

      /*---------Count the number of differences b/w each seq & consensus--*/
      /*  (Puts result in first_block->sequences[seq].undefined)   */
      if (first_block == NULL) first_block = block;
      cons_diff(bcur, first_block, sseq);

      bcur = bcur->next;
   }  /* end of block */

   /*----------Determine the closest sequence ---------*/
   /*   (Puts results in block list records)           */
   /*  Extract blist->next->block->sequences[blist->minseq].name  */
   closest(blist, first_block, sseq);

   free(sseq);
}  /* end of make_consensus */
/*========================================================================
        Figure out the consensus for this block based on percentage
        & store it in the block list record
=========================================================================*/
void percent_consensus(bcur)
struct blocks_list *bcur;
{
   double sum[MAXAA+1], tot, maxw;
   int seq, pos, aa, width, maxaa, dupmax;
   Block *block;

   block = bcur->block;
   width = block->width;

   /*-------------------------------------------------------------------*/
   for (pos = 0; pos < width; pos++)
   { 
      tot = 0.0;
      maxw = maxaa = dupmax = -1;
      for (aa = 0; aa < MAXAA+1; aa++) sum[aa] = 0.0;
  
      for (seq = 0; seq < block->num_sequences; seq++)
      {
         if (block->residues[seq][pos] >= 0 &&
                block->residues[seq][pos] < MAXAA)
         {
            sum[block->residues[seq][pos]] += block->sequences[seq].weight;
            tot += block->sequences[seq].weight;
         }
         else printf("Unknown residue: %d\n", block->residues[seq][pos]);
      }

      for (aa = 0; aa < MAXAA+1; aa++)
      {
         if (sum[aa] > maxw)
         {
            maxw = sum[aa]; maxaa = aa;
         }
         else if (sum[aa] > 0.0 && sum[aa] == maxw)
                  dupmax = aa;
      }
      /*-------  Print "x" if maximum weight for any aa is < CProp% ------*/
      if ((maxw / tot) < CProp) maxaa = MAXAA;

      /*--------Save the consensus sequence------------------------*/
      if (maxaa >= 0 && maxaa < MAXAA )
           bcur->consensus[pos] = maxaa;
      else
           bcur->consensus[pos] = MAXAA;	/* X==23 */
   }  /*  end of pos */

}   /*  end of percent_consensus  */
/*========================================================================
        Figure out the consensus for this block & store it in the
        block list record - use highest total pairwise score
        Prints x if the best total score is negative
>>>>>  need to add a type to block_to_matrix(block, 21) that returns
	counts & just use them (like score_pseudos() does);
	would take care of the sequence weights too (see insert_blist())
=========================================================================*/
void score_consensus(bcur)
struct blocks_list *bcur;
{
   double sum[MAXAA+1], maxw, weight;
   int seq1, pos, width, nseq, maxaa, aamark[MAXAA+1];
   int aa1, aa2;
   Block *block;

   block = bcur->block;
   width = block->width;
   nseq = block->num_sequences;

   /*-------------------------------------------------------------------*/
   for (pos = 0; pos < width; pos++)
   { 
      /*    good sums can be negative */
      maxw = -999999.99;
      maxaa = -1;
      for (aa1 = 0; aa1 < MAXAA+1; aa1++)
      {
         sum[aa1] = 0.0;
         aamark[aa1] = NO;	/* does this aa appear in the pos ? */
      }
  
      /*   Mark the aas that appear in this position */
      for (seq1 = 0; seq1 < nseq; seq1++)
      {
            aa1 = block->residues[seq1][pos];
            aamark[aa1] = YES;
      }

      /*    Only choose among the aas that appear in the pos  */
      for (aa1 = 0; aa1 < MAXAA; aa1++)
      {
         sum[aa1] = 0.0;
         if ( aamark[aa1] )
         {
            for (seq1 = 0; seq1 < nseq; seq1++)
            {
               aa2 = block->residues[seq1][pos];
               weight =  block->sequences[seq1].weight;
               sum[aa1] += weight * Scores[aa1][aa2];
            }
         }
      }

      /*    Only choose among the aas that appear in the pos  */
      for (aa1 = 0; aa1 < MAXAA; aa1++)
      {
         if (aamark[aa1] && sum[aa1] > maxw)
         {
            maxw = sum[aa1]; maxaa = aa1;
         }
      }
      if (maxw <= 0.0) maxaa = MAXAA;	/*  Use X if non-positive sum */

      /*--------Save the consensus sequence------------------------*/
      if (maxaa > 0 && maxaa < MAXAA )
           bcur->consensus[pos] = maxaa;
      else
           bcur->consensus[pos] = MAXAA;	/* X==23 */
   }  /* end of pos */

}  /*  end of score_consensus */

/*========================================================================
        Figure out the consensus for this block & store it in the
        block list record - use highest total pairwise score
        Prints x if the best total score is negative
	Variation using pseudo-counts
=========================================================================*/
void score_pseudos(bcur)
struct blocks_list *bcur;
{
   double sum[MAXAA+1], maxw;
   int seq1, pos, width, nseq, maxaa, aamark[MAXAA+1];
   int aa1, aa2;
   Block *block;
   Matrix *matrix;

   block = bcur->block;
   width = block->width;
   nseq = block->num_sequences;
   matrix = block_to_matrix(block, 20);		/* counts+pseudos */

   /*-------------------------------------------------------------------*/
   for (pos = 0; pos < width; pos++)
   { 
      /*    good sums can be negative */
      maxw = -999999.99;
      maxaa = -1;
      for (aa1 = 0; aa1 < MAXAA+1; aa1++)
      {
         sum[aa1] = 0.0;
         aamark[aa1] = NO;	/* does this aa appear in the pos ? */
      }
  
      /*   Mark the aas that appear in this position */
      for (seq1 = 0; seq1 < nseq; seq1++)
      {
            aa1 = block->residues[seq1][pos];
            aamark[aa1] = YES;
      }

      /*    Only score the aas that appear in the pos  */
      for (aa1 = 0; aa1 < MAXAA; aa1++)
      {
         sum[aa1] = 0.0;
         if ( aamark[aa1] )
         {
            /*  Just the major 20 aas */
            for (aa2=1; aa2 <= 20; aa2++)
               sum[aa1] += matrix->weights[aa2][pos] * Scores[aa1][aa2];
         }
      }

      /*    Only choose among the aas that appear in the pos  */
      for (aa1 = 0; aa1 < MAXAA; aa1++)
      {
         if (aamark[aa1] && sum[aa1] > maxw)
         {
            maxw = sum[aa1]; maxaa = aa1;
         }
      }
      if (maxw <= 0.0) maxaa = MAXAA;	/*  Use X if non-positive sum */

      /*--------Save the consensus sequence------------------------*/
      if (maxaa > 0 && maxaa < MAXAA )
           bcur->consensus[pos] = maxaa;
      else
           bcur->consensus[pos] = MAXAA;	/* X==23 */
   }  /* end of pos */

   free_matrix(matrix);
}  /*  end of score_pseudos */
/*=======================================================================
      Count the number of differences b/w each seq & consensus
      (Puts result in first_block->sequences[seq].undefined) 
========================================================================*/
void cons_diff(bcur, first_block, sseq)
struct blocks_list *bcur;
Block *first_block;
struct seqseq *sseq;
{
   int width, seq, pos;
   Block *block;

      block = bcur->block;
      width = block->width;
      /*----- Count the number of differences in this block ------*/
      for (seq = 0; seq < block->num_sequences; seq++)
         block->sequences[seq].undefined = 0;
      for (seq = 0; seq < block->num_sequences; seq++)
         for (pos = 0; pos < width; pos++)
            if (bcur->consensus[pos] >= 0 && bcur->consensus[pos] < MAXAA &&
                (int) block->residues[seq][pos] != bcur->consensus[pos])
                   block->sequences[seq].undefined += 1;
      /*------Total diffs for all blocks accumulated in first block -----*/
      if (first_block != NULL && first_block != block)
      {
         /*--- put block sequences in same order as first_block -----*/
         order_seq(sseq, first_block, block);
         for (seq=0; seq < block->num_sequences; seq++)
             first_block->sequences[seq].undefined += 
                   block->sequences[ sseq[seq].seq ].undefined;
      }

}  /*   end of cons_diff */
/*=====================================================================
   Determine which sequence is most like the consensus
   and update seqprev fields with its distances between blocks
=======================================================================*/
void closest(blist, first_block, sseq)
struct blocks_list *blist;
Block *first_block;
struct seqseq *sseq;
{
   Block *block, *save_block;
   struct blocks_list *bcur;
   int i, mindiff, maxdiff, width, seq, save_seq, nb;
   struct sorttemp stemp[26];

   /*--------Determine the closest sequence -------------------------*/
   /*  (cumulative differences are stored in first_block)            */
   mindiff = 999; maxdiff = save_seq = 0;
   for (seq=0; seq < blist->nseq; seq++)
      if (first_block->sequences[seq].undefined < mindiff)
      {
         mindiff = first_block->sequences[seq].undefined;
         blist->minseq = seq;
      }
      else if (first_block->sequences[seq].undefined > maxdiff)
      {
         maxdiff = first_block->sequences[seq].undefined;
         blist->maxseq = seq;
      }
   printf("%s %s\tis first sequence most like consensus (%d %d)\n",
            first_block->family,
            first_block->sequences[blist->minseq].name, 
	    blist->minseq, mindiff);
   printf("%s %s\tis first sequence least like consensus (%d %d)\n",
            first_block->family,
            first_block->sequences[blist->maxseq].name, 
            blist->maxseq, maxdiff);

   /*  The order of the blocks in minseq may be different than the
       ABC order, if repeats were allowed by PROTOMAT; get the
       correct order in minseq */
   i = 0;
   bcur = blist->next;
   while(bcur != NULL && bcur->block != NULL)
   {
      block = bcur->block;
      if (block == first_block)
      {   seq = blist->minseq;  }
      else
      {
         order_seq(sseq, first_block, block);
         seq = sseq[blist->minseq].seq;
      }
      stemp[i].blist = bcur;
      stemp[i].position = bcur->block->sequences[seq].position;
      i++;
      bcur = bcur->next;
   }
   /*   sort by position  */
   qsort(stemp, blist->nblock, sizeof(struct sorttemp), sortcmp);
  
   bcur = blist;
   for (i=0; i< blist->nblock; i++)
   {
      bcur->next_min = stemp[i].blist;
      bcur = bcur->next_min;
   }
   bcur->next_min = NULL;

   /*-------------------------------------------------------------------*/
   /*------ Determine the distance between blocks in the closest seq ---*/
   save_seq = nb = 0;
   save_block = NULL;
   bcur = blist->next_min;
   while(bcur != NULL && bcur->block != NULL)
   {
      block = bcur->block;
      width = block->width;
/*
      if (block == first_block)
      if (bcur == blist->next_min)
      {
         bcur->minseqprev = block->sequences[blist->minseq].position - 1;
         save_seq = blist->minseq;
      }
      else
*/
      order_seq(sseq, first_block, block);
      seq = sseq[blist->minseq].seq;
      if (nb == 0)
      {
         bcur->minseqprev = block->sequences[seq].position - 1;
      }
      else
      {
         /*  from end to last block to start of this one ... */
         bcur->minseqprev = block->sequences[seq].position - 
    (save_block->sequences[save_seq].position + save_block->width);
      }
      save_seq = seq;
      save_block = block;
      bcur = bcur->next_min;
      nb++;
   }  /* end of block */

}  /* end of closest */

/*=======================================================================
  Imbed the consensus sequence for a list of blocks
    Extract blist->next->block->sequences[blist->minseq].name 
    If Profile exists, output a profile as well in PrfOutType format
========================================================================*/
void embed_consensus(blist, ofp, pfp, seq)
struct blocks_list *blist;
FILE *ofp, *pfp;
Sequence *seq;
{
   int sngle, aa, pos, savpos, totpos, sumpos, width, aacount[25];
   int firstpos, firstaa, lastaa, cobblen, cobbpos;
   long ltemp;
   double dtemp;
   struct blocks_list *bcur;
   Block *block, *first_block;
   char fam[MAXAC+1], ctemp[12], *cobbler, seqname[MAXNAME];
   Matrix *pssm, *target;

   /*  Try to find the sequence, unless it was passed in */
   if (seq == NULL)
   {  
	seq = read_seq(Fdb, blist->next->block->sequences[blist->minseq].name); 
	if (seq == NULL)
        { printf ("%s: %s not found\n", 
		blist->next->block->number,
		blist->next->block->sequences[blist->minseq].name);  }
   }
   if (seq != NULL) { strcpy(seqname, seq->name);  }
   else { strcpy(seqname, blist->next->block->sequences[blist->minseq].name); }

   /*   Compute length of block region = sumpos */
   sumpos = 0;
   bcur = blist->next;
   while(bcur != NULL && bcur->block != NULL)
   {
      block = bcur->block;
      width = block->width;
      sumpos += width + bcur->minseqprev;
      bcur = bcur->next;
   }

   /*----------------------------------------------------------------*/
   /*     Now print out the sequence in lower case with the consensus
          blocks embedded in upper case    */

   for (aa=0; aa < 25; aa++) aacount[aa] = 0;
   /*  Set the first and last aas to print */
   firstaa = 0; 
   first_block = NULL;
   if (seq != NULL) lastaa = seq->length;
   else             lastaa = sumpos;
   if (Short)
   {
      bcur = blist->next_min;
      /*  First block */
      if (bcur->block != NULL)
      {
         first_block = bcur->block;
         firstaa = bcur->minseqprev - ShortTrim;
         if (firstaa < 0) firstaa = 0;
      }
      lastaa = 0;
      while(bcur != NULL && bcur->block != NULL)
      {
         lastaa += bcur->minseqprev;
         lastaa += bcur->block->width;
         bcur = bcur->next_min;
      }
      lastaa += ShortTrim;
   }
   if (firstaa < 0) firstaa = 0;
   if (seq != NULL)
   {
      if (lastaa > seq->length) lastaa = seq->length;
      if (lastaa < firstaa)
      {   firstaa = 0; lastaa = seq->length;   }
   }
   if (lastaa < firstaa) { lastaa = sumpos;  }

   /*-------------------------------------------------------------------*/
   /*  seq is binary, so can't distinguish upper/lower case
       put the cobbler sequence part of seq in cobbler array      */
   cobblen = lastaa - firstaa;
   cobbler = (char *) malloc((cobblen+1) * sizeof(char));
   strcpy(fam, blist->next->block->family);
   pssm = NULL;
   if (PrfOutType >= 0)
   {
      pssm = new_matrix((cobblen+1));
      strcpy(pssm->id, "COBBLER; MATRIX");
      strcpy(pssm->number, fam);
      strcpy(pssm->ac, pssm->number);
      sprintf(pssm->de, "%s %s from %d to %d with embedded PSSM",
           fam, seqname, firstaa+1, lastaa);
      sprintf(pssm->ma, "width=%d seqs=%d",
         cobblen+1, blist->next->block->num_sequences);
   }
   
   /* -------------------Now the body-------------------------------- */
   /*  This ASSUMES the blocks are in order in the chosen sequence,
	but they may not be if PROTOMAT allowed repeats, etc
	Need to fix this - eg BL50006 in Blocks 9.0   */
   cobbpos = 0;
   totpos = firstaa;
   bcur = blist->next_min;
   while(bcur != NULL && bcur->block != NULL)
   {
      block = bcur->block;
      width = block->width;
      if (block == first_block) firstpos = firstaa;
      else firstpos = 0;
      /*   Before the block  */
      for (pos = firstpos; pos < bcur->minseqprev; pos++)
      {	
          /* Avoid problems; can happen when blocks out of order for seq */
          if (cobbpos < cobblen)
          {
          if (lastaa > totpos)
          {
             if (seq != NULL)
             { ctemp[0] = aa_btoa[seq->sequence[totpos]]; }
             else { ctemp[0] = 'X'; }
          }
          else { ctemp[0] = 'X'; }
          cobbler[cobbpos] = tolower(ctemp[0]);
	  sngle = aa_atob[ ctemp[0] ];
          aacount[sngle]++;
          if (pfp != NULL)
          {
             for (aa=0; aa < MATRIX_AA_WIDTH; aa++)
             { pssm->weights[aa][cobbpos] = Profile->weights[aa][sngle]; }
          }

          totpos++; cobbpos++;
          }
      }  /* end of region before block */

      /*   Within the block region */
      for (pos = 0; pos < width; pos++)
      {
	 /*  In rare cases the sequence ends before the block does */
         if (cobbpos < cobblen)
         {
         if (bcur->consensus[pos] >= 0 && bcur->consensus[pos] < MAXAA )
         {
              ctemp[0] = aa_btoa[ bcur->consensus[pos] ];
              cobbler[cobbpos] = aa_btoa[ bcur->consensus[pos] ];
              aacount[ bcur->consensus[pos] ]++;
         }
         else
         {		/* no consensus residue selected */
             cobbler[cobbpos] = 'x';
             aacount[ aa_atob['X'] ]++;
         }

         if (pfp != NULL)
         {
            /*	Uses the 1/3 bit PSSM made by insert_blist()    */
            /* For PSI, want cobbler sequence from 1/3 bit PSSM but pssm
               from target frequencies */
            if (PrfOutType == PRF_PSI)
            {
               target = block_to_matrix(bcur->block, 20);
               for (aa=0; aa < MATRIX_AA_WIDTH; aa++)
               { pssm->weights[aa][cobbpos] = target->weights[aa][pos]; }
               free_matrix(target);
            }
            else
            {
               for (aa=0; aa < MATRIX_AA_WIDTH; aa++)
               { pssm->weights[aa][cobbpos] = bcur->matrix->weights[aa][pos]; }
            }
         }
         }

         totpos++; cobbpos++;
      }  /* end of region within block */
      bcur = bcur->next_min;
   }  /* end of a block */

   /* ---Print the rest of the sequence now after the blocks------------- */
   if (lastaa > totpos)
   {
      savpos = totpos;
      for (pos = savpos; pos < lastaa; pos++)
      {
          if (seq != NULL)
          { ctemp[0] = aa_btoa[seq->sequence[pos]]; }
          else {ctemp[0] = 'X'; }
          cobbler[cobbpos] = tolower(ctemp[0]);
	  sngle = aa_atob[ ctemp[0] ];
          aacount[sngle]++;

          if (pfp != NULL)   /* same as PrfOutType >= 0 */
          {
             for (aa=0; aa < MATRIX_AA_WIDTH; aa++)
             { pssm->weights[aa][cobbpos] = Profile->weights[aa][sngle]; }
          }

          totpos++; cobbpos++;
      }
   }  /* end of if sequence was found */

   /*--------------------------------------------------------------------*/
   /*     Write the embedded sequence out */
   fprintf(ofp, ">%s %s from %d to %d with embedded consensus blocks\n",
           fam, seqname, firstaa+1, lastaa);
   for (pos=0; pos < cobblen; pos++)
   {
      fprintf(ofp, "%c", cobbler[pos]);
      if ((pos+1)%MAXWIDTH == 0) fprintf(ofp, "\n");
   }
   fprintf(ofp, "\n");

   /* Write the embedded PSSM out */
   switch (PrfOutType)
   {
      case PRF_SWAT:
         fprintf(pfp, "#COBBLER Profile for %s %s from %d to %d\n#\n      ",
            fam, seqname, firstaa+1, lastaa);
         for (aa=1; aa < 21; aa++) fprintf(pfp, "  %c  ", aa_btoa[aa]);
         fprintf(pfp, "\n");
         for (pos=0; pos < cobblen; pos++)
         {
            fprintf(pfp, "%c    ", cobbler[pos]);
            for (aa=1; aa < 21; aa++)
               fprintf(pfp, "%4d ", (int) round(pssm->weights[aa][pos]));
            fprintf(pfp, "\n");
         }
         break;
      case PRF_PSI:
         ltemp = (long) cobblen;
         fwrite(<emp, sizeof(long), 1, pfp);
         for (pos=0; pos < cobblen; pos++)
         {
            ctemp[0] = toupper(cobbler[pos]);
            fwrite(&ctemp, sizeof(char), 1, pfp);
         }
         for (pos=0; pos < cobblen; pos++)
         {
            for (aa=1; aa < 21; aa++)
            {
               dtemp = pssm->weights[aa][pos];
               fwrite(&dtemp, sizeof(double), 1, pfp);
            }
         }
         break;
      case PRF_PFS:
         fprintf(pfp, "(Peptide) Length: %d\n", cobblen );
         fprintf(pfp, "COBBLER Profile for %s %s from %d to %d\n",
           fam, seqname, firstaa+1, lastaa);
         fprintf(pfp, "Cons  ");
         for (aa=1; aa < 23; aa++) fprintf(pfp, "  %c  ", aa_btoa[aa]);
         fprintf(pfp,"Gap Len ..\n");
         for (pos=0; pos < cobblen; pos++)
         {
            fprintf(pfp, "%c    ", cobbler[pos]);
            for (aa=1; aa < 23; aa++)
               fprintf(pfp, "%4d ", (int) round(10.0 * pssm->weights[aa][pos]));
            fprintf(pfp, " 100 100\n");
         }
         fprintf(pfp, "*    ");
         for (aa=1; aa<23; aa++) fprintf(pfp, "%4d ", aacount[aa]);
         fprintf(pfp, "\n");
         break;
      case PRF_BLI:
	 output_matrix(pssm, pfp);
         break;
      default:
         break;
   }

   if (cobbler != NULL) free(cobbler);
   if (seq != NULL) free_sequence(seq);
/*
   if (pssm != NULL) output_matrix_s(pssm, stdout, FLOAT_OUTPUT);
*/
   if (pssm != NULL) free_matrix(pssm);
}   /* end of embed_consensus  */
/*======================================================================
   Find first sequence with any part of name == "name", 
	assumes name parts are separated by "|" and input file is fasta
========================================================================*/
Sequence *read_seq(fin, name)
FILE *fin;
char *name;
{
   Sequence *seq;
   char ctemp[MAXNAME], *ptr;
   int done;

   /*  After rewind, read_a_sequence() lbuff[] is not reset, so must
       read to eof before rewinding. See notes in blimps/sequences.c */
   while ( !feof(fin) )
   {  seq = read_a_sequence(fin, FASTA, AA_SEQ); }
   rewind(fin);

/*
printf("\nread_seq(%s)\n", name);
fgets(ctemp, sizeof(ctemp), fin);
printf("%s\n", ctemp);
rewind(fin);
*/

   done = NO;
   seq = NULL;
   while ( !done && ((seq = read_a_sequence(fin, FASTA, AA_SEQ)) != NULL) )
   {
        if (strcmp(name, seq->name) == 0) { done = YES; }
        else
        {
           strcpy(ctemp, seq->name);
           ptr = strtok(ctemp, "|");
           while (ptr != NULL && strstr(name, ptr) == NULL)
	   {	ptr = strtok(NULL, "|");  }
           if (ptr == NULL)
	   {   free_sequence(seq); seq = NULL;   }
           else
           {    done = YES;   }
        }
   }
   return(seq);
}  /*  end of read_seq */

/*=======================================================================
  Print out the consensus sequence for a list of blocks
========================================================================*/
void print_consensus(blist, ofp)
struct blocks_list *blist;
FILE *ofp;
{
   int pos, itemp, width;
   struct blocks_list *bcur;
   Block *block;

   bcur = blist->next_min;
   while(bcur != NULL && bcur->block != NULL)
   {
      block = bcur->block;
      width = block->width;
      /*------- Print leading X's for minimum preceding distance ------*/
      for (pos = 0; pos < bcur->minseqprev; pos++)
      {
          fprintf(ofp, "X");
          if ( (pos+1)%MAXWIDTH == 0) fprintf(ofp, "\n");
      }
      itemp = (int) bcur->minseqprev/MAXWIDTH;
      itemp = bcur->minseqprev - itemp * MAXWIDTH;
      if ((itemp + width) > MAXWIDTH) fprintf(ofp, "\n");
  
      for (pos = 0; pos < width; pos++)
      {
         if (bcur->consensus[pos] >= 0 && bcur->consensus[pos] < MAXAA )
              fprintf(ofp, "%c", aa_btoa[ bcur->consensus[pos] ]);
         else
              fprintf(ofp, "x");
      }
      fprintf(ofp, "\n");
      bcur = bcur->next_min;
   }  /* end of block */
   fprintf(ofp, "\n");
}   /*  end of print_consensus  */

/*=======================================================================
      Turn a block into a random consensus sequence
========================================================================*/
void make_random(blist, ofp)
struct blocks_list *blist;
FILE *ofp;
{
   double rrand;
   int seq, pos, width, nseq, randaa[MAXWIDTH], itemp;
   struct blocks_list *bcur;
   Block *block;

   bcur = blist->next;
/*
   if (bcur->block != NULL)
       fprintf(ofp, ">%s %s\n", bcur->block->number, bcur->block->de);
*/
   while (bcur !=NULL && bcur->block != NULL)
   {
      block = bcur->block;
      width = block->width;
      nseq = block->num_sequences;
      for (pos = 0; pos < width; pos++)
      { 
         rrand = (double) ran0() / (RAND_MAX + 1.0);  /* bw 0.0 and 1.0 */
         seq = (int) (nseq - 1) * rrand;
         randaa[pos] = block->residues[seq][pos];
      }

      /*------- Print leading X's for minimum preceding distance ------*/
      for (pos = 0; pos < bcur->minprev; pos++)
      {
          fprintf(ofp, "X");
          if ( (pos+1)%MAXWIDTH == 0) fprintf(ofp, "\n");
      }
      itemp = (int) bcur->minprev/MAXWIDTH;
      itemp = bcur->minprev - itemp * MAXWIDTH;
      if ((itemp + width) > MAXWIDTH) fprintf(ofp, "\n");
  
      /*--------Print the consensus block now ---------------------------*/
      for (pos = 0; pos < width; pos++)
      {
         if (randaa[pos] >= 0 && randaa[pos] < MAXAA )
            fprintf(ofp, "%c", aa_btoa[randaa[pos]]);
         else fprintf(ofp, "x");
      }
      fprintf(ofp, "\n");
      bcur = bcur->next;
   }  /*  end of block */
}  /* end of make_random */
/*=================================================================
   From Press, et al, "Numerical Recipes in C", pp.207-208
   Improved random number generator (breaks up sequential correlations)

   Assumes random number generator has been seeded elsewhere (does
   not call srand).
   Assumes caller will divide results by RAND_MAX+1 (so it can be
   used the same as rand()).
========================================================================*/
int ran0()
{
   static int y, v[98];
   static int iff=0;			/* first call flag */
   int j;

   if (iff == 0)	/* fill array on first call */
   {
      iff=1;
      for (j=0; j<=97; j++) v[j] = random();
      y=random();
   }
   j = 1 + 97.0 * y / (RAND_MAX+1.0);
   if (j >=0 && j <= 97)
   {
      y=v[j];
      v[j] = random();
   }
   else y=random();
   return (y);
}  /* end of ran0 */
/*=======================================================================
     routines for a list of blocks
========================================================================*/
struct blocks_list *make_blist()
{
   struct blocks_list *new;
   
   new = (struct blocks_list *) malloc (sizeof(struct blocks_list));
   new->nblock = new->nseq = new->totwidth = new->minprev = new->maxprev = 0;
   new->minseq = new->minseqprev = new->query_pos = 0;
   new->maxseq = new->maxseqprev = 0;
   new->consensus = NULL;
   new->block = NULL;
   new->matrix = NULL;
   new->next = new->next_min = NULL;

   return(new);
}  /* end of make_blist */

/*---------------------------------------------------------------------
       Inserts the block in a list of blocks
       Computes the 1/3 bit PSSM for the block
-----------------------------------------------------------------------*/
void insert_blist(blist, block)
struct blocks_list *blist;
Block *block;
{
   struct blocks_list *cur;
   char *ptr, ctemp[MAXNAME];
   double sum;
   int seq;

   /*------ Accumulate totals in header record ------*/
   blist->nblock += 1;
   blist->nseq = block->num_sequences;
   blist->totwidth += block->width;

   /*--- Insert a new record for the current block at the end of the list ---*/
   cur = blist;
   while (cur->next != NULL)
      cur = cur->next;

   cur->next = make_blist();
   cur->next_min = cur->next;
   cur->next->consensus = (int *) malloc(block->width * sizeof(int));
   cur->next->block = block;

   /*  Make sure the block has sequence weights in it;
	block_to_matrix() takes care of this, but other routines
	here might get caught */
   sum = 0.0;
   for (seq=0; seq < block->num_sequences; seq++)
   {    sum += block->sequences[seq].weight;   }
   if (sum <= 0.0)
   {  pb_weights(block);  }

   /*  Following requires global vars Qij and frequency[]  */
   /*   NOTE:  For Gribskov-type PSSM change 6 to 30 in block_to_matrix()
               and Qij should be a substitution matrix    */
   if (Qij != NULL)
      cur->next->matrix = block_to_matrix(block, 6);	/* third bit PSSM */
   /*------- get minimum preceding distance ------*/
   cur->next->minprev = cur->next->maxprev = 0;
   strcpy(ctemp, block->ac);
   ptr = strtok(ctemp, "(");
   if (ptr != NULL)
   {
      ptr = strtok(NULL, ",");
      if (ptr != NULL) cur->next->minprev = atoi(ptr);
   }
   if (cur->next->minprev < 0) cur->next->minprev = 0;
   
}  /* end of insert_blist */

void free_blist(blist)
struct blocks_list *blist;
{
   struct blocks_list *cur, *last;

   cur = last = blist;
   while (cur->next != NULL)
   {
      last = cur;  cur = cur->next;
   }
   if (cur != blist)
   {
      if (cur->consensus != NULL) free(cur->consensus);
      if (cur->block!= NULL) free_block(cur->block);
      if (cur->matrix != NULL) free_matrix(cur->matrix);
      free(cur);
      last->next = last->next_min = NULL;
      free_blist(last);
   }
   else free(blist);

}  /* end of free_blist */
/*=======================================================================*/
/*  Sequences may not be in the same order both blocks. If not, then
    set sseq[s1] = s2  where
    b1->sequences[s1].name == b2->sequences[s2].name
=========================================================================*/
void order_seq(sseq, b1, b2)
struct seqseq *sseq;
Block *b1, *b2;
{
   int nseq, i1, i2;

   nseq = b1->num_sequences;
   if (b2->num_sequences < nseq) nseq = b2->num_sequences;
   for (i1 = 0; i1 < nseq; i1++)
   {
      if (b1 == b2) sseq[i1].seq = i1;
      else
      {
         sseq[i1].seq = -1;
         i2 = 0;
         while (sseq[i1].seq < 0 && i2 < nseq)
         {
            if (strcmp(b1->sequences[i1].name, b2->sequences[i2].name) == 0)
               sseq[i1].seq = i2;
            i2++;
         }
      }
   }
}  /*  end of order_seq */
/*======================================================================
	Read an integer-valued substitution matrix
	MAXAA == 25 - should use 24 here?
========================================================================*/
void load_sij(fin, scores)
FILE *fin;
int scores[MAXAA][MAXAA];
{
   char line[132], *ptr;
   int alpha[MAXAA], nrows, ncols, row, col, i;

/*----------Read file until first non-blank line --------------*/
/* Skip comments at beginning of file - 1st char = #, > or ;   */
   line[0] = '\0';
   while (((int) strlen(line) < 1 || line[0]=='#' || line[0]=='>' || 
                                     line[0]==';')
          && fgets(line, sizeof(line), fin) != NULL)
	    ;
/*------See if the first line has characters on it ------------*/
   for (col=0; col < MAXAA; col++) alpha[col] = -1;
   if (strstr(line, "A") != NULL)	/* This line has characters */
   {
      row = 0;	/* # of alphabetic characters on the line */
      for (i=0; i< (int) strlen(line); i++)
      {
	 col = aa_atob[ line[i] ];
	 if (col >= 0 && col < MAXAA)
	 {
	    alpha[row] = col;
	    row++;
	 }
	 else if (isalpha(line[i])) row++;
      }
   }
/*-------Get the data values now ------------*/
   for (row=0; row 1 && nrows < MAXAA)
      {
	 if (alpha[nrows] >= 0 && alpha[nrows] < MAXAA)
	 {
	    row = alpha[nrows]; ncols = 0;
	    ptr = strtok(line, " ,\n");
	    while (ptr != NULL)
	    {
	       if (strspn(ptr, "+-0123456789") == strlen(ptr))
	       {
		  col = alpha[ncols];
		  if (col >= 0 && col < MAXAA)
		     scores[row][col] = atoi(ptr);
		  ncols++;
	       }
	       ptr = strtok(NULL, " ,\n");
	    }
	 }
	 nrows++;
      }
   }

/*-------If some entries are still missing, assume symmetry ---------*/
   for (row=0; row D */
	   scores[row][col] = scores[3][col];
	if (row==21 && scores[row][col]==-999)	/* Z -> E */
	   scores[row][col] = scores[6][col];
	if (col==20 && scores[row][col]==-999)	/*  B -> D */
	   scores[row][col] = scores[row][3];
	if (col==21 && scores[row][col]==-999)	/* Z -> E */
	   scores[row][col] = scores[row][6];
     }
   }

}  /* end of load_sij */
/*=======================================================================
   Read in query sequence, align it with blocks, embed consensus
   at alignment points if all blocks align in the right order without
   overlapping.
========================================================================*/
void query_consensus(blist, ofp, pfp)
struct blocks_list *blist;
FILE *ofp, *pfp;
{
   int lastpos, sumpos, width;
   Sequence *seq;
   struct blocks_list *bcur;

   seq = read_a_sequence(Fsq, UNI, AA_SEQ);
   rewind(Fsq);

   /*   If query is shorter than the sum of the block widths
        just print a message  */
   sumpos = 0;
   bcur = blist->next;
   while (bcur != NULL && bcur->block != NULL)
   {
      /* don't count the aas before the first block */
      if (bcur != blist->next) sumpos += bcur->minprev;
      sumpos += bcur->block->width;
      bcur = bcur->next;
   }
   if (seq->length < sumpos)
   {
      printf("Query sequence %s is shorter than minimum path width\n",
              seq->name);
      free_sequence(seq);
      seq = NULL;
   }
 
   /*--------------------------------------------------------------------*/
   /*   Align the sequence with each block & get the value of
        minseqprev  */
   lastpos = 0;
   if (seq != NULL)
   {
      bcur = blist->next;
      while (bcur != NULL && bcur->block != NULL)
      {
         width = bcur->block->width;
/*       matrix = block_to_matrix(bcur->block, 3);   scaled 0-99  */
/*		Uses 1/3 bit PSSM made by insert_blist()          */
         bcur->query_pos = best_pos(bcur->matrix, seq); 
         if (bcur->query_pos < lastpos - 1)
         {
            printf("WARNING: Aligned blocks overlap!!! ");
            printf(" block=%s, pos=%d, last pos = %d\n",
             bcur->block->number, bcur->query_pos, lastpos);
         }
	 else
	 {
            printf(" block=%s, pos=%d\n",
             bcur->block->number, bcur->query_pos);
         }
         bcur->minseqprev = bcur->query_pos - lastpos;
         lastpos = bcur->query_pos + width;
         bcur = bcur->next;
      }

      /*------------------------------------------------------------*/
      embed_consensus(blist, ofp, pfp, seq);    /* frees seq */

   } /*  end of if sequence was found */
  
}   /*  end of query_consensus */
/*=======================================================================
            Score all alignments of matrix with sequence & return
	     position of best alignment
============================================================================*/
int best_pos(matrix, seq)
Matrix *matrix;
Sequence *seq;
{
  int scan_pos, seq_pos, mat_pos, best_position;
  double seq_score, max_seq_score;

  max_seq_score = 0.0;
  best_position = -999;
  
  /* for every alignment of the matrix and sequence score the alignment. */
  /* there are (seq_length + matrix_length  - 1) different alignments. */
  /* Note: seq_pos is the relative position of the 1st matrix column to the */
  /*       1st sequence column */
  /* Note: the indexing is shifted to make the calculation of scan_pos */
  /*       (see below) easier/faster */
  for (seq_pos= -matrix->width+1; seq_pos < seq->length; seq_pos++) {


    /* 
     * score this alignment
     */
    seq_score = 0.0;

    /* for each position in the matrix add the weight to the total score */
    /* Note: mat_pos is the current column of the matrix */
    for (mat_pos=0; mat_pos < matrix->width; mat_pos++) {

      /* make sure the sequence and the matrix overlap at this point */
      /* Note: scan_pos is where the current matrix column is in the */
      /*       sequence */
      scan_pos = seq_pos + mat_pos;
      if ((scan_pos >= 0) && (scan_pos < seq->length)) { /* if in the seq */
	seq_score += matrix->weights[ seq->sequence[scan_pos] ][mat_pos];
      }
      else {			/* not in the sequence */
	seq_score += matrix->weights[aa_atob['-']][mat_pos]; 
	/* score as if it was a gap */
      }

    } /* end score this alignment */

/*    alignments_done++; */
    
      if (seq_score > max_seq_score) {
	max_seq_score = seq_score;
	best_position = seq_pos;
      }
    
  } /* end of pairwise lineup */
  
  return(best_position);

}  /* end of best_pos */
/*========================================================================
        Figure out the consensus for this block & store it in the
        block list record - use highest PSSM score
        Prints x if the best total score is negative
=========================================================================*/
void pssm_consensus(bcur)
struct blocks_list *bcur;
{
   double maxw;
   int aa1, seq1, pos, width, nseq, maxaa, aamark[MAXAA+1];
   Block *block;

   block = bcur->block;
   width = block->width;
   nseq = block->num_sequences;

   /*-------------------------------------------------------------------*/
   for (pos = 0; pos < width; pos++)
   { 
      /*    good sums can be negative */
      maxw = -999999.99;
      maxaa = -1;
      for (aa1 = 0; aa1 < MAXAA+1; aa1++)
         aamark[aa1] = NO;	/* does this aa appear in the pos ? */
  
      /*   Mark the aas that appear in this position */
      for (seq1 = 0; seq1 < nseq; seq1++)
      {
            aa1 = block->residues[seq1][pos];
            if (aa1 >= 0 && aa1 <= MAXAA)
               aamark[aa1] = YES;
      }

      /*    Only choose among the aas that appear in the pos  */
      for (aa1 = 0; aa1 < MAXAA; aa1++)
         if ( aamark[aa1] )
         {
            if (bcur->matrix->weights[aa1][pos] > maxw)
            {   maxw = bcur->matrix->weights[aa1][pos]; maxaa = aa1;  }
         }

      if (maxw <= 0.0) maxaa = MAXAA;	/*  Use X if non-positive sum */

      /*--------Save the consensus sequence------------------------*/
      if (maxaa > 0 && maxaa < MAXAA )
           bcur->consensus[pos] = maxaa;
      else
           bcur->consensus[pos] = MAXAA;	/* X==23 */
   }  /* end of pos */

}  /*  end of pssm_consensus */
/*=======================================================================*/
int sortcmp(t1, t2)
struct sorttemp *t1, *t2;
{
   return(t1->position - t2->position);
}  /* end of sortcmp */

/*========================================================================
   Write out the results
   Need: ac, sequence name, firstaa & lastaa for heading;
	 length, cobbler sequence, pssm values
	 aacount[] for PRF_PFS
=========================================================================*/
void write_cobbler(cfp, pfp, cobbler, pssm)
FILE *cfp, *pfp;
char *cobbler;
Matrix *pssm;
{
   int cobblen;
 
   cobblen = (int) strlen(cobbler);

}  /* end of write_cobbler */
/*========================================================================
	Retrieve & print a sequence
	blist->minseq is ML, blist->maxseq is LL
========================================================================*/
void get_seq(fam, name, fdb, fout)
char *fam, *name;
FILE *fdb, *fout;
{
   Sequence *seq;
   char seqname[MAXNAME];

   /* read_seq rewinds fdb */
   seq = read_seq(fdb, name); 
   if (seq == NULL)
   { 
      printf ("Sequence %s not found\n", name);
   }
   else
   {
      sprintf(seqname, "%s %s", fam, name);
      strcpy(seq->name, seqname);
      output_sequence(seq, fout);
   }
}  /* end of get_seq */
ct seqseq *sseq;
Block *b1, *b2;
{
   int nseq, i1, i2;

   nseq = b1->num_sequences;
   if (b2->num_sequences < nseq) nseq = b2->num_sequences;
   for (i1 = 0; i1 < nseq; i1++)
   {
      if (b1 == b2) sseq[i1].seq = i1;
      else
      {
         sseq[i1].seq = -1;
         i2 = 0;
         while (sseq[i1].seq < 0 && i2 < nseq)
         {
  blimps-3.9/blimps/codehop.c000064400001460000012000002013761013361752400162340ustar00jorjastaff00000400000027/* COPYRIGHT 1997-2004 Fred Hutchinson Cancer Research Center, Seattle, WA, USA
   CODEHOP - COnsensus-DEgenerate Hybrid Oligonucleotide Primers
   (formerly BASE_PRIDE - Blocks ASistEd PRImer DEsign)
   This program will suggest degenerate PCR primers from blocks data.   
==========================================================================
12/ 7/97 1. Changed Base Pride to Codehop
12/30/97 1. Extend temperature calculation to non-degenerate portion of
	    core adjacent to clamp. compute_thermo().
 1/ 2/98 1. Increased CLAMP_MAX_LEN from 30 to 165bps == max block width
         2. Skip degenerate clamp residues from nt_clamp[] in compute_thermo();
		the clamp temperature is really undefined if the most common
		codon is not used (esp. if equal codon usage)
            Use nsres instead of nres when computing core degeneracy (IE,
		apply Core_Strictness).
 1/ 3/98 1. Use average entropy/enthalpy values if degen. codons in clamp.
 1/ 7/98 1. Changed criteria for best_oligo in a clump to not use clamp info.
 1/ 9/98 1. Don't use clamp strictness; if degenerate residues in clamp then
	    pick one at random (changed content of ->nt_max[]).
 1/ 9/98 1. Added clamp probability score (->clamp_prob).
 1/10/98 1. Don't use clamp strictness; if degenerate residues in clamp then
	    pick one at random (changed content of ->nt_max[]).
         2. Allow core to be 12 if ROSE=FALSE. Fixed ->clamp_prob.
 1/11/98 1. Format modifications.
         2. Added -Begin100 option: If FALSE, use core strictness to
            determine eligible starting points.
         3. Include ->clamp_prob in best_oligo determination.
 3/27/98 1. Modified compute_max() per Tim Rose.
    Never use codons AAA [0], CCC [21], GGG [42] or TTT [63] in nt_common[],
    but still are used to compute DNA PSSM - compute_max(), fix_codons().
 3/28/98 1. Adjusted core length for complements: core_len in find_oligos()
 4/13/98 1. New option to specify max length of runs (-Apolyx).
         2. Break up runs > polyx value: break_runs()
 4/14/98 1. Fixed compute_thermo(); was computing temperature incorrectly 
		for complement.
 4/16/98 1. Added nt_max[]; break_runs() once from compute_max().
	    Undid 3/27/98 change for nt_common[].
 5/ 6/98 1. Add OutOligo to be max number of oligos to show per block.
	    Activated display_oligos(). But now the oligos are always
	    printed in sorted order, not in geographical order any more.
 4/14/99 1. Error message if no blocks found in input
12/ 9/99 1. Fix memory problems
12/17/99 1. Longer AC (family name)
-----------------------Version 3.6--------------------------------------------
10/14/04.1  Problems with genetic code, incomplete blocks in input file
            Revise search for codon usage table
=================================================================================
*/

#define EXTERN

#include 
#include "codehop.h"

#define USAGE "Usage: %s [blocks-input_file_name [output_file_name]]\n [-Ffamily_name]\n [-Ppssm_type]\n [-Ccodon_usage_file]\n [-Ggenetic_code_type]\n [-Dcore_degeneracy_parameter]\n [-Score_strictness_parameter]\n [-Lclamp_strictness_parameter]\n [-Tclamp_temperature]\n [-Nconcentration]\n [-Rose_restrictions]\n [-Most_common_codon]\n [-Verbose]\n [-Output]\n [-Begin]\n [-ApolyX_parameter]\n\n"


#define DEFAULTS "Defaults: in-\"%s\" out-\"%s\"\n family-\"%s\"\n pssm_type-\"%d\"\n codon_usage-\"%s\"\n genetic_code_type-\"%d\"\n core_degeneracy-\"%3.1f\"\n core_strictness-\"%3.1f\"\n clamp_strictness-\"%3.1f\"\n clamp-temperature-\"%3.1f\"\n concentration-\"%3.1f\"pM\n Rose-FALSE\n most_common_codon-FALSE\n verbose-FALSE\n begin_oligo-TRUE\n polyX-\"%d\"\n\n"


#define AA_ALPHABET_SHRT "ACDEFGHIKLMNPQRSTVWXY"

/*
 * Local variables and data structures
 */

#define is_res(x) (x==aa_atob['A'] || x==aa_atob['C'] || x== aa_atob['G'] ||   \
                x==aa_atob['T']) ? TRUE : FALSE
/*	Clamp temperate: a = AT content, g = GC content of clamp region */
#define cltemp(a,g) (3.0 + 4.0 * g + 2.0 * a)

void getargs() ;
void fprint_matrix1() ;
void fprint_matrix1_3spaced() ;

void fix_codons();
void process_block();

struct dna_matrix *new_dna_matrix();
void free_dna_matrix();
struct dna_matrix *unpssm_pssm();
struct dna_matrix *complement_pssm();
void compute_max();

struct oligo_list *make_oligo();
void find_oligos();
void insert_oligo();
void display_oligos();
void display_oligo();
void score_clamp();
void score_clamp_prob();
void display_consensus();
int get_clump();

double clamp_freier();
double clamp_rychlik();
void compute_thermo();
void break_runs();
int oligocmp();

/*---------------------- Global variables ----------------------------*/
char Version[12] = "10/14/04.1";		/* Version date */
Boolean  WWW_FLAG = TRUE ;

double Clamp_Strictness = MAX_STRICTNESS;	/* clamp codon strictness */
double Core_Strictness = MIN_STRICTNESS;	/* core codon strictness  */
double Core_Degeneracy = DEFAULT_CORE_DEG;	/* core degeneracy */
double Clamp_Temperature = DEFAULT_TEMP;	/* clamp temperature */
double Concentration = DEFAULT_CONC;		/* concentration in nM */
double Koncentration = DEFAULT_KONC;		/* K+ concentration in mM */
double ProdLen = DEFAULT_PRODLEN;		/* Product length */
int PolyX = DEFAULT_POLYX;			/* Max run of any nuc */
int Rose = FALSE;	/* Enforces Tim Rose's restrictions on core region */
int Most_Common_Codon = FALSE;	/* use most common codon in clamp */
int Verbose = FALSE;		/* verbose output */
int OutOligo = 0;		/* number of oligos to print */
int Begin100 = TRUE;		/* begin core on conserved residue */
int Debug = FALSE;		/* debugging output */

char  Frqname[MAXNAME]="";
char  IDname[MAXNAME]="";
int   Pssm_Type = PSSM_TYPE_DFLT, Gcode_Type = GCODE_TYPE_DFLT ;
unsigned char Gcode[64], RevGcode[64];
/*  Codons in Blimps order: use T instead of U to use amino acid routines  */
char Codons[64][3] = {
"AAA","AAC","AAG","AAT", "ACA","ACC","ACG","ACT", "AGA","AGC","AGG","AGT",
"ATA","ATC","ATG","ATT", "CAA","CAC","CAG","CAT", "CCA","CCC","CCG","CCT",
"CGA","CGC","CGG","CGT", "CTA","CTC","CTG","CTT", "GAA","GAC","GAG","GAT",
"GCA","GCC","GCG","GCT", "GGA","GGC","GGG","GGT", "GTA","GTC","GTG","GTT",
"TAA","TAC","TAG","TAT", "TCA","TCC","TCG","TCT", "TGA","TGC","TGG","TGT",
"TTA","TTC","TTG","TTT" };

/*  Breslauer, et al entropy & enthalpy for nearest neighbors, order is
     AA AC AG AT CA CC CG CT    GA GC GG GT TA TC TG TT          */
double Bres_Enthalpy[16]  = {  9.1,  6.5,  7.8,  8.6,  5.8, 11.0, 11.9,  7.8,
                              5.6, 11.1, 11.0,  6.5,  6.0,  5.6,  5.8,  9.1 };
double Bres_Entropy[16] = { 24.0, 17.3, 20.8, 23.9, 12.9, 26.6, 27.8, 20.8,
                             13.5, 26.7, 26.6, 17.3, 16.9, 13.5, 12.9, 24.0 };
/*=======================================================================*/
/*
 * main
 *   controls flow of program
 *   Parameters: argc, argv
 *   Error codes:
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE  *inpf=stdin, *outf=stdout ;
  FILE  *fcod, *fqij;
  char  inpfname[MAXNAME]="stdin", outfname[MAXNAME]="stdout" ;
  char  src_fam_name[BLOCK_AC_LEN]="" ;
  char  *blimps_dir, tmp[MAXNAME] ;
  Block *block;
  int   i1, nblock, prev_num;
  char  codon_usage_file[MAXNAME] = CODON_USAGE_FILE_DFLT ;
  char  *pssm_defs[] = PSSM_DEFS ;
  char  qijname[MAXNAME]="";
  struct timeval tv;

  ErrorLevelReport = 2;		/* suppress BLIMPS errors */
  blimps_dir = getenv("BLIMPS_DIR");

  printf("CODEHOP Version %s\n", Version);
  printf("COPYRIGHT 1997-2004, Fred Hutchinson Cancer Research");
  printf(" Center, Seattle, WA, USA\n");
  if (Debug)
  {
     for (i1=0; i1< argc; i1++) printf("%s ", argv[i1]);
     printf("\n");
  }

  /* show usage and what defaults are used */
  if (argc < 2 || (argc == 2 && strstr(HELP_REQUEST, argv[1]) != NULL) )
    {
    fprintf(stderr, USAGE, argv[0]) ;
    fprintf(stderr, DEFAULTS, inpfname, outfname, "first_in_input", 
       Pssm_Type, codon_usage_file, Gcode_Type, Core_Degeneracy,
       Core_Strictness, Clamp_Strictness, Clamp_Temperature, Concentration,
       PolyX) ;
    fprintf(stderr, COMMENTS) ;
    exit(0) ;
    }
  else
     getargs(argc, argv, inpfname, outfname, src_fam_name, codon_usage_file) ;

/*printf (">>>inpfname=%s<<<\n", inpfname); */


/* check arguments */

  sprintf (tmp, " %d ", Pssm_Type) ;
  if (strstr(PSSM_TYPES, tmp) == NULL) 
     {
     fprintf(stderr, "Warning: Unspecified pssm type (%d) requested.\nUsing default pssm type (%d).\n\"%s help\" for help.\n\n",
             Pssm_Type, PSSM_TYPE_DFLT, argv[0]) ;
     Pssm_Type = PSSM_TYPE_DFLT ;
     }

  if (Gcode_Type < 0 || Gcode_Type > NUMBER_OF_GENETIC_CODES)
     {
     fprintf(stderr, "Warning: Unspecified gcode type (%d) requested.\nUsing default gcode type (%d).\n\"%s help\" for help.\n\n",
             Gcode_Type, GCODE_TYPE_DFLT, argv[0]) ;
     Gcode_Type = GCODE_TYPE_DFLT ;
     }

  if (Core_Strictness < MIN_STRICTNESS ||
      Core_Strictness > MAX_STRICTNESS)
     {
     fprintf(stderr, "Warning: Core strictness parameter requested (%3.2f) is out of range (%3.2f to %3.2f)\nUsing default value (%3.2f).\n",
             Core_Strictness, MIN_STRICTNESS, MAX_STRICTNESS, MIN_STRICTNESS) ;
     Core_Strictness = MIN_STRICTNESS ;
     }

  if (Clamp_Strictness < MIN_STRICTNESS ||
      Clamp_Strictness > MAX_STRICTNESS)
     {
     fprintf(stderr, "Warning: Clamp strictness parameter requested (%3.2f) is out of range (%3.2f to %3.2f)\nUsing default value (%3.2f).\n",
             Clamp_Strictness, MIN_STRICTNESS, MAX_STRICTNESS, MAX_STRICTNESS) ;
     Clamp_Strictness = MAX_STRICTNESS ;
     }

  if (Clamp_Strictness < Core_Strictness)
     {
     fprintf(stderr, "Warning: Clamp strictness parameter requested (%3.2f) is less than core strictness parameter (%3.2f)\nUsing default values (%3.2f, %3.2f).\n",
             Clamp_Strictness, Core_Strictness, MAX_STRICTNESS, MIN_STRICTNESS) ;
     Core_Strictness = MIN_STRICTNESS;
     Clamp_Strictness = MAX_STRICTNESS;
     }

   if (Clamp_Temperature < 0.0 )
     {
     fprintf(stderr, "Warning: Clamp temperature requested (%3.2f) is negative\nUsing default value (%3.2f).\n", Clamp_Temperature, DEFAULT_TEMP);
     Clamp_Temperature = DEFAULT_TEMP;
     }

   if (Concentration < 0.0 )
     {
     fprintf(stderr, "Warning: Concentration requested (%3.2f) is negative\nUsing default value (%3.2f).\n", Concentration, DEFAULT_CONC);
     Concentration = DEFAULT_CONC;
     }

                                                               /* open files */
/* Input */
  if (strcmp(inpfname,"stdin") !=0 && (inpf=fopen(inpfname, "r")) == NULL)
     {
     fprintf(stderr, "Cannot open input file %s\n", inpfname);
     exit(-1);
     }

/* output */
  outf = NULL;
  if (strcmp(outfname,"stdout") !=0 && (freopen(outfname, "w", stdout)) == NULL)
     {
     fprintf(stderr, "Cannot open output file %s\n", outfname);
     exit(-1);
     }


/* Amino acid frequency */
  if (blimps_dir != NULL) 
  {
       sprintf(Frqname, "%s/docs/%s", blimps_dir, "default.amino.frq");
       sprintf(IDname, "%s/docs/%s", blimps_dir, "identity.frq");
  }
  else
  {
       sprintf(Frqname, "%s", AA_FREQUENCY_FNAME) ;
       sprintf(IDname, "%s", ID_FREQUENCY_FNAME) ;
  }

/* don't load_frequencies() yet because we equal freqs of 1 for nuc pssm */

  if (blimps_dir != NULL) sprintf(qijname, "%s/docs/", blimps_dir);

  if (Pssm_Type == 30) strcat(qijname, "default.iij"); /*average score*/
  else                 strcat(qijname, "default.qij");

  Qij = NULL;
  if ( (fqij=fopen(qijname, "r")) != NULL)
     { Qij = load_qij(fqij); fclose(fqij); }
  RTot = LOCAL_QIJ_RTOT;

/*  Gcode[i] = aa # with i in Blimps = ACGT order */
  init_gcode(&gcodes[Gcode_Type], Gcode, RevGcode);

/* Codon usage, look in current dir, then in blimps_dir, then try default */
/*printf (">>>blimps_dir=%s<<<\n", blimps_dir); */
  if ((fcod=fopen(codon_usage_file, "r")) == NULL)
  {
     fprintf(stderr, "Cannot open codon usage file %s\n", codon_usage_file);

     /*  Try to find it elsewhere */
     if (blimps_dir != NULL) 
     {
        strcpy(tmp, codon_usage_file);
        sprintf(codon_usage_file, "%s/docs/%s", blimps_dir, tmp); 
        fprintf(stderr, "...trying %s ...\n", codon_usage_file);
        if ((fcod = fopen(codon_usage_file, "r")) == NULL)
        {
           fprintf(stderr, "Cannot open codon usage file %s\n", codon_usage_file);

           sprintf(codon_usage_file, CODON_USAGE_FILE_DFLT);
           fprintf(stderr, "...trying %s ...\n", codon_usage_file);
           if ((fcod = fopen(codon_usage_file, "r")) == NULL)
           {
              fprintf(stderr, "Cannot open codon usage file %s\n", codon_usage_file);
              strcpy(tmp, codon_usage_file);
              sprintf(codon_usage_file, "%s/docs/%s", blimps_dir, tmp); 
              fprintf(stderr, "...trying %s ...\n", codon_usage_file);
              if ((fcod = fopen(codon_usage_file, "r")) == NULL)
              {
                 fprintf(stderr, "Cannot open codon usage file %s\n", codon_usage_file);
                 exit(-1);
              }
           }
        }
     }
     else  /* no $BLIMPS_DIR */
     {
        sprintf(codon_usage_file, CODON_USAGE_FILE_DFLT);
        fprintf(stderr, "...trying %s ...\n", codon_usage_file);
        if ((fcod = fopen(codon_usage_file, "r")) == NULL)
        {
           fprintf(stderr, "Cannot open codon usage file %s\n", codon_usage_file);
           exit(-1);
        }
     }
  } /* end of codon usage file */

  load_codons(fcod);
  /*  Fix up the codons for use here, they are in Codon_Usage[64]  */
  fix_codons();

/*----------------------------------------------------------------------*/
/* print parameters used */
     printf( 
       "\nParameters:\n Amino acids PSSM calculated with %s\n and back-translated with %s genetic code\n and codon usage table \"%s\"\n Maximum core degeneracy %3.0f    Core strictness %3.2f\n Clamp strictness %3.2f   Target clamp temperature %3.2f C\n DNA Concentration %3.2f nM   Salt Concentration %3.2f mM\n Codon boundary %d   Most common codon %d\n Verbose %d   Output %d\n Begin %d   PolyX %d\n",
        pssm_defs[Pssm_Type], gcodes[Gcode_Type].name, codon_usage_file, Core_Degeneracy, Core_Strictness, Clamp_Strictness, Clamp_Temperature, Concentration, Koncentration, Rose, Most_Common_Codon, Verbose, OutOligo, Begin100, PolyX) ;
     printf("Suggested CODEHOPS: The degenerate region (core) is printed in lower case,\nthe non-degenerate region (clamp) is printed in upper case.\n");

/*-------------------------------------------------------------------------*/
/*  Initialize the random number generator */
   gettimeofday(&tv, NULL);
   srand(tv.tv_sec^tv.tv_usec);

  /*  Process all blocks, or all blocks with specified AC. Sequences and
      their number can differ from block to block  */
  nblock = 0;
  prev_num = -1;
  while ((block = read_a_block(inpf)) != NULL)
  {
      /* Trying to make sure blocks are from the same group here */
      /* sometimes users cut-paste incomplete blocks and we abort...*/
      if ( (!strlen(src_fam_name) ||
            !strncasecmp(src_fam_name, block->family, strlen(src_fam_name)) )
          && (prev_num < 0 || block->num_sequences == prev_num) )
      {	         
         process_block(block); 
         nblock++;  
         prev_num = block->num_sequences;
      }
      free_block(block);
  }
  if (nblock < 1) printf("\nNo correctly formatted blocks found to process\n");
   
  fclose(inpf);
  if (outf != NULL) fclose(outf);

  exit(0);
}  /* end of main */

/*****************************************************************************
 * get input and output file names and other program parameters.
 *
 * All parameters, except explicit input and output file names, 
 * should be preceded by a "-".
 * A sole "-" (implicitly) specifies a default for a file name.
 * The first explicit or implicit file name will be assigned to the input file
 * and the second to the output file.
 *
 * NOTE:  Most of the returned variables are global...
 *
 *****************************************************************************/

void getargs(argc, argv, inpfname, outfname, fam_name, codon_usage_fname)

int    argc;
char   *argv[];
char   inpfname[], outfname[], fam_name[], codon_usage_fname[] ;
{

   int i1 ;
   int fnames=0 ;
   char *chr_ptr ;


   for(i1=1; i1 0) Verbose = FALSE;
*/
   if (Verbose) OutOligo = 0;
   if (!Verbose && OutOligo < 1) OutOligo = 1;

   return ;
}  /*   end of getargs */

/*==================================================================
      Process a block
====================================================================*/
void process_block(block)
Block *block;
{
Matrix *matrix;
struct dna_matrix *nuc_matrix, *rev_matrix;

        /* load the frequencies for converting blocks to matrices */
/* this has to be done each time since we load other values for converting the nuc PSSM */
	load_frequencies(Frqname);	/* freqs for AA PSSM */

        matrix = block_to_matrix(block, Pssm_Type) ;
/*output_matrix(matrix, stdout, FLOAT_OUTPUT, AA_SEQ); */

        /* convert the aa PSSM to a nuc PSSM */
        load_frequencies(IDname);	/*  use 1.0 */

        nuc_matrix = unpssm_pssm(matrix);
        printf("\nProcessing Block %s\n", block->number);
        /* Compute nt_core[], nt_common[], nt_max[],  nt_clamp[],
	 nres[], nsres[] & max_weight[] for each position of matrix */
        compute_max(nuc_matrix, matrix);
	/* Print nt_common[] == the consenus amino acids */
        display_consensus(nuc_matrix);
/*fprint_matrix1(nuc_matrix, stdout, nt_adegen[ALPHABET].list) ;*/
        find_oligos(nuc_matrix);

        rev_matrix = complement_pssm(nuc_matrix);
        printf("\nProcessing Complement of Block %s\n", block->number);
        compute_max(rev_matrix, matrix);
        display_consensus(nuc_matrix);
        find_oligos(rev_matrix);

        free_matrix(matrix);
        free_dna_matrix(nuc_matrix);
        free_dna_matrix(rev_matrix);

}  /* end of process_block */

/*=====================================================================
 * unpssm_pssm
 *   Translates an animo acid pssm into a  DNA pssm of degenerate
 *    codons
 *   Parameters:
 *     Matrix *pssm: the amino acid pssm 
 *   Return code: a pointer to the new DNA pssm
 *   Notes: this method only works because ACGT are valid amino acid codes
 */

struct dna_matrix *unpssm_pssm(pssm)
     Matrix *pssm;
{
  Matrix *tmp_pssm;
  struct dna_matrix *dna_pssm;
  Block *tmp_block;

  int i, aa, pos, cod, res;
  unsigned char c;

  /* make sure it is an AA PSSM: can only tell this if the undefined
     pointer is set, which is usually isn't */
/*
  if ( pssm->undefined != AA_SEQ ) {
    sprintf(ErrorBuffer, 
    "unpssm_pssm(): Not an amino acid pssm, not unpssming.");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer, 
	    "                      Returning the original pssm.\n");
    ErrorReport(PROGRAM_ERR_LVL);
    return pssm;
  }
*/

   /* Allocate the DNA pssm  */
   dna_pssm = new_dna_matrix(3 * pssm->width);
   dna_pssm->block = pssm->block;
   dna_pssm->strand = 1;

   /* Make the DNA block, it's 3 wide, used for each PSSM column  */
   tmp_block = new_block(3, 64);
   /*  Each block "sequence" is a codon  */
   for (cod = 0; cod < 64; cod++) 
   {
         for (i=0; i< 3; i++)
         {
            c = Codons[cod][i];
            tmp_block->sequences[cod].sequence[i] = aa_atob[c];
         }
   }


   /*  Compute the DNA PSSM one AA PSSM position at a time */
   for (pos = 0; pos < pssm->width; pos++)
   {
      /* Set the "sequence" weight for each codon  =
         AA PSSM weight for aa x codon usage   */
      for (cod=0; cod < 64; cod++)
      {
         aa = Gcode[cod];
         tmp_block->sequences[cod].weight = pssm->weights[aa][pos];
         tmp_block->sequences[cod].weight *= Codon_Usage[cod];
/*
printf("cod=%d aa=%d pssm=%f usage=%f weight=%f\n",
  cod, aa, pssm->weights[aa][pos], Codon_Usage[cod],
  tmp_block->sequences[cod].weight);
*/
      }
      /*  Convert the block to a PSSM, odds ratios with freqs = 1,
          normalized to add to 100 for each position. May want to
          use other PSSM types ?   */
      tmp_pssm = block_to_matrix(tmp_block, Pssm_Type);

      /* Move the weights to the DNA PSSM, adjust residue index  */
      for (i=0; i< 3; i++)	/* i is the position within the codon */
         for (aa = 0; aa < 25; aa++)
            if (is_res(aa))
               for (res = 0; res < 4; res++)
                  if (nt_btoa[res] == aa_btoa[aa])
                     dna_pssm->weights[res][3*pos+i] =
                     tmp_pssm->weights[aa][i];

      free_matrix(tmp_pssm);
   }   /* end of AA PSSM position */

   free_block(tmp_block);
   return(dna_pssm);

}  /*  end of unpssm_pssm */
/*====================================================================
	Allocate memory for a new DNA PSSM
=====================================================================*/
struct dna_matrix *new_dna_matrix(length)
int length;
{
   struct dna_matrix *new;
   int res;

   new = (struct dna_matrix *) malloc(sizeof(struct dna_matrix));
   new->length = length;
   new->weights[0] = malloc(4*length*sizeof(MatType));
   for (res=0; res< 4; res++) new->weights[res] = new->weights[0] + res*length;
   new->max_weight = malloc(length*sizeof(MatType));
   new->nres = malloc(length*sizeof(int));
   new->nsres = malloc(length*sizeof(int));
   new->nt_core = malloc(length*sizeof(int));
   new->nt_clamp = malloc(length*sizeof(int));
   new->nt_common = malloc(length*sizeof(int));
   new->nt_max = malloc(length*sizeof(int));

   return(new);
}  /* end of new_dna_matrix */
/*====================================================================
	De-allocate memory for a new DNA PSSM
=====================================================================*/
void free_dna_matrix(dna_matrix)
struct dna_matrix *dna_matrix;
{
   free(dna_matrix->nt_max);
   free(dna_matrix->nt_common);
   free(dna_matrix->nt_clamp);
   free(dna_matrix->nt_core);
   free(dna_matrix->nsres);
   free(dna_matrix->nres);
   free(dna_matrix->max_weight);
   free(dna_matrix->weights[0]);
   free(dna_matrix);

}  /* end of free_dna_matrix */
/*=================================================================
	Reverse complement a DNA pssm
	complement offset = (DNA length-1) - offset
	forward aa# = (DNA length - 1 - complement_offset) / 3
===================================================================*/
struct dna_matrix *complement_pssm(pssm)
struct dna_matrix *pssm;
{
    struct dna_matrix *rev;
    int nuc, pos, revpos;

    rev = new_dna_matrix(pssm->length);
    rev->block = pssm->block;
    rev->strand = -1;

    for (pos=0; pos < rev->length; pos++)
    {
       revpos = pssm->length - pos - 1;
       for (nuc=0; nuc < 4; nuc++)
       { 
          if (nuc == nt_atob['A'])
              rev->weights[nuc][revpos] = pssm->weights[nt_atob['T']][pos];
          else if (nuc == nt_atob['T'])
              rev->weights[nuc][revpos] = pssm->weights[nt_atob['A']][pos];
          else if (nuc == nt_atob['C'])
              rev->weights[nuc][revpos] = pssm->weights[nt_atob['G']][pos];
          else if (nuc == nt_atob['G'])
              rev->weights[nuc][revpos] = pssm->weights[nt_atob['C']][pos];
       }
    }
    return(rev);
}  /*  end of complement_pssm */
/*==================================================================
      Find degenerate region & extend 
      Be sure pssm->length is >= CORE_MIN_LEN before calling this routine
      Core degenerate region is 11 nucleotides from 3' to 5', 
      followed by 21 nuc. clamp continuing 3' to 5' (left side of pssm
      is the 5' end, so have to read it backwards).

      For each DNA pssm, should pre-compute two arrays (in rgr array?)
	For each position: # diff. nucs
	For each position: consensus nuc
=====================================================================*/
void find_oligos(pssm)
struct dna_matrix *pssm;
{
   int pos, posmod3, len, pos1, i, new_core, core_len;
   int new_clump, clamp_len, noligo, nclump;
   double ln4, max_score, core_score;
   double a_count, t_count, g_count, c_count;
   double entropy, enthalpy;
   struct oligo_list *oligo_clump, *oligo, *best_oligo, *prev_oligo, *tmp_oligo;
   char dna[CORE_MAX_LEN + CLAMP_MAX_LEN];

   ln4 = log(4.0);
   max_score = log(Core_Degeneracy) / ln4;
   nclump = noligo = 0;
   /*    List of oligos in a clump */
   if (!Verbose) oligo_clump = make_oligo(0);

/*
   printf("Best oligo for %s", pssm->block->number);
   if (pssm->strand < 0) printf(" Complement\n");
   else printf("\n");
*/

   best_oligo = NULL;			/* Highest scoring oligo for PSSM */
   prev_oligo = NULL;			/* Previous oligo found for PSSM */
   /*  Temporary storage area for clamp temperate calculations  */
   tmp_oligo = make_oligo(CORE_MAX_LEN + CLAMP_MAX_LEN);

/*>>>>> Rose conditions:  
	  first TWO positions of core are conserved (not just one) ???
          core ends on codon boundary => core_last % 3 == 0 
          minus strand core region is always 12 long, not 11, and always
            starts on the 1st res of a codon => core_first % 3 == 2 
          plus strand core region can be 12 long if the 3rd res of the 1st
            codon is conserved (eg W) => core_first % 3 == 2,
            otherwise it is 11 long and starts on the 2nd res of a 
            codon => core_first % 3 == 1
<<<<<<<<<<*/
   if (pssm->length >= CORE_MIN_LEN)
   {
      /*   Go from 3' to 5'     */
      for (pos = pssm->length - 1; pos >= CORE_MIN_LEN; pos--)
      {
         posmod3 = pos % 3;
         /*   Start core region with a conserved column; optionally
              apply core strictness to determine this */
         if ( ( Begin100 && pssm->nres[pos] == 1) ||
              (!Begin100 && pssm->nsres[pos] == 1)  )
         { 
            if (!Rose ||
                (Rose && 
                 ( (pssm->strand < 0 && posmod3 == 2)   ||
                   (pssm->strand > 0 && posmod3 >  0)  )  )   )
            {
               /* nt_max contains residue with max weight   */
               dna[0] = nt_btoa[ pssm->nt_max[pos] ];	/* 1st position */
               dna[1] = '\0';
               pos1 = pos - 1;  len = 1;

               /*  Core length is pre-determined:
                   Forward: If core starts on a codon boundary, 
			make it 12 long, otherwise it will be 11 long 
		   Complement: If starts on codon boundary 11 else 12
	       */
               core_len = CORE_MIN_LEN;
               if (pssm->strand > 0 && posmod3 == 2) core_len = CORE_MAX_LEN;
	       if (pssm->strand < 0 && posmod3 == 2 && Rose)
			 core_len = CORE_MAX_LEN;
	       if (pssm->strand < 0 && posmod3 != 2) core_len = CORE_MAX_LEN;
               
               core_score = 0.0; 
               /* Try to extend the core region to its predetermined length */
               while (pos1 >= 0 && core_score <= max_score &&
                      len < core_len)
               {
                  core_score += log( (double) pssm->nsres[pos1]) / ln4 ;
                  dna[len] = nt_adegen[ pssm->nt_core[pos1] ].residue;
                  pos1--; len++;
               }  /* end of while pos1 */

               dna[len] = '\0';

               if (Debug) printf("end:   pos=%d, len=%d, core_score=%.1f\n",
                       pos, len, core_score);
               if ( (len == core_len) && (core_score <= max_score) )
               {
                  if (Debug)
                     printf("oligo start: pos=%d, len=%d, core_score=%.1f,",
                       pos, len, core_score);

                  /* For Rose f this core region starts on the same amino acid as for the
                     previous oligo, then don't save this one */
                  if (Rose && prev_oligo != NULL &&
                      (prev_oligo->core_first / 3) ==  (pos / 3) )
                            new_core = FALSE;
                  else      new_core = TRUE;

/*>>> Following code only reports core if min clamp length fits in block
                  if ( new_core && (len + CLAMP_MIN_LEN) <= pos + 1)
<<<<<*/
                  if ( new_core )
                  {
                     /*  Use temporary oligo space for temperate calcs */
                     tmp_oligo->pssm = pssm;
                     tmp_oligo->strand = pssm->strand;
		     tmp_oligo->core_first = pos;			/* 3'end */
		     tmp_oligo->core_last = pos - core_len + 1;	/* 5'end */
                     tmp_oligo->core_score = core_score;

                     /*   Now add the clamp region  */
                     /* NOTE: clamp is built from 3' to 5', but NN temperature
                         calc has to be done from 5' to 3' */
                     tmp_oligo->clamp_temp = tmp_oligo->clamp_temp_nn = 0.0;
                     a_count = t_count = g_count = c_count = 0.0;
                     clamp_len = 0; 

                     /*-----------------------------------------------------*/
                     while ( pos1 >= 0 && len < core_len + CLAMP_MAX_LEN &&
                             tmp_oligo->clamp_temp_nn < Clamp_Temperature )
                     {
			i = pssm->nt_clamp[pos1];
                        dna[len] = nt_adegen[ i ].residue;

                        /*  update temperature stuff */
                        if ( dna[len] == 'A' )      a_count += 1.0;
                        else if ( dna[len] == 'T' ) t_count += 1.0;
                        else if ( dna[len] == 'G' ) g_count += 1.0;
                        else if ( dna[len] == 'C' ) c_count += 1.0;

                        if (clamp_len > 0)  /* need at least 2 for temp calc */
                        {
                           tmp_oligo->clamp_first = tmp_oligo->core_last - 1; /* 3'end */
                           tmp_oligo->clamp_last = pos1;	/* 5'end */

                           tmp_oligo->clamp_temp = 
                               cltemp((a_count+t_count), (g_count+c_count));
                           /*  Calc entropy & enthalpy from 5' to 3'*/
                           compute_thermo(tmp_oligo, &entropy, &enthalpy);
                           /*  Get a nearest neighbor temp */
                           tmp_oligo->clamp_temp_nn = clamp_rychlik(entropy, enthalpy, 
                                    (g_count/clamp_len), (c_count/clamp_len));
                        }
                        pos1--; len++; clamp_len++;
                     }  /* end of while pos1 */
                     /*-----------------------------------------------------*/

                     dna[len] = '\0';

                     if (Debug) printf("\n last pos=%d, core score=%.2f %s\n", 
                             (pos1 + 1), core_score, dna );

                     oligo = make_oligo(pos - pos1 + 1);

                     oligo->pssm = pssm;
                     oligo->strand = pssm->strand;
		     oligo->core_first = pos;			/* 3'end */
		     oligo->core_last = pos - core_len + 1;	/* 5'end */
                     oligo->core_score = core_score;
                     oligo->clamp_first = oligo->core_last - 1; /* 3'end */
                     oligo->clamp_last = pos1 + 1;		/* 5'end */

                     /* >>> compute_thermo(), etc. give same
			results as above for tmp_oligo - why do it again? <<< */
                     oligo->clamp_temp = 
                         cltemp((a_count+t_count), (g_count+c_count));
                     /*  Recalc entropy & enthalpy from 5' to 3'*/
                     compute_thermo(oligo, &entropy, &enthalpy);
                     /*  Get a nearest neighbor temp */
                     oligo->clamp_temp_nn = clamp_rychlik(entropy, enthalpy, 
                                    (g_count/clamp_len), (c_count/clamp_len));

		     /* NOTE: assumes Core_Strictness <= Clamp_Strictness */
                     score_clamp(oligo, Core_Strictness, Clamp_Strictness);
		     score_clamp_prob(oligo);

                     /*  Clump stuff only needs to be done if !Verbose  */
                     if (!Verbose)
                     {
		        new_clump = get_clump(oligo, prev_oligo);
                        if (new_clump)
                        {
		   	   display_oligos(oligo_clump);
                           oligo_clump->next_oligo = NULL;
                           nclump++; noligo = 0;
                        }
		        oligo->clump = nclump;
                        noligo++;
     		        oligo->number = noligo;
                        insert_oligo(oligo_clump, oligo);
                     }
                     else { display_oligo(oligo); }

                     prev_oligo = oligo;		/* save previous */
		     /*  Update best */
                     /*  If same total score, check for best core */
                     if ( best_oligo == NULL ||
                          (best_oligo != NULL &&
                           ((oligo->core_score < best_oligo->core_score) ||
                            (oligo->core_score == best_oligo->core_score &&
                             oligo->clamp_prob > best_oligo->clamp_prob))
                           )
                         )
                               best_oligo = oligo;
                  }  /* end of a good oligo new_core */
               }   /* end of a good core + room for extension */
            } /*  end of conserved pos */
         }  /* end of Rose check */
      } /* end of pos */

      if (best_oligo == NULL) printf("No suggested primers found.\n");
      else if (!Verbose)  /*  Print last clump */
           {
              display_oligos(oligo_clump);
              oligo_clump->next_oligo = NULL;
           }
   }
   else
   {
        printf("Block is too narrow\n");
   }

   free(tmp_oligo);
   if (!Verbose) free(oligo_clump);

}  /* end of find_oligos */
/*=======================================================================
	len isn't used here ... why pass it?
========================================================================*/
struct oligo_list *make_oligo(len)
int len;
{
   struct oligo_list *new;

   new = (struct oligo_list *) malloc(sizeof(struct oligo_list));

   new->core_first = new->core_last = new->clamp_first = new->clamp_last = 0;
   new->core_score = new->clamp_score = new->clamp_prob = 0.0;
   new->clamp_temp = new->clamp_temp_nn = 0.0;
   new->pssm = NULL;
   new->strand = new->out_order = 0;
   new->number = new->clump = -1;
   new->next_oligo = NULL;
   new->pssm = NULL;

   return (new);
}  /* end of make_oligo */
/*=======================================================================
	Insert oligo into a sorted list, sorted by
        clump and number.
        Lower key is better, so complements get sorted first
        First oligo in list isn't used
========================================================================*/
void insert_oligo(list, new)
struct oligo_list *list, *new;
{
   struct oligo_list *cur;
   double curkey, newkey;
   int done;

/*
   newkey = (double) new->strand * (new->core_score + new->clamp_prob);
   newkey = (double) new->core_score;
*/
   /*  Assumes never more than 100 clumps per block */
   newkey = (double) 100 * new->clump + new->number;

   cur = list;		/* first element in list is a dummy */

   done = FALSE;
   while (!done && cur->next_oligo != NULL)
   {
/*
      curkey = (double) cur->strand * (cur->core_score + cur->clamp_prob);
      curkey = (double) cur->next_oligo->core_score;
*/
      curkey = (double) 100 * cur->next_oligo->clump + cur->next_oligo->number;
      if (newkey < curkey)
      {
         new->next_oligo = cur->next_oligo;
         cur->next_oligo = new;
         done = TRUE;
      }
      cur = cur->next_oligo;
   }
   if (!done) cur->next_oligo = new;

   
}  /* end of insert_oligo */
/*===================================================================
      Compute max residue & consensus residues for each column of
      a DNA PSSM: 
       maxaa = highest scoring res in position of AA pssm
       nt_core[] = highest scoring res in DNA pssm (degenerate, for core)
       nt_common[] = most common codon from maxaa (nondegenerate, for clamp)
       nt_max[] = highest scoring res in DNA pssm (degenerate, for clamp)
       nt_clamp[] = either nt_common[] or nt_max[]
       nres[] = actual number of residues in position
       nsres[] = number of residues using strictness
       max_weight[] = max nuc weight in position (used in score_clamp() )
===================================================================*/
void compute_max(dna_pssm, aa_pssm)
struct dna_matrix *dna_pssm;
Matrix *aa_pssm;
{
   int pos, res, dna_res[3], i, ic, aapos, maxaa, maxcod;
   char ctemp[6];
   double maxwt, dtemp;

   for (pos = 0; pos < dna_pssm->length; pos++)
   {
         /*-------------------------------------------------------------*/
         /*  Get the codon corresponding to the consensus amino acid  &
             save it for display in the non-degenerate (clamp) region */
         if ( (pos%3) == 0 )
         {
             aapos = pos / 3;
             if (dna_pssm->strand < 0) aapos = aa_pssm->width - 1 - aapos;
             /*   Get consensus aa from amino acid PSSM */
             maxwt = 0.0; maxaa = -1;
             for (res=1; res <= 20; res++)
                if (aa_pssm->weights[res][aapos] > maxwt)
                {
                   maxwt = aa_pssm->weights[res][aapos];
                   maxaa = res;
                }
      
             /*   Get codon corresponding to maxaa
                  from codon usage table, put it in pos, pos+1, pos+2 ,
		  should be a better way to find all codons for an aa,
                  see aa_acodon[] in gcode.h */
             maxwt = 0.0; maxcod = -1;
             for (ic=0; ic < 64; ic++)
             {
/* >>>> Too severe? AAACTA should be okay if PolyX >= 3
  	      Don't consider AAA [0], CCC [21], GGG [42] or TTT [63] 
              Only affects most common codons for clamp, not clamp if
		taken from DNA PSSM; see fix_codons() 
                if ( (ic%21) > 0 &&
<<<< */
                if (Gcode[ic] == maxaa && Codon_Usage[ic] > maxwt)
                {
                   maxwt = Codon_Usage[ic]; maxcod = ic;
                }
             }
             if (maxcod >= 0 && maxcod < 64)
             {
                dna_pssm->nt_common[pos]   = nt_atob[ Codons[maxcod][0] ];
                dna_pssm->nt_common[pos+1] = nt_atob[ Codons[maxcod][1] ];
                dna_pssm->nt_common[pos+2] = nt_atob[ Codons[maxcod][2] ];
                if (dna_pssm->strand < 0)	/* complement */
                {
                   for (i=0; i< 3; i++)  /* save the forward values */
                   {
                      dna_res[i] = dna_pssm->nt_common[i+pos];
                   }
                   for (i=0; i< 3; i++)  /* reverse & complement */
                   {
                      if (dna_res[i] == nt_atob['A'])
                       dna_pssm->nt_common[2-i+pos] = nt_atob['T'];
                      else if (dna_res[i] == nt_atob['T'])
                       dna_pssm->nt_common[2-i+pos] = nt_atob['A'];
                      else if (dna_res[i] == nt_atob['C'])
                       dna_pssm->nt_common[2-i+pos] = nt_atob['G'];
                      else if (dna_res[i] == nt_atob['G'])
                       dna_pssm->nt_common[2-i+pos] = nt_atob['C'];
                   }
                }
             }
             
         }  /*  end of amino acid */

         /*-------------------------------------------------------------*/
         /*  Get the number of residues in this col of the DNA pssm &
             the max weight in each col, which will be used later to
             apply the strictness criteria */
         /*  Also puts  all the residues with the max weight in ctemp,
             but these aren't currently used */
         dna_pssm->nres[pos] = dna_pssm->nsres[pos] = 0;
         dna_pssm->max_weight[pos] = 0.0;
         for (res=0; res < 4; res++)
         {
            if (dna_pssm->weights[res][pos] > 0.0)
            {
                dna_pssm->nres[pos] += 1;
                if (dna_pssm->weights[res][pos] > dna_pssm->max_weight[pos])
                {
                   dna_pssm->max_weight[pos] = dna_pssm->weights[res][pos];
                   ctemp[0] = nt_btoa[res];
                   ctemp[1] = '\0';
                   ic = 1;
                }
                else if (dna_pssm->weights[res][pos] ==
                         dna_pssm->max_weight[pos])
                { 
                   ctemp[ic++]=  nt_btoa[res];
                   ctemp[ic] = '\0';
                }
             }
         }     /* end of for res */

         /*-------------------------------------------------------------*/
         /*   Get the degenerate residue for the core region */
         /*  ctemp contains all the residues with weight/max > Core_Strictness */
         ctemp[0] = '\0'; ic = 0;
         for (res=0; res < 4; res++)
         {
            dtemp = dna_pssm->weights[res][pos] / dna_pssm->max_weight[pos];
            if ( (Core_Strictness  < 1.0 && dtemp  > Core_Strictness) ||
                 (Core_Strictness == 1.0 && dtemp >= Core_Strictness) )
            {
               ctemp[ic++] = nt_btoa[res]; ctemp[ic] = '\0';
            }
         }
         dna_pssm->nsres[pos] = (int) strlen(ctemp);
         ic = 0;
         while (ic < 16 &&
                         (strcmp(ctemp, nt_adegen[ic].list) != 0)) ic++;
                  dna_pssm->nt_core[pos] = ic;   /* nt_adegen[ic].residue */

         /*-------------------------------------------------------------*/
         /*   Get the nuc with max weight from the PSSM */
         /*  ctemp contains the residues with weight/max > Clamp_Strictness */
         ctemp[0] = '\0'; ic = 0;
         for (res=0; res < 4; res++)
         {
            dtemp = dna_pssm->weights[res][pos] / dna_pssm->max_weight[pos];
            if ( (Clamp_Strictness  < 1.0 && dtemp >  Clamp_Strictness) ||
                 (Clamp_Strictness == 1.0 && dtemp >= Clamp_Strictness) )
            {
               ctemp[ic++] = nt_btoa[res]; ctemp[ic] = '\0';
            }
         }
         /*  Pick a residue a random */
         i = (rand() >> 3) % strlen(ctemp);
         dna_pssm->nt_max[pos] = nt_atob[ ctemp[i] ];

/*>>>>>>>>> Don't want degen residues in the clamp: 
         ic = 0;
         while (ic < 16 &&
                         (strcmp(ctemp, nt_adegen[ic].list) != 0)) ic++;
                  dna_pssm->nt_max[pos] = ic;  
<<<<<<*/

         /*---------------------------------------------------------------*/
         /*   Now set up the clamp depending on what the user wants there */
         if (Most_Common_Codon)
         { dna_pssm->nt_clamp[pos] = dna_pssm->nt_common[pos];}
         else                  
         { dna_pssm->nt_clamp[pos] = dna_pssm->nt_max[pos];   }
   }  /* end of pos */


   /*   Edit nt_clamp[] and break up runs  */
   break_runs(dna_pssm);

}  /* end of compute_max */

/*=============================================================================
     First oligo is the list isn't used
     Scan through all oligos for a clump & flag the best three for printing
=============================================================================*/
void display_oligos(oligos)
struct oligo_list *oligos;
{
   struct oligo_list *cur;
   struct sort_array *stemp;
   int i, noligo;

   noligo = 0;

   /*   Count the number of oligos */
   noligo = 0;
   cur = oligos;
   while (cur->next_oligo != NULL)
   {  
      noligo++;
      cur = cur->next_oligo;
   }

   /*  Make an array for sorting */
   stemp = (struct sort_array *) malloc(noligo * sizeof(struct sort_array));
   noligo = 0;
   cur = oligos;
   while (cur->next_oligo != NULL)
   {  
      stemp[noligo].oligo = cur->next_oligo;
      stemp[noligo].clump = cur->next_oligo->clump;
      stemp[noligo].number = cur->next_oligo->number;
      stemp[noligo].core_score = cur->next_oligo->core_score;
      stemp[noligo].clamp_score = cur->next_oligo->clamp_score;
      noligo++;
      cur = cur->next_oligo;
   }

   /*  Sort by clump and core_score  */
   qsort(stemp, noligo, sizeof(struct sort_array), oligocmp);

   /*  Fill in output order - should do something about ties */
   for (i=0; iout_order = i;
   }
   /*  Print out all oligos with same score as last one  */
   for (i=OutOligo; i< noligo; i++)
   {
      if (stemp[i].core_score == stemp[OutOligo-1].core_score)
 		stemp[i].oligo->out_order = OutOligo-1;
   }

   cur = oligos;
   while (cur->next_oligo != NULL)
   {  
      cur = cur->next_oligo;
      if (cur->out_order < OutOligo) display_oligo(cur);
   }

   free(stemp);
}   /*  end of display_oligos  */

/*=============================================================================
  Sample data: Forward: core_first=31, core_last=21, clamp_first=20, _last= 0
               Comple (cpos)       65            55              54        34
               pos                 15            25              26        46
=============================================================================*/
void display_oligo(oligo)
struct oligo_list *oligo;
{
   int pos, cpos, res;

   if (Debug)
   {
      printf("%s", oligo->pssm->block->number);
      if (oligo->strand < 0) printf(" Complement\n");
      else printf("\n");
   }

   /*  Print the oligo */
   for (pos=0; pos < oligo->pssm->length; pos++)
   {
      if (oligo->strand > 0)  /* Plus is printed 5' to 3' */
      {
          /*  Use degenerate codon in the core & non-degen in the clamp */
          if (pos < oligo->clamp_last) { printf(" "); }
          else if (pos >= oligo->clamp_last && pos <= oligo->clamp_first)
          {
              res = oligo->pssm->nt_clamp[pos];
              printf("%c", nt_btoa[res]);
          }
          else if (pos >= oligo->core_last && pos <= oligo->core_first)
          {  res = oligo->pssm->nt_core[pos];
             printf("%c", tolower( nt_btoa[res]) ); }
      }
      else     	/*  complement  is printed 3' to 5' */
      {
          cpos = oligo->pssm->length - 1 - pos;    /* complement position */
          if (cpos > oligo->core_first) { printf(" "); }
          else if (cpos >= oligo->clamp_last && cpos <= oligo->clamp_first)
          {
              res = oligo->pssm->nt_clamp[cpos];
              printf("%c", nt_btoa[res]);
          }
          else if (cpos >= oligo->core_last && cpos <= oligo->core_first)
          { res = oligo->pssm->nt_core[cpos];
            printf("%c", tolower( nt_btoa[res]) ); }
      }
   }   /* end of pos */

/*
   if (oligo->strand > 0) printf(" -3\'  %.2f + %.2f = %.2f", 
           oligo->core_score, oligo->clamp_prob, 
          (oligo->core_score + oligo->clamp_prob) );
   else  printf(" -5\'  %.2f + %.2f = %.2f", 
           oligo->core_score, oligo->clamp_prob, 
          (oligo->core_score + oligo->clamp_prob) );
*/
   if (oligo->strand > 0) printf(" -3\'  "); 
   else                   printf(" -5\'  ");
   printf("Core: ");
   printf("degen=%.0f", pow(4.0, oligo->core_score));
   printf(" len=%d  Clamp: score=%d, len=%d temp=% .1f",
           (oligo->core_first - oligo->core_last + 1),
            round(oligo->clamp_prob),
           (oligo->clamp_first - oligo->clamp_last + 1),
            oligo->clamp_temp_nn );
   if (oligo->clamp_temp_nn < Clamp_Temperature)
      printf(" *** CLAMP NEEDS EXTENSION\n");
   else printf("\n");
   

}  /* end of display_oligo  */
/*=======================================================================
    Scoring an oligo:
	strictness parameters = a number between 0 and 1
         0.0 is most degenerate, count all nucs in position
         1.0 is least degenerate, count only highest nuc in position
	 0 => position score == # diff nucs in position
	>0 => position score == # diff nucs in position with
				weight >= max weight
	If strict_low != strict_high, strictness is varied across
	clamp, from strict_low at the start (next to the core) to strict_high
=======================================================================*/
void score_clamp(oligo, strict_low, strict_high)
struct oligo_list *oligo;
double strict_low, strict_high;
{
   int pos, res, clamp_len, nres;
   double ln4, strict, strict_inc, dtemp;

   ln4 = log(4.0);
   clamp_len = oligo->clamp_first - oligo->clamp_last;
   strict_inc = (strict_high - strict_low) / clamp_len;

   oligo->clamp_score = 0.0;
   for (pos = oligo->clamp_last, strict = strict_high;
        pos <= oligo->clamp_first; pos++, strict -= strict_inc)
   {
      nres = 0;
      for (res=0; res < 4; res++)
      {
         /*   Strictness of 0.0 is handled separately */
         dtemp = oligo->pssm->weights[res][pos] / oligo->pssm->max_weight[pos];
         if ( (strict >  0.0 && dtemp >= strict) ||
              (strict <= 0.0 && dtemp >  strict) )
                  nres++;
      }
      oligo->clamp_score += log((double) nres) / ln4;
   }

}  /*  end of score_clamp */
/*=======================================================================
   Clamp probability score: (really isn't a probability ...)
       Weighted average of max weight in DNA PSSM columns.
       Weight is distance from core/clamp boundary: (n+1-i)/n where n
	is the clamp length.
       Total weight = sum(i=1,n){(n+1-i)/n} = sum(i=1,n){i/n} = n(n+1)/2n
		= (n+1)/2
  Sample oligos:
	strand	core_first core_last clamp_first clamp_last
	1	91		81	80		65
	-1	46		36	35		15
=======================================================================*/
void score_clamp_prob(oligo)
struct oligo_list *oligo;
{
   int pos, res, clamp_len, ipos;
   double dtemp, maxwt;

   clamp_len = oligo->clamp_first - oligo->clamp_last + 1;

   oligo->clamp_prob = 0.0;
   ipos = 0;
   for (pos = oligo->clamp_first; pos >= oligo->clamp_last; pos--)
   {
      maxwt = 0.0;
      for (res=0; res < 4; res++)
      {
         if (oligo->pssm->weights[res][pos] > maxwt)
             maxwt = oligo->pssm->weights[res][pos];
      }
      ipos++;  /* ipos is distance away from core/clamp boundary */
      dtemp =  ((double) clamp_len + 1 - ipos) / ((double) clamp_len);
/*
      oligo->clamp_prob += ( dtemp * log(maxwt / 100.0) );
*/
      oligo->clamp_prob += ( dtemp * maxwt );
   }
   dtemp = ((double) (clamp_len + 1)) / 2.0 ;	/* total weight */
   oligo->clamp_prob /= dtemp;

}  /*  end of score_clamp_prob */
/*=====================================================================*/
void display_consensus(dna_pssm)
struct dna_matrix *dna_pssm;
{
   int pos, res;

   /*   Print the consensus amino acid */
   if (dna_pssm->strand > 0)
   {
      for (pos=0; pos < dna_pssm->length; pos++)
      {
          if ((pos%3) == 2 )
          {
             res = codon2aa(Gcode, dna_pssm->nt_common[pos-2], 
		dna_pssm->nt_common[pos-1], dna_pssm->nt_common[pos]);
             printf("%c  ", aa_btoa[res]);
          }
      }
   }
   printf("\n");

}  /* end of display_consensus */
/*=================================================================
     Determine whether an oligo belongs in a new clump 
     It does if its core region doesn't overlap with the
     previous oligo. core_first is always > core_last:
   
	same clump:    old_last = 104	 old_first = 114
		    new_last = 102    new_first = 112
        different clump:
new_last = 90    new_first = 100
=================================================================*/
int get_clump(new_oligo, old_oligo)
struct oligo_list *new_oligo, *old_oligo;
{
   if (old_oligo == NULL || new_oligo == NULL ||
       new_oligo->core_first < old_oligo->core_last)
	return TRUE;
   else	return FALSE;

}   /*  end of get_clump */
/*=================================================================
    Equation [2] from Freier, et al, PNAS 83:9373-9377
=================================================================*/
double clamp_freier(entropy, enthalpy)
double entropy, enthalpy;
{
   double tm, top, bot;

   top = 0.0 - 1000.0 * enthalpy;
   /*   Assumes concentration is given in nM units  */
   bot = 1.987 * (log(Concentration/4.0) + log(0.000000001));
   bot -= entropy;
   if (bot < 0.0)
      tm = top / bot - 273.15;
   else
      tm = 0.0;

   return(tm);
}  /* end of clamp_freier */
/*=================================================================
    Equation [] from Rychlik, et al (1990), NAR 18:6409
	Ta = 0.3Tm_primer + 0.7Tm_product - 14.9
=================================================================*/
double clamp_rychlik(entropy, enthalpy, g_percent, c_percent)
double entropy, enthalpy, g_percent, c_percent;
{
   double tm_primer, salt;

   /*  Assumes Koncentration is in mM = 10-3 */
   salt = 16.6 * ( log10(Koncentration) + log10(0.001) );
   tm_primer = clamp_freier(entropy, enthalpy) + salt;

/* NOTE: tm_prod & t_a give bad temps ! Aren't used here 
   tm_prod = 0.41 * (g_percent + c_percent) + salt - 675 / ProdLen;
   ta = 0.3 * tm_primer + 0.7 * tm_prod - 14.9;
*/

   return(tm_primer);
}  /* end of clamp_rychlik */
/*=================================================================
   Compute entropy & enthalpy for an oligo clamp
	clamp_last is the 5' end, clamp_first is the 3' end
	Compute from the 5' to the 3' end
    5' clamp_last, clamp_first, core_last, core_first 3'
=================================================================*/
void compute_thermo(oligo, entropy, enthalpy)
struct oligo_list  *oligo;
double *entropy, *enthalpy;
{
   int pos, prev_res, res, bi, done;
   int firstpos, lastpos;

   res = prev_res = -99;
   *entropy = 10.8;  *enthalpy = 0.0;
   done = FALSE;
   firstpos = oligo->clamp_last; lastpos = oligo->core_first;
   for (pos=firstpos; pos <= lastpos; pos++)
   {
      /*  pos is the actual position in the array */
      if (pos >= oligo->clamp_last && pos <= oligo->clamp_first)
      {
          res = oligo->pssm->nt_clamp[pos];
          /* Be careful: nt_clamp[] could be a degenerate residue! */
          if ( (prev_res >= 0 && prev_res < 4) && 
               (res >= 0 && res < 4) )
          {
             bi = prev_res * 4 + res;
             *entropy += Bres_Entropy[bi]; 
             *enthalpy += Bres_Enthalpy[bi];
          }
          else if ( (prev_res >= 0 && prev_res < 16) && 
               (res >= 0 && res < 16) )
          {
             *entropy += 20.3;			/* average values */
             *enthalpy += 8.1;
          }
          prev_res = res;
      }
      /*  Continue into the core region until a degenerate position */
      if (pos >= oligo->core_last && !done)
      {
          if (oligo->pssm->nsres[pos] > 1) { done = TRUE; }
          else
          {
             res = oligo->pssm->nt_clamp[pos];
             if (prev_res >= 0 && prev_res < 4) 
             {
                bi = prev_res * 4 + res;
                *entropy += Bres_Entropy[bi]; 
                *enthalpy += Bres_Enthalpy[bi];
             }
             prev_res = res;
          }
      }
   }  
}   /* end of compute_thermo */

/*=====================================================================
    Reads along nt_clamp[].
	When max number of nuc of any type is passed, breaks the
	run by replacing the lowest scoring member of the run with the
	next highest value from the DNA PSSM, even if the
	clamp is made from the most common codons.
=======================================================================*/
void break_runs(pssm)
struct dna_matrix *pssm;
{
   int pos, firstpos, lastpos, prev_res, res, i, done, nrun, minpos, maxres;
   double minwt, maxwt;

   res = prev_res = -99;
   done = FALSE;
   firstpos = 0; lastpos = pssm->length;
   pos = firstpos; nrun = 1;
   while (!done && pos < lastpos)
   {
      /*  pos is the actual position in the array */
      res = pssm->nt_clamp[pos];
      /* Be careful: nt_clamp[] could be a degenerate residue! */
      if (res >= 0 && res < 4) 
      {
         if (res == prev_res) nrun++;
         else                 nrun = 1;
      }
      prev_res = res;
      if (nrun > PolyX)
      {
         /* Find the position with the lowest weight for the res */
         minpos = pos-nrun+1;
         minwt = pssm->weights[res][minpos];
         for (i= pos-nrun+2; i < pos; i++)
         {
            if (pssm->weights[res][i] < minwt)
            {
               minpos = i;
               minwt = pssm->weights[res][i];
            }
         }
         /* Find the next highest weight and use it instead */
/*>>>>> What if nres = 1 in this position???   */
         maxwt = -99.9;
         maxres = -1;
         for (i=0; i<4; i++)
         {
            if (i != res && pssm->weights[i][minpos] > maxwt)
            {
               maxwt = pssm->weights[i][minpos];
               maxres = i;
            }
         }
         pssm->nt_clamp[minpos] = maxres;
         /*  Go back to the beginning of the run */
         pos = pos-nrun; nrun = 1;
      } /* end of a run */
      pos++;
   }  
}  /* end of break_runs() */

/*=====================================================================
     Revise the codon usage table: As read, the 64 usages add up to 1.0,
	want the entries for the codons for each AA to add up to 1.0
     Assumes the global table Codon_Usage[64] has been loaded
=======================================================================*/
void fix_codons()
{
   int aa, ic;
   double totaa;

   for (aa=1; aa<=20; aa++)
   {
      totaa = 0.0;
      for (ic=0; ic < 64; ic++)
         if (Gcode[ic] == aa)  totaa += Codon_Usage[ic];
      for (ic=0; ic < 64; ic++)
         if (Gcode[ic] == aa)  Codon_Usage[ic] /= totaa;
   }

   /*    Set AAA, CCC, GGG & TTT to zero so they are never used in clamp */
/*  Affects values in DNA PSSM as well as in clamp here
   Codon_Usage[0] = Codon_Usage[21] = Codon_Usage[42] = Codon_Usage[63] = 0.0;
*/

}  /* end of fix_codons */

/*=====================================================================
 * fprint_matrix1
 *
 *  Prints a Matrix data structure to a file in a generic format. 
 *  adapted from fprint_matrix
 *
 *   Parameters: 
 *     Matrix *matrix:   the matrix to print
 *     FILE   *omfp:     the output matrix file pointer
 *     char   *alphabet: the printed matrix residues and their order
 *   Error Codes: none
 *
 */

void fprint_matrix1(matrix,omfp,alphabet)
     struct dna_matrix *matrix;
     FILE *omfp;
     char *alphabet ;
{
  int  pos, low, high, matrix_print_width ;
  char *ptr ;


  if (WWW_FLAG)
     matrix_print_width = WWW_MATRIX_PRINT_WIDTH ;
  else
     matrix_print_width = SHL_MATRIX_PRINT_WIDTH ;

  high = matrix_print_width;
  for (low=0; 
       lowlength; 
       low = (high+=matrix_print_width) - matrix_print_width) {

  fprintf(omfp,"\n%s", matrix->block->number);
  if (matrix->strand < 0) fprintf(omfp, " Complement\n");
  else fprintf(omfp, "\n");

  if (matrix->length > 99) {
    fprintf(omfp,"  |");
    for (pos=low; poslength; pos++) {
      if (pos+1 > 99) {
	fprintf(omfp,"% 4d", (pos+1-(((pos+1)/1000)*1000)) / 100);
      }
      else {
	fprintf(omfp,"    ");
      }
    }
  fprintf(omfp,"\n");
  }

  if (matrix->length > 9) {
    fprintf(omfp,"  |");
    for (pos=low; poslength; pos++) {
      if (pos+1 > 9) {
	fprintf(omfp,"% 4d", (pos+1-(((pos+1)/100)*100)) / 10);
      }
      else {
	fprintf(omfp,"    ");
      }
    }
  fprintf(omfp,"\n");
  }
  
  fprintf(omfp,"  |");
  for (pos=low; poslength; pos++) {
    fprintf(omfp,"%4d", ((pos-((pos/10)*10))+1)%10);
  }
  
  fprintf(omfp,"\n");
  fprintf(omfp,"--+");
  for (pos=low; poslength; pos++) {
    fprintf(omfp,"----");
  }

  fprintf(omfp,"\n");

  for (ptr=alphabet; *ptr != '\0'; ptr++)
      {
      fprintf(omfp,"%c |", *ptr);
      for (pos=low; poslength; pos++) 
          {
          fprintf(omfp,"% 4d", 
                  round(matrix->weights[nt_atob[*ptr]][pos]));
          }
      fprintf(omfp,"\n");
      }

  }

}  /* end of fprint_matrix1 */

/*====================================================================
 * fprint_matrix1_3spaced
 *   Prints a Matrix data structure to a file.
 *  Positions are spaced to be 2 empty positions apart so
 *  that if the matrix positions will be aligned with the positions in 
 *  nucleotide derived matrices
 *
 *  Adapted from fprint_matrix1 and fprint_matrix_3spaced
 *
 *   Parameters: 
 *     Matrix *matrix:  the matrix to print
 *     FILE   *omfp:   the output matrix file pointer
 *     char   *alphabet: the printed matrix residues and their order
 *   Error Codes: none
 */

void fprint_matrix1_3spaced(matrix,omfp,alphabet)
     struct dna_matrix *matrix;
     FILE *omfp;
     char *alphabet ;
{
  int pos;
  int low, high;
  char *ptr;

  int matrix_print_width ;

  if (WWW_FLAG)
     matrix_print_width = WWW_MATRIX_PRINT_WIDTH ;
  else
     matrix_print_width = SHL_MATRIX_PRINT_WIDTH ;

/* divide print width by 3 since it is specified in actual positions
   and in this procedure each position takes the printed space of 3 */
  matrix_print_width = floor(matrix_print_width/3) ;

  high = matrix_print_width;
  for (low=0; 
       lowlength; 
       low = (high+=matrix_print_width) - matrix_print_width) {

  fprintf(omfp,"\n");

/* modified following statements to 
  print matrix column number starting from 1 not 0 and properly show numbers >99 */

  fprintf(omfp,"%s\n", matrix->block->number);

  if (matrix->length > 99) {
    fprintf(omfp,"  |");
    for (pos=low; poslength; pos++) {
      if (pos+1 > 99) {
	fprintf(omfp,"% 4d", (pos+1-(((pos+1)/1000)*1000)) / 100);
      }
      else {
	fprintf(omfp,"    ");
      }
    }
  fprintf(omfp,"\n");
  }

  if (matrix->length > 9) {
    fprintf(omfp,"  |");
    for (pos=low; poslength; pos++) {
      if (pos+1 > 9) {
	fprintf(omfp,"% 4d        ", (pos+1-(((pos+1)/100)*100)) / 10);
      }
      else {
	fprintf(omfp,"            ");
      }
    }
  fprintf(omfp,"\n");
  }
  
  fprintf(omfp,"  |");
  for (pos=low; poslength; pos++) {
    fprintf(omfp,"%4d        ", ((pos-((pos/10)*10))+1)%10);
  }
  
  fprintf(omfp,"\n");
  fprintf(omfp,"--+");
  for (pos=low; poslength; pos++) {
    fprintf(omfp,"------------");
  }

  fprintf(omfp,"\n");
  

  for (ptr=alphabet; *ptr != '\0'; ptr++)
      {
      fprintf(omfp,"%c |", *ptr);
      for (pos=low; poslength; pos++) 
          {
          fprintf(omfp,"% 4d        ", 
                  round(matrix->weights[nt_atob[*ptr]][pos]));
          }
      fprintf(omfp,"\n");
      }

  }

} /*  end of fprint_matrix1_3spaced */
/*=========================================================================
	Sort by clump, core_score & clamp_score (D)
=========================================================================*/
int oligocmp(s1, s2)
struct sort_array *s1, *s2;
{
   if (s1->clump != s2->clump) return(s1->clump - s2->clump);
   /*  core_score is double, smaller is better */
   else if (s1->core_score > s2->core_score) return(1);
   else if (s1->core_score < s2->core_score) return(-1);
   /*  clamp_score is double, bigger is better */
   else if (s2->clamp_score > s1->clamp_score) return(1);
   else if (s2->clamp_score < s1->clamp_score) return(-1);
   else return(0);
}  /* end of oligocmp  */
he 5' end, clamp_first is the 3' end
	Compute from the 5' to the 3' end
    5' clamp_last, clamp_first, core_last, core_first 3'
=================================================================*/
void compute_thermo(oligo, entropy, enthalpy)
struct oligo_liblimps-3.9/blimps/coduse.c000064400001460000012000000125150774312247700161030ustar00jorjastaff00000400000027/*=====================================================================
(C) Copyright 1997-2000, Fred Hutchinson Cancer Research Center           
	coduse.c: Read a CUTG codon usage file & make a BLIMPS
		codon.use file for an organism

CUTG .spsum file entry format:

organism: number of compiled CDS
CGA CGC CGG CGU AGA AGG CUA CUC CUG CUU UUA UUG UCA UCC UCG UCU AGC AGU ACA ACC ACG ACU CCA CCC CCG CCU GCA GCC GCG GCU GGA GGC GGG GGU GUA GUC GUG GUU AAA AAG AAC AAU CAA CAG CAC CAU GAA GAG GAC GAU UAC UAU UGC UGU UUC UUU AUA AUC AUU AUG UGG UAA UAG UGA
-----------------------------------------------------------------------
 2/12/97 J. Henikoff
=======================================================================*/

#define EXTERN				/*  Needed for Blimps routines */
#define MAXNAME 80

#include 

double read_cutg();


/*   Blimps2Gcode[Blimps order (ACGU)] = Gcode order (UCAG)                */
int Blimps2Gcode[64] = {
 42, 41, 43, 40,  38, 37, 39, 36,  46, 45, 47, 44,  34, 33, 35, 32,     /*A*/
 26, 28, 27, 24,  22, 21, 23, 20,  30, 29, 31, 28,  18, 17, 19, 16,     /*C*/
 58, 57, 59, 56,  54, 53, 55, 52,  62, 61, 63, 60,  50, 49, 51, 48,     /*G*/
 10,  9, 11,  8,   6,  5,  7,  4,  14, 13, 15, 12,   2,  1,  3,  0  };  /*U*/

/*   Blimps2CUTG[Blimps order] = CUTG order                     */
int Blimps2CUTG[64] = {
 38, 40, 39, 41,  18, 19, 20, 21,   4, 16,  5, 17,  56, 57, 59, 58,     /*A*/
 42, 44, 43, 45,  22, 23, 24, 25,   0,  1,  2,  3,   6,  7,  8,  9,     /*C*/
 46, 48, 47, 49,  26, 27, 28, 29,  30, 31, 32, 33,  34, 35, 36, 37,     /*G*/
 61, 50, 62, 51,  12, 13, 14, 15,  63, 52, 60, 53,  10, 54, 11, 55  };  /*U*/

/*   CUTG2Blimps[CUTG order] = Blimps order                     */
int CUTG2Blimps[64] = {
 24, 25, 26, 27,   8, 10, 28, 29,  30, 31, 60, 62,  52, 53, 54, 55,
  9, 11,  4,  5,   6,  7, 20, 21,  22, 23, 36, 37,  38, 39, 40, 41,
 42, 43, 44, 45,  46, 47,  0,  2,   1,  3, 16, 18,  17, 19, 32, 34,
 33, 35, 49, 51,  57, 59, 61, 63,  12, 13, 15, 14,  58, 48, 50, 56  };  /*U*/

/*  Codons in Blimps order  */
char Codons[64][3] = {
"AAA","AAC","AAG","AAU", "ACA","ACC","ACG","ACU", "AGA","AGC","AGG","AGU",
"AUA","AUC","AUG","AUU", "CAA","CAC","CAG","CAU", "CCA","CCC","CCG","CCU",
"CGA","CGC","CGG","CGU", "CUA","CUC","CUG","CUU", "GAA","GAC","GAG","GAU",
"GCA","GCC","GCG","GCU", "GGA","GGC","GGG","GGU", "GUA","GUC","GUG","GUU",
"UAA","UAC","UAG","UAU", "UCA","UCC","UCG","UCU", "UGA","UGC","UGG","UGU",
"UUA","UUC","UUG","UUU" };

/*======================================================================*/
int main(argc, argv)
int argc;
char *argv[];
{
   FILE *fin, *fout;
   char infile[MAXNAME], outfile[MAXNAME], organism[MAXNAME], line[MAXLINE];
   int first, done;
   double tot_codons;

   printf("CODUSE: (C) Copyright 1997");
   printf(" Fred Hutchinson Cancer Research Center\n");
   if (argc > 1) strcpy(infile, argv[1]);
   else
   {
      printf("\nEnter name of CUTG spsum file: ");
      gets(infile);
   }
   if ( (fin=fopen(infile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", infile);
      exit(-1);
   }

   first = TRUE;
   if (argc > 2)  strcpy(organism, argv[2]);
   else
   {
      printf("Enter organism name (leave blank for first organism in file): ");
      gets(organism);
   }
   if (strlen(organism))
   {
      printf("Looking for organism %s in %s\n", organism, infile);
      first = FALSE;
   }
   else
   {
      printf("Taking first organism in %s", infile);
      first = TRUE;
   }

   if (argc > 3) strcpy(outfile, argv[3]);
   else
   {
      printf("\nEnter name of Blimps codon usage output file: ");
      gets(outfile);
   }
   if ( (fout=fopen(outfile, "w")) == NULL)
   {
      printf("\nCannot open file %s\n", outfile);
      exit(-1);
   }

/*---------------------------------------------------------------------*/
   done = FALSE;
   while(!done && fgets(line, MAXLINE, fin) != NULL)
   {
      if (first ||
          (strncasecmp(line, organism, strlen(organism)) == 0) )
      {
         strcpy(organism, line);
         tot_codons = read_cutg(fin, fout);
         done = TRUE;
      }
   }
/*---------------------------------------------------------------------*/
   fprintf(fout, "---------------------------------------------\n");
   fprintf(fout, "%s\n", outfile);
   fprintf(fout, "Codon usage for %s from %s:", organism, infile);
   fprintf(fout, " %.0f codons\n", tot_codons);
   fclose(fin);  fclose(fout);
   exit(0);
}  /*  end of main */
/*=========================================================================*/
double read_cutg(fin, fout)
FILE *fin, *fout;
{
   char line[MAXLINE], *ptr, ctemp[6];
   double cutg[64], total;
   int i, b;

   total = 0.0;
   if (fgets(line, MAXLINE, fin) != NULL)
   {
      ptr = strtok(line, " \t\r\n");
      i = 0;
      while (i < 64) 
      {
         if (ptr != NULL)
         {
            cutg[i] = atof(ptr); 
	    total += cutg[i++];
            ptr = strtok(NULL, " \t\r\n");
         }
         else cutg[i++] = 0.0;
      }

      for (i=0; i< 64; i++)
      {
         b = Blimps2CUTG[i];
         strncpy(ctemp, Codons[i], 3); ctemp[3] = '\0';
/*         fprintf(fout, "%12.4f	-- [%2d] %s\n", cutg[b], i, ctemp); */
         fprintf(fout, "%8.6f	-- [%2d] %s\n", cutg[b]/total, i, ctemp);
      }
   }
/*   printf("%f\n", total); */
   return(total);
}   /*  end of read_cutg */

/*======================================================================*/
6, 37,  38, 39, 40, 41,
 42, 43, 44, 45,  46, 47,  0,  2,   1,  3, 16, 18,  17, 19, 32, 34,
 33, 35, 49, 51,  57, 59, 61, 63,  12, 13, 15, 14,  58, 48, 50, 56  };  /*U*/

/*  Codoblimps-3.9/blimps/config.c000064400001460000012000000602030774312247700160630ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* config.c: reads the configuration file. */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */


/*	system headers not in global.h  */
/*	blimps library headers */
#include 
#include 
#include 
#include 
#include  
/*	headers in current directory */
#include "config.h"
#include "blimps.h"
#include "scoring.h"		/* for DoHistogram */
#include "lists.h"


/*
 * Exported variables and data structures
 */
 
/*
 * Local variables and data structures
 */
 
static Boolean BL_field_seen = FALSE;
static Boolean MA_field_seen = FALSE;

static void read_config_file_end();


/*
 * Function definitions
 */
 
/* 
 * Configuration file related functions
 *
 *   int read_config_file (filename) 
 *   void read_config_file_end()
 *   
 */

/* 
 * read config file functions
 *   These are functions for each posible config file entry.  The first
 *   two characters of the function name are usually the config file
 *   field.
 *   Parameters: See the individual functions code.  Most do not have
 *               parameters and rely on the global buffer and get_token.
 *   Return codes: Most are none.  See the individual functions code. 
 *   Error codes:  Most are none.  See the individual functions code. 
 */

static void unknown_conf_key(buf_token)
     char *buf_token;
{
  sprintf(ErrorBuffer, 
	  "Unknown configuration file key: %s\n", buf_token);
  ErrorReport(INFO_ERR_LVL);
}

static void BL_block_filename()
{
  char *buf_token;

  BL_field_seen = TRUE;
  if (MA_field_seen) {
    sprintf(ErrorBuffer,
	    "MA field already used.  Cannot have both the BL and the MA");
    ErrorReport(WARNING_ERR_LVL);
    sprintf(ErrorBuffer,
	    "fields.  Ignoring the BL line.\n");
    ErrorReport(WARNING_ERR_LVL);
  }

  buf_token = get_token(NULL);
  insert_file(buf_token, BLOCK_FILES);
}

static void PA_pattern_filename()
{
  char *buf_token;

  sprintf(ErrorBuffer,
	  "Using the PAttern switch causes the REpeats switch to be ignored.");
  ErrorReport(WARNING_ERR_LVL);
  sprintf(ErrorBuffer,
	  "Alignments reported will include repeats.\n");
  ErrorReport(WARNING_ERR_LVL);

  UsePatterns = TRUE; 
  buf_token = get_token(NULL);
/*printf("Saw pattern filename: %s\n", buf_token);*/
  insert_file(buf_token, PATTERN_FILES); 
/*printf("%d pattern files\n", number_of_files(PATTERN_FILES));*/
}

static void CO_conversion_method()
{
  char *buf_token;

  /* the scoring method to use */
  buf_token = get_token(NULL);
  sscanf(buf_token, "%d", &BlockToMatrixConversionMethod);
}

static void DB_db_filename()
{
  char *buf_token;

  buf_token = get_token(NULL);
  insert_file(buf_token, DATABASE_FILES);
}

static void ER_error_level_to_report()
{
  char *buf_token;

  /* the reporting level to do */
  buf_token = get_token(NULL);
  sscanf(buf_token, "%d", &ErrorLevelReport);
}

static void EX_export_matr_filename()
{
  char *buf_token;

  buf_token = get_token(NULL);
  strncpy(ExportMatrixFile, buf_token, SMALL_BUFF_LENGTH);
}

static void FR_freq_filename()
{
  char *buf_token;

  buf_token = get_token(NULL);
  insert_file(buf_token, FREQUENCY_FILE);
}

static void GE_genetic_code()
{
  char *buf_token;

  /* the genetic code to use */
  buf_token = get_token(NULL);
  sscanf(buf_token, "%d", &GeneticCodeInitializer);
}

static void HI_histogram()
{
  char *buf_token;
	
  buf_token = get_token(NULL);
  if ((strcasecmp(buf_token, "TRUE") == 0) ||
      (strcasecmp(buf_token, "YES") == 0) ||
      (strcasecmp(buf_token, "T") == 0) ||
      (strcasecmp(buf_token, "Y") == 0) ||
      ((isdigit(buf_token[0])) && (strcmp(buf_token, "0") != 0))) {
    DoHistogram = TRUE;
  }
  else {
    DoHistogram = FALSE;
  }
}

static void MA_Matrix_db_filename()
{
  char *buf_token;

  MA_field_seen = TRUE;
  if (BL_field_seen) {
    sprintf(ErrorBuffer,
	    "BL field already used.  Cannot have both the MA and the BL");
    ErrorReport(WARNING_ERR_LVL);
    sprintf(ErrorBuffer,
	    "fields.  Ignoring the MA line.\n");
    ErrorReport(WARNING_ERR_LVL);
  }

  buf_token = get_token(NULL);
  insert_file(buf_token, BLOCK_FILES);
}

static void NU_number_to_report()
{
  char *buf_token;

  /* the number of results to save/report */
  buf_token = get_token(NULL);
  sscanf(buf_token, "%d", &NumberToReport);
}

static void OP_options_for_algs()
{
  insert_into_options(NULL);
}

static void OU_output_filename()
{
  char *buf_token;

  buf_token = get_token(NULL);
  strncpy(OutputFile, buf_token, SMALL_BUFF_LENGTH);
}

static void RE_repeats_allowed()
{
  char *buf_token;
	
  buf_token = get_token(NULL);
  if ((strcasecmp(buf_token, "TRUE") == 0) ||
      (strcasecmp(buf_token, "YES") == 0) ||
      (strcasecmp(buf_token, "T") == 0) ||
      (strcasecmp(buf_token, "Y") == 0) ||
      ((isdigit(buf_token[0])) && (strcmp(buf_token, "0") != 0))) {
    RepeatsAllowed = TRUE;
  }
  else {
    RepeatsAllowed = FALSE;
  }
}

static void SC_scoring_method()
{
  char *buf_token;

  /* the scoring method to use */
  buf_token = get_token(NULL);
  sscanf(buf_token, "%d", &SequenceMatrixScoringMethod);
}

static void SE_search_type()
{
  char *buf_token;

  sprintf(ErrorBuffer,
	  "Old style configuration file.");
  ErrorReport(INFO_ERR_LVL);
  sprintf(ErrorBuffer,
	  "New style does not use the SE field.\n");
  ErrorReport(INFO_ERR_LVL);

  buf_token = get_token(NULL);
  if (!strcasecmp(buf_token, "MATRIX")) {
    SearchType = SEARCH_TYPE_MATRIX;
  }
  else if (!strcasecmp(buf_token, "BLOCK")) {
    SearchType = SEARCH_TYPE_BLOCK;
  }
  else {
    SearchType = SEARCH_TYPE_UNKNOWN;
    sprintf(ErrorBuffer, 
	    "Unknown search type: %s\n", buf_token);
    ErrorReport(WARNING_ERR_LVL);
  }
}

static void SQ_sequence_filename()
{
  char *buf_token;
  
  buf_token = get_token(NULL);
  insert_file(buf_token, SEQUENCE_FILES);
}

static void ST_strands_to_search()
{
  char *buf_token;

  /* number of strands to search: 1 (forward), -1 (reverse), 2 (both) */
  buf_token = get_token(NULL);
  sscanf(buf_token, "%d", &StrandsToSearch);
  if (StrandsToSearch < 0) StrandsToSearch = -1;
  if (StrandsToSearch == 0 || StrandsToSearch > 2) StrandsToSearch = 2;
}

static void SV_saved_scores()
{
  char *buf_token;
	
  buf_token = get_token(NULL);
  if ((strcasecmp(buf_token, "TRUE") == 0) ||
      (strcasecmp(buf_token, "YES") == 0) ||
      (strcasecmp(buf_token, "T") == 0) ||
      (strcasecmp(buf_token, "Y") == 0) ||
      ((isdigit(buf_token[0])) && (strcmp(buf_token, "0") != 0))) {
    SavedScoresFlag = TRUE;
  }
  else {
    SavedScoresFlag = FALSE;
  }
}

static void TY_sequence_type()
{
  char *buf_token;
  
  /* DNA => force DNA, AA => force AA  */
  buf_token = get_token(NULL);
  if (!strcasecmp(buf_token, "DNA"))   { SequenceType = NA_SEQ; }
  else 
  {
     if (!strcasecmp(buf_token, "AA")) { SequenceType = AA_SEQ; }
     else                              { SequenceType = UNKNOWN_SEQ; }
  }
}



/*
 * init_config_vars
 *   Sets the initial and default values of the configuration file related
 *   variables.
 *   Parameters: none
 *   Error codes: none
 */

static void init_config_vars()
{

  /* initialize the file lists */
  BlockFiles.fp    = NULL;
  DatabaseFiles.fp = NULL;
  FrequencyFile.fp = NULL;
  SequenceFiles.fp = NULL;

  BlockFiles.db_type    = -1;
  DatabaseFiles.db_type = -1;
  FrequencyFile.db_type = -1;
  SequenceFiles.db_type = -1;
  
  BlockFiles.seq_type    = UNKNOWN_SEQ;
  DatabaseFiles.seq_type = UNKNOWN_SEQ;
  FrequencyFile.seq_type = UNKNOWN_SEQ;
  SequenceFiles.seq_type = UNKNOWN_SEQ;
  
  BlockFiles.num_files    = 0;
  DatabaseFiles.num_files = 0;
  FrequencyFile.num_files = 0;
  SequenceFiles.num_files = 0;
  
  BlockFiles.max_files    = 0;
  DatabaseFiles.max_files = 0;
  FrequencyFile.max_files = 0;
  SequenceFiles.max_files = 0;
  
  BlockFiles.cur_file    = 0;
  DatabaseFiles.cur_file = 0;
  FrequencyFile.cur_file = 0;
  SequenceFiles.cur_file = 0;

  /* initialize some of the other variables to their default values */
  GeneticCodeInitializer = 0;		/* the standard genetic code */

  StrandsToSearch = 2;		/* == 2 if want to search both strands */
  RepeatsAllowed  = TRUE;	/*  RE  */
  SavedScoresFlag = FALSE;	/*  SV  */
  NumberToReport  = 0;		/* <0 means all, 0 means judge, */
				/* >0 means use that number */
  SearchType      = SEARCH_TYPE_UNSET;
  SequenceType	= UNKNOWN_SEQ;		/* sequence type */
  DoHistogram = FALSE;

  BlockToMatrixConversionMethod = 3; /* default method is pseudo-counts */
  SequenceMatrixScoringMethod   = 0; /* default method is zero */

  ErrorLevelReport = WARNING_ERR_LVL; /* report all errors */

}


/*
 * read_config_file
 *   reads the configuration file given by the filename
 *   Parameters:
 *     char * filename  : the configuration filename
 *   Return codes: 1 (TRUE) if read file sucessfully
 *                 0 (FALSE) if had problems, but without a major error
 *   Error codes:
 */

int read_config_file(filename) 
     char *filename;
{
  FILE *cfp;  /* the configuration file pointer */
  char *buf_token;
  int str_length;


  /* initialize the variabls and set the defaults */
  init_config_vars();


  /* create the error file by removing the config file extension and adding *
   * the suffix .err .  If there is no extension, just add .err to the name */
  /* NOTE: this is written to be un*x specific */
  
  strncpy(Buffer, filename, LARGE_BUFF_LENGTH);
  str_length = strlen(Buffer);
  str_length--;
  while ((Buffer[str_length] != '.') &&
	 (Buffer[str_length] != '/')) {
    str_length--;
  }
  if (Buffer[str_length] == '.') { /* there is an extension */
    strncpy(&(Buffer[str_length]), ".err\0", 
	    LARGE_BUFF_LENGTH - str_length);
  }
  else {			/* there was no extension */
    strncpy(&(Buffer[strlen(Buffer)]), ".err\0", 
	    LARGE_BUFF_LENGTH - strlen(Buffer));
  }
  set_error_file_name(Buffer);

  /* open the configuration file for reading */
  cfp = fopen(filename, "r");

  if (cfp == NULL) {
    sprintf(ErrorBuffer, 
	    "Configuration file \"%s\" not found.  Exiting\n", 
	    filename);
    ErrorReport(FATAL_ERR_LVL);	/* exit with an error */
  }


  /* read in the parameters */
  /* loop until EOF or '//' (detected in the switch) */
  while (!feof(cfp) && fgets(Buffer, LARGE_BUFF_LENGTH, cfp)) {
    if (!blank_line(Buffer)) { /* don't want to look if this is a blank line */

      buf_token = get_token(Buffer);

      /* huge switch statement of chars to determine which config entry */
      switch ( toupper(buf_token[0]) ) {
      case 'B':
	switch ( toupper(buf_token[1]) ) {
	case 'L': /* BL: Block filename */
	  BL_block_filename();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      case 'C':
	switch ( toupper(buf_token[1]) ) {
	case 'O': /* CO: Conversion method for converting a block to a */
		  /*     matrix */
	  CO_conversion_method();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      case 'D':
	switch ( toupper(buf_token[1]) ) {
	case 'B': /* DB: Database filename */
	  DB_db_filename();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      case 'E':
	switch ( toupper(buf_token[1]) ) {
	case 'R': /* ER: Error level to report */
	  ER_error_level_to_report();
	  break;
	case 'X': /* EX: Export Matrix filename */
	  EX_export_matr_filename();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      case 'F':
	switch ( toupper(buf_token[1]) ) {
	case 'R': /* FR: Codon Frequency Filename */
	  FR_freq_filename();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      case 'G':
	switch ( toupper(buf_token[1]) ) {
	case 'E': /* GE: Genetic code */
	  GE_genetic_code();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      case 'H':
	switch ( toupper(buf_token[1]) ) {
	case 'I': /* HI: Histogram */
	  HI_histogram();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      case 'M':
	switch ( toupper(buf_token[1]) ) {
	case 'A': /* MA: Matrix database filename*/
	  MA_Matrix_db_filename();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      case 'N':
	switch ( toupper(buf_token[1]) ) {
	case 'U':	/* NU: Number to report */
	  NU_number_to_report();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      case 'O':
	switch ( toupper(buf_token[1]) ) {
	case 'P': /* OP: Options for algorithms */
	  OP_options_for_algs();
	  break;
	case 'U': /* OU: Output filename */
	  OU_output_filename();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      case 'P':
	switch ( toupper(buf_token[1]) ) {
	case 'A': /* PA: The pattern file(s) */
	  PA_pattern_filename();
	  break;
	case '4': /* P4: Parameter, for backward compatibility */
	  sprintf(ErrorBuffer,
		  "Old style configuration file.");
	  ErrorReport(INFO_ERR_LVL);
	  sprintf(ErrorBuffer,
		  "New style uses the ST field instead of P4.\n");
	  ErrorReport(INFO_ERR_LVL);
	  ST_strands_to_search();
	  break;
	case '5': /* P5: Parameter, for backward compatibility */
	  sprintf(ErrorBuffer,
		  "Old style configuration file.");
	  ErrorReport(INFO_ERR_LVL);
	  sprintf(ErrorBuffer,
		  "New style uses the RE field instead of P5.\n");
	  ErrorReport(INFO_ERR_LVL);
	  RE_repeats_allowed();
	  break;
	case '9': /* P9: Parameter, for backward compatibility */
	  sprintf(ErrorBuffer,
		  "Old style configuration file.");
	  ErrorReport(INFO_ERR_LVL);
	  sprintf(ErrorBuffer,
		  "New style uses the NU field instead of P9.\n");
	  ErrorReport(INFO_ERR_LVL);
	  NU_number_to_report();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      case 'R':
	switch ( toupper(buf_token[1]) ) {
	case 'E':	/* RE: Repeats allowed */
	  RE_repeats_allowed();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      case 'S':
	switch ( toupper(buf_token[1]) ) {
	case 'C': /* SC: Scoring method */
	  SC_scoring_method();
	  break;
	case 'E': /* SE: Search type */
	  SE_search_type();
	  break;
	case 'Q': /* SQ: Sequence filename */
	  SQ_sequence_filename();
	  break;
	case 'T': /* ST: Strands to search */
	  ST_strands_to_search();
	  break;
	case 'V': /* SV: Sequence filename */
	  SV_saved_scores();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      case 'T':
	switch ( toupper(buf_token[1]) ) {
	case 'Y': /* TY: Sequence type  */
	  TY_sequence_type();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
      case '/':
	switch ( toupper(buf_token[1]) ) {
	case '/': /* //: end of configuration file */
	  /* close the configuration file */
	  fclose(cfp);
	  
	  read_config_file_end();
	  
	  /* return */
	  return TRUE;
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      default:
	unknown_conf_key(buf_token);
	break;
      } /* end switch */
    } /* end if not a blank line */
  } /* end while loop */

  /* close the configuration file */
  fclose(cfp);

  read_config_file_end();

  /* return */
  return FALSE; /* didn't read a "//", hit the end of the file */
}


/*
 * read_config_file_end
 *   Does the final clean up of reading the configuration file.  Makes
 *   sure the database files are in the right places.
 *   Parameters: none
 *   Error codes: none
 */

static void read_config_file_end()
{
  FILE *tfp;			/* temp file pointer */

  /* move the database to the correct list */

  /* NOTE: In the future there will be DB, SQ, BL, and matrix fields.  The */
  /*       if statements will be very bad.  Mayb have a number and each time */
  /*       one of the fields is seen, set a flag in the number.  Then have */
  /*       a case statement based off of that number. */
  /* SOLUTION: The matricies are stored in the blocks files until after this */
  /*           phase.  After we figure out the search type then determine if */
  /*           the files are blocks or matricies.  Since there can be only */
  /*           blocks or matricies, not both, we can do this. */

  switch (SearchType) {
  case SEARCH_TYPE_UNSET :

    /* determine the type of search. */
    /* SQ vs DB = BLOCK; BL vs DB = MATRIX; SQ vs BL = UNKNOWN; */

    /* if there are database files, should be ok */
    if (number_of_files(DATABASE_FILES) != 0) {

      /* if no sequence files, probably BL vs DB = SEARCH_TYPE_MATRIX */
      if (number_of_files(SEQUENCE_FILES) == 0) {

	/* make sure there is a block to use, */
	/* if not, there is no way to search */
	if (number_of_files(BLOCK_FILES) != 0) {
	  SearchType = SEARCH_TYPE_MATRIX;
	  SequenceFiles = DatabaseFiles;
	}
	else {
	  sprintf(ErrorBuffer,
		  "No block file (BL) or sequence file (SQ) given, aborting.\n");
	  ErrorReport(FATAL_ERR_LVL);
	}

      }

      /* since there is sequence files, if no block files, */
      /* probably SQ vs DB = SEARCH_TYPE_BLOCK */
      else if (number_of_files(BLOCK_FILES) == 0) {

	/* make sure there is a sequence file to use, */
	/* if not, there is no way to search */
	if (number_of_files(SEQUENCE_FILES) != 0) {
	  SearchType = SEARCH_TYPE_BLOCK;
	  BlockFiles = DatabaseFiles;
	}
	else {
	  /* won't be reached, left incase of re-arrangement */
	  sprintf(ErrorBuffer,
		  "No sequence file (SQ) or block file (BL) given, aborting.\n");
	  ErrorReport(FATAL_ERR_LVL);
	}

      }

      /* since there is all three kinds of files (SQ, BL and DB), guess that */
      /* the search will be UNKNOWN */
      else {
	sprintf(ErrorBuffer,
		"Configuration file has SQ, BL, and DB entries.");
	ErrorReport(WARNING_ERR_LVL);
	sprintf(ErrorBuffer,
		"Unable to determine the type of search.");
	ErrorReport(WARNING_ERR_LVL);
	sprintf(ErrorBuffer, 
		"Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.\n");
	ErrorReport(WARNING_ERR_LVL);
	SearchType = SEARCH_TYPE_UNKNOWN;
      }

    }

    /* since there is no database file (no DB line) if there are both */
    /* sequence and block files we can try an UNKNOWN search */
    else {

      /* if either one of the sequence files or block files are missing, */
      /* the search cannot be done */
      if ((number_of_files(SEQUENCE_FILES) == 0) ||
	  (number_of_files(BLOCK_FILES) == 0)) {
	/* missing one of BL and SQ */
	sprintf(ErrorBuffer,
		"Missing either the BL or SQ field, aborting.\n");
	ErrorReport(FATAL_ERR_LVL);
      }

      /* both sequence and block files are present (but no database files), */
      /* we can try an UNKNOWN search */
      else {
	/* has both SQ and BL, make SEARCH_TYPE_UNKNOWN */
	sprintf(ErrorBuffer,
		"Configuration file has SQ and BL entries.");
	ErrorReport(WARNING_ERR_LVL);
	sprintf(ErrorBuffer,
		"Unable to determine the type of search.");
	ErrorReport(WARNING_ERR_LVL);
	sprintf(ErrorBuffer, 
		"Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.\n");
	ErrorReport(WARNING_ERR_LVL);
	SearchType = SEARCH_TYPE_UNKNOWN;
      }

    } /* end if there are database files */

    break;
  case SEARCH_TYPE_MATRIX :
    /* blocks vs databases (sequences) */
    /* check if there are files in the database files */
    if (number_of_files(DATABASE_FILES) == 0) {
      if (number_of_files(SEQUENCE_FILES) == 0) {
	sprintf(ErrorBuffer,
		"No sequence files given for the sequence database, aborting.\n");
	ErrorReport(FATAL_ERR_LVL);
      }
      else {
	sprintf(ErrorBuffer,
		"No DB field given, assuming data is in the SQ field.\n");
	ErrorReport(WARNING_ERR_LVL);
      }
    }
    else {
      if (number_of_files(BLOCK_FILES) == 0) {
	sprintf(ErrorBuffer,
		"No block file given (BL field), aborting.\n");
	ErrorReport(FATAL_ERR_LVL);
      }
      else {
	SequenceFiles = DatabaseFiles;
      }
    }
    break;
  case SEARCH_TYPE_BLOCK :
    /* sequences vs databases (blocks) */
    /* check if there are files in the database files */
    if (number_of_files(DATABASE_FILES) == 0) {
      if (number_of_files(BLOCK_FILES) == 0) {
	sprintf(ErrorBuffer,
		"No block files given for the block database, aborting.\n");
	ErrorReport(FATAL_ERR_LVL);
      }
      else {
	sprintf(ErrorBuffer,
		"No DB field given, assuming data is in the BL field.\n");
	ErrorReport(WARNING_ERR_LVL);
      }
    }
    else {
      if (number_of_files(SEQUENCE_FILES) == 0) {
	sprintf(ErrorBuffer,
		"No sequence file given (SQ field), aborting.\n");
	ErrorReport(FATAL_ERR_LVL);
      }
      else {
	BlockFiles = DatabaseFiles;
      }
    }
    break;
  case SEARCH_TYPE_UNKNOWN :
    /* unknown search type, assuming sequences vs blocks is OK */
    sprintf(ErrorBuffer, 
	    "Unknown search type given, assuming SQ vs BL search.\n");
    ErrorReport(WARNING_ERR_LVL);
    break;
  default:
    /* BIG ERROR, should never get here.  Memory corrupted */
    sprintf(ErrorBuffer, 
	    "read_config_file_end(): SearchType variable corrupted.");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "                        Should never have reached this part of the program.");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "                        Possible memory problems.");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "                        The rest of the run may be invalid.");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer, 
	    "                        Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.\n");
    ErrorReport(PROGRAM_ERR_LVL);
    SearchType = SEARCH_TYPE_UNKNOWN;
    break;
  }

  /* determine if there are blocks or matricies in the BlockFiles */
  SiteSpecificScoringMatrixType = SSSM_BLOCK;
  if (MA_field_seen) {		/* the user says it is matricies */
    MatrixFiles = BlockFiles;
    SiteSpecificScoringMatrixType = SSSM_PRECOMP_MAT;
  }
  else if (! BL_field_seen) {	/* the user didn't say it's blocks so check */
    rewind_file(BLOCK_FILES);
    tfp = get_file(BLOCK_FILES);
    if (! (tfp == NULL)) {
      /* there is data in the files, so check the type */
      /* search for the MA line in a matrix */
      while (fgets(Buffer, LARGE_BUFF_LENGTH, tfp) &&
	     !(((Buffer[0] == 'M') && (Buffer[1] == 'A')) ||
	       ((Buffer[0] == 'B') && (Buffer[1] == 'L'))) &&
	     !feof(tfp));
      if ((Buffer[0] == 'M') && (Buffer[1] == 'A')) {
	MatrixFiles = BlockFiles;
	SiteSpecificScoringMatrixType = SSSM_PRECOMP_MAT;
      } /* else leave it as a blocks database */
    }
    /* if no data at all let it default to blocks and let the rest handle it */
    /* The system needs these to be rewound to start */
    rewind_file(BLOCK_FILES);	
    /* being safe, the fp was copied from BlockFiles */
    rewind_file(MATRIX_FILES);
  }
    


  /* determine sequence database db_type and seq_type */
  /* NOTE: doing direct accessing because need to set various fields */
  SequenceFiles.fp = fopen(SequenceFiles.file_names[0], "r");
  
  if (SequenceFiles.fp != NULL) {
    SequenceFiles.db_type = type_dbs(SequenceFiles.fp, DbInfo);
    if (SequenceFiles.db_type < 0 || SequenceFiles.db_type >= MAXDB) {
      /* unknown database type */
      sprintf(ErrorBuffer, 
	      "Unknown sequence format.  Known formats are:");
      ErrorReport(WARNING_ERR_LVL);
      sprintf(ErrorBuffer,
	      "Fasta, GenBank, PIR, Swiss Prot, and GCG.");
      ErrorReport(WARNING_ERR_LVL);
      sprintf(ErrorBuffer,
	      "Assuming there is no title and just sequence.\n");
      ErrorReport(WARNING_ERR_LVL);
      SequenceFiles.db_type = FLAT;
    }
    SequenceFiles.seq_type = seq_type_dbs(SequenceFiles.fp, DbInfo, 
			  SequenceFiles.db_type, SequenceType);
  }
  else {
    sprintf(ErrorBuffer, "Unable to read sequence file: %s ",
	    SequenceFiles.file_names[0]);
    ErrorReport(SERIOUS_ERR_LVL);
    sprintf(ErrorBuffer, "to determine the type of database\n");
    ErrorReport(SERIOUS_ERR_LVL);
  }

  fclose(SequenceFiles.fp);
  SequenceFiles.fp = NULL;	/* NOTE: make sure to set to NULL.  This */
				/* field is checked in various file */
				/* functions and is assumed to be NULL at */
				/* the first time called */
}

/* Change log information follows. 
  Changes since version 3.2.5:
   1/23/99 Added SV option to activate SavedScores
           Added lists.h
  Changes since version 3.2.4:
  12/12/98 Modified TY to differentiate between values DNA & AA.
           Modified ST to accept value = -1 => minus strand only.
  Changes since version 3.0.0:
   4/22/96 Added TYpe option to specify sequence type as DNA or protein.
  Changes for version 3.0.0:
   9/16/95 Changed default conversion method from 2 to 3, line 342.  JGH
*/
d_scores();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
	break;
      case 'T':
	switch ( toupper(buf_token[1]) ) {
	case 'Y': /* TY: Sequence type  */
	  TY_sequence_type();
	  break;
	default:
	  unknown_conf_key(buf_token);
	  break;
	}
      case '/':
	switch ( toupper(buf_token[1]) ) {
	case '/': /* //: end of configuration file */
	  /* close the confiblimps-3.9/blimps/convert.c000064400001460000012000001572160774312247700163110ustar00jorjastaff00000400000027/* (C) Copyright 1993-2001, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* convert.c: functions for different methods of converting a block into a */
/*            matrix */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */


/*	system headers not in global.h */
#include 
#include 
/*	blimps library headers */
#include 
#include 
#include 	/* includes sequences.h, output.h */
#include 	/* includes pattern.h */
#include 
#include 
#include 	/* for MAXLINE */
#include 
/*	headers in current directory */
#include "blimps.h"


/*
 * Exported variables and data structures
 */
double RTot;
struct float_qij *Qij;

/*
 * Local variables and data structures
 */


/*
 * Function definitions
 */


/*
 * --OLD-- Sequence weighting methods.  Various methods of giving different
 * weights to the sequences.
 */

static double *clustered_weights(/*block*/);
static double *pre_weighted_sequences(/*block*/);



/*
 * --OLD-- Matrix construction methods.  Build matricies from blocks and 
 * sequence weights.
 */

static void basic_matrix_construction(/*block, seq_weight, matrix*/);







/* 
 * Conversion methods
 *   void default_conversion_method(block, matrix)
 *   void original_conversion_method_cleaned_up(block, matrix) 
 *   void original_conversion_method(block, matrix)
 *   void pre_weighted_conversion_method(block, matrix)
 *   void altschul_data_dependent_conversion_method(block, matrix)
 *   void gribskov_conversion_method(block, matrix)
 */




/*
 * block_to_matrix
 *   converts a block into a matrix (possition specific matrix?) according
 *   to the rule specified in BlockToMatrixConversionMethod.  The block field
 *   of the matrix is set in this function.
 *   Parameters:
 *     Block *block: the block to convert
 *   Return codes: Returns the pointer to the new Matrix.
 *   Error codes:
 */

Matrix *block_to_matrix(block, conversion_method)
     Block *block;
     int conversion_method;
{
  Matrix *matrix;
  char *tmp;

  /* get new matrix */
  matrix = new_matrix(block->width);

  /* initialize the pattern */
  matrix->patterns = NULL;

  /* copy the relevant block information into the matrix */
  matrix->block = block;
  
  strncpy(Buffer, block->id, SMALL_BUFF_LENGTH);
  /* NOTE: Chance to goof by replacing the wrong "BLOCK" */
  tmp = strstr(Buffer, "BLOCK");
  if (tmp != NULL) {
    strncpy(strstr(Buffer, "BLOCK"), "MATRIX\0", 7);
    strncpy(matrix->id, Buffer, SMALL_BUFF_LENGTH);
  }
  else {
    strncpy(matrix->id, 
	    strncat(Buffer, "; MATRIX", SMALL_BUFF_LENGTH - strlen(Buffer)),
	    SMALL_BUFF_LENGTH);
  }

  strcpy(matrix->ac, block->ac);
  strncpy(matrix->de, block->de, DESC_WIDTH);
  strncpy(matrix->ma, block->bl, SMALL_BUFF_LENGTH);
  /* Just leave it BLxxxxx */
  strcpy(matrix->number, block->number);
  strncpy(matrix->motif, block->motif, 20); 
  /* This 20 is from the size in the struct */

  matrix->width = block->width;
  matrix->max_length = matrix->width;
  matrix->percentile = block->percentile;
  matrix->strength = block->strength;
  matrix->num_sequences = block->num_sequences;


  switch (conversion_method) {
  case 0:   /* seq wts from clumps, odds ratios */
    original_conversion_method_cleaned_up(block, matrix); 
    break;
  case 1:   /* seq wts from clumps, odds ratios */
    original_conversion_method(block, matrix);
    break;
  case 2:   /* seq wts from block else pb_weights(), odds ratios */
    pre_weighted_conversion_method(block, matrix);
    break;

  /*  DEFAULT is case 3 (scale=0)  */
  /* cases 3-40 use seq wts from block else pb_weights()  */
  /* cases 3-6, 10, 20 use position-specific pseudo counts */
  /*  require frequency[] = default.amino.frq, RTot and  */
  /*  Qij = default.qij which must be initialized by calling program */
  case 3:   /* Altschul's data-dependent method of computing a PSSM */
	    /* log_e(odds ratios)=nats, positive values */
    altschul_data_dependent_conversion_method(block, matrix, 0);
    break;
  case 4:   /* log_2(odds ratios)=bits, signed integers */
    altschul_data_dependent_conversion_method(block, matrix, 1);
    break;
  case 5:   /* log_2(odds ratios)/2= half bits, signed integers */
    altschul_data_dependent_conversion_method(block, matrix, 2);
    break;
  case 6:   /* log_2(odds ratios)/3= third bits, signed integers */
    altschul_data_dependent_conversion_method(block, matrix, 3);
    break;
  case 9:   /* pseudo-counts close to zero */
	    /* log_e(odds ratios)=nats, positive values */
    altschul_data_dependent_conversion_method(block, matrix, 9);
    break;

  case 10:   /* odds ratios */
    altschul_data_dependent_conversion_method(block, matrix, 10);
    break;
  case 20:   /* (count[aa]+pseudo-count[aa])/(totcount+totpseudo) */
    altschul_data_dependent_conversion_method(block, matrix, 20);
    break;
  case 21:   /* count[aa]/totcount */
    altschul_data_dependent_conversion_method(block, matrix, 21);
    break;

  case 30:   /* Gribskov's average score method; loads default.sij */
    gribskov_conversion_method(block, matrix);
    break;

  case 40:   /* SIFT method; requires default.rank, default.diri   */
	     /* which are loaded here */
    SIFT_conversion_method(block, matrix);
    break;

  default:  /* the default case */

    sprintf(ErrorBuffer, 
	    "Invalid block to matrix conversion method specified, %d.",
	    conversion_method);
    ErrorReport(WARNING_ERR_LVL);

    sprintf(ErrorBuffer,     /* ^^^^----------------vvvvvvvvvvvvvvvvvvv */
	    "Using the default conversion method of Altschul's data-dependent method.\n");
    ErrorReport(WARNING_ERR_LVL);
    altschul_data_dependent_conversion_method(block, matrix, 0);
    break;

  } /* end switch of conversion types */

  /* return the matrix */
  return matrix;
}



/*
 * original_conversion_method_cleaned_up
 *   The original conversion method.  This is done by weighted average of the 
 *   clusters.  This follows the method in patmat but has been written in
 *   a more legible manner and has the following changes:
 *     no more reliance on flag values for B, Z, and X
 *     X, '-', '*', & non-code scores are read straight from the frequencies
 *     the frequencies for B and Z are ignored, when a B or Z is encountered
 *       it is partitioned between D & N or E & Q.
 *     the matrix scores for B and Z are computed from the matrix scores of 
 *       D & N and E & Q.
 *   Parameters:
 *     Block *block:   the block to be converted
 *     Matrix *matrix: where the resulting matrix will be put
 *   Error codes: none
 */

void original_conversion_method_cleaned_up(block, matrix) 
     Block *block;
     Matrix *matrix;
{
  double *seq_weight;		/* the contribution of this sequence to the */
				/* block.  = 1/(num seq in cluster) */

  /* get the weights of the sequences */
  seq_weight = clustered_weights(block);

  basic_matrix_construction(block, seq_weight, matrix);

  free(seq_weight);
}
  


/*
 * pre_weighted_conversion_method
 *   This conversion method uses the pre-weighted sequence scores and
 *   uses the basic matrix construction method.  This method has the
 *   following properties:
 *     X, '-', '*', & non-code scores are read straight from the frequencies
 *     the frequencies for B and Z are ignored, when a B or Z is encountered
 *       it is partitioned between D & N or E & Q.
 *     the matrix scores for B and Z are computed from the matrix scores of 
 *       D & N and E & Q.
 *   Parameters:
 *     Block *block:   the block to be converted
 *     Matrix *matrix: where the resulting matrix will be put
 *   Error codes: none
 */

void pre_weighted_conversion_method(block, matrix)
     Block *block;
     Matrix *matrix;
{
  double *seq_weight;		/* the contribution of this sequence to the */
				/* block.  = the value given in the block */

  /* get the weights of the sequences */
  seq_weight = pre_weighted_sequences(block);

  if (seq_weight != NULL) {
    basic_matrix_construction(block, seq_weight, matrix);
    
    free(seq_weight);
  }
  else {
    /* remember that seq_weight has been freed already if NULL is returned */
    sprintf(ErrorBuffer,
	    "All weights in the block were less than or equal to zero.");
    ErrorReport(WARNING_ERR_LVL);
    sprintf(ErrorBuffer,
	    "Computing position-based sequence weights.\n");
    ErrorReport(WARNING_ERR_LVL);

    pb_weights(block);
    seq_weight = pre_weighted_sequences(block);

    if (seq_weight != NULL) {
       basic_matrix_construction(block, seq_weight, matrix);
       free(seq_weight);
    }
    

  }
    
} /* end of pre_weighted_convertion_method */




/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>*/

/*
 * altschul data dependent conversion method aux. structures/defines
 */

/* these are from JGH's makealts, I am not sure where these are from exctly. */
/* I think they are the actual values from the aabet.h structures. */
/* AAS and AASALL are not matched up with any of the aabet.h defines. */
#define AASALL 26
/* 0- 1A 2R 3N 4D 5C 6Q 7E 8G 9H 10I 11L 12K 13M 14F 15P 16S 17T 18W 19Y
   20V 21B 22Z 23X 24* 25J,O,U */

#define MAXWIDTH 400			/* Max. block width */

struct working {	/* Working information for one column */
  double cnt[AASALL];		/* Sequence-weighted counts */
  double totcnt;
  double raw[AASALL];		/* unweighted counts */
  double totraw;
  double reg[AASALL];		/*  pseudo counts */
  double totreg;
  double probn[MAXDIRI];        /* for dirichlet */
  double probj[MAXDIRI];        /* for dirichlet */

};

struct work_pssm {              /* Working PSSM area */
  double** value;   /* double value[MAXWIDTH][AASALL]*/
  double* sum ;   /* double sum[MAXWIDTH] */
};

struct rank_cell {
        int aa;
        double value;
};

/*
 * altschul data dependent conversion method aux. functions
 */

/*==================================================================*/
static struct working *make_col()
{
  struct working *col;
  int aa;
  
  CheckMem(
	   col = (struct working *) malloc(sizeof(struct working))
	   );
  
  col->totcnt = col->totreg = 0.0;
  for (aa=0; aa < AASALL; aa++) {
    col->cnt[aa] = col->reg[aa] = 0.0;
  }

  return col;
}  /* end of make_col */


/*=====================================================================*/
static struct work_pssm *make_work_pssm(length)
int length;
{
  struct work_pssm *pssm;
  int pos, aa;
  double* double_pointer;

  CheckMem(
           pssm = (struct work_pssm *) malloc(sizeof(struct work_pssm))
           );

        double_pointer = (double*) calloc (length * AASALL, sizeof (double));
        pssm->value = (double **) calloc (length, sizeof (double*));
        pssm->sum = (double *) calloc (length, sizeof (double));

  for (pos = 0; pos < length; pos++) {
        pssm->value[pos] = &(double_pointer[pos * AASALL]);
  }

  for (pos = 0; pos < length; pos++) {
    pssm->sum[pos] = 0.0;
    for (aa=0; aa < AASALL; aa++) {
      pssm->value[pos][aa] = 0.0;
    }
  }  

  return pssm;
}  /* end of make_work_pssm */
/*=====================================================================*/
void free_work_pssm(pssm)
struct work_pssm *pssm;
{
  free(pssm->value[0]); 
  free(pssm->value);
  free(pssm->sum);
  free(pssm);
}  /* end of free_work_pssm */


/*======================================================================*/
static void counts(block, col, pos)
     Block *block;
     struct working *col;
     int pos;
{
  int seq, aa, aa1;

  col->totcnt = col->totraw = col->totreg = 0.0;
  for (aa = 0; aa < AASALL; aa++) { 
    col->cnt[aa] = col->raw[aa] = col->reg[aa] = 0.0;
  }

  /*  Only count the real 20 aas, combine B(21) with D & Z(22) with E  */
  for (seq = 0; seq < block->num_sequences; seq++) {
    aa = block->residues[seq][pos];
    if (aa == 21) aa = 4;			/* combine B with D */
    if (aa == 22) aa = 7;			/* combine Z with E */
    if (aa >= 1 && aa < AAS) {
      col->cnt[aa] += block->sequences[seq].weight;
      col->totcnt += block->sequences[seq].weight;
      col->raw[aa] += 1.0;
      col->totraw += 1.0;
    }
    else {
/*
      sprintf(ErrorBuffer,
	      "Uncounted \"residue\" character for %s: %c\n",
	      block->number, aa_btoa[block->residues[seq][pos]]);
      ErrorReport(INFO_ERR_LVL);
*/
      /* If not one of the basic aas, divide the count among them */
      for (aa1 = 1; aa1 < AAS; aa1++)
      {
         col->cnt[aa1] += (block->sequences[seq].weight / 20.0);
         col->raw[aa1] += (1.0 / 20.0) ;
      }
      col->totcnt += block->sequences[seq].weight;
      col->totraw += 1.0;
    }
  }
}  /* end of counts */


/*=====================================================================*/
static int count_residues(col)
     struct working *col;
{
  int aa, nr;
  
  nr = 0;
  for (aa = 1; aa < AAS; aa++) {
    if (col->cnt[aa] > 0.0) nr++;
  }

  return nr;
}  /*  end of count_residues */


/*=======================================================================*/
static void pseudo_alts(col, qij, epsilon)
     struct working *col;
     struct float_qij *qij;
     double epsilon;
{
  int aa, row;
  
  /*---------- get the pseudo counts -------------------------------*/
  for (aa=1; aa < AAS; aa++) {
    col->reg[aa] = 0.0;
    for (row = 1; row < AAS; row++) {
      col->reg[aa] += (col->cnt[row] * qij->value[aa][row] / qij->marg[row]);
    }
    col->reg[aa] *= epsilon;
    if (col->totcnt > 0.0) col->reg[aa] /= col->totcnt;
    col->totreg += col->reg[aa];
  }
}  /* end of pseudo_alts */


/*========================================================================
	Computes scores for B, Z, X, -(gap) and *(stop) in a column
	of a PSSM using other scores in the column
	frequency[] is a global array created by load_frequencies()
	why is it an argument here?
==========================================================================*/
/* SOME DUPLICATE CODE FROM basic_matrix_construction(). */
static void compute_BZX(frequency, matrix, col)
     double *frequency;
     Matrix *matrix;
     int col;
{
  int aa;
  double dmean, dmin;
  double part_D;		/* the partition of D for B. */
				/* = freq[D] / ( freq[D] + freq[N] ) */
  double part_N;		/* the partition of N for B. */
				/* = freq[N] / ( freq[D] + freq[N] ) */
  double part_E;		/* the partition of E for Z. */
				/* = freq[E] / ( freq[E] + freq[Q] ) */
  double part_Q;		/* the partition of Q for Z. */
				/* = freq[Q] / ( freq[E] + freq[Q] ) */
  /*
   * find the partitions of D, N, E, and Q for B and Z
   */
  part_D = frequency[aa_atob['D']] / 
    ( frequency[aa_atob['D']] + frequency[aa_atob['N']] );
  part_N = frequency[aa_atob['N']] / 
    ( frequency[aa_atob['D']] + frequency[aa_atob['N']] );
  part_E = frequency[aa_atob['E']] / 
    ( frequency[aa_atob['E']] + frequency[aa_atob['Q']] );
  part_Q = frequency[aa_atob['Q']] / 
    ( frequency[aa_atob['E']] + frequency[aa_atob['Q']] );

    /* fill in the matrix for B, Z, X, gap, stop and non */
    matrix->weights[aa_atob['B']][col] = 
      (part_D * matrix->weights[aa_atob['D']][col] +
       part_N * matrix->weights[aa_atob['N']][col]);
    matrix->weights[aa_atob['Z']][col] =
      (part_E * matrix->weights[aa_atob['E']][col] +
       part_Q * matrix->weights[aa_atob['Q']][col]);

    /*   X or unk gets the weighted average score; - and * get the min score */
    dmin = 999.99;
    dmean = 0.0;
    for (aa=1; aa<20; aa++)
    {
       dmean += frequency[aa] * matrix->weights[aa][col];
       if (matrix->weights[aa][col] < dmin) dmin = matrix->weights[aa][col];
    }
    matrix->weights[aa_atob['X']][col] = dmean;
    matrix->weights[aa_atob[25]][col] = dmean;		/* unknown res */
    matrix->weights[aa_atob['-']][col] = dmin;
    if (dmin > 0.0) matrix->weights[aa_atob['*']][col] = 0.0;
    else            matrix->weights[aa_atob['*']][col] = dmin;

}  /* end of compute_BZX */


/*=========================================================================
      Adds negative minval to give all positive matrix,
      then multiplies by 99/maxval to give scores ranging from 0 to 99 
      NOTE: Not 0 to 100 because "output_matrix" routine might not leave
	    enough space.
===========================================================================*/
static void positive_matrix(freqs, pssm, matrix)
     double *freqs;
     struct work_pssm *pssm;
     Matrix *matrix;
{
  int pos, aa;
  double factor, maxval, minval, dtemp;

  minval = 9999.9;
  maxval = -9999.9;
  for (pos = 0; pos < matrix->width; pos++) {
    for (aa=1; aa < AAS; aa++) {
      if (pssm->value[pos][aa] < minval) minval = pssm->value[pos][aa];
      if (pssm->value[pos][aa] > maxval) maxval = pssm->value[pos][aa];
    }
  }
   
  if (minval < 0.0) {
    factor = 99.0 / (maxval - minval);
  }
  else {
    factor = 99.0 / maxval;
  }
  if (factor < 1.0) {
    factor = 1.0;
  }
  for (pos = 0; pos < matrix->width; pos++) {
    for (aa=1; aa < AAS; aa++) {
      if (minval < 0.0) {
	dtemp = factor * (pssm->value[pos][aa] - minval);
      }
      else {
	dtemp = factor * pssm->value[pos][aa];
      }
      matrix->weights[aa][pos] = (MatType) dtemp;
    }
    compute_BZX(freqs, matrix, pos);
  }  /*  end of for pos */
}  /* end of positive_matrix */


/*==========================================================================
     Uses Altschul's method of getting pseudo-counts with a qij matrix,
	scale=0 => DEFAULT nats, positive integers
	scale=1 => bits, signed integers
	scale=2 => half bits, signed integers
	scale=3 => third bits, signed integers
	scale=9 => few pseudo counts, bits, positive integers
	scale=10 => odds ratios
	scale=20 => counts + pseudo counts
	scale=21 => counts
===========================================================================*/
static void make_alts(block, matrix, freqs, qij, RTot, scale)
     Block *block;
     Matrix *matrix;
     double *freqs;
     struct float_qij *qij;
     double RTot;		/* Total R for Altschul */
     int scale;
{
  double factor, dtemp, epsilon;
  int pos, aa;
  struct working *col;
  struct work_pssm *pssm;

  factor = 1.0;
  if (scale > 0 && scale < 9) factor = (double) scale / log(2.0);
  col = make_col();
  pssm = make_work_pssm(block->width);
  
  /*--------------  Do one position at a time -------------------*/
  for (pos = 0; pos < block->width; pos++) 
  {
    /*-------- count the number of each aa in this position ------------*/
    counts(block, col, pos);
    
    /*-------- determine total number of pseudo-counts in column ------*/
    /*  9 => compute minimal number of pseudo-counts; RTot should
	be a large number in this case, such as 1000  */
    if (scale == 9)
/*
    {  epsilon = (double) col->totcnt / RTot ; }
*/
    {  epsilon = (double) 1.0 / RTot ; }
    else
    {  epsilon = (double) RTot * count_residues(col);  }
    
    /*---------- get the pseudo counts -------------------------------*/
    pseudo_alts(col, qij, epsilon);
    
    /*---------   Fill in the matrix entries --------------------*/
    pssm->sum[pos] = 0.0;
    for (aa=1; aa < AAS; aa++)
    {
       /*    Count proportions; returned if scale == 21   */
       if (scale == 21)
       {
          pssm->value[pos][aa] = col->cnt[aa];
          if ( col->totcnt > 0.0)
             pssm->value[pos][aa] /= col->totcnt;
       }

       /*    Count+pseudo proportions; returned if scale == 20   */
       if (scale <= 20)
       {
          pssm->value[pos][aa] = col->cnt[aa] + col->reg[aa];
          if ( (col->totcnt + col->totreg) > 0.0)
             pssm->value[pos][aa] /= (col->totcnt + col->totreg);
       }
    
       /*     Odds ratios; returned if scale == 10   */
       if (scale < 20 && freqs[aa] > 0.0)
          pssm->value[pos][aa] /= freqs[aa];

       /*   take the log of the odds ratio  */
       if (scale < 10 && pssm->value[pos][aa] > 0.0) 
          pssm->value[pos][aa] = log(pssm->value[pos][aa]);
 
       pssm->sum[pos] += pssm->value[pos][aa];

       /*  scale the matrix  */
       dtemp = factor * pssm->value[pos][aa];
       matrix->weights[aa][pos] = dtemp;

     }  /* end of aa */

     compute_BZX(freqs, matrix, pos); 
  }  /*  end of for pos */

  /*------ Now make the final scores; make log scores non-neg    */
  /*       by subtracting the min. value for all positions ----- */
  if (scale==0 || scale==9) positive_matrix(freqs, pssm, matrix);
  
  free(col);
  free_work_pssm(pssm);
}  /* end of make_alts */

/*==========================================================================
     Uses Gribskov's method 
     Assumes a non-negative substition matrix (min. value = 0)
     Sets 20 aas plus B and Z from the matrix; X, etc to zero = min. value
     Index for B is 21, for Z is 22
===========================================================================*/
void make_gribs(block, matrix, subst)
Block *block;
Matrix *matrix;
struct float_qij *subst;
{
   double dtemp, sum, temp[AASALL];
   int pos, aa, aa1;
   struct working *col;

   col = make_col();

   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      counts(block, col, pos);

      sum = 0.0;
      for (aa=0; aa <= 22; aa++)
      {
         temp[aa] = 0.0;
         for (aa1=1; aa1 <= 22 ; aa1++)
         {
            temp[aa] += col->cnt[aa1] * subst->value[aa][aa1];
         }
         temp[aa] /= col->totcnt;
         sum += temp[aa];
      }
      for (aa=1; aa <= 22; aa++)
      {
/*		ends up rounding to zero!
         dtemp = temp[aa];
         matrix->weights[aa][pos] = round(dtemp);
*/
         matrix->weights[aa][pos] = temp[aa];
      }
      /*  Set X, * and - to zero */
      matrix->weights[0][pos] = matrix->weights[23][pos] = 0.0;
      matrix->weights[24][pos] = matrix->weights[25][pos] = 0.0;
   }  /*  end of for pos */

   free(col);
}   /*  end of make_gribs */

/*======================================================================*/
struct float_qij *load_qij(fin)
     FILE *fin;
{
  char line[LARGE_BUFF_LENGTH], *ptr;
  double total;
  int alpha[AAS], nrows, ncols, row, col, i;
  struct float_qij *new;
  
  CheckMem (
	    new = (struct float_qij *) malloc(sizeof(struct float_qij))
	    );
  
  /*----------Read file until first non-blank line --------------*/
  /* Skip comments at beginning of file - 1st char = #, > or ;   */
  line[0] = '\0';
  while (((int) strlen(line) < 1 ||
           line[0]=='#' || line[0]=='>' || line[0]==';')
	 && fgets(line, sizeof(line), fin) != NULL)
    ;

  /*------See if the first line has characters on it ------------*/
  for (col=0; col < AAS; col++) alpha[col] = -1;
  if (strstr(line, "A") != NULL) {	/* This line has characters */
    row = 0;	/* # of alphabetic characters on the line */
    for (i=0; i< (int) strlen(line); i++) {
      col = -1;
      col = aa_atob[line[i]];
      if (col >= 0 && col < AAS) {
	alpha[row] = col;
	row++;
      }
      else if (isalpha(line[i])) {
	row++;
      }
    }
  }

  /*-------Get the data values now ------------*/
  for (row=0; rowvalue[row][col] = -1.0;		/* Null value */
    }
  }
   
  nrows = 0;
  line[0] = '\0';
  while (fgets(line, sizeof(line), fin) != NULL) {
    if ((int) strlen(line) > 1 && nrows < AAS) {
      if (alpha[nrows] >= 0 && alpha[nrows] < AAS) {
	row = alpha[nrows]; ncols = 0;
	ptr = strtok(line, " ,\n");
	while (ptr != NULL) {
	  if (strspn(ptr, ".+-0123456789") == strlen(ptr)) {
	    col = alpha[ncols];
	    if (col >= 0 && col < AAS) {
	      new->value[row][col] = (double) atof(ptr);
	    }
	    ncols++;
	  }
	  ptr = strtok(NULL, " ,\n");
	}
      }
      nrows++;
    }
  }
  
  /*-------If some entries are still missing, assume symmetry ---------*/
  for (row=0; rowvalue[row][col] < 0.0) {
	new->value[row][col] = new->value[col][row];
      }
    }
  }

  /*-------compute the marginal probabilities ---------*/
  total = 0.0;
  for (row=1; rowmarg[row] = 0.0;
    for (col=1; colmarg[row] += new->value[row][col];
    }
    total += new->marg[row];
  }
  
  return new;
}  /* end of load_qij */


/*=========================================================================
    Normalize sequence weights to add up to the number of sequences
=========================================================================*/
void normalize(block)
     Block *block;
{
  double sum, factor;
  int seq;
  
  sum = 0.0;
  for (seq = 0; seq < block->num_sequences; seq++) {
    sum += block->sequences[seq].weight;
  }
  if (sum <= 0.0)   /*  All seqs have zero weight! Add pb weights */
  {
      sprintf(ErrorBuffer,
	    "All weights in the block were less than or equal to zero.");
      ErrorReport(WARNING_ERR_LVL);
      sprintf(ErrorBuffer,
	    "Computing position-based sequence weights.\n");
      ErrorReport(WARNING_ERR_LVL);

      pb_weights(block);
      for (seq = 0; seq < block->num_sequences; seq++) {
        sum += block->sequences[seq].weight;
      }
  }
  if (sum > 0.0) factor = block->num_sequences / sum;
  else factor = 1.0;
  for (seq = 0; seq < block->num_sequences; seq++) {
    block->sequences[seq].weight *= factor;
  }
}  /*  end of normalize */


/*
 * altschul_data_dependent_conversion_method
 *   Expects global variables frequency[], Qij[][] and RTot
 *   Parameters:
 *     Block *block:   the block to be converted
 *     Matrix *matrix: where the resulting matrix will be put
	scale = 0	log odds ratios, positive values
		1	bits, log odds ratios
		2	half bits, log odds ratios
         	3	third bits, log odds ratios
		9	few pseudo counts
		10	odds ratios
		20	(counts+pseudo counts)/tot
		21	counts
 *   Error codes: Checks MAXWIDTH, global variables
 */
void altschul_data_dependent_conversion_method(block, matrix, scale)
     Block *block;
     Matrix *matrix;
     int scale;
{
  int itemp;

  if (block->width > MAXWIDTH)
  {
      itemp = MAXWIDTH;
      sprintf(ErrorBuffer, "convert: Block is too wide, unable to continue (max=%d).\n",
		itemp);
      ErrorReport(FATAL_ERR_LVL);
  }
  if (Qij == NULL) {
      sprintf(ErrorBuffer, "Qij matrix missing, unable to continue.\n");
      ErrorReport(FATAL_ERR_LVL);
    }

  /* check to see if the block has sequence weights */

  normalize(block);   /*  Make weights sum to number of sequences */
  make_alts(block, matrix, frequency, Qij, RTot, scale); 

} /* end of altschul_data_dependent_conversion_method  */

/*
 * gribskov_dependent_conversion_method
 *   Expects global variables frequency[]
 *   Loads default.sij
 *   Parameters:
 *     Block *block:   the block to be converted
 *     Matrix *matrix: where the resulting matrix will be put
 *   Error codes: none
 */

void
gribskov_conversion_method(block, matrix)
     Block *block;
     Matrix *matrix;
{
  char sijname[SMALL_BUFF_LENGTH], *blimps_dir;
  struct float_qij *sij_matrix;
  FILE *fp;

  /*  load the substitution matrix */
  blimps_dir = getenv("BLIMPS_DIR");
  if (blimps_dir != NULL)
  {
     sprintf(sijname, "%s/docs/default.sij", blimps_dir);
  }
  else
  {
     sprintf(sijname, "default.sij");
  }

  sij_matrix = load_qij(fp);
  fclose(fp);
  if (sij_matrix == NULL) 
  {
      sprintf(ErrorBuffer,
	      "gribskov_conversion_method: default.sij matrix missing, Cannot continue.\n");
      ErrorReport(FATAL_ERR_LVL);
  }

  /* check to see if the block has sequence weights */
  normalize(block);   /*  Make weights sum to number of sequences */
  make_gribs(block, matrix, sij_matrix); 

}  /* end of gribskov_dependent_conversion_method
/*<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/

/*
 * Sequence weighting methods.  Various methods of giving different
 * weights to the sequences.
 */

/*
 * static double *clustered_weights(block)
 * static double *pre_weighted_sequences(block)
 * void pb_weights(block)
 */


/*
 * clustered_weights
 *   This sequence weighing depends on the clustering of the block.
 *   The weight of a sequence is one over the number of sequences in
 *   that cluster.
 *   Parameters:
 *     Block* block: the block that the sequences are from.
 *   Return codes: a pointer to the sequence weights array.
 *   Error codes: 
 */
 
static double *clustered_weights(block)
     Block* block;
{
  double *seq_weight;		/* the contribution of this sequence to the */
				/* block.  = 1/(num seq in cluster) */

  int clust;			/* a cluster counter */
  int seq;			/* a sequence counter */

  int seq_num;			/* keep's track of where to start when */
				/* filling seq_weight*/

  double weight;		/* a temporary holder for the weight */


  /*
   * create and fill the seq_weight array.
   */
  /* allocate space */
  CheckMem(
	   seq_weight = (double *) calloc(block->num_sequences, sizeof(double))
	   );

  /* fill the seq_weight array */
  seq_num = 0;
  for (clust=0; clustnum_clusters; clust++) {
    weight = 1.0/(double)block->clusters[clust].num_sequences;
    /* fill each sequence in the cluster */
    for (seq=seq_num; seqclusters[clust].num_sequences; 
	 seq++) {
      seq_weight[seq] = weight;
    }
    seq_num += block->clusters[clust].num_sequences;
  }

  return seq_weight;
} /* end of clustered_weights */

/*
 * pre_weighted_sequences
 *   This sequence weighing was done beforehand.  The weight of the
 *   sequence was read from the block.
 *   Parameters:
 *     Block* block: the block that the sequences are from.
 *   Return codes: a pointer to the sequence weights array.
 *   Error codes: NULL if all of the weights in the block are <= zero.
 */
 
static double *pre_weighted_sequences(block)
     Block* block;
{
  double *seq_weight;		/* the contribution of this sequence to the */
				/* block. */

  int seq;			/* a sequence counter */

  int num_seqs;			/* keep's track of total sequences */

  double max_weight;

  /*
   * create and fill the seq_weight array.
   */
  /* allocate space */
  CheckMem(
	   seq_weight = (double *) calloc(block->num_sequences, sizeof(double))
	   );
  
  num_seqs = block->num_sequences;
  
  /* fill each sequence weight from the block */
  max_weight = 0.0;
  for (seq=0; seqsequences[seq].weight;
    if (seq_weight[seq] > max_weight) {
      max_weight = seq_weight[seq];
    }
  }

  if (max_weight <= 0) {
    /* all weights were zero */
    free(seq_weight);
    
    return NULL;  /* the error is handled in the calling function */
  }	    

  return seq_weight;
}  /* end of pre_weighted_sequences  */

/*=======================================================================
      Compute Steve's position-based sequence weights      
	NOTE:  Characters - (0), X (23) and * (24) are ignored
	       Characters 1-22 are the 20 basic aas plus B & Z
	MATRIX_AA_WIDTH = 26, defined in matrix.h
========================================================================*/
void pb_weights(block)
Block *block;
{
   struct pb_counts *pb;
   double factor, dtemp;
   int seq, pos, aa, width;

   width = block->width;
   CheckMem( 
	pb = (struct pb_counts *) malloc(width*sizeof(struct pb_counts))
    );

   for (pos = 0; pos < width; pos++)
   { 
      pb[pos].diffaas = 0.0;
      for (aa = 0; aa < MATRIX_AA_WIDTH; aa++)
         pb[pos].naas[aa] = (double) 0.0;
   }
  
   for (pos = 0; pos < width; pos++)
      for (seq = 0; seq < block->num_sequences; seq++)
      {
         if (block->residues[seq][pos] >= 1 &&
             block->residues[seq][pos] <= 22)
         {
            pb[pos].naas[block->residues[seq][pos]] += 1;
         }
         else
         {
            sprintf(ErrorBuffer, "pb_weights:%d ignored for %s\n",
                 block->residues[seq][pos], block->number);
	    ErrorReport(INFO_ERR_LVL);
         }
      }

   factor = 1.0;
   for (pos = 0; pos < width; pos++)
   { 
      for (aa = 1; aa <= 22; aa++)
      {
         if (pb[pos].naas[aa] > 0.0)
         {
            pb[pos].diffaas += 1;	/* # of different types of aas in pos */
         }
      }
   }

   for (seq = 0; seq < block->num_sequences; seq++)
   {
      block->sequences[seq].weight = 0.0;
      for (pos = 0; pos < width; pos++)
      {
         aa = block->residues[seq][pos];
         dtemp = pb[pos].diffaas * pb[pos].naas[aa];
         if (dtemp > 0.0)
            block->sequences[seq].weight += 1.0 / dtemp;
      } 
   }

   free(pb);
}  /* end of pb_weights */




/*
 * Matrix construction methods.  Build matricies from blocks and 
 * sequence weights.
 */

/*
 * static void basic_matrix_construction(block, seq_weight, matrix)
 *
 */


/* 
 * basic_matrix_construction
 *   This is the most general matrix construction method.  Each
 *   occurence of a residue in a sequence contributes the sequence
 *   weight of the sequence divided by the frequency of the residue to
 *   the total weight of the residue in the matrix at that column.
 *   This contribution is scaled by the total of the other residue
 *   contributions for the column of the matrix.  The following are
 *   exceptions to the method:
 *     X, '-', '*', & non-code scores are read straight from the frequencies
 *     the frequencies for B and Z are ignored, when a B or Z is encountered
 *       it is partitioned between D & N or E & Q.
 *     the matrix scores for B and Z are computed from the matrix scores of 
 *       D & N and E & Q.
 *   Parameters:
 *     Block *block:       the block to be converted
 *     double *seq_weight: the weights of each sequence.
 *     Matrix *matrix:     where the resulting matrix will be put
 *   Error codes: none
 */

static void basic_matrix_construction(block, seq_weight, matrix)
     Block *block;
     double *seq_weight;
     Matrix *matrix;
{
  int seq;			/* a sequence counter */
  int col;			/* a column counter */
  int aa;			/* an amino acid counter */

  int num_sequences;		/* the number of sequences in the block */

  Residue res;			/* a residue.  Used for keeping hold of */
				/* block->residues[seq][col] */

  double total;			/* the sum of the seq_weight/freq[] for each */
				/* column (every amino acid).  This is used */
				/* to scale each matrix entry for a column */
				/* to a percentage */

  double count[MATRIX_AA_WIDTH]; /* the sum of the weights for each amino */
				 /* acid in the column */

  double part_D;		/* the partition of D for B. */
				/* = freq[D] / ( freq[D] + freq[N] ) */
  double part_N;		/* the partition of N for B. */
				/* = freq[N] / ( freq[D] + freq[N] ) */
  double part_E;		/* the partition of E for Z. */
				/* = freq[E] / ( freq[E] + freq[Q] ) */
  double part_Q;		/* the partition of Q for Z. */
				/* = freq[Q] / ( freq[E] + freq[Q] ) */


  /*
   * find the partitions of D, N, E, and Q for B and Z
   */
  part_D = frequency[aa_atob['D']] / 
    ( frequency[aa_atob['D']] + frequency[aa_atob['N']] );
  part_N = frequency[aa_atob['N']] / 
    ( frequency[aa_atob['D']] + frequency[aa_atob['N']] );
  part_E = frequency[aa_atob['E']] / 
    ( frequency[aa_atob['E']] + frequency[aa_atob['Q']] );
  part_Q = frequency[aa_atob['Q']] / 
    ( frequency[aa_atob['E']] + frequency[aa_atob['Q']] );


  /*
   * make the matrix
   */
  /* for every column in the block, count up the countribution of each aa, */
  /* and fill the matrix column */
  for (col=0; colwidth; col++) {
    /* reset the counts array and the total */
    for (aa=0; aanum_sequences;
    for (seq=0; seqresidues[seq][col];
      /* if not B, Z, X, gap, stop and non, do the regular */
      if ((res != aa_atob['B']) &&
	  (res != aa_atob['Z']) &&
	  (res != aa_atob['X']) &&
	  (res != aa_atob['-']) && /* gap */
	  (res != aa_atob['*']) && /* stop */
	  (res != AAID_NAR)) {     /* non */
	if (frequency[res] != 0.0) { /* try to protect from div by zero */
	  count[res] += seq_weight[seq] / frequency[res];
	  total      += seq_weight[seq] / frequency[res];
	}
      }
      /* otherwise, if it is B, partition B between D and N */
      else if (res == aa_atob['B']) {
	if (frequency[aa_atob['D']] != 0.0) { /* try to protect div by zero */
	  count[aa_atob['D']] += 
	    (part_D * seq_weight[seq]) / frequency[aa_atob['D']];
	  total +=
	    (part_D * seq_weight[seq]) / frequency[aa_atob['D']];
	}
	if (frequency[aa_atob['N']] != 0.0) { /* try to protect div by zero */
	  count[aa_atob['N']] += 
	    (part_N * seq_weight[seq]) / frequency[aa_atob['N']];
	  total +=
	    (part_N * seq_weight[seq]) / frequency[aa_atob['N']];
	}
      }
      /* otherwise, if it is Z, partition Z between E and Q */
      else if (res == aa_atob['Z']) {
	if (frequency[aa_atob['E']] != 0.0) { /* try to protect div by zero */
	  count[aa_atob['E']] += 
	    (part_E * seq_weight[seq]) / frequency[aa_atob['E']];
	  total +=
	    (part_E * seq_weight[seq]) / frequency[aa_atob['E']];
	}
	if (frequency[aa_atob['Q']] != 0.0) { /* try to protect div by zero */
	  count[aa_atob['Q']] += 
	    (part_Q * seq_weight[seq]) / frequency[aa_atob['Q']];
	  total +=
	    (part_Q * seq_weight[seq]) / frequency[aa_atob['Q']];
	}
      }
      /* otherwise, if it is X, gap, stop or non, don't calculate */
    }

    /* for every amino acid, fill in the matrix for this column, unless it */
    /* is B, Z, X, gap, stop or non */
    for (aa=0; aaweights[aa][col] = count[aa] * 100.0 / total;
	}
	else {
	  matrix->weights[aa][col] = 0.0;
	}
      }
    }

    /* fill in the matrix for B, Z, X, gap, stop and non */
    matrix->weights[aa_atob['B']][col] = 
      (part_D * matrix->weights[aa_atob['D']][col] +
       part_N * matrix->weights[aa_atob['N']][col]);
    matrix->weights[aa_atob['Z']][col] =
      (part_E * matrix->weights[aa_atob['E']][col] +
       part_Q * matrix->weights[aa_atob['Q']][col]);
    matrix->weights[aa_atob['X']][col] = frequency[aa_atob['X']];
    matrix->weights[aa_atob['-']][col] = frequency[aa_atob['-']];
    matrix->weights[aa_atob['*']][col] = frequency[aa_atob['*']];
    matrix->weights[AAID_NAR][col]     = frequency[AAID_NAR];

  } /* end for each column */

} /* end of basic_matrix_construction */









/*
 * The original PATMAT method.  Hardly ever done anymore.
 */

/*
 * original_conversion_method
 *   The original conversion method.  This is done by weighted average of the 
 *   clusters.  This follows the method in patmat.
 *   Parameters:
 *     Block *block:   the block to be converted
 *     Matrix *matrix: where the resulting matrix will be put
 *   Error codes: none
 */

void original_conversion_method(block, matrix)
     Block *block;
     Matrix *matrix;
{
  int aa, pos, clust, seq;
  int num_clusters, num_sequences, width;
  Residue *sequence;
  double *divisor;

  double tmp_double;

  double *number_occurred[MATRIX_AA_WIDTH]; /* [amino acid][position] */

  
  
  /* allocate the space for the number occured 2-d array ([amino acid][pos]) */
  CheckMem(
	 number_occurred[0] = (double *) calloc(matrix->width*MATRIX_AA_WIDTH,
						sizeof(double))
	   );
  
  /* setup the array of pointers */
  for (aa=0; aa < MATRIX_AA_WIDTH; aa++) {
    number_occurred[aa] = number_occurred[0] + aa*matrix->width;
  }
  
  /* get the space for the divisor array */
  CheckMem(
	   divisor = (double *) calloc(block->width, sizeof(double))
	   );
  
  
  
  width = block->width;

  /* 
   * get the number of residues at each position.  clusters use 
   * fractional values.
   */

  /* for each cluster */
  num_clusters = block->num_clusters;
  for (clust=0; clust < num_clusters; clust++) {
    
    /* for each sequence in the cluster */
    num_sequences = block->clusters[clust].num_sequences;
    for (seq=0; seq < num_sequences; seq++) {
      
      /* for each position in the sequence */
      sequence = block->clusters[clust].sequences[seq].sequence;
      for (pos=0; pos < width; pos++) {
	
	/* increase the number of amino acids seen at this position */
	/* in the number_occured matrix */
	number_occurred[sequence[pos]][pos] += 
	  (double) 1.0/(double)num_sequences; /* type casting to be safe */
	
      } /* end for each position */
    } /* end for each sequence */
  } /* end for each cluster */
  
  /*
   * calculate the divisor for later use.
   * divisor[i] = summation over all amino acids of 
   *                ( num_occured[aa][i] / frequency[aa] )
   */
  
  /* for each position */
  for (pos=0; pos < width; pos++) {
    
    /* for all amino acids */
    for (aa=0; aa < MATRIX_AA_WIDTH; aa++) {
      
      if (frequency[aa] > 0.0) {
	if (number_occurred[aa][pos] > 0.0) {
	  divisor[pos] += number_occurred[aa][pos] / frequency[aa];
	}
      }
      
    } /* end for all amino acids */
  } /* end for each position */
  
  
  /*
   * calculate the matrix weights.
   *                              ( num_occur[aa][i] / freq[aa] ) * 100
   * in general: weights[aa][i] = -------------------------------------
   *                                     divisor[i]
   */
  
  /* for each amino acid */
  for (aa=0; aa < MATRIX_AA_WIDTH; aa++) {
    
    /* if there is a valid weight (frequency is not -1.0) */
    if ((int)frequency[aa] != -1) { /* typecast to be safe */
      
      /* for each position */
      for (pos=0; pos < width; pos++) {
	
	if (frequency[aa] < -1.0) {
	  tmp_double = frequency[aa];
	}
	else if (number_occurred[aa][pos] > 0) {
	  tmp_double = ( (number_occurred[aa][pos] / frequency[aa]) * 100 ) 
	               / divisor[pos];
	}
	else {
	  tmp_double = 0.0;
	}
	
	matrix->weights[aa][pos] = tmp_double; 
	
      } /* end for each position */
    } /* end if valid weight */
  } /* end for each amino acid */
  
  /* free temporarily allocated space */
  free(divisor);
  free(number_occurred[0]);
  
}  /* end of original_conversion_method  */

/*===================================================================*/
/*  Pauline's additions to convert.c for SIFT */

void SIFT_conversion_method(block, pssm)
     Block *block;
     Matrix *pssm;
{
     int diri_option, gap_option, exp_option, subtract_option;

	diri_option = gap_option = exp_option = TRUE;
	subtract_option = FALSE;

      if (Qij == NULL) {
          sprintf(ErrorBuffer, "Qij matrix missing, unable to continue.\n");
          ErrorReport(FATAL_ERR_LVL);
        }
        normalize  (block);
        SIFT_pssm(block, pssm, frequency, Qij, diri_option, gap_option,
                          exp_option, subtract_option);
}  /* end of SIFT_conversion_method */

/*==========================================================================
10/20/00 SIFT pseudocounts
13-dirichlet component
option:  diri_pseudocounts
	  TRUE: use 13-component Dirichlet
	  FALSE use BLOSUM62 qij's
option:  gap: TRUE -allow everything 
	      FALSE - just look at 20 amino acids
option:  exp (m)
	 m=0 # of amino acids at pos (default)
	 m=1  similiarity scale (more conservative)

option:	subtract_threshold TRUE : scores -= SIFT_TOLERANCE
			   FALSE: leave as original scores
===========================================================================*/
void SIFT_pssm(block, matrix, freqs, qij, 
		diri_pseudocounts, gap_option, 
		exp_option, subtract_threshold)
Block *block;
Matrix *matrix;
double *freqs;
struct float_qij *qij;
int diri_pseudocounts, gap_option, exp_option, subtract_threshold;
{
  FILE *rfp;
  double dtemp, epsilon;
  int pos, aa,  itemp;
  struct working *col;
  struct work_pssm *pssm;
  int original_aa;
  struct diri* diric;
  int max_aa;
  double min_freq;
  int div_by_max;
  struct float_qij *rank_matrix;
  char *blimps_dir, diriname[SMALL_BUFF_LENGTH], rankname[SMALL_BUFF_LENGTH];

  blimps_dir = getenv("BLIMPS_DIR");
   if (blimps_dir != NULL)
   {
      sprintf(diriname, "%s/docs/default.diri", blimps_dir);
      sprintf(rankname, "%s/docs/default.rank", blimps_dir);
/*>>>>> Need to check that rankname & diriname actually exists
        for WWW servers would be better to check in current
        directory first  <<<<<<*/
   }
   else
   {
      sprintf(diriname, "default.diri");
      sprintf(rankname, "default.rank");
   }

  diric = load_diri (diriname);
  rank_matrix = NULL;

  if (exp_option == 1)
  {
     if ( (rfp = fopen(rankname, "r") ) == NULL)
     {
         sprintf(ErrorBuffer, "SIFT_pssm(): Cannot open %s\n", rankname);
         ErrorReport(FATAL_ERR_LVL);
     }
     else
     {
        rank_matrix = load_qij(rfp);
        fclose(rfp);
     }
  }

  div_by_max = TRUE;
  col = make_col();
  pssm = make_work_pssm(block->width);

  /*--------------  Do one position at a time -------------------*/
  for (pos = 0; pos < block->width; pos++) 
  {
    /*-------- count the number of each aa in this position ------------*/
    if (gap_option) {
	counts (block,col, pos);
    } else {
	counts_nogaps(block, col, pos); 
   } 
    /*-------- determine total number of pseudo-counts in column ------*/
    epsilon = 0;
    itemp = count_residues (col);
    original_aa = block->residues[0][pos];

    if (exp_option == 1) {
	/*printf ("pos %d :  ", pos); */
	dtemp = similarity_dependent_scale(col, rank_matrix, original_aa);
	if (itemp == 1) { 
		epsilon = 0; 
	} else { 
		epsilon = exp (dtemp);
	}
    } else { 
	if (itemp == 1) { epsilon = 0; }
        else if (itemp > 7) { epsilon = 1000; }
        else { epsilon = exp( (double) itemp) ; }
 
   } 
	
    /*---------- get the pseudo counts -------------------------------*/
    if (diri_pseudocounts) {
	pseudo_diri (col, diric, epsilon ); 
    } else {
	pseudo_alts(col, qij, epsilon);
    } 

    /*---------   Fill in the matrix entries --------------------*/
    pssm->sum[pos] = 0.0;
    for (aa=1; aa < AAS; aa++)
    {

	pssm->value[pos][aa] = col->cnt[aa] + epsilon * col->reg[aa];
        if ( (col->totcnt + col->totreg) > 0.0)
             pssm->value[pos][aa] /= (col->totcnt + epsilon);


    } /* end of aa, pssm->values filled for a given pos */

   if (div_by_max) {
        max_aa = find_max_aa_pssm (pssm, pos);
	min_freq = pssm->value[pos][max_aa];
       for (aa = 1; aa < AAS; aa++) {
		pssm->value[pos][aa] /= min_freq;
	}
   } 

   if (subtract_threshold) {
	   for (aa = 1; aa < AAS; aa++) {
	        pssm->value[pos][aa] -= SIFT_TOLERANCE;
   	}
   }

       pssm->sum[pos] += pssm->value[pos][aa];

    	for (aa = 1; aa < AAS; aa++) {
	  matrix->weights[aa][pos] = pssm->value[pos][aa];
	}
	original_aa = block->residues[0][pos];
        if ( (matrix->weights[original_aa][pos] < SIFT_TOLERANCE
                         && (!subtract_threshold)) ||
              (matrix->weights[original_aa][pos] < 0.0 && subtract_threshold) )
        {
	   sprintf (ErrorBuffer, "SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.\n", 
		aa_btoa[original_aa], pos);
           ErrorReport(WARNING_ERR_LVL);
	}

	} /* end of for pos */

  if (diri_pseudocounts) {
	free (diric);
  }

  free(col);
  free_work_pssm(pssm);

}  /* end of SIFT_pssm */

/*======================================================================
   Dirichlet input file order (0-19) is  ARNDCQEGHILKMFPSTWYV
   Blimps order (0-24) is               -ARNDCQEGHILKMFPSTWYVBZX*
   Store Dirichlet alphas in positions 1-20 to match blimps
=======================================================================*/
struct diri *load_diri (filename)
char filename[LARGE_BUFF_LENGTH];
{
   FILE* fin;
   int i, aa, numc, type;
   char line[MAXLINE], *ptr;
   struct diri *diric;
   double denom;
   double background_frequency[AAS];

   if ((fin = fopen (filename, "r")) == NULL) 
   {
      sprintf (ErrorBuffer, "dirichlet(): Cannot open dirichlet file %s\n",
			 filename);
      ErrorReport(FATAL_ERR_LVL);
   }

   diric = (struct diri *) malloc(sizeof(struct diri));
   if (diric == NULL)
   {
      sprintf (ErrorBuffer, "dirichlet(): OUT OF MEMORY\n");
      ErrorReport(FATAL_ERR_LVL);
   }
   numc = 0;
   while (numc < MAXDIRI && !feof(fin) && fgets(line, MAXLINE, fin) != NULL)
   {
      type = 0;
      if (strstr(line, "Mixture=") != NULL) type = 1;
      if (strstr(line, "Alpha=") != NULL)  type = 2;
      if (type > 0)
      {
         ptr = strtok(line, "="); ptr = strtok(NULL, "\t\n\r ");
         switch (type)
         {
            case 1:
               diric->q[numc] = atof(ptr);
               break;
            case 2:
               diric->altot[numc] = atof(ptr);
               aa = 1;
               while (aa < AAS && ptr != NULL)
               {
                  ptr = strtok(NULL, "\t\n\r ");
                  diric->alpha[numc][aa++] = atof(ptr);
               }
               numc++;
               break;
            default:
               break;
         }
      }
   }  /* end of while */
   diric->ncomp = numc;
	for (i = 0; i < numc; i++) {
		for (aa = 1; aa < AAS; aa++) {
			diric->alpha_normalized[i][aa] = diric->alpha[i][aa]/diric->altot[i];
		}
	}

	for (aa = 1; aa < AAS; aa++) {
		denom = 0.0;
		for (i = 0; i < numc; i++) {
			denom += (diric->q[i] * diric->alpha[i][aa] / 
							diric->altot[i]);
		}
		background_frequency[aa] = denom;
	}
	for (i =0; i < numc; i++) {
	/*	printf ("Component %d ratio of aa relative to background \n", i); */
		for (aa = 1; aa < AAS; aa++) {
			diric->frequency_to_background_ratio[i][aa] =  
	diric->alpha[i][aa]/(diric->altot[i] * background_frequency[aa]);
		}
	}
   fclose(fin);
   return(diric);
}   /* end of load_diri */

/*========================================================================
==========================================================================*/
/* only count valid amino acids, no considerationto gaps */
void counts_nogaps (block, col, pos)
Block *block;
struct working *col;
int pos;
{
 int seq, aa;

  col->totcnt = col->totraw = col->totreg = 0.0;
  for (aa = 0; aa < AASALL; aa++) {
    col->cnt[aa] = col->raw[aa] = col->reg[aa] = 0.0;
  }

  /*  Only count the real 20 aas, combine B(21) with D & Z(22) with E  */
  for (seq = 0; seq < block->num_sequences; seq++) {
    aa = block->residues[seq][pos];
    if (aa >= 1 && aa < AAS) {
      col->cnt[aa] += block->sequences[seq].weight;
      col->totcnt += block->sequences[seq].weight;
      col->raw[aa] += 1.0;
      col->totraw += 1.0;
    }
  } /* end of for */
} /* end of counts_nogaps */


/*========================================================================
==========================================================================*/
double similarity_dependent_scale (col, rank_matrix, original_aa)
struct working *col;
struct float_qij *rank_matrix;
int original_aa;
{
  int aa, rank; double sum;
   int n;
  int max_aa;

  max_aa = find_max_aa_col(col);
  original_aa = max_aa; /* change to max aa 10/24/00 */

  n = 0;
  sum = 0.0; 
  for (aa = 1; aa <= 20 ; aa++) {
        if (col->cnt[aa] > 0.0) {
                n++;
              rank = (int) rank_matrix->value[original_aa][aa];
              sum += rank * col->cnt[aa]/col->totcnt;
/*		printf ("\taa %c rank %d weight %.3f", aa_btoa[aa], rank, col->cnt[aa]/col->totcnt); */
        }
   }
/*   printf (" sim score %.3f\n", sum); */
  return sum;

} /* end of similarity_dependent_scale */


/*=====================================================================*/
/*========================================================================
==========================================================================*/
void pseudo_diri(col, diric, epsilon)
struct working *col;
struct diri *diric;
double epsilon;
{
   int j, aa;
   double denom, dtemp;
   double total;

      /*-----------   compute equation (3), Prob(n|j) ------------  */
      for (j = 0; j < diric->ncomp; j++)
      {
         col->probn[j] = lgamma(col->totcnt + 1.0) + lgamma(diric->altot[j]);
         col->probn[j] -= lgamma(col->totcnt + diric->altot[j]);

	/*   Note range on aa varies; Diric values only for 1-20 */
         for (aa = 1; aa < AAS; aa++)
         {
         /*  ni = cnt[i] */
	    if (col->cnt[aa] >= 0.0)
            {
               dtemp = lgamma(col->cnt[aa] + diric->alpha[j][aa]);
/*  printf ("aa %c cnt %.3f alpha %.3f dtemp %.3f\n", aa_btoa[aa], col->cnt[aa], diric->alpha[j][aa], dtemp); */
		dtemp -= lgamma(col->cnt[aa] + 1.0);
	   	dtemp -= lgamma(diric->alpha[j][aa]);
		col->probn[j] += dtemp;
/*               printf ("col->probn is now %.3f prob is %.3f \n\n", col->probn[j], exp (col->probn[j])) ; */
	     } /* end of if > = 0.0 */
         } /* end of for amino acids */
      } /* end of for all j components */

      /*------ compute sum qk * p(n|k) using logs & exponents ----------*/
      denom = log(diric->q[0]) + col->probn[0];
      for (j = 1; j < diric->ncomp; j++)
      {
         dtemp = log(diric->q[j]) + col->probn[j];
         denom = add_logs(denom, dtemp);
      }
/* printf ("%.3f denom number of comp %d\n", denom, diric->ncomp); */

      /*   compute equation (3), Prob(j|n)  */
      for (j = 0; j < diric->ncomp; j++)
      {
         col->probj[j] = log(diric->q[j]) + col->probn[j] - denom;
/*       printf("j=%d probn[j]=%f probj[j]=%f\n",
             j, exp(col->probn[j]), exp(col->probj[j])); */ 

      }

      /* ----- compute equation (4), ni + bi, bi = Prob(j|n) * alpha[j][i]  */

	 for (aa = 1; aa < AAS; aa++)
      {
         for (j = 0; j < diric->ncomp; j++) {
		col->reg[aa] +=   
				(exp(col->probj[j]) * diric->alpha[j][aa]);
			/*  * epsilon); */ 
            }
	 col->totreg += col->reg[aa];
	}
/*	printf (" total prob. %.2f\n", col->totreg); */
/* scale dirichlet to probabilities */      
	total = 0.0;
	for (aa = 1; aa < AAS; aa ++) {
		col->reg[aa] /= col->totreg;
		total += col->reg[aa];
	}
/*	printf ("%.2f total\n", total); */
 
/*	printf ("%c %.3f", aa_btoa[aa], col->reg[aa]);
	if (col->cnt[aa] > 0.0) {printf ("*\n"); } else { printf ("\n");} */ 

}  /* end of pseudo_diri */

/*========================================================================
==========================================================================*/
int find_max_aa_col (col)
struct working *col;
{
	int aa, max_aa;
	double max = 0.0;
	
        max_aa = -1;
	for (aa = 1; aa < AAS; aa++) {
		if (col->cnt[aa] > max) {
			max = col->cnt[aa];
			max_aa = aa;
		}
	}
	return max_aa;

} /* end of find_max_aa_col */

/*========================================================================
==========================================================================*/
int find_max_aa_pssm (pssm, pos)
struct work_pssm *pssm;
int pos;
{
	int aa, max_aa;
	double max;

        max_aa = -1;
	max = 0.0;
	for (aa = 1; aa < AAS; aa++) {
		if (pssm->value[pos][aa] > max) {
			max_aa = aa;
			max = pssm->value[pos][aa];
		}
	}
	return max_aa;
} /* end of find_max_aa_pssm */
		

/*===============================================================
      Returns log(e^x + e^y)
================================================================*/
double add_logs(lx, ly)
double lx, ly;
{
   if (lx > ly)  return(lx + log(1.0 + exp(ly - lx)));
   else          return(ly + log(1.0 + exp(lx - ly)));
}  /*  end of add_logs */


/*=========================================================================*/
/* Change log information follows. */
/*
 Changes since version 3.5:
  8/27/03 Fix problem in make_alts() with scale=10,20,21,30
 Changes since version 3.4:
 12/29/00 Added Pauline's routines for SIFT (SIFT_prediction, etc.)
	  Modified struct working, struct work_pssm and make_work_pssm()
	  (width is now dynamic) Added free_work_pssm()
  6/16/00 Added type 22 (pseudo-counts nearly zero) to block_to_matrix()
 Changes since version 3.3.2:
  5/24/00 Increased MAXWIDTH from 100 to 400, but need to do away with
	  this restriction!
 Changes since version 3.3:
  9/ 4/99 Added type 21 (counts only) to block_to_matrix()
 Changes since version 3.2.5:
  2/22/99  Removed block from positive_matrix()
 Changes since version 3.2.4:
 12/12/98  compute_BZX(): Use 0 for * column instead of min value, unless
	   min value is negative.
 Changes since version 3.2.3:
  8/11/98  convert.c: MAXWIDTH increased, error check added.
  4/ 8/98  Avoid division by zero in pseudo_alts() & block_to_matrix().
           Divide counts of aas other than the basic 20 among those 20.
 Changes since version 3.1:
  1/30/97  Changed no weights error message from SERIOUS to WARNING.
 10/10/96  Fixed bug in pb_weights() when X (#23) in sequence.
  9/25/96  Changed compute_BZX() to compute average score for X.
*/

 = 1; aa < AAS; aa++) {
	        pssm->value[pos][aa] -= SIFT_TOLERANCE;
   	}
   }

       pssm->sum[pos] += pssm->value[pos][aa];

    	for (aa = 1; aa < AAS; aa++) {
	  matrix->weights[aa][pos] = pssm->value[pos][aa];
	}
	original_aa = block->residues[0][pos];
        if ( (matrix->weights[original_aa][pos] < SIFT_TOLERANCE
                         && (!subtract_thblimps-3.9/blimps/email.c000064400001460000012000000045640774312247700157150ustar00jorjastaff00000400000027/* COPYRIGHT 2000 Fred Hutchinson Cancer Research Center 
	email.c
	Read a file sequences and submit them at intervals
	to the blocks server; interval is determined by
	sequence length and type
		email  
--------------------------------------------------------------------
 9/ 4/00
====================================================================*/

#define EXTERN
#define MAXNAME 80	/* Maximum file name length */
#define EMAILADD "blocks@blocks.fhcrc.org"	/* email server address */

#include 

/*=======================================================================*/
/*
 * main
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *bfp, *ofp;
  Sequence *sequence;
  char filename[MAXNAME], outname[MAXNAME], ctemp[MAXNAME];
  int seconds, pid;
  int db_type, seq_type;

  /* ------------1st arg = sequence file -----------------------------------*/
   if (argc > 1)
      strcpy(filename, argv[1]);
   else
   {
      printf("\nEnter name of sequence file: ");
      gets(filename);
   }
   if ( (bfp=fopen(filename, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", filename);
      exit(-1);
   }
   /*  Making a unique temporary file name here */
   pid = (int) getpid();
   sprintf(outname, "%d.seq", pid);

   db_type = type_dbs(bfp, DbInfo);
   seq_type = seq_type_dbs(bfp, DbInfo, db_type);

  /*-----------------------------------------------------------------*/

  while ((sequence = read_a_sequence(bfp, db_type, seq_type)) != NULL)
  {
     /*  Assuming rate of 150aas/min, 2.5/sec   */
     seconds = round((double) sequence->length/2.5);
     if (seq_type == NA_SEQ) seconds *= 2;

     if ( (ofp=fopen(outname, "w")) != NULL)
     {
        /* Add or modify parameters; see
		http://blocks.fhcrc.org/help/email.html  */
        fprintf(ofp, "#OU sum\n");
        fprintf(ofp, "#EX 1\n");
        fprintf(ofp, "#SQ\n");
        output_sequence(sequence, ofp);
        fclose(ofp);

	/* mailx is the Solaris mail program, yours might be in
		/bin/mail or someplace else */
        sprintf(ctemp, "/usr/bin/mailx -s %s %s < %s",
	   sequence->name, EMAILADD, outname);
        printf("Submitting %s (len=%d %d seconds)\n", 
              sequence->name, sequence->length,  seconds);
        system(ctemp);
        sleep(seconds);
     }
  }
  fclose(bfp);
  sprintf(ctemp, "rm %s", outname);
  system(ctemp);

  exit(0);

}  /* end of main */
blimps-3.9/blimps/errors.c000064400001460000012000000142060774312250000161170ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* errors.c: error reporting functions */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */


/*	system headers not in global.h  */
/*	blimps library headers */
#include 

/*
 * Exported variables and data structures
 */

char ErrorBuffer[LARGE_BUFF_LENGTH];
int  ErrorLevelReport;


/*
 * Exported variables and data structures
 */

static char ErrorFile[SMALL_BUFF_LENGTH];

/*
 * Function definitions
 */

/*
 * set_error_file_name
 *   Sets the name of the error output file to use.
 *   Parameters:
 *     char *error_file: the name of the file.
 *   Error codes: None
 */

void set_error_file_name(error_file)
     char *error_file;
{
  strncpy(ErrorFile, error_file, SMALL_BUFF_LENGTH);
}

/*
 * ErrorReport
 *   ErrorReport prints out the error message in the ErrorBuffer to stderr and
 *   the ErrorFile if it can be opened.
 *   Note: The error message must be placed in ErrorBuffer before ErrorReport
 *         is called.
 *   Parameters:
 *     int err_level:  The error level reporting at.  If the error level is
 *                     >= FATAL_ERR_LVL, exit() is called with the error level.
 *   Error codes: None
 */

void ErrorReport(err_level)
     int err_level;
{
  FILE *efp; 
  Boolean dont_skip_error_file_report;
  
  /* check to see if we report */
  if ((err_level >= ErrorLevelReport) || (err_level == FATAL_ERR_LVL)) {

    /* open the error file for appending */
    efp = fopen(ErrorFile, "a");
    
    if (efp == NULL) {
      dont_skip_error_file_report = FALSE;
    }
    else {
      dont_skip_error_file_report = TRUE;
    }
  
    switch (err_level) {
    case INFO_ERR_LVL:
      fprintf(stderr, "Information: %s\n", ErrorBuffer);
      if (dont_skip_error_file_report) {
	fprintf(efp, "Information: %s\n", ErrorBuffer);
      }
      break;
    case WARNING_ERR_LVL:
      fprintf(stderr, "Warning: %s\n", ErrorBuffer);
      if (dont_skip_error_file_report) {
	fprintf(efp, "Warning: %s\n", ErrorBuffer);
      }
      break;
    case SERIOUS_ERR_LVL:
      fprintf(stderr, "Serious: %s\n", ErrorBuffer);
      if (dont_skip_error_file_report) {
	fprintf(efp, "Serious: %s\n", ErrorBuffer);
      }
      break;
    case PROGRAM_ERR_LVL:
      fprintf(stderr, "Program Error: %s\n", ErrorBuffer);
      if (dont_skip_error_file_report) {
	fprintf(efp, "Program Error: %s\n", ErrorBuffer);
      }
      break;
    case FATAL_ERR_LVL:
    default:
      fprintf(stderr, "Fatal Error: %s\n", ErrorBuffer);
      if (dont_skip_error_file_report) {
	fprintf(efp, "Fatal Error: %s\n", ErrorBuffer);
      }
      if (dont_skip_error_file_report) {
	fclose(efp);		/* close the file */
      }
      
      /* exit(????); choose a good error level to return */
      exit(FATAL_ERR_LVL);	/* closes all the open files */
    }
    
    ErrorBuffer[0] = '\0';	/* clear the string incase the caller does */
				/* not setup ErrorBuffer correctly for the */
				/* next call */
    if (dont_skip_error_file_report) {
      fclose(efp);		/* close the file */
    }
  }
}



/*
 * ABRT_signal_handler
 *   Catches the SIGABRT signal and announces the probable cause that was
 *   seen in testing.  It appears that when there is very little memory
 *   left free() has a hard time deallocating memory.  I'm guessing that it
 *   is when it is trying to put the free memory block into a list, the
 *   error that occurs is: "getfreehdr: out of memory".  The error seems to
 *   have only occured in the function call free() after many small blocks
 *   of memory have been freed.  It probably cannot handle as many free 
 *   blocks of memory as it is getting.
 *   NOTE: The memory recover functions "should" work.  The only
 *     problem appears to be in the function free().  The function is
 *     always called with a valid pointer to a busy block, allocated
 *     previously by a malloc function, when the error occurs.  And for
 *     about 10 calls before the error the pointer is OK too.  The
 *     problem I'm having with free() may be particular to this
 *     development system (SunOS Release 4.1.3) or I might have done
 *     something that causes this side effect.
 *   NOTE: The function recover_memory() in memory.c handles the recovery
 *     of memory when there is no more allocatable memory.  See the macro
 *     CheckMem(A) in memory.h to see how the function is called.
 *   Parameters: none
 *   Error codes: none, aborts the program.
 */

void ABRT_signal_handler()
{
  sprintf(ErrorBuffer,
	  "Caught the SIGABRT (6) signal error.");
  ErrorReport(PROGRAM_ERR_LVL);
  sprintf(ErrorBuffer,
	  "In testing, this signal occured when all the available");
  ErrorReport(PROGRAM_ERR_LVL);
  sprintf(ErrorBuffer,
	  "memory was filled and when trying to free memory to continue,");
  ErrorReport(PROGRAM_ERR_LVL);
  sprintf(ErrorBuffer,
	  "by using free(), after many small blocks had been freed.");
  ErrorReport(PROGRAM_ERR_LVL);
  sprintf(ErrorBuffer,
	  "If that is the case, try setting the number of scores to");
  ErrorReport(PROGRAM_ERR_LVL);
  sprintf(ErrorBuffer,
	  "report to a lower value than at the point memory was filled. ");
  ErrorReport(PROGRAM_ERR_LVL);
  sprintf(ErrorBuffer,
	  "Sorry for the inconvienience, but the memory recovery");
  ErrorReport(PROGRAM_ERR_LVL);
  sprintf(ErrorBuffer,
	  "functions \"should\" have worked.  ");
  ErrorReport(PROGRAM_ERR_LVL);
  sprintf(ErrorBuffer,
	  "See the errors.c source code for programming details.\n");
  ErrorReport(PROGRAM_ERR_LVL);

  sprintf(ErrorBuffer,
	  "Aborting due to the SIGABRT signal.\n");
  ErrorReport(FATAL_ERR_LVL);
}


/* Change log information follows. */
/* 
 * Revision 1.1  1993/08/17  04:18:16  billa
 * Added INFO_ERR_LVL for low level messages/errors and ErrorLevelReport
 * to control the level of error reporting.
 *
 * Revision 0.51  1993/07/23  17:40:18  billa
 * Changed the exit return number to FATAL_ERR_LVL.  Was empty.
 *
 * Revision 0.20  1993/06/23  16:46:49  billa
 * creation, error reporting to stderr and to the error file from
 * ErrorReport()
 *
 */



blimps-3.9/blimps/fastaseqs.c000064400001460000012000000046050774312250000165770ustar00jorjastaff00000400000027/*  COPYRIGHT 1998, Fred Hutchinson Cancer Research Center
    fastaseqs.c  Read a file of sequences and converts them to FASTA format
           fastaseqs  
--------------------------------------------------------------------
 1/15/98 J. Henikoff
====================================================================*/

#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#include 

/*=======================================================================*/
/*
 * main
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *fin, *fout;
  Sequence *seq;
  char infile[MAXNAME], outfile[MAXNAME];
  int db_type, seq_type, nseq;

   if (argc < 2)
   {
      printf("COPYRIGHT 1998, Fred Hutchinson Cancer Research Center\n");
      printf("fastaseqs: Converts a file of sequences to FASTA format\n");
      printf("USAGE: fastaseqs  \n");
      printf("     = input file of seqences in a common format\n");
      printf("    = output file of sequences in FASTA format\n");
   }

/* ------------1st arg = file of sequences------------------------------*/
   if (argc > 1)
      strcpy(infile, argv[1]);
   else
   {
      printf("\nEnter name of input sequence file: ");
      gets(infile);
   }
   if ( (fin=fopen(infile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", infile);
      exit(-1);
   }
/* ------------2nd arg = output file  -----------------------------------*/
   if (argc > 2)
      strcpy(outfile, argv[2]);
   else
   {
      printf("\nEnter name of output file: ");
      gets(outfile);
   }
   if ( (fout=fopen(outfile, "w")) == NULL)
   {
      printf("\nCannot open file %s\n", outfile);
      exit(-1);
   }

/*-----------------------------------------------------------------*/
   db_type = type_dbs(fin, DbInfo);
   if (db_type < 0) db_type = FLAT;
   seq_type = UNKNOWN_SEQ;
   seq_type = seq_type_dbs(fin, DbInfo, db_type, seq_type);

/*-----------------------------------------------------------------*/
/*   Have to read all the sequences into memory                    */

  rewind(fin);
  nseq = 0;
  while ( (seq = read_a_sequence(fin, db_type, seq_type)) != NULL)
  {
     nseq++;
     output_sequence(seq, fout);
     free_sequence(seq);
  }
   
  fclose(fin); fclose(fout);
  printf("%d sequences read\n", nseq);
  if (nseq > 0) exit(0);
  else          exit(-1);

}  /* end of main */
blimps-3.9/blimps/files.c000064400001460000012000000412430774312250000157060ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* files.c: access to configuration and database files */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */


/*	system headers not in global.h  */
/*	blimps library headers */
#include 
#include 
#include 

/*
 * Exported variables and data structures definitions
 */

char ExportMatrixFile[SMALL_BUFF_LENGTH];
char OutputFile[SMALL_BUFF_LENGTH];
char ErrorFile[SMALL_BUFF_LENGTH];

FileList BlockFiles;
FileList MatrixFiles;
FileList DatabaseFiles;
FileList FrequencyFile;		/* Note: should be only one file in the list */
FileList SequenceFiles; 
FileList PatternFiles; 


/*
 * Local variables and data structures
 */


#define FILE_LIST_INCREASE_SIZE 20





/*
 * Function definitions
 */

static FileList *get_file_list();




/*
 * Basic File routines
 *
 *   static FileList *get_file_list(file_group)
 *   void insert_file(file_name, file_group)
 *   FILE *get_file(file_group)
 *   void rewind_file(file_group)
 *   char *get_current_file_name(file_group) 
 *   char *get_file_name(file_num, file_group) 
 *   int number_of_files(file_group) 
 *   void close_file(file_group)
 *   int type_dbs(fin,dbs)
 *   int get_sequence_db_seq_type()
 *   int get_sequence_db_db_type()
 *
 */


/* 
 * get_file_list
 *   returns a pointer to the file list of the requested file group.
 *   Parameters:
 *     int file_group: the group to get a file pointer for.
 *   Retrun codes: the pointer to the file list
 *   Error codes:  NULL if the requested file group is unknown
 */

static FileList *get_file_list(file_group)
     int file_group;
{
  FileList *this_list;

  switch (file_group) {
  case BLOCK_FILES :
    this_list = &(BlockFiles);
    break;
  case MATRIX_FILES :
    this_list = &(MatrixFiles);
    break;
  case DATABASE_FILES :
    this_list = &(DatabaseFiles);
    break;
  case FREQUENCY_FILE :		/* Note: should be only one in the list */
    this_list = &(FrequencyFile);
    break;
  case SEQUENCE_FILES :
    this_list = &(SequenceFiles);
    break;
  case PATTERN_FILES :
    this_list = &(PatternFiles);
    break;
  default:
    sprintf(ErrorBuffer, 
	    "get_file_list(): Unknown file group %d.", file_group);
    ErrorReport(PROGRAM_ERR_LVL);
    this_list = NULL;
  } /* end switch */

  return this_list;
}


/*
 * insert_file
 *   insert_file inserts the file_name into the file_group list
 *   Parameters:
 *     char *file_name: the name of the file
 *     int file_group: the group to get a file pointer for.
 *   Return codes: none
 *   Error codes:
 */

void insert_file(file_name, file_group)
     char *file_name;
     int file_group;
{
  FileList *this_list;

  this_list = get_file_list(file_group);

  if (this_list == NULL) {
    sprintf(ErrorBuffer, 
	    "insert_file(): Bad file list, not entering filename \"%s\"",
	    file_name);
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "               into a file list\n");
    ErrorReport(PROGRAM_ERR_LVL);
  }

  /* if this is the first time (this_list->num_files == 0) allocate space */
  if (this_list->num_files == 0) {
    CheckMem(
	     this_list->file_names = (char **) calloc(FILE_LIST_INCREASE_SIZE,
						      sizeof(char *))
	     );
    this_list->max_files = FILE_LIST_INCREASE_SIZE;
  }

  /* increase file number count */
  this_list->num_files++;

  /* if this is a frequency file list and there is already a file, */
  /* warn that extras will be ignored */
  if ((file_group == FREQUENCY_FILE) && (this_list->num_files > 1)) {
    sprintf(ErrorBuffer, "Already have a frequency file: %s",
	   this_list->file_names[0]);
    ErrorReport(WARNING_ERR_LVL);
    sprintf(ErrorBuffer, "The file %s will be ignored.\n", file_name);
    ErrorReport(WARNING_ERR_LVL);
  }

  /* if there is no room, allocate more space */
  if (this_list->num_files > this_list->max_files) {
    char **tmp_ptr;		/* don't want to ruin pointer in case there */
				/* is a repeated realloc call */
    
    CheckMem(
	     tmp_ptr = (char **) realloc(this_list->file_names,
					 (this_list->max_files +
					  FILE_LIST_INCREASE_SIZE) *
					 sizeof(char *))
	     );
    this_list->file_names = tmp_ptr;
    this_list->max_files += FILE_LIST_INCREASE_SIZE;
  }

#ifndef NO_STRDUP
  this_list->file_names[this_list->num_files - 1] = strdup(file_name);
#else
  CheckMem(
          this_list->file_names[this_list->num_files - 1] = (char *)
            calloc(strlen(file_name) + 1, sizeof(char))	/* +1 for '\0' */
          );
  strncpy(this_list->file_names[this_list->num_files - 1], file_name, 
         strlen(file_name));
  this_list->file_names[this_list->num_files - 1][strlen(file_name)+1] = '\0'; 
#endif

}

/*
 * get_file
 *   get_file retrieves the file pointer of the requested group.
 *   Parameters:
 *     int file_group: the group to get a file pointer for.
 *   Return codes: Returns the file pointer to the requested file group
 *   Error codes:
 */

FILE *get_file(file_group) 
     int file_group;
{
  FileList *this_list;
  register char c;

  this_list = get_file_list(file_group);

  if (this_list == NULL) {
    sprintf(ErrorBuffer, "get_file(): Bad file list, unable to open a file\n");
    ErrorReport(PROGRAM_ERR_LVL);
    return NULL;
  } /* end switch */
  
  if (this_list->fp == NULL) {  /* initially set to NULL in declaration */
    this_list->fp = fopen(this_list->file_names[this_list->cur_file], "r");
    /* the sequence info was set at the end of the reading of the */
    /* configuration file and when the file group is rewound.  At this */
    /* time db_type and seq_type are set */
  }
  if (this_list->fp == NULL) {
    /* report error */
    switch (file_group) {
    case BLOCK_FILES :
      sprintf(ErrorBuffer, "Unable to open block file: %s\n", 
	      this_list->file_names[this_list->cur_file]);
      ErrorReport(SERIOUS_ERR_LVL);
      return NULL;
      break;
    case MATRIX_FILES :
      sprintf(ErrorBuffer, "Unable to open matrix file: %s\n", 
	      this_list->file_names[this_list->cur_file]);
      ErrorReport(SERIOUS_ERR_LVL);
      return NULL;
      break;
    case DATABASE_FILES :
      sprintf(ErrorBuffer, "Unable to open database file: %s\n", 
	      this_list->file_names[this_list->cur_file]);
      ErrorReport(SERIOUS_ERR_LVL);
      return NULL;
      break;
    case FREQUENCY_FILE :	/* Note: should be only one in the list */
      sprintf(ErrorBuffer, "Unable to open frequency file: %s\n", 
	      this_list->file_names[this_list->cur_file]);
      ErrorReport(SERIOUS_ERR_LVL);
      return NULL;
      break;
    case SEQUENCE_FILES :
      sprintf(ErrorBuffer, "Unable to read sequence file: %s\n", 
	      this_list->file_names[this_list->cur_file]);
      ErrorReport(SERIOUS_ERR_LVL);
      return NULL;
      break;
    case PATTERN_FILES :
      sprintf(ErrorBuffer, "Unable to read pattern file: %s\n", 
	      this_list->file_names[this_list->cur_file]);
      ErrorReport(SERIOUS_ERR_LVL);
      return NULL;
      break;
    default:
      sprintf(ErrorBuffer, "get_file(): Unknown file group");
      ErrorReport(PROGRAM_ERR_LVL);
      sprintf(ErrorBuffer, "            Unable to open a file\n");
      ErrorReport(PROGRAM_ERR_LVL);
    }
  }
  
  /* HACK!!! since fgets stops reading at a newline, it doesn't see the EOF */
  /* and does not set it.  This is a way to make sure that the EOF is raised */
  c = getc(this_list->fp);
  ungetc(c, this_list->fp);

  if (feof(this_list->fp)) {
    /* if more files to look at */
    if (this_list->cur_file < this_list->num_files -1) { /* -1 because */
			/* cur_files starts at zero, num_files starts at one */
      this_list->cur_file++;
      fclose(this_list->fp); 
      this_list->fp = fopen(this_list->file_names[this_list->cur_file], "r");

  /*-------------------------------------------------------------------*/
  /* determine sequence database db_type and seq_type */
  /* Code take from config.c   */
  /* NOTE: doing direct accessing because need to set various fields */
  
      if (file_group == SEQUENCE_FILES)
      {
  if (this_list->fp != NULL) {
    this_list->db_type = type_dbs(this_list->fp, DbInfo);
    if (this_list->db_type < 0 || this_list->db_type >= MAXDB) {
      /* unknown database type */
      sprintf(ErrorBuffer, 
	      "Unknown sequence format.  Known formats are:");
      ErrorReport(WARNING_ERR_LVL);
      sprintf(ErrorBuffer,
	      "Fasta, GenBank, PIR, Swiss Prot, and GCG.");
      ErrorReport(WARNING_ERR_LVL);
      sprintf(ErrorBuffer,
	      "Assuming there is no title and just sequence.\n");
      ErrorReport(WARNING_ERR_LVL);
      this_list->db_type = FLAT;
    }
    this_list->seq_type = seq_type_dbs(this_list->fp, DbInfo, 
			  this_list->db_type, this_list);
  }
  else {
    sprintf(ErrorBuffer, "Unable to read sequence file: %s ",
	    this_list->file_names[0]);
    ErrorReport(SERIOUS_ERR_LVL);
    sprintf(ErrorBuffer, "to determine the type of database\n");
    ErrorReport(SERIOUS_ERR_LVL);
  }
     }  /* end of SEQUENCE_FILES  */
  /*-------------------------------------------------------------------*/


      if (this_list->fp == NULL) {
	/* report error */
	switch (file_group) {
	case BLOCK_FILES :
	  sprintf(ErrorBuffer, "Unable to open block file: %s\n", 
		  this_list->file_names[this_list->cur_file]);
	  ErrorReport(SERIOUS_ERR_LVL);
	  return NULL;
	  break;
	case MATRIX_FILES :
	  sprintf(ErrorBuffer, "Unable to open matrix file: %s\n", 
		  this_list->file_names[this_list->cur_file]);
	  ErrorReport(SERIOUS_ERR_LVL);
	  return NULL;
	  break;
	case DATABASE_FILES :
	  sprintf(ErrorBuffer, "Unable to open database file: %s\n", 
		  this_list->file_names[this_list->cur_file]);
	  ErrorReport(SERIOUS_ERR_LVL);
	  return NULL;
	  break;
	case FREQUENCY_FILE :	/* Note: should be only one in the list */
	  sprintf(ErrorBuffer, "Unable to open frequency file: %s\n", 
		  this_list->file_names[this_list->cur_file]);
	  ErrorReport(SERIOUS_ERR_LVL);
	  return NULL;
	  break;
	case SEQUENCE_FILES :
	  sprintf(ErrorBuffer, "Unable to read sequence file: %s", 
		  this_list->file_names[this_list->cur_file]);
	  ErrorReport(SERIOUS_ERR_LVL);
	  return NULL;
	  break;
	case PATTERN_FILES :
	  sprintf(ErrorBuffer, "Unable to read pattern file: %s", 
		  this_list->file_names[this_list->cur_file]);
	  ErrorReport(SERIOUS_ERR_LVL);
	  return NULL;
	  break;
	default:
	  sprintf(ErrorBuffer, "get_file(): Unknown file group");
	  ErrorReport(PROGRAM_ERR_LVL);
	  sprintf(ErrorBuffer, "            Unable to open a file\n");
	  ErrorReport(PROGRAM_ERR_LVL);
	}
      }
    }
    else { /* no more files, close and exit */
      fclose(this_list->fp); 
      return NULL;
    }
  }
  return (this_list->fp);
  
}


/*
 * rewind_file
 *   rewind_file sets/resets the file pointer of the specified group back to
 *   the first file, first character.
 *   Parameters:
 *     int file_group: the group rewind.
 *   Return codes: none
 *   Error codes:
 */

void rewind_file(file_group) 
     int file_group;
{
  FileList *this_list;

  this_list = get_file_list(file_group);

  if (this_list == NULL) {
    sprintf(ErrorBuffer, 
	    "rewind_file(): Bad file group, unable to rewind file list\n");
    ErrorReport(PROGRAM_ERR_LVL);
  }
  
  if (this_list->fp != NULL) {
    fclose(this_list->fp); 
  }

  /* set the current file to the first file */
  this_list->cur_file = 0;

  /* If want to check the sequence database type and sequence */
  /* type for each file, put the code here.  The database type and */
  /* the sequence type are set at the end of reading the */
  /* configuration file. */ 

  /* set the file pointer to null so that the next call to get_file will */
  /* start at the beginning */
  this_list->fp = NULL;

}


/*
 * get_current_file_name
 *   Returns a pointer to the string of the current file name. 
 *   Parameters:
 *     int file_group: the file group for the name
 *   Return codes: a string of the filename
 *   Error codes:  NULL if there is no filename
 */

char *get_current_file_name(file_group) 
     int file_group;
{
  FileList *this_list;

  this_list = get_file_list(file_group);

  if (this_list == NULL) {
    sprintf(ErrorBuffer, 
	    "get_current_file_name(): Bad file group, unable to return a file name\n");
    ErrorReport(PROGRAM_ERR_LVL);
    return NULL;
  }
  
  if (this_list->num_files <= 0) {
    sprintf(ErrorBuffer, 
	    "get_current_file_name(): No files in the file group");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer, 
	    "                         Unable to return a file name\n");
    ErrorReport(PROGRAM_ERR_LVL);
    return NULL;
  }
  
  /* return a pointer to the current file name */
  return (char *) this_list->file_names[this_list->cur_file];

}


/*
 * get_file_name
 *   Returns a pointer to the string of the requested file name.  
 *   Parameters:
 *     int file_num:   which file to return (0..num_files);
 *     int file_group: the file group for the name
 *   Return codes: a string of the filename
 *   Error codes:  NULL if there is no filename
 */

char *get_file_name(file_num, file_group) 
     int file_num;
     int file_group;
{
  FileList *this_list;

  this_list = get_file_list(file_group);

  if (this_list == NULL) {
    sprintf(ErrorBuffer, 
	    "get_file_name(): Bad file group, unable to return a file name\n");
    ErrorReport(PROGRAM_ERR_LVL);
    return NULL;
  }
  
  if (this_list->num_files <= 0) {
    sprintf(ErrorBuffer, "get_file_name(): No files in the file group");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer, "                 Unable to return a file name\n");
    ErrorReport(PROGRAM_ERR_LVL);
    return NULL;
  }
  
  if (this_list->num_files < file_num) {
    sprintf(ErrorBuffer, 
	    "get_file_name(): Requested file out of the range of the files");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "                 in the file group");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer, 
	    "                 Unable to return a file name\n");
    ErrorReport(PROGRAM_ERR_LVL);
    return NULL;
  }

  /* return a copy of the current file name */
  return (char *) this_list->file_names[file_num];

}


/*
 * number_of_files
 *   Returns the number of files in the file group.
 *   Parameters: 
 *     int file_group: the group rewind.
 *   Return codes: the number of files in the file group.
 *   Error codes:  -1 if the file group is unknown
 */

int number_of_files(file_group) 
     int file_group;
{
  FileList *this_list;

  this_list = get_file_list(file_group);

  if (this_list == NULL) {
    sprintf(ErrorBuffer, 
	    "number_of_files(): Bad file group, unable to report number of files\n");
    ErrorReport(PROGRAM_ERR_LVL);
    return -1;
  }

  return this_list->num_files;
}


/*
 * close_file
 *   closes the selected file group.
 *   Parameters: 
 *     int file_group: the group rewind.
 *   Return codes: none
 *   Error codes:
 *   Note: right now this function is identical to rewind_file() except it
 *         does not set the current file to the beginning.
 */

void close_file(file_group) 
     int file_group;
{
  FileList *this_list;

  this_list = get_file_list(file_group);

  if (this_list == NULL) {
    sprintf(ErrorBuffer, 
	    "close_file() : Bad file group, unable to rewind file list\n");
    ErrorReport(PROGRAM_ERR_LVL);
  }
  
  if (this_list->fp != NULL) {
    fclose(this_list->fp); 
  }
  
  /* set the file pointer to null so that the next call to get_file will */
  /* start at the beginning */
  this_list->fp = NULL;

}



/* NOTE: it might be good in the future to make these into generic */
/*       functions that are passed the type of file structure.  There */
/*       might become situations where there are sequence and database */
/*       types for blocks. */

/*
 * get_sequence_db_seq_type
 *   Returns the type of sequences of the databases.  
 *   NOTE: this assumes that all the sequences in a database file are
 *         of the same type, and that all of the database files are of
 *         the same type.
 *   NOTE: SequenceFiles.db_type is set only at the end of reading the 
 *         configuration file.
 *   Parameters: none
 *   Return codes: the different sequence types
 *   Error codes:  none
 */

int get_sequence_db_seq_type()
{
  return SequenceFiles.seq_type;    
}

/*
 * get_sequence_db_db_type
 *   Returns the kind of the database of the seqeuence database file 
 *   currently being read.  
 *   NOTE: SequenceFiles.db_type is set each time a new sequence file is
 *         opened.
 *   Parameters: none
 *   Return codes: the different sequence db types
 *   Error codes:  none
 */

int get_sequence_db_db_type()
{
  return SequenceFiles.db_type;    
}


/* Change log information follows. */
/*  Changes since version 3.0.0:
 7/11/96  Set SequenceFiles.db_type & .seq_type in get_file().
*/
 "Unable to read sequence file: %s\n", 
	      this_list->file_names[this_list->cur_file]);
      ErrorReport(SERIOUS_ERR_LVL);
      return NULL;
      break;
    case PATTERN_FILES :
      sprintf(ErrorBuffer, "Unable to read pattern file: %s\n", 
	      this_list->file_names[this_list->cur_file]);
      ErrorReport(SERIOUS_ERR_LVL);
      returblimps-3.9/blimps/find_biassed_blocks.c000064400001460000012000001111510774312250000205470ustar00jorjastaff00000400000027/*-----------------------------------------------------------------------------
Copyright 1997-2000: Fred Hutchinson Cancer Research Center, Seattle, WA  USA
 find_biassed_blocks.c - identify blocks with biassed composition

Revised criteria June 2000:
1. Compute correlation coeff for each pair of columns
2. Clump columns based on 1. with correlation coeffs >= col_score_cutoff
3. Biassed if max clump from 2. has >= bias_cutoff percent of cols in block
   and has >= min_cols

 A biassed block is one with a significant number of conserved columns similar 
to one another. The degree of similarity and fraction of similar columns are
program parameters. The r correlation coefficient is used to compare the 
columns. A potential problem with the use of this column comparison measure is 
that non conserved columns with similar distribution of aa will get high scores.
Biological examples of such columns are hydrophobic positions. Blocks of 
transmembrane regions have such columns.

July 96, spruced up this version (2) for use in WWW page. Only output format
 affected. 

      Aug 20, 96' - blimps 3.1 defines matrix->weights as double (was int)
                    matrix->weights values are rounded before printing.

                    changed width of printed matrix lines to depend on www 
                    flag - if flag is on up to 55 positions are printed per 
                    line, else 18.
  11/25/98 Simplify output. Look for amino.frq in $BLIMPS_DIR
   5/24/00 Apply fraction of similar columns to # of columns, not to
		# of pairs of columns
   6/ 1/00 Clump columns based on correlation score & apply fraction to
	   clump size; require a minimum of MIN_COLS
   9/27/00 Make MIN_COLS a parameter
-----------------------------------------------------------------------------*/

#define EXTERN

#define SEARCH_TYPE_UNSET  -1

#define COL_SCORE_CUTOFF 0.25
#define BIAS_CUTOFF 0.50
#define MIN_COLS 3
#define MAXROWS 100
#define INDEX(n, col, row) (col*n - (col*(col+3))/2 - 1 + row)

#include "blocksprogs.h"
#include "blkvblk.h"

/* variables set by the configuration file in blimps program */

int StrandsToSearch;
int NumberToReport;
int SearchType;
int GeneticCodeInitializer;
int SiteSpecificScoringMatrixType;
int BlockToMatrixConversionMethod; /* default method is two */
int SequenceMatrixScoringMethod;   /* default method is zero */

/*
 * Local variables and data structures
 */

int    getargs(), data_read() ;

void   set_defaults(), fprint_matrix() ;

double cols_score(), cols_scoreNPrd() ;

char   DBtype() ;

Block  *read_a_prodom_entry() ;
int cluster();

int         alloctd_algnmnts ;
int         alignments_done = 0 ;
int         dbg_lvl = 0 ;
Boolean     WWW_FLAG = TRUE ;

/*=======================================================================*/
/*
 * main
 *   controls flow of program
 *   Parameters: argc, argv
 *   Error codes:
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  int           i1, i2, similar_pairs, similar_cols, max_clump, flag;
  int           read_entries = 0, hits = 0 , min_cols;
  FILE          *bfp, *out ;
  Block         *block ;
  Matrix        *matrix ;
  char          bdbname[MAXNAME], outname[MAXNAME], ctemp[MAXNAME] ;
  char          line[MAXLINELEN], db_type, percent_char[5] ;
  char		*blimps_dir;
  double        col_score, col_score_cutoff, bias_cutoff, frac_similar_pairs ; 
  double	frac_similar_cols, frac_max_clump ;
  struct pair *pairs;
  int npair, px;


/* set column score cutoff.
   Columns with scores above the cutoff are considered similar */
  col_score_cutoff = COL_SCORE_CUTOFF ;  

/* set bias fraction cutoff.
   Blocks that have more then this fraction of similar scores are considered 
   biassed */
  bias_cutoff = BIAS_CUTOFF ;  
  min_cols = MIN_COLS ;

                /* If no parameters passed on command line show how to do it */
  if (argc == 1) 
     printf("\n%s blocks_db [column score cutoff [bias fraction cutoff [min biased cols [debug level]]]]\n", 
            argv[0]) ;

                                      /* getting input and output file names */
  if ((getargs(argc,argv,bdbname,&bfp,&col_score_cutoff,&bias_cutoff,&min_cols)) != OK) 
     exit(ERROR) ; 

  sprintf(outname,"%s.biassed_blocks", bdbname) ;
  out = NULL;
  if ( ! WWW_FLAG && (out=fopen(outname, "w")) == NULL)
     {
     printf("\nCannot open output file file \"%s\"\n", outname);
     return(ERROR);
     }

                                                    /*set the default values */
  set_defaults();

                                                         /* find out DB type */
  if ((db_type = DBtype(&bfp)) == ERROR) exit(ERROR) ; 

  if (WWW_FLAG) strcpy(percent_char,"%") ;
  else          strcpy(percent_char,"%") ;

                             /* print parameters used and scores header line */ 
  if (! WWW_FLAG) printf("%s.\n", argv[0]) ;

  sprintf(line,
"Normalized Sum-of-Products column score\nColumn score cutoff %.3f. Bias-fraction cutoff %2d percent (minimum %d columns).\n", 
         col_score_cutoff, (int) (bias_cutoff*100.), min_cols ) ;

  printf("%s\n",line) ;
  if (! WWW_FLAG) fprintf(out,"%s\n",line) ;


                   /* load the frequencies for converting blocks to matrices */
  blimps_dir = getenv("BLIMPS_DIR");
                   /* load the frequencies for converting blocks to matrices */
  if ( ! load_frequencies(AA_FREQUENCY_FNAME) )
  {
     if (blimps_dir != NULL)
     {
        sprintf(ctemp, "%s/docs/%s", blimps_dir, AA_FREQUENCY_FNAME);
	fprintf(stderr, "Trying %s...\n", ctemp);
        load_frequencies(ctemp) ;
     }
  }


  printf("               Pairs                 Columns         Clumps\n");
  printf("Block    Width Total Biassed Percent Biassed Percent Biassed Percent\n");
                                      /* looping through all the entry pairs */
  while (data_read(&bfp,&block,&matrix,db_type) == OK) 
  {
     read_entries++ ;

     if (dbg_lvl > 4)
        printf("%-10s (%2d columns)\n", matrix->number, matrix->width) ;

     similar_pairs = similar_cols = max_clump = 0 ;
     npair = matrix->width * (matrix->width - 1)/2;
     pairs = (struct pair *) malloc (npair * sizeof(struct pair));
     /* compare all matrix columns with each other. */
     for (i1=0; i1 < matrix->width; i1++)
     {
         flag = 0;
         for (i2=i1+1; i2 < matrix->width; i2++)
 	 {
             /* col_score is correlation coeff between 0.0 and 1.0  */
             col_score = cols_scoreNPrd(matrix->weights,i1,matrix->weights,i2) ;
             px = INDEX(matrix->width, i1, i2);
             pairs[px].score = (int) 100.0 * col_score;
             if (col_score >= col_score_cutoff) 
             { similar_pairs++ ; flag = 1; }

             if (dbg_lvl > 5)
                printf(" %2d %2d  %.3f\n", i1, i2, col_score) ;
             else if 
                (dbg_lvl > 4 && col_score >= col_score_cutoff)
                printf(" %2d %2d  %.3f\n", i1, i2, col_score) ;

	 }
         if (flag) similar_cols++;
     }
     max_clump = cluster(col_score_cutoff, min_cols,  matrix->width, pairs);
     frac_max_clump = (double) max_clump / matrix->width;
     frac_similar_cols = (double) similar_cols/matrix->width;
     frac_similar_pairs = (double) 
                     similar_pairs/(matrix->width * (matrix->width - 1) / 2) ;


          /* check if the fraction of similar scores is above the cutoff to 
                                            be identified as biassed blocks. */
     if (frac_max_clump >= bias_cutoff)
     {
        hits++ ;

        sprintf(line, "%-10s %2d   %4d  %4d   %3d      %4d   %3d      %4d   %3d",
                matrix->number, matrix->width, 
                (matrix->width * (matrix->width - 1) / 2),
		similar_pairs, (int) (frac_similar_pairs*100),
		similar_cols,  (int) (frac_similar_cols*100.),
		max_clump,     (int) (frac_max_clump*100.));

	 
        printf("%s\n",line) ;
        if (! WWW_FLAG) fprintf(out,"%s\n",line) ;

        if (dbg_lvl == 1)
        {
           if (db_type != MATRIX_DB) { output_block(block, stdout); }
           else                      { fprint_matrix(matrix,stdout); }

        }
        if (dbg_lvl == 2)
           if (db_type != MATRIX_DB) fprint_matrix(matrix,stdout) ;
     }
     else if (dbg_lvl > 2)
/*
        printf(
          "Block %-10s (%2d columns) has         %2d%s (%d/%d) similar column pairs.\n",
               matrix->number, matrix->width, 
               (int) (frac_similar_pairs*100.), percent_char, similar_pairs,
               (matrix->width * (matrix->width - 1) / 2)) ;
*/
        printf("%-10s %2d   %4d  %4d   %3d      %4d   %3d      %4d   %3d\n",
                matrix->number, matrix->width, 
                (matrix->width * (matrix->width - 1) / 2),
		similar_pairs, (int) (frac_similar_pairs*100),
		similar_cols,  (int) (frac_similar_cols*100.),
		max_clump,     (int) (frac_max_clump*100.));


     if (db_type != MATRIX_DB) free_block(block) ;
     free_matrix(matrix) ;
     free(pairs);
  }

  if (WWW_FLAG)
     sprintf(line,"%d biassed blocks found in the %d blocks.", 
             hits, read_entries) ;
  else
     sprintf(line,"%d biassed blocks found in the %d blocks from file %s.", 
             hits, read_entries, bdbname) ;

  printf("\n%s\n",line) ;
  if (! WWW_FLAG) fprintf(out,"%s\n",line) ;

  fclose(bfp); if (! WWW_FLAG) fclose(out);         /* close files */

  if (! WWW_FLAG) printf ("Output written in file %s.\n", outname) ;
  exit(0);

}  /* end of main */


/*****************************************************************************
 * get input and output file names and other program parameters interactively
 * or from command line. 
 *****************************************************************************/

int getargs(argc,argv,bdbname,bfp,col_score_cutoff,bias_cutoff,min_cols)

int    argc;
char   *argv[];
char   bdbname[] ;
FILE   **bfp;
double *col_score_cutoff, *bias_cutoff ;
int *min_cols;

{
/* ------------1st arg = block file --------------------------------------*/
   if (argc > 1) strcpy(bdbname, argv[1]);
   else                                   /* get input file interactively */
      {
      printf("\nEnter name of a file with blocks or block matrices: ");
      gets(bdbname);
      }

   if ( (*bfp=fopen(bdbname, "r")) == NULL)
      {
      printf("\nCannot open file \"%s\"\n", bdbname);
      return(ERROR);
      }


/* ------------optional 2nd arg = column score cutoff ------------------*/

   if (argc > 2) *col_score_cutoff = atof(argv[2]) ;

   if (*col_score_cutoff == 0)
      *col_score_cutoff = COL_SCORE_CUTOFF ;
   else if (*col_score_cutoff < -1.0 || *col_score_cutoff > 1.0)
      {
      printf("\nColumn score cutoff has to be between -1 and 1 !\n") ;
      printf("The value given (%f) is out of range.\n", *col_score_cutoff) ;
      return(ERROR) ;
      }

/* ------------optional 3rd arg = bias fraction cutoff ------------------*/

   if (argc > 3) *bias_cutoff = atof(argv[3]) ;

   if (*bias_cutoff == 0)
      *bias_cutoff = BIAS_CUTOFF ;
   else if (*bias_cutoff <= 0 || *bias_cutoff > 1.0)
      {
      printf("\nBias fraction cutoff has to be between 0 and 1 !\n") ;
      printf("The value given (%f) is out of range.\n", *bias_cutoff) ;
      return(ERROR) ;
      }

/* ------------optional 4th arg = bias fraction cutoff ------------------*/

   if (argc > 4) *min_cols = atoi(argv[4]) ;

   if (*min_cols <= 0) *min_cols = MIN_COLS ;

/* ------------optional 5th arg = debug level ------------------*/

   if (argc > 5) dbg_lvl = atoi(argv[5]) ;

   return(OK) ;

}

/****************************************************************************
 * set the default values for some of the variables.
 ****************************************************************************/

void set_defaults()
{

  GeneticCodeInitializer = 0;           /* the standard genetic code */

  StrandsToSearch = 2;          /* == 2 if want to search both strands */
  NumberToReport  = 0;          /* <0 means all, 0 means judge, */
                                /* >0 means use that number */
  SearchType      = SEARCH_TYPE_UNSET;

  BlockToMatrixConversionMethod = 2; /* default method is two */
  SequenceMatrixScoringMethod   = 0; /* default method is zero */

  ErrorLevelReport = WARNING_ERR_LVL; /* report all errors */

}


/*****************************************************************************
 * cols_score
 * compare a pair of matrix columns (positions)
 ****************************************************************************/

double cols_score(mat1,col1,mat2,col2)

MatType *mat1[], *mat2[] ;
int     col1, col2 ;

{
   double score ;
   double p1=0.0, p2=0.0, p3a=0.0, p3b=0.0, p4a=0.0, p4b=0.0 ;
   int    aa ;

                 /* Calculate Pearson's r score between the 2 matrix columns */

   for (aa=0; aa 0 && mat2[aa][col2] > 0)
         score += mat1[aa][col1] * mat2[aa][col2] ;

 /* normalize maximal score to 1.0 */ 
   score /= 10000.0 ;
   
   return(score) ;

}

/****************************************************************************
 * find out if a file (DB) is of blocks, ProDom multiple alignments or matrices
 * The first entry in the file (ending with a "//") will be read.
 * If the entry contains a line begining with "BL   " it will be declared a
 * blocks database, if it will contain a line begining with "MA   " it will be 
 * declared a matrices database. If none or both are found than it will be
 * declared as neither
 ****************************************************************************/

char DBtype(dbfile)

FILE  **dbfile ;

{

   char    *first_entry, *tmp_ptr ;
   char    rc = '\0' ;
   int     entrysize ;
   int     entrylen = 0 ;
   Boolean check = FALSE ;

   entrysize = ENTRYSIZE ;

   first_entry = (char *) malloc(entrysize*sizeof(char)) ;

     /* read first line to determine if file has ProDom multiple alignment
        format - "># (#)", where # is one or more digits */

   if (fgets(first_entry, ENTRYSIZE-1, *dbfile) != NULL && 
       (int) strlen(first_entry) >= 6)
      {
      if (first_entry[0] == '>')              /* check if first char is ">" */
	 {
                                         /* check if second char is a digit */
         if (isdigit(first_entry[1]) != 0)
	    {
                                             /* read all consecutive digits */
            for (entrysize=2; 
                 entrysize" */
   while((fgets(line, MAXLINELEN, db)) != NULL && line[0] != '>') ;

   if (line[0] != '>') return(NULL) ;

                                                /* allocate space for block */
     CheckMem(block = (Block *) malloc(sizeof(Block))) ;

/* process first line - the description line */

   line[0] = ' ' ;                                        /* get rid of '>' */
                                          /* get first word - sequence name */
   if ((ptr = get_token(line)) == NULL) 
      {
      printf("Error ! Problem in format of ProDom entry description -line\n") ;
      return(NULL) ;
      }

                            /* create accession prefix - "PD" + preceding 0s,
                                entry presumed not to be longer then 5 chars */
   word[0] = 'P' ;   word[1] = 'D' ; 
   i2 = 2 ;
   for(i1=0; i1<(5 - (int) strlen(ptr)); i1++) word[i2++] = '0' ;
   word[i2] = '\0' ;

   strcpy(entry_name, ptr) ;
                                       /* save first word in block accession */
   sprintf(block->ac, "%s%s;", word, entry_name) ;
   sprintf(block->number, "%s%s", word, entry_name) ;

                                              /* save first word in block ID */
   sprintf(block->id, "%s; ProDom_mul", entry_name) ;

                 /* get second word - number of sequences between parethesis */
   if ((ptr = get_token(NULL)) == NULL) 
      {
      printf("Error ! Problem in format of ProDom entry description-line\n") ;
      return(NULL) ;
      }

                                                        /* strip parenthesis */
   if (ptr[0] != '(')
      {
      printf("Error ! Problem in ProDom entry %s\n", entry_name) ;
      printf("second word in description line doesn't begin with a (\n") ;
      return(NULL) ;
      }
   else
      ptr[0] = '0' ;

   if (ptr[strlen(ptr)-1] != ')')
      {
      printf("Error ! Problem in ProDom entry %s\n", entry_name) ;
      printf("second word in description line doesn't end with a )\n") ;
      return(NULL) ;
      }
   else
      ptr[strlen(ptr)-1] = ' ' ;

               /* check that second word is composed of digits and copy it */
   for(iptr=ptr; *iptr != ' ' && isdigit(*iptr); iptr++) ;
   if (*iptr != ' ')
      {
      printf("Error ! Problem in format of ProDom entry %s\n", entry_name) ;
      printf("A non-digit in the number-of-sequences field \"%s\"\n", ptr) ;
      return(NULL) ;
      }

   block->num_sequences = atoi(ptr) ;

   if (block->num_sequences <= 1) 
      {
      printf(
       "Error ! Number of sequences in ProDom entry %s (%d) is less than 2\n",
       entry_name, block->num_sequences) ;
      return(NULL) ;
      }
   else 
      block->max_sequences = block->num_sequences ;

                                                        /* get rest of line */
   for(iptr=ptr; *iptr != '\0'; iptr++) ;       /* find end of current word */

                            /* get rid of leading and trailing white spaces */
   ptr = eat_whitespace(iptr+1) ;
   remove_trailing_whitespace(ptr) ;

                                   /* save string in block description line */
   strncpy(block->de, ptr, SMALL_BUFF_LENGTH) ;
                           /* in case word is longer than SMALL_BUFF_LENGTH 
                                      and thus the last char copied isnt \0 */ 
   block->de[SMALL_BUFF_LENGTH-1] = '\0' ;

   block->num_clusters = block->max_clusters = 1 ; 
   block->motif[0] = '\0';
   block->percentile = 0 ;
   block->strength = 0 ;

                                         /* allocate space for the clusters */
   CheckMem(block->clusters = (Cluster *) 
                             calloc(block->max_clusters, sizeof(Cluster))) ;

/* process next lines - the sequence lines */
  
          /* read all lines until a line starting with a space, EOL or '>' */
/* Note that if a line begining with '>' was read (the description line of 
   the next entry) it won't be read in fetching the next entry and that 
   entry will be lost */

   
   for(num_seqs=0;
       (fgets(line, MAXLINELEN, db)) != NULL && 
       line[0] != '\n' && line[0] != ' '  && line[0] != '>' ;
       num_seqs++)
      {
                                          /* get first word - sequence name */
      if ((ptr = get_token(line)) == NULL) 
         {
         printf(
            "Error ! Problem in format of ProDom entry %s sequence-line %d\n",
                entry_name, num_seqs+1) ;
         return(NULL) ;
         }

           /* temporarily store sequence name, if this is first sequence 
              the sequences length isn't known and no memory allocated yet, 
              place it in block sequence structure after memory is allocated */
      strcpy(word, ptr) ;

                               /* get second word - sequence start position */
      if ((ptr = get_token(NULL)) == NULL) 
         {
         printf(
            "Error ! Problem in format of ProDom entry %s sequence-line %d\n",
                entry_name, num_seqs+1) ;
         return(NULL) ;
         }

           /* temporarily store start position, if this is first sequence 
              the sequences length isn't known and no memory allocated yet, 
              place it in block sequence structure after memory is allocated */

      for(iptr=ptr; *iptr != '\0' && isdigit(*iptr); iptr++) ;
      if (*iptr != '\0')
         {
         printf(
            "Error ! Problem in format of ProDom entry %s sequence-line %d\n",
                entry_name, num_seqs+1) ;
         printf("A non-digit in the sequence start position %s\n", ptr) ;
         return(NULL) ;
         }

      temp = atoi(ptr) ;

                    /* get 3rd word - sequence end position (no use for it) */
      if ((ptr = get_token(NULL)) == NULL) 
         {
         printf(
            "Error ! Problem in format of ProDom entry %s sequence-line %d\n",
                entry_name, num_seqs+1) ;
         return(NULL) ;
         }

                                              /* get 4th word - the sequence */
      if ((ptr = get_token(NULL)) == NULL) 
         {
         printf(
            "Error ! Problem in format of ProDom entry %s sequence-line %d\n",
                entry_name, num_seqs+1) ;
         return(NULL) ;
         }


           /* should have arrived at the begining of 4th word - the sequence */
                /* find out from the first sequence the sequence length 
                   and use it to allocate memory for the sequence structures */
      if (num_seqs == 0)
	 {
         block->width = strlen(ptr) ;

                          /* following part adapted from 
                             blimps procedure read_block_body by Bill Alford */

         /* allocate space for all the Sequences of the block sequence array */
         CheckMem(
             sequence_pointer = 
                  (Sequence *) 
		  calloc(block->max_sequences,sizeof(Sequence))) ;

	                             /* initialize the block sequences array */
	 block->sequences = sequence_pointer ;

	                                  /* allocate space for all residues */
	 CheckMem(
             residue_pointer = 
                 (Residue *) 
                 calloc(block->width * block->max_sequences, 
			sizeof(Residue))) ;

	                                /* initialize the residues 2-d array */
	 CheckMem(
             block->residues = 
                 (Residue **) calloc(block->max_sequences, sizeof(Residue *))) ;

	                                /* initialize sequences and residues */
         for(i1=0; i1max_sequences; i1++) 
            {
	    sequence_pointer[i1].length = block->width;
	    sequence_pointer[i1].sequence =
 		              &(residue_pointer[i1 * block->width]) ;
	    block->residues[i1] = 
                              &(residue_pointer[i1 * block->width]) ;
	    }
         }

                         /* memory now allocated to block sequence structure 
                                              copy name, position and length */
      strncpy(block->sequences[num_seqs].name, word, SMALL_BUFF_LENGTH) ;
                           /* in case word is longer than SMALL_BUFF_LENGTH 
                                      and thus the last char copied isnt \0 */ 
      block->sequences[num_seqs].name[SMALL_BUFF_LENGTH-1] = '\0' ; 

      block->sequences[num_seqs].position = temp ;

      block->sequences[num_seqs].length = block->width ;

/* process next word - the sequence, check length, change gap symbol "." to "-" */

      if (strlen(ptr) != block->width)
	 {
         printf(
            "Error ! Problem in format of ProDom entry sequence-line %d\n",
                num_seqs+1) ;
         printf("Sequence %s has length of %d instead of expected %d\n",
                block->sequences[num_seqs].name, strlen(ptr), 
	        block->width) ;
         return(NULL) ;
         }

      for(iptr=ptr; *iptr != '\0'; iptr++) if (*iptr == '.') *iptr = '-' ;

    /* next part adopted from blimps  procedure next_cluster by Bill Alford */
                     /* read the sequence from the string into the Sequence */

       rc = read_sequence(&(block->sequences[num_seqs]), AA_SEQ, 0, ptr) ; 
				   /* the Sequence, sequence type, starting */
   				   /* position, string with the sequence    */

                                      /* check to see if there was an error */    
       if (rc < 0) 
          {
                      /* Error, more residues in the sequence than expected */
          printf("Error reading sequence %s in block %s,", 
                 block->sequences[num_seqs].name, block->number) ;
          printf("%d more residues in the sequence than the expected %d.\n",
	         -rc, block->sequences[num_seqs].length) ;
          }
       else if (rc < block->sequences[num_seqs].length) 
          {
        /* Error, not enough residues for the sequence, filling with blanks */
          printf("Error reading sequence %s in block %s,", 
                 block->sequences[num_seqs].name, block->number) ;
          printf("not enough residues to fill the sequence.");
          printf("Filling the rest of the sequence with blanks.\n");

                                                     /* filling with blanks */
    	  for(i1=rc; i1sequences[num_seqs].length; i1++) 
	     block->sequences[num_seqs].sequence[i1] = aa_atob['-'];
          }
       else if (rc > block->sequences[num_seqs].length) 
          {
              /* BIG Error, an undocumented return value from read_sequence */
          printf(
              "read_a_prodom_entry(): Error reading sequence %s in block %s,",
 	         block->sequences[num_seqs].name,
                 block->number) ;
          printf("Undocumented return value, %d, from read_sequence().\n",
                 rc) ;
          } /* else, ret_value == seq.length, OK */

                 /* sequences have no weights give all equal weights of 100 */
       block->sequences[num_seqs].weight =  100.0 ;

          /* assign the sequences to the cluster (space has been allocated) */

       block->clusters[0].num_sequences = block->num_sequences ;

       block->clusters[0].sequences = &(block->sequences[0]) ;

       }

      if (num_seqs < 2)
	 {
         printf("Error ! Not enough sequences (%d) in ProDom entry %s\n",
                num_seqs, block->number) ;
         return(NULL) ;
         }
      else if (num_seqs != block->num_sequences)
         {
         printf("Error ! Actual number of sequences in ProDom entry %s\n",
                block->number) ;
         printf("different than what the entry reports\n") ;
         return(NULL) ;
         }

      min_pos = 10000 ;  /* find min and max start positions of sequences */
      max_pos = 0 ;
      for(i1=0; i1sequences[i1].position > max_pos) 
            max_pos = block->sequences[i1].position ;
         if (block->sequences[i1].position < min_pos) 
            min_pos = block->sequences[i1].position ;
	 }

/* add min and max distance from previous block (sequence start) to Ac line */
      sprintf(word, " distance from previous block=(%d,%d)", 
              min_pos, max_pos);
      strcat(block->ac, word) ;

      sprintf(block->bl, "adapted from ProDom entry; width=%d; seqs=%d;",
              block->width, block->num_sequences) ; 

   return(block) ;
}

/*
 * fprint_matrix
 *   Prints a Matrix data structure to a file.  Primarily for debugging purposes.
 * adapted from blimps3.0.0 print_matrix
 *   Parameters: 
 *     Matrix *matrix:  the matrix to print
 *     FILE   *omfp:   the output matrix file pointer
 *   Error Codes: none
 */

void fprint_matrix(matrix,omfp)
     Matrix *matrix;
     FILE *omfp;
{
  int pos;
  int low, high;
  char c;

  int MATRIX_PRINT_WIDTH ;

  if (WWW_FLAG)
     MATRIX_PRINT_WIDTH = 55 ;
  else
     MATRIX_PRINT_WIDTH = 18 ;

  high = MATRIX_PRINT_WIDTH;
  for (low=0; 
       lowwidth; 
       low = (high+=MATRIX_PRINT_WIDTH) - MATRIX_PRINT_WIDTH) {



  fprintf(omfp,"\n");

/* modified following statements to 
  print matrix column number starting from 1 not 0*/

  if (matrix->width > 99) {
    fprintf(omfp,"  |");
    for (pos=low; poswidth; pos++) {
      if (pos+1 > 99) {
	fprintf(omfp,"% 4d", (pos+1)%100);
      }
      else {
	fprintf(omfp,"    ");
      }
    }
  }

  fprintf(omfp,"\n");
  if (matrix->width > 9) {
    fprintf(omfp,"  |");
    for (pos=low; poswidth; pos++) {
      if (pos+1 > 9) {
	fprintf(omfp,"% 4d", (pos+1-(((pos+1)/100)*100)) / 10);
      }
      else {
	fprintf(omfp,"    ");
      }
    }
  }
  
  fprintf(omfp,"\n");
  fprintf(omfp,"  |");
  for (pos=low; poswidth; pos++) {
    fprintf(omfp,"%4d", ((pos-((pos/10)*10))+1)%10);
  }
  
  fprintf(omfp,"\n");
  fprintf(omfp,"--+");
  for (pos=low; poswidth; pos++) {
    fprintf(omfp,"----");
  }

  fprintf(omfp,"\n");
  
/* following part modified not to show B, J, O, U and Z */
  for (c='A'; c<='Y'; c++) {
    switch (c)
      {
      case 'B' : continue ;
      case 'J' : continue ;
      case 'O' : continue ;
      case 'U' : continue ;
      }
    fprintf(omfp,"%c |", c);
    for (pos=low; poswidth; pos++) {
      fprintf(omfp,"% 4d", round(matrix->weights[aa_atob[c]][pos]));
    }
    fprintf(omfp,"\n");
  }

/* removed printing of c='*' */

  c = '-';
  fprintf(omfp,"%c |", c);
  for (pos=low; poswidth; pos++) {
    fprintf(omfp,"% 4d", round(matrix->weights[aa_atob[c]][pos]));
  }
  fprintf(omfp,"\n");

  }

} /* end of fprint_matrix */
/*---------------------------------------------------------------------
	cluster pairwise scores
-----------------------------------------------------------------------*/
int cluster(score_cutoff, min_cols,  width, pairs)
double score_cutoff;
int min_cols, width;
struct pair *pairs;
{
   int iclus, npair, threshold, s1, s2, px, i, i1, i2;
   int nclus[MAXROWS], icluster[MAXROWS], minclus, oldclus;
   int maxnclus;

   if (min_cols > width) min_cols = width;
   npair = width*(width-1)/2;
   threshold = (int) (100.0 * score_cutoff);

/*  Print scores */
/*   printf("\nThreshold=%d", threshold);
   for (s2=1; s2= threshold)	/*  cluster this pair */
	 {
/*
printf("s1=%d s2=%d score=%d\n", s1, s2, pairs[px].score);
*/
	    if (icluster[s1] < 0)          /* s1 not yet clustered */
	    {
	       if (icluster[s2] < 0)       /* new cluster */
	       {
		  icluster[s1] = iclus++;
		  icluster[s2] = icluster[s1];
	       }
	       else  				/* use s2's cluster  */
		  icluster[s1] =  icluster[s2];
	    }
	    /*  use s1's cluster if it has one and s2 doesn't */
	    else if (icluster[s1] >= 0 && icluster[s2] < 0)
	       icluster[s2] = icluster[s1];
	    /* merge the two clusters into the lower number */
	    else if (icluster[s1] >= 0 && icluster[s2] >= 0)
	    {
	       minclus = icluster[s1]; oldclus = icluster[s2];
	       if (icluster[s2] < icluster[s1])
	       {
		  minclus = icluster[s2]; oldclus = icluster[s1];
	       }
	       for (i1=0; i1 maxnclus) maxnclus = nclus[i];
   }

/*
for (i=0; i= min_cols) return(maxnclus);
   else return(0);

}  /* end of cluster */
               /* initialize the residues 2-d array */
	 CheckMem(
             block->residues = 
                 (Residue **) calloc(block->max_sequences, sizeof(Residue *))) ;

	                                /* initialize sequences and residues */
         for(i1=0; i1max_sequences; i1++) 
            {
	    sequence_pointer[i1].length = block->width;
	    sequence_pointer[i1].sequence =
 	blimps-3.9/blimps/format_block.c000064400001460000012000000660051054325714200172540ustar00jorjastaff00000400000027/*  Copyright 1997-2003: 
     Fred Hutchinson Cancer Research Center, Seattle, WA, USA */
/*      format_block.c                                    */

/* SP May 96' - modifications :
  Made the sequence names and start positions optional. If the fields 
  (windows) for these are totaly empty the program will give default values.
  Fixed spelling mistake and bug in message when a sequence is too short.
  SP July 19 96. 
     removed tags ('-') as suffixes to weight type and scale parameters
     when calling blweight. After this program was updated its behavoir
     changed.
  SP Aug 27 96.
     added fasta format reading from sequences box.
11/15/97 Moved home directory defs to homedir.h - but always executes from
	 btest anyway (??)
12/ 8/98 Execute logo.csh instead of logoscript.www.BFormatter
         Execute pssm.sh instead of PSSMscript.www
         Added btest_flag
 6/20/99 Increased sequence name length from 10 to 18
 2/ 8/00 Allow ACs of 7-10 chars
12/23/06 Increased sequence name length from 18 to 20
*/

/*===========================================================================*/
/* blimps stuff */
#define EXTERN

#include 

#define BTEST_HOME   "/home/btest"
#define BLOCKS_HOME  "/home/blocks"

typedef struct {
    char *name;
    char *val;
} entry;

/* from util.c */
char *makeword(char *line, char stop);
char *fmakeword(FILE *f, char stop, int *len);
char x2c(char *what);
void unescape_url(char *url);
void plustospace(char *str);
 
entry entries[10000];

#define BLOCK_SEQUENCE_INCREASE_SIZE 50  /* default number of sequences to allocate */
#define MIN_BLOCK_LENGTH 3
#define MINAC 7
#define MAXAC 10

#define UNKNOWN_SEQ_NAME "unknown"
#define UNKNOWN_SEQ_POS 9999


#define TMP_SUBDIR   "/tmp"
#define BIN_SUBDIR   "/bin"
#define LOG_SUBDIR   "/log"

char extblock_stdout[LARGE_BUFF_LENGTH];
char Block_file[LARGE_BUFF_LENGTH];
char Block_fileNW[LARGE_BUFF_LENGTH];
char Blweight[LARGE_BUFF_LENGTH];
char Weight_type[LARGE_BUFF_LENGTH];
char Weight_scale[LARGE_BUFF_LENGTH];
char log_dir[LARGE_BUFF_LENGTH];
char log_file[LARGE_BUFF_LENGTH];
char error_file[LARGE_BUFF_LENGTH];
char tmp_dir[LARGE_BUFF_LENGTH];
char home_dir[LARGE_BUFF_LENGTH];
char buf[LARGE_BUFF_LENGTH];

int btest_flag;
int pid;

int no_seq_names, no_seq_pos ;

entry *ID_Ptr = NULL;
entry *AC_Ptr = NULL;
entry *MIN_DIST_Ptr = NULL;
entry *MAX_DIST_Ptr = NULL;
entry *DE_Ptr = NULL;
entry *MA_METH_Ptr = NULL;
entry *MA_WIDTH_Ptr = NULL;
entry *MA_SEQS_Ptr = NULL;
entry *SEQ_NAMES_Ptr = NULL;
entry *SEQ_POS_Ptr = NULL;
entry *SEQS_Ptr = NULL;

void read_startup_info()
{
  int i;
  char *script, *ptr;
  FILE *logdate, *curr_year_month;

  script = getenv("SCRIPT_NAME");

  btest_flag = 0;
  ptr = getenv("BLOCKS_HOME");
  if (ptr != NULL)
  {
     sprintf(home_dir, "%s", ptr);
  }
  else
  {
     if (strstr(script, "btest")) {
       sprintf(home_dir, "%s", BTEST_HOME);
       btest_flag = 1;
     }
     else if (strstr(script, "blocks")) {
       sprintf(home_dir, "%s", BLOCKS_HOME);
     }
     else {
    /* problems, raise an error */
    /* this is the only way I know how to get mosaic to raise an error. */
       printf(0);
       exit(1);
     }
   }

  pid = getpid();
  curr_year_month = popen("date '+%y%m'", "r");
  logdate = popen("date \"+%y%m%d\"", "r");

  sprintf(extblock_stdout, "%s%s/extblock_stdout", home_dir, BIN_SUBDIR);
  sprintf(Blweight, "%s%s/blweight", home_dir, BIN_SUBDIR);
  sprintf(Block_fileNW, "%s%s/%d.blk.NW.temp", home_dir, TMP_SUBDIR, pid);
  sprintf(Block_file, "%s%s/%d.blk", home_dir, TMP_SUBDIR, pid);
  sprintf(Weight_type, "P");
  sprintf(Weight_scale, "M");
  fgets(buf, LARGE_BUFF_LENGTH, curr_year_month);
  remove_trailing_whitespace(buf);
  sprintf(log_dir, "%s%s/%s", home_dir, LOG_SUBDIR, buf);
  fgets(buf, LARGE_BUFF_LENGTH, logdate);
  remove_trailing_whitespace(buf);
  sprintf(tmp_dir, "%s%s", home_dir, TMP_SUBDIR);

  pclose(curr_year_month);
  pclose(logdate);
}   /*  end of read_startup_info */


int parse()
{
/* parse the input */

  register int i,num_entries=0;
  char *entry_string;
  int cl;

  /* check that there is something to use. */
  entry_string = getenv("QUERY_STRING");

/*
  if (entry_string == NULL) 
     {
     printf("No query information to decode.\n");
     exit(1);
     }
*/

  /* parse the query string into individual entries */

  cl = atoi(getenv("CONTENT_LENGTH"));

  for(i=0;cl && (!feof(stdin));i++) 
     {
     num_entries=i;
     entries[i].val = fmakeword(stdin,'&', &cl);
     plustospace(entries[i].val);
     unescape_url(entries[i].val);
     entries[i].name = makeword(entries[i].val,'=');

     if (!strncmp(entries[i].name, "ID", 14)) 
        {
	ID_Ptr = &entries[i]; 
        }

     if (!strncmp(entries[i].name, "AC", 14)) 
        {
	AC_Ptr = &entries[i]; 
        }

     if (!strncmp(entries[i].name, "MIN_DIST", 14)) 
        {
	MIN_DIST_Ptr = &entries[i]; 
        }

     if (!strncmp(entries[i].name, "MAX_DIST", 14)) 
        {
	MAX_DIST_Ptr = &entries[i]; 
        }

     if (!strncmp(entries[i].name, "DE", 14)) 
        {
	DE_Ptr = &entries[i]; 
        }

     if (!strncmp(entries[i].name, "MA_METH", 14)) 
        {
	MA_METH_Ptr = &entries[i]; 
        }

     if (!strncmp(entries[i].name, "MA_WIDTH", 14)) 
        {
	MA_WIDTH_Ptr = &entries[i]; 
        }

     if (!strncmp(entries[i].name, "MA_SEQS", 14)) 
        {
	MA_SEQS_Ptr = &entries[i]; 
        }

     if (!strncmp(entries[i].name, "SEQ_NAMES", 14)) 
        {
	SEQ_NAMES_Ptr = &entries[i]; 
        }

     if (!strncmp(entries[i].name, "SEQ_POS", 14)) 
        {
	SEQ_POS_Ptr = &entries[i]; 
        }

     if (!strncmp(entries[i].name, "SEQS", 14)) 
        {
	SEQS_Ptr = &entries[i]; 
        }

    }


  return num_entries;
} /*  end of parse */


void clean_temp_files()
{
/* weighted block file won't be deleted so it can be used to make a logo */
  sprintf(buf, "rm -f %s%s/%d*temp", home_dir, TMP_SUBDIR, pid); 
  system(buf);
}

/* 
 * resize_block_sequences
 *   Increases the memory for the storage of the sequences of a block.
 *   Parameter:
 *     Block *block: the block to resize
 *   Error codes: none
 */

static void resize_block_sequences(block)
     Block *block;
{
  int i;
  void *tmp_ptr;		/* don't want to ruin pointer in case there */
				/* is a repeated realloc call */

  /* announce info */
  sprintf(ErrorBuffer, 
	  "Allocating more space for sequences in block %s.\n",
	  block->number);
/*  ErrorReport(INFO_ERR_LVL); */ /* turned off SP */

  /* get more space */
  block->max_sequences += BLOCK_SEQUENCE_INCREASE_SIZE;
  
  CheckMem(
	   tmp_ptr = 
	   (Sequence *) realloc(block->sequences,
				sizeof(Sequence) *
				block->max_sequences)
	   );
  block->sequences = (Sequence *) tmp_ptr;
  
  CheckMem(
	   tmp_ptr = 
	   (Residue *) realloc(block->sequences[0].sequence,
			       sizeof(Residue) *
			       block->width *
			       block->max_sequences)
	   );
  block->sequences[0].sequence = (Residue *) tmp_ptr;

  CheckMem(
	   tmp_ptr = 
	   (Residue **) realloc(block->residues,
				sizeof(Residue *) *
				block->max_sequences)
	   );
  block->residues = (Residue **) tmp_ptr;
  
  /* re-initialize sequences and residues, same data, just different place */
  for(i=0; imax_sequences; i++) {
    block->sequences[i].length = block->width;
    block->sequences[i].sequence = 
      &(block->sequences[0].sequence[i * block->width]);
    block->residues[i] = 
      &(block->sequences[0].sequence[i * block->width]);
  }
}


void make_block()
{
  FILE  *bfp ;
  Block *block ;
  char  string[LARGE_BUFF_LENGTH], string2[SMALL_BUFF_LENGTH] ;
  char  chr, end_chr, *ptr ;
  int   stringlen, i, seqs_start, j, k, rc ;
  Sequence *sequence_pointer ;
  Residue  *residue_pointer ;
  Boolean is_fasta = FALSE, seq_header = FALSE ;

  /* check that obligatory fields have something */

/* Note if sequence names and start positions not supplied */
  if (SEQ_NAMES_Ptr->val[0] == NULL) no_seq_names = 1 ;
  else                               no_seq_names = 0 ; 

  if (SEQ_POS_Ptr->val[0] == NULL) no_seq_pos = 1 ;
  else                             no_seq_pos = 0 ; 

  if (SEQS_Ptr->val[0] == NULL) 
    {
      printf("
      Error
      \n");
      printf("No sequences specified.
      \n");
      exit(0);
    }

                                                /* allocate space for block */
    CheckMem(block = (Block *) malloc(sizeof(Block))) ;

        /* if first non blank char is '>' the sequences are in FASTA format */
    for (seqs_start=0; 
         (chr = SEQS_Ptr->val[seqs_start]) != '\0' && 
         chr != '>' && isspace(chr);
         seqs_start++) ;
    if (chr == '>') 
       {
       is_fasta = TRUE ;
       seqs_start++ ;                                          /* skip '>' */
       }
    else            
       {
       is_fasta = FALSE ;
       seqs_start = 0 ;
       }

                  /* get length of first sequence to use as alignment width */
    if (is_fasta)
       {
                                         /* find begining of first sequence */
       for (ptr=strchr(SEQS_Ptr->val, '>'); *ptr != '\n' && *ptr != '\0';
            ptr++) ;
       if (*ptr == '\0')
          {
          printf("
      Error
      \n");
          printf("No sequences specified.
      \n");
          exit(0);
          }
       else
	  {
          ptr++ ;
          end_chr = '>' ;
          seq_header = TRUE ;

          if (!(no_seq_names))
	     {
             printf("
      Warning
      \n");
             printf("Sequence names box is used and the alignment is in FASTA format.
      \n") ;
             printf("Sequence names will be taken from the alignment
      \n") ;
             printf("(first word in the sequence header lines -
      \n") ;
             printf("'>seq_name 123 aa example protein').
      \n") ;
             }
	  }
       }
    else
       {
       ptr = SEQS_Ptr->val ;           
       end_chr = '\n' ;
       seq_header = FALSE ;
       }


    for(block->width = 0;
        *ptr != end_chr && *ptr != '\0'; ptr++)
      if (isalpha(*ptr) || *ptr == '-') block->width++ ;

    if (block->width > LARGE_BUFF_LENGTH)
       {
       printf("
      Error
      \n");
       printf("Judging by the first sequence length (%d) the alignment is too long. The maximal length is %d.
      \n", 
              block->width, LARGE_BUFF_LENGTH);
       exit(0);
       }

    if (block->width < MIN_BLOCK_LENGTH)
       {
       printf("
      Error
      \n");
       printf("Judging by the first sequence length (%d) the alignment is too short. The minimal length is %d.
      \n", 
              block->width, MIN_BLOCK_LENGTH);
       exit(0);
       }

    if (MA_WIDTH_Ptr->val[0] != NULL && 
        block->width != atoi (MA_WIDTH_Ptr->val))
       {
       printf("
      Warning
      \n");
       printf("The alignment width you gave (%s) is different than the first sequence length (%d).
      \n", 
              MA_WIDTH_Ptr->val, block->width);
       }


                                            /* allocate memory for sequences*/

   block->num_clusters = block->max_clusters = 1 ; 
                                 /* since number of sequences not known yet */
   block->max_sequences = BLOCK_SEQUENCE_INCREASE_SIZE ;


                                         /* allocate space for the clusters */
   CheckMem(block->clusters = (Cluster *) 
                             calloc(block->max_clusters, sizeof(Cluster))) ;

                          /* following part adapted from 
                             blimps procedure read_block_body by Bill Alford */

         /* allocate space for all the Sequences of the block sequence array */
         CheckMem(
             sequence_pointer = 
                  (Sequence *) 
		  calloc(block->max_sequences,sizeof(Sequence))) ;

	                             /* initialize the block sequences array */
	 block->sequences = sequence_pointer ;

	                                  /* allocate space for all residues */
	 CheckMem(
             residue_pointer = 
                 (Residue *) 
                 calloc(block->width * block->max_sequences, 
			sizeof(Residue))) ;

	                                /* initialize the residues 2-d array */
	 CheckMem(
             block->residues = 
               (Residue **) calloc(block->max_sequences, sizeof(Residue *))) ;

	                                /* initialize sequences and residues */
         for(j=0; jmax_sequences; j++) 
            {
	    sequence_pointer[j].length = block->width;
	    sequence_pointer[j].sequence =
 		              &(residue_pointer[j * block->width]) ;
	    block->residues[j] = 
                              &(residue_pointer[j * block->width]) ;
	    }

 /* get block sequence data */
 /* sequences */
 
    stringlen = (int) strlen(SEQS_Ptr->val) ;

    block->num_sequences = 0;
    j = 0 ;

             /* go along the string containing all the sequence-window data */
    for (i=seqs_start; i<=stringlen; i++)
      if (seq_header)
	 {
                                                            /* skip blanks */
         for(; isspace(SEQS_Ptr->val[i]) && SEQS_Ptr->val[i] != '/n' && 
               SEQS_Ptr->val[i] != '/0'; i++) ;
         if (SEQS_Ptr->val[i] == '/n')      /* no name is found in line */
             sprintf(block->sequences[block->num_sequences].name, 
                     "%s%d", UNKNOWN_SEQ_NAME, block->num_sequences+1) ;
         else
                        /* copy first 20 chars or until a space is reached */
         for(k=0; !(isspace(SEQS_Ptr->val[i])) && k<20 &&
                  SEQS_Ptr->val[i] != '/n' ; i++, k++) 
            block->sequences[block->num_sequences].name[k] = SEQS_Ptr->val[i];

                                                            /* end string */
         block->sequences[block->num_sequences].name[k] = '\0' ;

                                   /* move along until the end of the line */
         for(; SEQS_Ptr->val[i] != '\n' && SEQS_Ptr->val[i] != '\0'; i++) ;
                          /* if end of string reached - sequence is missing */
         if (SEQS_Ptr->val[i] != '\n')
	    {
            printf("
      Error
      \n");
            printf("Sequence %d not found.
      \n", block->num_sequences+1) ;
            exit(0);            
            }

         seq_header = FALSE ;
         }
                      /* else-if end of sequence-string reached process it */
/* end of sequence is end of string OR the end-character (eol or >) + 
   checking that the end-chararcter is precede by an eol for fasta seqs */
      else if (SEQS_Ptr->val[i] == '\0' ||
          (SEQS_Ptr->val[i] == end_chr && 
           (!(is_fasta) || SEQS_Ptr->val[i-1] == '\n')) )
	 {
         if (j==0)
            {
                              /* skip until end of string or no space char */
            while(isspace(SEQS_Ptr->val[i]) && SEQS_Ptr->val[i] != '\0') ;
 /* if we are the end-of-string this is just an extra line beyond the seqs */
            if (SEQS_Ptr->val[i] == '\0') break ;
            else
               {
               printf("
      Error
      \n");
               printf("Sequence %d not found.
      \n", 
                      block->num_sequences+1) ;
               exit(0);
	       }
            }
         string[j] = '\0' ;

         if (block->max_sequences <= block->num_sequences+1) 
            resize_block_sequences(block) ;

	                                            /* process the sequence */

    /* next part adopted from blimps  procedure next_cluster by Bill Alford */
                     /* read the sequence from the string into the Sequence */

         rc = read_sequence(&(block->sequences[block->num_sequences]), 
                            AA_SEQ, 0, string) ; 
				   /* the Sequence, sequence type, starting */
   				   /* position, string with the sequence    */

                                      /* check to see if there was an error */
         if (rc < 0) 
            {
                      /* Error, more residues in the sequence than expected */
            printf("
      Warning
      \n");
            printf("Error reading sequence %d. %d more residues in the sequence than the expected %d.
      \n",
                   block->num_sequences+1, -rc, 
                   block->sequences[block->num_sequences].length) ;
            }
         else if (rc < block->sequences[block->num_sequences].length) 
            {
            if (rc < MIN_BLOCK_LENGTH)
               {
               printf("
      Error
      \n");
               printf("Sequence (%d) is too short (%d). The minimal length is %d.
      \n", 
                      block->num_sequences+1, rc, MIN_BLOCK_LENGTH);
               exit(0);
	       }

          /* Error, not enough residues for the sequence, filling with gaps */
            printf("
      Warning
      \n");
            printf("Error reading sequence %d. It is shorter (%d) than the apparent alignment length. Padding the end of the sequence with gaps.
      \n",
                   block->num_sequences+1, rc);

                                                       /* filling with gaps */
    	    for(j=rc; jsequences[block->num_sequences].length; j++) 
	       block->sequences[block->num_sequences].sequence[j] = 
                                                                 aa_atob['-'];
	    }
         else if (rc > block->sequences[block->num_sequences].length) 
            {
              /* BIG Error, an undocumented return value from read_sequence */
            printf("
      Error
      \n");
            printf("Error reading sequence %d.
      \n", block->num_sequences+1);
            exit(0);            
            } /* else, ret_value == seq.length, OK */

                 /* sequences have no weights give all equal weights of 100 */
         block->sequences[block->num_sequences].weight =  100.0 ;

 /* if this is fasta format and it is not the last seq next is a seq header */
         if (is_fasta && SEQS_Ptr->val[i] != '\0') seq_header = TRUE ;

         j = 0 ;
         block->num_sequences++ ;         
         }
      else         /* if end of seq not reached add char to sequence string */
	 {
         string[j++] = SEQS_Ptr->val[i] ;
         }

 /* sequence names */

    if (! (is_fasta)) /* in fasta format sequence names given with sequences*/
    if (no_seq_names) 
       for (i=0; inum_sequences; i++) 
          sprintf(block->sequences[i].name, "%s%d", UNKNOWN_SEQ_NAME, i+1) ;
    else 
       {
       stringlen = (int) strlen(SEQ_NAMES_Ptr->val) ;

/* if the string doesn't end with eol, put one there instead of 
   end-of-string */
       if (SEQ_NAMES_Ptr->val[stringlen-1] != '\n') 
          SEQ_NAMES_Ptr->val[stringlen] = '\n' ;       

       k = 0;
       j = 0 ;

       for (i=0; i<=stringlen; i++)
         if (SEQ_NAMES_Ptr->val[i] != '\n') 
	    {
            if (!isspace(SEQ_NAMES_Ptr->val[i]))
               string[j++] = SEQ_NAMES_Ptr->val[i] ;
            }
         else
	    {
         /* check if this is an "extra" name (with no sequence to attach to) */
            if (k == block->num_sequences) break ;

            if (j==0)
               {
               printf("
      Error
      \n");
               printf("No name found for sequence %d.
      \n", 
                      k+1) ;
               exit(0);
               }

            string[j] = '\0' ;

            if (block->max_sequences <= k) 
               resize_block_sequences(block) ;

                                       /* copy up to first 20 chars of name */
            strncpy(block->sequences[k].name,string,20) ;

            j = 0 ;
            k++ ;         
	    }

                        /* check that number of sequence names is equal to 
                                                       number of sequences */
       if (k != block->num_sequences)
          {
          if (k < block->num_sequences) printf("
      Error
      \n");
          else                          printf("
      Warning
      \n");
          printf("Number of sequence names (%d) is different than number of sequences (%d).
      \n", 
                 k, block->num_sequences) ;
          if (k < block->num_sequences) exit(0);
          }
       }


 /* sequence positions */
 
    if (no_seq_pos) for (i=0; inum_sequences; i++) 
       block->sequences[i].position = UNKNOWN_SEQ_POS ;
    else
       {
       stringlen = (int) strlen(SEQ_POS_Ptr->val) ;

/* if the string doesn't end with eol, put one there instead of 
   end-of-string */
       if (SEQ_POS_Ptr->val[stringlen-1] != '\n') 
          SEQ_POS_Ptr->val[stringlen] = '\n' ;       

       k = 0;
       j = 0 ;

       for (i=0; i<=stringlen; i++)
         if (SEQ_POS_Ptr->val[i] != '\n') 
	    {
            if (isalnum(SEQ_POS_Ptr->val[i]))
                string[j++] = SEQ_POS_Ptr->val[i] ;
            }
         else
	    {
  /* check if this is an "extra" position (with no sequence to attach to) */
            if (k == block->num_sequences) break ;

            if (j==0)
               {
               printf("
      Error
      \n");
               printf("No start position found for sequence %d.
      \n", 
                      k+1) ;
               exit(0);
               }
            string[j] = '\0' ;

            if (block->max_sequences <= k+1) resize_block_sequences(block) ;

            block->sequences[k].position = atoi(string) ;

            j = 0 ;
            k++ ;         
	    }

                /* check that number of sequence start positions is equal to 
                   number of sequences */
       if (k != block->num_sequences)
          {
          if (k < block->num_sequences) printf("
      Error
      \n");
          else                          printf("
      Warning
      \n");
          printf("Number of sequence start positions (%d) is different than number of sequences (%d).
      \n", 
                 k, block->num_sequences) ;
          if (k < block->num_sequences) exit(0);
          }
       }

                       /* check that actual number of sequences is equal to 
                          what the user gave */
    if (MA_SEQS_Ptr->val[0] != NULL && 
        block->num_sequences != atoi (MA_SEQS_Ptr->val))
       {
       printf("
      Warning
      \n");
       printf("The number of sequences you gave (%s) is different from the number found (%d).
      \n", 
              MA_SEQS_Ptr->val, block->num_sequences);
       }

          /* assign the sequences to the cluster (space has been allocated) */

    block->clusters[0].num_sequences = block->num_sequences ;

    block->clusters[0].sequences = &(block->sequences[0]) ;

 /* get block header data */

    if (ID_Ptr->val[0] == NULL) 
       strcpy(block->id, "None") ;
    else
       strncpy(block->id,ID_Ptr->val, SMALL_BUFF_LENGTH) ;

    strcat(block->id, "; BLOCK") ;


    if (AC_Ptr->val[0] == NULL) 
    {
       strncpy(block->number, block->sequences[0].name, MAXAC) ;
    }
    else
    { strcpy(block->number,AC_Ptr->val) ;   }
    block->number[MAXAC] = '\0';
    if (strlen(block->number) < MINAC)
    {
       for (i=strlen(block->number); i< MINAC; i++) block->number[i] = 'x';
       block->number[MINAC] = '\0';
    }
    for (i=0; inumber); i++)
    {
       if (!isalnum(block->number[i])) block->number[i] = 'x';
    }

    strcpy(block->ac,block->number) ;

    if (MIN_DIST_Ptr->val[0] == NULL) 
       {
       j = 10000 ;
       for(i=0; inum_sequences; i++) 
         if (block->sequences[i].position < j) j = block->sequences[i].position ;
       }
    else j = atoi(MIN_DIST_Ptr->val) ;

    sprintf(block->ac, "%s; distance from previous block = (%d",
            block->ac, j) ;


    if (MAX_DIST_Ptr->val[0] == NULL) 
       {
       j = 0 ;
       for(i=0; inum_sequences; i++) 
         if (block->sequences[i].position > j) j = block->sequences[i].position ;
       }
    else j = atoi(MAX_DIST_Ptr->val) ;

    sprintf(block->ac, "%s,%d)",
            block->ac, j) ;
  
    if (DE_Ptr->val[0] == NULL) 
       strcpy(block->de, "None") ;
    else
       strncpy(block->de,DE_Ptr->val, SMALL_BUFF_LENGTH) ;

    if (MA_METH_Ptr->val[0] != NULL) 
       strncpy(block->bl,MA_METH_Ptr->val, SMALL_BUFF_LENGTH-25) ;
    else
       strcpy(block->bl,"Method unspecified") ;

    sprintf(block->bl, "%s; width=%d; seqs=%d;",
            block->bl, block->width, block->num_sequences) ;

    block->motif[0] = '\0';
    block->percentile = 0 ;
    block->strength = 0 ;

    /* open up the block file to write to */
    bfp = fopen(Block_fileNW, "w");

    output_block(block, bfp) ;
      
    free_block(block) ;
    fclose(bfp);
      
} 
  
void weight_block()
{

  sprintf(buf, "%s %s %s %s %s > /dev/null", 
         Blweight, Block_fileNW, Block_file, Weight_type, Weight_scale); 

  if (system(buf)) 
    {
    printf("
      Error
      \n");
    printf("An error occured weighting the block.\n");
    printf("Please try again at a later time.\n");
    printf("If it fails again contact the maintainer of these pages\n");
    printf("and describe what caused the problem with an example.
      \n");

    clean_temp_files() ;

    exit(0);
    }
}


void display_output()
{

  FILE  *bfp ;
  Block *block;

  printf("Block Formatter output\n");
  printf("
      Block Formatter output
      \n");

  printf("Sequences weighted by") ;
  switch (Weight_type[0])
     {
     case 'P' :
        printf(" position-based weights") ;
        break ;
     case 'V' :
        printf(" Voronoi weights") ;
        break ;
     case 'A' :
        printf(" Vingron & Argos weights") ;
        break ;
     case 'C' :
        printf(" %% clustering") ;
        break ;
     }

   printf(". The weights were scaled to 1-100, 100 having most weight.
      \n") ;

   if (btest_flag)
   {
      printf("[block logo",
          Block_file) ;
      printf(" (GIF image)]") ;
      printf(" [block PSSM",
          Block_file) ;
      printf(" (what is a PSSM)]") ;
   }
   else
   {
      printf("[block logo",
          Block_file) ;
      printf(" (GIF image)]") ;
      printf(" [block PSSM",
          Block_file) ;
      printf(" (what is a PSSM)]") ;
   }

   printf("
      \n") ;

    /* open up the block file */
   bfp = fopen(Block_file, "r");

   block = read_a_block(bfp) ;

   printf("
      ");
   output_block(block, stdout) ;
   printf("
      ");

   free_block(block) ;
   fclose(bfp);

}


void main(int argc, char *argv[]) {

  printf("Content-type: text/html\n\n\n");


  if(strcmp(getenv("REQUEST_METHOD"),"POST")) {
    printf("This script should be referenced with a METHOD of POST.\n");
    printf("If you don't understand this, see this ");
    printf("forms overview.%c",10);

    printf("
      What could have happened is that you just reloaded this page rather than redoing the search.\n");

    printf("
      If you use NETSCAPE it has a tendency to try to reload a page when you go back to it.  This may be why you have this error.\n");

    exit(1);
  }

  if(strcmp(getenv("CONTENT_TYPE"),"application/x-www-form-urlencoded")) {
    printf("This script can only be used to decode form results. \n");
    exit(1);
  }

  /*    Set file permissions to "rw-rw----"     */
  system("umask 006");

  read_startup_info();

  parse();

  make_block();
  
  weight_block();
  
  display_output(); 

  clean_temp_files() ;

  exit(0) ;
}

r, an undocumented return value from read_sequence */
            printf("
      Error
      \n");
            printf("Error reading sequence %d.
      \n", block->num_sequences+1);
            exit(0);            
            } /* else, ret_value == seq.length, OK */

                 /* sequences have no weights give all equal weights of 100 */
         block->sequences[block->num_sequences].weight =  100.0 ;

 /* if this is fasta format and it is not the last seq next is a seq header */
         if (is_fastablimps-3.9/blimps/gcode.c000064400001460000012000000132660774312250000156710ustar00jorjastaff00000400000027/* (C) Copyright 1993-9, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* gcode.c: Functions for the translation of nucleotides to amino acids */
/* Modified by: Bill Alford */
/* Change log information is at the end of the file. */

#include 
#include 
#include 


/* -----------------------   initialize a genetic code   -------------------*/
void
init_gcode(gp, xltab, rcxltab)
    GeneticCodePtr  gp;
    register unsigned char   xltab[64], rcxltab[64];
{
    register char   *code;
    register int    i, j, k, tot;
    /* gctrans -- used to translate from the binary alphabet used in ntbet.h
    into a binary alphabet appropriate for the GeneticCode strings */
    static unsigned char    gctrans[] = { '\003', '\001', '\000', '\002' };

    code = gp->code;

    for (i=0; i<4; ++i) {
        for (j=0; j<4; ++j) {
            for (k=0; k<4; ++k, ++code) {
                tot = gctrans[i]*4*4 + gctrans[j]*4 + gctrans[k];
                xltab[tot] = aa_atob[*code];
                tot = (3-gctrans[i])*4*4 + (3-gctrans[j])*4 + (3-gctrans[k]);
                rcxltab[tot] = aa_atob[*code];
            }
        }
    }    

	return;
}



/*
codon2aa

Translate 3 binary-encoded nucleotides (n1, n2, and n3) into a binary
amino acid in the specified genetic code.
*/
unsigned char
codon2aa(gcode, n1, n2, n3)
    unsigned char   *gcode;
    unsigned    n1, n2, n3;
{
    if (n1 < 4 && n2 < 4 && n3 < 4)
        return gcode[n1*4*4 + n2*4 + n3];

    if (n1 >= NUCID_MAX || n2 >= NUCID_MAX || n3 >= NUCID_MAX)
        return (unsigned char)aa_atob[UNKNOWN_AA_CHR];

    {
        unsigned char   aa;
        unsigned char   b1, b2, b3;
        int i1, i2, i3;

        b1 = nt_bdegen[n1].list[0];
        b2 = nt_bdegen[n2].list[0];
        b3 = nt_bdegen[n3].list[0];
        aa = gcode[b1*4*4 + b2*4 + b3];

        for (i1=0; i1 < nt_bdegen[n1].ndegen; ++i1) {
            b1 = nt_bdegen[n1].list[i1]*4*4;
            for (i2=0; i2 < nt_bdegen[n2].ndegen; ++i2) {
                b2 = b1 + nt_bdegen[n2].list[i2]*4;
                for (i3=0; i3 < nt_bdegen[n3].ndegen; ++i3) {
                    b3 = nt_bdegen[n3].list[i3];
                    if (gcode[b2 + b3] != aa)
                        return (unsigned char)aa_atob[UNKNOWN_AA_CHR];
                }
            }    
        }
        return aa;
    }
/*NOTREACHED*/
}   /* end of codon2aa */


/*
aa2codon

Translate a single binary-encoded amino acid into 3 binary-encoded
nucleotides (n1, n2, and n3)
Note:  Could add translation tables to gcode.h
	The translations here are simplified to one degenerate codon per aa
	and therefore not quite correct for:
	Arg (R) = CGT, CGC, CGA, CGG; AGA, AGG = CGN or AGR
	Leu (L) = CTT, CTC, CTA, CTG; TTA, TTG = CTN or TTR
	Ser (S) = TCT, TCC, TCA, TCG; AGT, AGC = TCN or AGY
*/
void aa2codon(aa, n1, n2, n3)
Residue aa, *n1, *n2, *n3;
{
	switch (aa)
	{
	case 0: /*  -  => --- */
		{ *n1 = *n2 = *n3 = nt_atob['-']; }
	break;
	case 1: /*  A  => GCN */
		{ *n1 = nt_atob['G']; *n2 = nt_atob['C']; *n3 = nt_atob['N']; }
	break;
	case 2: /*  R  => MGN */
		{ *n1 = nt_atob['M']; *n2 = nt_atob['G']; *n3 = nt_atob['N']; }
	break;
	case 3: /*  N  => AAY */
		{ *n1 = nt_atob['A']; *n2 = nt_atob['A']; *n3 = nt_atob['Y']; }
	break;
	case 4: /*  D  => GAY */
		{ *n1 = nt_atob['G']; *n2 = nt_atob['A']; *n3 = nt_atob['Y']; }
	break;
	case 5: /*  C  => UGY */
		{ *n1 = nt_atob['U']; *n2 = nt_atob['G']; *n3 = nt_atob['Y']; }
	break;
	case 6: /*  Q  => CAR */
		{ *n1 = nt_atob['C']; *n2 = nt_atob['A']; *n3 = nt_atob['R']; }
	break;
	case 7: /*  E  => GAR */
		{ *n1 = nt_atob['G']; *n2 = nt_atob['A']; *n3 = nt_atob['R']; }
	break;
	case 8: /*  G  => GGN */
		{ *n1 = nt_atob['G']; *n2 = nt_atob['G']; *n3 = nt_atob['N']; }
	break;
	case 9: /*  H  => CAY */
		{ *n1 = nt_atob['C']; *n2 = nt_atob['A']; *n3 = nt_atob['Y']; }
	break;
	case 10: /*  I  => ATH */
		{ *n1 = nt_atob['A']; *n2 = nt_atob['T']; *n3 = nt_atob['H']; }
	break;
	case 11: /*  L  => YTN */
		{ *n1 = nt_atob['Y']; *n2 = nt_atob['T']; *n3 = nt_atob['N']; }
	break;
	case 12: /*  K  => AAR */
		{ *n1 = nt_atob['A']; *n2 = nt_atob['A']; *n3 = nt_atob['R']; }
	break;
	case 13: /*  M  => ATG */
		{ *n1 = nt_atob['A']; *n2 = nt_atob['T']; *n3 = nt_atob['G']; }
	break;
	case 14: /*  F  => TTY */
		{ *n1 = nt_atob['T']; *n2 = nt_atob['T']; *n3 = nt_atob['Y']; }
	break;
	case 15: /*  P  => CCN */
		{ *n1 = nt_atob['C']; *n2 = nt_atob['C']; *n3 = nt_atob['N']; }
	break;
	case 16: /*  S  => WSN */
		{ *n1 = nt_atob['W']; *n2 = nt_atob['S']; *n3 = nt_atob['N']; }
	break;
	case 17: /*  T  => ACN */
		{ *n1 = nt_atob['A']; *n2 = nt_atob['C']; *n3 = nt_atob['N']; }
	break;
	case 18: /*  W  => TGG */
		{ *n1 = nt_atob['T']; *n2 = nt_atob['G']; *n3 = nt_atob['G']; }
	break;
	case 19: /*  Y  => TAY */
		{ *n1 = nt_atob['T']; *n2 = nt_atob['A']; *n3 = nt_atob['Y']; }
	break;
	case 20: /*  V  => GTN */
		{ *n1 = nt_atob['G']; *n2 = nt_atob['T']; *n3 = nt_atob['N']; }
	break;
	case 21: /*  B (D or N)  => RAY */
		{ *n1 = nt_atob['R']; *n2 = nt_atob['A']; *n3 = nt_atob['Y']; }
	break;
	case 22: /*  Z (E or Q)  => SAR */
		{ *n1 = nt_atob['S']; *n2 = nt_atob['A']; *n3 = nt_atob['R']; }
	break;
	case 23: /*  X => NNN  */
		{ *n1 = nt_atob['N']; *n2 = nt_atob['N']; *n3 = nt_atob['N']; }
	break;
	case 24: /*  * => TRR  (stop) */
		{ *n1 = nt_atob['T']; *n2 = nt_atob['R']; *n3 = nt_atob['R']; }
	break;
	default: /*  Unknown */
		{ *n1 = nt_atob['N']; *n2 = nt_atob['N']; *n3 = nt_atob['N']; }
	break;
	}
}   /*  end of aa2codon  */


/* Change log information follows. */
/* Changes since Blimps Version 3.1:
 * 1/19/1997 Added aa2codon() routine.
 * 
 */

blimps-3.9/blimps/frequency.c000064400001460000012000000206720774312250000166100ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* frequency.c: amino acid frequency information  */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

/*	system headers not in global.h */
/*	blimps library headers */
#include 
#include 	/* includes sequences.h for NA_SEQ */
#include 	/* includes pattern.h */
#include 
#include 	/* For Qij stuff */
#include 
#include 

/*
 * Exported variables and data structures
 */

double frequency[MATRIX_AA_WIDTH];
double Codon_Usage[64];


/*
 * Local variables and data structures
 */




/*
 * Function definitions
 */

static double read_freq();

/*
 * Frequency file related functions
 *
 *   Boolean load_aa_frequencies()
 *   static double read_freq(ffp)
 *
 */

/*
 * load_frequencies
 *   reads in the frequencies if there is a frequency file.
 *   puts them in global array frequency[]
 *   Parameters:
 *     char *fname: The frequency file filename
 *   Return codes: TRUE if there was a frequency file and the data was 
 *                 sucessfully read in, FALSE if not.
 *   Error codes: none
 */

Boolean load_frequencies(fname)
     char *fname;		/* the frequency file filename */
{
  int i;
  FILE *ffp;			/* the frequency file pointer */
  double J_weight, O_weight, U_weight;

  ffp = fopen(fname, "r");

  if (ffp == NULL) {
    sprintf(ErrorBuffer, "load_frequencies: Unable to open frequency file: %s", 
	    fname);
    ErrorReport(WARNING_ERR_LVL);
/*
    sprintf(ErrorBuffer, 
	    "load_frequencies: Setting all frequencies to one.");
    ErrorReport(SERIOUS_ERR_LVL);
*/
    for(i=0; i>>>> Need to check that frqname & qijname actually exist;
	for WWW servers would be better to check in current
	directory first  <<<<<<*/
   }
   else
   {
      sprintf(frqname, "default.amino.frq");
      sprintf(qijname, "default.qij");
   }
   load_frequencies(frqname);		/* creates frequency[]  */
   Qij = NULL;
   if ( (fqij=fopen(qijname, "r")) != NULL)
   { Qij = load_qij(fqij); fclose(fqij);  }
   RTot = LOCAL_QIJ_RTOT;
/*
   Matrix *matrix = block_to_matrix(Block *block, 3);
*/
}  /* end of frq_qij */

/* Change log information follows. */
/* 
 * Changes since 3.5:
   7/29/02  Modified error messages
 * Changes since 3.2:
   2/11/99  Added frq_qij()  JGH
 * Changes since 3.1:
   2/14/97  Added load_codons()  JGH
 */

blimps-3.9/blimps/htmlize-LAMA.c000064400001460000012000000136420775576037000170120ustar00jorjastaff00000400000027/*  Copyright 1999-2003 Fred Hutchinson Cancer Research Center
	htmlize-LAMA.c

   This program will insert html links in LAMA output.
   Input - query blocks file name, target blocks file name, 
   LAMA output file name (default stdin), output file (default stdout) 

   Jan 97 - added link to "show_block_alignment", made use of icons. SP
   2/7/97 Check for btest in script name rather than using hard-coded names.JGH
   6/20/99 Renamed (used to be htmlink_LAMA-out) & updated for Blimps 3.2.6 &
	   for longer sequence names (10->18 chars).
*/

#include 
#include 


#define TRUE 1
#define FALSE 0

#define MAXLINELEN 1000
#define SMALLBUFF   200

#define HELP_ICON "?"
#define LOGOS_ICON "\"Logos\""
#define ALIGNMENT_ICON "\"alignment\""

  /* specific strings in score lines of lama output files. 
     Used for identifying score lines. */
#define SCORELINESTR1 " : "
#define SCORELINESTR2 ") score "

void dehtmlize_str() ;

/*
 * main
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE   *inpf, *outf ;
  char   inpfname[MAXLINELEN], outfname[MAXLINELEN] ;
  char   readline[MAXLINELEN], prcssdline[MAXLINELEN] ;
  char   Qfname[MAXLINELEN], Tfname[MAXLINELEN] ;
  char   link_string1[SMALLBUFF], link_string2[SMALLBUFF], link_string3[SMALLBUFF] ;
  char   help_icon[SMALLBUFF], logos_icon[SMALLBUFF], alignment_icon[SMALLBUFF] ;
  char   block1[SMALLBUFF], block2[SMALLBUFF], *ptr, *script;
  int    pos_blk1, pos_blk2, algnmnt_len ;

   script = getenv("SCRIPT_NAME");
 
/* ------------ 1st arg = Query blocks file name ----------------------------*/
   if (argc > 1)
      strncpy(Qfname, argv[1], MAXLINELEN);
   else
      {
      fprintf(stderr, "%s query_blocks_file_name target_blocks_file_name LAMA_output_file_name\n",
             argv[0]) ;
      exit(-1) ;
      }

/* ------------ 2nd arg = Target blocks file name --------------------------*/
   if (argc > 2)
      strncpy(Tfname, argv[2], MAXLINELEN);
   else
      {
      fprintf(stderr, "%s query_blocks_file_name target_blocks_file_name LAMA_output_file_name\n",
             argv[0]) ;
      exit(-1) ;
      }

/* ------------ 3rd optional arg = output file ---------------------------*/
   if (argc > 3 && argv[3][0] != '-')
      {
      strncpy(inpfname, argv[3], MAXLINELEN);
      if ( (inpf=fopen(inpfname, "r")) == NULL)
         {
         fprintf(stderr, "Program %s cannot open input file %s\n", 
                argv[0], inpfname);
         exit(-3);
         }
      }
   else inpf = stdin ;

/*
   if (argc > 3)
      strncpy(inpfname, argv[3], MAXLINELEN);
   else
      {
      fprintf(stderr, "%s query_blocks_file_name target_blocks_file_name LAMA_output_file_name\n",
             argv[0]) ;
      exit(-1) ;
      }

   if ( (inpf=fopen(inpfname, "r")) == NULL)
      {
      fprintf(stderr, "Program %s cannot open input file %s\n", 
              argv[0], inpfname);
      exit(-2);
      }
*/

/* ------------ 4th optional arg = output file ---------------------------*/
   if (argc > 4 && argv[4][0] != '-')
      {
      strncpy(outfname, argv[4], MAXLINELEN);
      if ( (outf=fopen(outfname, "w")) == NULL)
         {
         fprintf(stderr, "Program %s cannot open output file %s\n", 
                argv[0], outfname);
         exit(-3);
         }
      }
   else outf = stdout ;

   if (strstr(script, "btest")) {
       sprintf(link_string1, "");
     }
   else  {
       sprintf(link_string3, "");
     }

   strcpy(help_icon, HELP_ICON) ;
   strcpy(logos_icon, LOGOS_ICON) ;
   strcpy(alignment_icon, ALIGNMENT_ICON) ;

/* loop through all the input file lines */

   while ((fgets(readline, MAXLINELEN, inpf)) != NULL)
      {
                                           /* copy line without html code */
      dehtmlize_str(readline,prcssdline) ;

                                      /* identify if line is a score line */
      if (strstr(prcssdline,SCORELINESTR1) != NULL &&
          strstr(prcssdline,SCORELINESTR2) != NULL)
	 {
         sscanf(prcssdline, "%s %d %*c %*d %*s %s %d %*c %*d %*c%d ", 
               block1, &pos_blk1, block2, &pos_blk2, &algnmnt_len) ;

                                                        /* get rid of EOL */
         if ((ptr=strchr(readline,'\n')) != NULL) *ptr = '\0' ;
 
         fprintf(outf, "%s [%s%s+%s+%d+%s+%s+%d+%d\">%s \
%s%s+%s+%d+%s+%s+%d+%d\">%s%s%s]\n", 
                readline, 
                link_string1,
                Qfname, block1, pos_blk1, 
                Tfname, block2, pos_blk2, algnmnt_len,
                alignment_icon,
                link_string2,
                Qfname, block1, pos_blk1, 
                Tfname, block2, pos_blk2, algnmnt_len,
                logos_icon,
                link_string3,
                help_icon) ;
         }
      else
         fprintf(outf,"%s", readline) ;
      }

   fclose(inpf) ;
   fclose(outf) ;

   exit(0);

}  /* end of main */



/* remove html code (anything bounded by '<' and '>' and the '<' + '>' 
   themselves */

void dehtmlize_str(instr,outstr) 

char instr[], outstr[] ;

{
   int i1, i2, htmlcode ;

   htmlcode = FALSE ;

   for(i1=0, i2=0; instr[i1] != '\0'; i1++)
      if (htmlcode)
	 {
         if (instr[i1] == '>') htmlcode = FALSE ;
         }
      else
	 {
         if (instr[i1] != '<') outstr[i2++] = instr[i1] ;
         else htmlcode = TRUE ;
         }

   outstr[i2] = '\0' ;

   return ;
}
 char   help_icon[SMALLBUFF], logos_icon[SMALLBUFF], alignment_icon[SMALLBUFF] ;
  char   blocblimps-3.9/blimps/htmlize-codehop.c000064400001460000012000000247630776201650700177210ustar00jorjastaff00000400000027/*  COPYRIGHT 1998-2003: Fred Hutchinson Cancer Research Center
      hmtlize-codehop 

Insert html links into codehop output

--------------------------------------------------------------
3/28/98 Changes to match codehop.c
5/ 5/98 Changes per Tim Rose.
1/25/99 Correct spelling
11/28/03 Increased MAXLINE
--------------------------------------------------------------
*/
#include 
#include 
#include 

#define FNAMELEN 80
#define MAXLINE 640
#define NO 0
#define YES 1

/*	List of oligos    */
struct olist {
   int linenum;
   int firstpos, lastpos;
   char line[MAXLINE];
   int extend;		/* clamp needs extension */
   int degen;		/* core degeneracy */
   double ctemp;	/* clamp temperature */
   struct olist *next_olist;
};
/*	List of blocks   */
struct blist {
   int linenum;
   int strand;
   int firstpos, lastpos;
   char name[FNAMELEN];
   char line[MAXLINE];
   struct olist *bolist;
   struct blist *next_blist;
};
struct olist *make_olist();
struct blist *make_blist();
void insert_blist();
void insert_oend();
void insert_ohead();
void condense();

/*======================================================================*/
void main(argc, argv)
int argc;
char *argv[];
{
   FILE *fin;
   char filename[FNAMELEN], line[MAXLINE], stemp[MAXLINE], *ptr, *ptr1, *ptrt;
   int i, nline, nblock, noligo, blen, olen, verbose;
   struct blist *blist, *bfor, *brev, *bcur;
   struct olist *onew, *ocur;

   if (argc > 1)
   {
      strcpy(filename, argv[1]);
      if ( (fin=fopen(filename, "r")) == NULL)
      {
         printf("\nCannot open file %s\n", filename);
         exit(-1);
      }
   }
   else
   {
      fin=stdin;
   }
   /*-------------------------------------------------------------------*/
   /*  Read through the output and make a list of oligos for each block */
   
   blist = make_blist();
   nline = nblock = noligo = 0;
   verbose = NO;
   while (!feof(fin) && fgets(line, MAXLINE, fin) != NULL)
   {
      nline++;
      if (strncmp(line, "Processing Block", 16) == 0)
      {
         nblock++;
         bfor = make_blist();
         bfor->linenum = nline;
         bfor->strand = 1;
         ptr = strtok(line+16, " \n\r\t");
         strcpy(bfor->name, ptr);
         fgets(line, MAXLINE, fin); nline++;
         strcpy(bfor->line, line);
         bfor->bolist = make_olist();
         insert_blist(blist, bfor);
         bcur = bfor;
      }
      if (strncmp(line, "Processing Complement of Block", 30) == 0)
      {
         nblock++;
         brev = make_blist();
         brev->linenum = nline;
         brev->strand = -1;
         ptr = strtok(line+30, " \n\r\t");
         strcpy(brev->name, ptr);
         strcpy(brev->line, bfor->line);
         brev->bolist = make_olist();
         insert_blist(blist, brev);
         bcur = brev;
      }
      if ((ptr = strstr(line, "degen=")) != NULL)
      {
         noligo++;
         onew = make_olist();
         onew->linenum = nline;
         strcpy(onew->line, line);
         if (strstr(line, "CLAMP NEEDS EXTENSION") != NULL)
         {  
	   onew->extend = YES;
         }
         ptrt = strstr(ptr, "temp=");
         ptr1 = strtok(ptr, " \n\r\t");
         if (ptr1 != NULL) onew->degen = atoi(ptr1+6);
         ptr = strstr(ptrt, "temp=");
         if (ptr != NULL)
         {
            ptr1 = strtok(ptr, "\n\r\t");
            if (ptr1 != NULL) onew->ctemp = atof(ptr1+5);
         }
         /*  Plus oligos are stored backwards, in geographical
             order on the protein */
         if (bcur->strand < 0) insert_oend(bcur->bolist, onew);
         else insert_ohead(bcur->bolist, onew);
      }
      if (strstr(line, "Verbose 1") != NULL) verbose = YES;
   }
   rewind (fin);

   /*-------------------------------------------------------------------*/
   printf("\n");
   printf("CODEHOP Results\n");
   printf("
      CODEHOP Results
      \n");
   printf("
        ");
   printf("
      • Oligo Summary");
   if (!verbose) printf ("   Not all overlapping primers are shown\n");
   else printf("\n");
   printf("
      ");

   /*-------------------------------------------------------------------*/
   /*  Read throught the output again & print is as-is                  */
   nline = 0;
   bcur = blist->next_blist;
   while (!feof(fin) && fgets(line, MAXLINE, fin) != NULL)
   {
      nline++;
      if (bcur != NULL && nline == bcur->linenum)
      {
          printf("
      ");
          if (bcur->strand < 0)
          {
             printf("Complement of Block %s\n",
                  bcur->name, bcur->name);
             if (bcur->bolist->next_olist != NULL)
                printf("Oligos\n", bcur->name);
          }
          else
          {
             printf("Block %s\n",
                  bcur->name, bcur->name);
             if (bcur->bolist->next_olist != NULL)
                printf("Oligos\n", bcur->name);
          }
          printf("
      ");
          bcur = bcur->next_blist;
      }
      /*  Don't want to see the "Processing Block ... " lines     */
      if (strstr(line, "No suggested primers found") != NULL)
      { printf("No suggested primers found.\n"); }
      else if (strstr(line, "Processing ") != NULL) { printf("\n");}
           else if ((ptr=strstr(line, "CLAMP NEEDS EXTENSION")) != NULL)
                {
		   ptr = strtok(line, "*");
		   printf("%s", ptr);
                   printf("*** CLAMP NEEDS EXTENSION\n"); 
                }
                else { printf("%s", line); }
   }
   fclose(fin);

   /*-----------------------------------------------------------------*/
   /*  Now condense the oligos    */
   condense(blist);

   printf("
      Oligos
      ");
   printf("Degenerate alphabet\n");

   bcur = blist->next_blist;
   while (bcur != NULL)
   {
      if (bcur->bolist->next_olist != NULL)
      {
         if (bcur->strand < 0)
            printf("
      Complement of Block %s
      \n",
              bcur->name, bcur->name);
         else
            printf("
      Block %s
      \n", 
              bcur->name, bcur->name);
         ocur = bcur->bolist->next_olist;
         while (ocur != NULL)
         {
            olen = strcspn(ocur->line + ocur->firstpos, " ");
            blen = strlen(bcur->line + ocur->firstpos);
            if (olen < blen) blen = olen;
            strncpy(stemp, bcur->line + ocur->firstpos, blen);
            stemp[blen] = '\0';
            /*  Print the consensus aas */
            if (bcur->strand < 0) printf("%s\n", stemp);
            else printf("         %s\n", stemp);

            strncpy(stemp, ocur->line + ocur->firstpos, olen);
            stemp[olen] = '\0';
            if (bcur->strand < 0) printf("%s oligo:5'-", stemp);
            else                  printf("oligo:5'-%s-3'", stemp);

            if (bcur->strand < 0)  /*  reverse it */
            {
               for (i=0; idegen, ocur->ctemp);
            if (ocur->extend)
            {
/*
               printf("
      Edit
      \n");
*/
               printf("   Extend clamp\n"); 
            }
            else
            {   printf("\n");  }
            ocur = ocur->next_olist;
         }
      }
      bcur = bcur->next_blist;
   }

   printf("
      \n");
   /*-----------------------------------------------------------------*/
/*
   printf("\nnline=%d, nblock=%d, noligo=%d\n", nline, nblock, noligo);
   printf("\n%d blocks, %d oligos processed\n", nblock, noligo);
*/

   exit(0);
}  /* end of main */
/*=========================================================================*/
struct olist *make_olist()
{
   struct olist *new;

   new = (struct olist *) malloc(sizeof(struct olist));
   new->linenum = new->lastpos = 0;
   new->firstpos = MAXLINE;
   new->line[0] = '\0';
   new->degen = 0; new->ctemp = 0.0;
   new->extend = NO;
   new->next_olist = NULL;
   return(new);
}  /*  end of make_olist  */
/*=========================================================================*/
struct blist *make_blist()
{
   struct blist *new;

   new = (struct blist *) malloc(sizeof(struct blist));
   new->linenum = new->strand = new->lastpos = 0;
   new->firstpos = MAXLINE;
   new->name[0] = '\0';
   new->line[0] = '\0';
   new->bolist = NULL;
   new->next_blist = NULL;
   return(new);
}  /*  end of make_olist  */
/*==========================================================================
     Inserts at end of list: First member of list has no data
==========================================================================*/
void insert_oend(list, new)
struct olist *list, *new;
{
   struct olist *cur;

   cur = list;
   while (cur->next_olist != NULL) cur = cur->next_olist;
   cur->next_olist = new;

}  /* end of insert_oend */
/*==========================================================================
     Inserts at head of list
==========================================================================*/
void insert_ohead(list, new)
struct olist *list, *new;
{
   new->next_olist = list->next_olist;
   list->next_olist = new;

}  /* end of insert_ohead */
/*==========================================================================*/
void insert_blist(list, new)
struct blist *list, *new;
{
   struct blist *cur;

   cur = list;
   while (cur->next_blist != NULL) cur = cur->next_blist;
   cur->next_blist = new;

}  /* end of insert_blist */
/*==========================================================================*/
void condense(blist)
struct blist *blist;
{
   struct blist *bcur;
   struct olist *ocur;

   bcur = blist->next_blist;
   while (bcur != NULL)
   {
      ocur = bcur->bolist->next_olist;
      while (ocur != NULL)
      {
         /*  find the first  & last non-blank character on the line  */
         ocur->firstpos = strspn(ocur->line, " ");
         ocur->lastpos = strlen(ocur->line);
         if (ocur->firstpos < bcur->firstpos) bcur->firstpos = ocur->firstpos;
         if (ocur->lastpos > bcur->lastpos) bcur->lastpos = ocur->lastpos;
         ocur = ocur->next_olist;
      }
      bcur = bcur->next_blist;
   }
}  /*  end of condense  */
list();
     blimps-3.9/blimps/interpro.c000064400001460000012000000400310774312250000164400ustar00jorjastaff00000400000027/*>>>>> dups isn't right; need to make an auxillary file of dups values
somehow; maybe read prosite.dat? <<<<*/
/* Interpro Copyright 2000 Fred Hutchinson Cancer Research Center
   Read an Interpro xml file and make .lis files for protomat

   interpro interpro.xml  [-x]
	Extracts sequence information for one or all entries
	Outputs one .lis file for each entry listing all TP/FN
		sequences - can't determine repeats info?

   Interpro entry is assumed to have this format:
	 => AC
	... => DE
	Domain|Family|Repeat
		Take all types, differences are clear
	
	
		Skip PROFILE, use name from first dbxref as ID 
	
		Take status="T" or "N"
		Could be multiple entries for same sequence:
			PROSITE => repeated domain; use to estimate dups
			PRINTS => multiple domains
	
	
	
		....
	
	

  Output .lis file has this format:
	>AC ;ID;DE;MOTIFJ=[4,npos=T+N,dups,17];$
	pros/
	sptr_ac		PS=T|N DB=ac,ac,ac...
	...

--------------------------------------------------------------------
 2/ 9/00  J. Henikoff
 2/21/00  Added -x option to just make xref file
 3/27/00  Always make xref if all
 3/30/00  Modifications for Interpro 1.0 format
 4/15/00  Try to fix dups (was always 1 for PROSITE!)
 4/16/00  Write interpro.motifj = motifj parameters
 4/17/00  Change AC from IPR to IPB per Rolf's request
====================================================================*/

#define EXTERN
#define MAXNAME 80	/* Maximum file name length */
#define MINWIDTH 10	/* Minimum block width */
#define MAXWIDTH 55	/* Maximum block width */
#define MAXSEQ 1500	/* Maximum number of sequences */
#define MAXKEY 10	/* Max dbkeys per IPR entry */
#define MAXGROUP 2000	/* Max #lines in repeats.dat */

#include 

int get_iprs();
struct db_id *insert_id();
void free_ids();
int read_repeats();
int get_repeats();

/*  Additional info for a struct db_id sequence */
struct db_extra {
	char dbkey[IDLEN];
	int count;			/* #times seq is in dbkey */
};

struct working {
	char ac[MAXAC+1];
	int num;
} Repeats[MAXGROUP];
int NRepeat, MaxRepeat, All, Xonly;

/*=======================================================================*/
int main(argc, argv)
     int argc;
     char *argv[];
{
   FILE *fip, *fxref;
   char iprfile[MAXNAME], xreffile[MAXNAME], iprname[MAXAC];
   int nipr;

   ErrorLevelReport = 4;	/* BLIMPS error level */

   if (argc < 4)
   {
      printf("INTERPRO: Copyright 2000 Fred Hutchinson Cancer Research");
      printf(" Center\nUSAGE: interpro interpro.xml \n");
   }
   /* ------------1st arg = interpro.xml  -------------------------------*/
   if (argc > 1)
      strcpy(iprfile, argv[1]);
   else
   {
      printf("\nEnter name of interpro xml file: ");
      gets(iprfile);
   }
   if ( (fip=fopen(iprfile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", iprfile);
      exit(-1);
   }

   /* ------------2nd arg = entry number -----------------------------------*/
   if (argc > 2)
      strcpy(iprname, argv[2]);
   else
   {
      printf("\nEnter name of interpro entry or all : ");
      gets(iprname);
   }
   if (!strlen(iprname)) strcpy(iprname, "all");
   All = NO;
   if (strcmp(iprname, "all") == 0) All = YES;

   /* ------------3rd arg optionally == -x for xref file only---------------*/
   fxref = NULL; Xonly = NO;
   if (argc > 3 && (strncmp(argv[3], "-x", 2) == 0) )
   {
      Xonly = YES;
   }
   if (Xonly || All)
   {
      strcpy(xreffile, iprfile);
      strcat(xreffile, ".xref");
      fxref = fopen(xreffile, "w");
   }

   /*----------------------------------------------------------------------*/
   NRepeat = read_repeats();		/* repeats.dat in current dir */
   nipr = get_iprs(fip, fxref, iprname);
   fclose(fip);
   printf("%d entries processed from %s\n", nipr, iprname);
   exit(0);
}  /* end of main */

/*========================================================================
========================================================================*/
int get_iprs(fip, fxref, iprname)
FILE *fip, *fxref;
char iprname[MAXNAME];
{
   FILE *flis, *fmot;
   char line[MAXLINE], ac[MAXNAME], id[MAXNAME], de[MAXLINE], *ptr, *ptr1;
   char ctemp[MAXLINE], ctemp1[MAXNAME], fname[MAXNAME], status[MAXNAME];
   char db[MAXKEY+1][MAXNAME], dbkey[MAXKEY+1][MAXNAME];
   struct db_id *ids, *did;
   int i, ndb, maxdb, nipr, nac, nseq, occurs, dups, reps, done, member_flag;
   int maxrep, firstps, nseqps;

   fmot = fopen("interpro.motifj", "w");
   ids = makedbid();
   nipr = nac = nseq = nseqps = firstps = occurs = 0;
   done = NO;
   ac[0] = id[0] = de[0] = '\0';

   /*=====================================================================*/
   while (!done && !feof(fip) && fgets(line, MAXLINE, fip) != NULL)
   {
      if (strstr(line, "\n  */
         nipr++;
         nseq = nseqps = occurs = firstps = ndb = 0;
         member_flag = NO;
         ptr = strtok(line, "\"");
         if (ptr != NULL)
         {
            ptr = strtok(NULL, "\"");
            if (ptr != NULL)
            { 
               strcpy(ac, ptr);
		/* change IPR to IPB */
	       if (strlen(ac) > 3 && ac[2] == 'R') ac[2] = 'B';
               nac++; ndb = 0;
               member_flag = NO;
               if (fxref != NULL)
               {
                  fprintf(fxref, "%s", ac);
               }
               if (strlen(ac) > MAXAC-1) ac[MAXAC-1] = '\0';
               if ( All || (strcmp(iprname, ac) == 0) )
               {
	          sprintf(fname, "%s.lis", ac);
                  flis = fopen(fname, "w");
               }
            }
            else printf("ERROR no ac found");
         }

         while (!done && !feof(fip) && fgets(line, MAXLINE, fip) != NULL &&
                 strstr(line, "") == NULL )
         {
            if (strstr(line, "") != NULL)
            {
               strcpy(de, ac);
               ptr = strtok(line, "> \t\r\n");
               if (ptr != NULL)
               {
                  ptr = strtok(NULL, "<\t\r\n");
                  if (ptr != NULL) { strcpy(de, ptr); }
                  else  /* look for name on next line  (e.g. IPR002128) */
                  {
printf("%s:   not found\n", ac);
                  }
               }
            }

            /*-------------Database---------------------------------*/
            
            if ( (strstr(line, "") != NULL) )
                   member_flag = YES;
            if ( (strstr(line, "") != NULL) )
                   member_flag = NO;

      /*  */
            if ( member_flag && (strstr(line, " */
              /*  Don't use PROFILE or PREFILE, not reliable  */
              if( (strstr(line, "/") == NULL) &&
                  (strstr(line, "PROSITE") != NULL ||
                   strstr(line, "PRINTS")  != NULL ||
                   strstr(line, "PFAM")    != NULL) )
              {
	       /*  Flag first PROSITE entry, will use it to count dups */
               if (strstr(line, "PROSITE") != NULL)
	       {
			if (!firstps) firstps = 1;
			else firstps = 0;
               }
	       else { firstps = 0; }
               strcpy(ctemp, line);
               ptr = strstr(line, "db=");
               if (ptr != NULL)
               {
                  ptr1 = strtok(ptr,"\"");
                  ptr1 = strtok(NULL,"\"");
                  strcpy(db[ndb], ptr1);
               }
               strcpy(line, ctemp);
               ptr = strstr(line, "dbkey=");
               if (ptr != NULL)
               {
                  ptr1 = strtok(ptr,"\"");
                  ptr1 = strtok(NULL,"\"");
                  strcpy(dbkey[ndb], ptr1);
               }
               ptr = strstr(ctemp, "name=");
               if (ptr != NULL)
               {
                  ptr1 = strtok(ptr,"\"");
                  ptr1 = strtok(NULL,"\"");
                  strcpy(id, ptr1);
               }

               /*--------Sequences for Database--------------------------*/
               /*---A sequence may exist multiple times for same dbxref--*/
/*>>>> sometimes there is no ; need to stop if hit
    or     <<<<*/
               while ( !feof(fip) && fgets(line, MAXLINE, fip) != NULL &&
                       strstr(line, "") == NULL )
               {
                  if (strstr(line, "found)  /* new seq for ac */
                              {
                                 nseq++;
				 if (firstps) nseqps++;
                                 strcpy(did->ps, status);
                                 sprintf(did->info, "%s", dbkey[ndb]);
                                 did->found = YES;
				 did->rank = 1;		/* # of dbkeys */
				 did->score = 0;	/* reps */
                              }
                              else   /* existing seq for ac */
                              {
                                 strcpy(ctemp1, did->info);
                                 if (strstr(ctemp1, dbkey[ndb]) == NULL)
                                 {
                                    sprintf(ctemp1, " %s", dbkey[ndb]);
                                    strcat(did->info, ctemp1);
				    did->rank += 1;	/* # of dbkeys */
                                 }
                              }
/*>>> need to increment did->score = PROSITE repeats here; not so
	easy because there may be multiple PROSITE entries 
        assuming if there is a PROSITE, it's first   
>>>*/
                              if ( (strcmp(db[0], "PROSITE") == 0) &&
				   (strcmp(dbkey[0], dbkey[ndb]) == 0) )
                              {
           			   did->score += 1;   /* maxrep */
                              }
                                 
                           }  /* end of did */
                        }
                     }
                  }
               }  /* end of sequences for dbxref */ 

               if (ndb < MAXKEY) ndb++;
               else printf("Too many dbxref entries for %s\n", ac);
             }
             else
             {
               printf("Skipping %s %s", ac, line);
               while ( !feof(fip) && fgets(line, MAXLINE, fip) != NULL &&
                       strstr(line, "") == NULL &&
                       strstr(line, "") == NULL )
                                ;
             }
            }  /*  end of dbxref   */

         }  /* end of interpro */

         /*-------------Repeats from PROSITE-----------*/
         maxrep = 1; maxdb = 0;
         did = ids->next;
         while (did != NULL)
         {
            if ( did->score > maxrep )  maxrep = did->score;
	    if (did->rank > maxdb) maxdb = did->rank;
            did = did->next;
         }
         /*------------Repeats from repeats.dat---------------------*/
         if (NRepeat > 0)
         {
            for (i=0; i= 0 && (reps+1) < maxrep) maxrep = reps+1;
            }
         }

         /*--------------Output the results---------------------------*/
         dups = occurs - nseq;
	 if (dups < 0) dups = 0;
         if (flis != NULL)
         {
            fprintf(flis, ">%s ;%s;%s;MOTIFJ=[4,%d,%d,17];$\n", 
                 ac, id, de, nseq, dups);
            fprintf(flis, "pros/\n");
            did = ids->next;
            while (did != NULL)
            {
/*  Only print sequences that are true for all dbxrefs 
               if (did->rank == ndb)
*/
               fprintf(flis, "%s\tPS=%s %s\n", did->entry, did->ps, did->info);
               did = did->next;
            }
            fclose(flis);
         }
         free_ids(ids);
         if (fmot != NULL)
         {  fprintf(fmot, "%s %d %d %d\n", ac, nseq, dups, maxrep);  }
         if (fxref != NULL)
         {
            for (i=0; i < ndb; i++) fprintf(fxref, " %s", dbkey[i]);
            fprintf(fxref, " %d %d\n", maxrep, dups);
         }

      }   /*  end of  */

   }   /*  end of fip  */

   fclose(fmot);
   return(nipr);

}  /* end of get_iprs */
/*==========================================================================
 Insert a new sequence in the list of sequences if it's not already there
 The list is sorted by entry (sequence name)
===========================================================================*/
struct db_id *insert_id(seqname, ids)
char seqname[MAXNAME];
struct db_id *ids;
{
   struct db_id *did, *new, *last;
   int insert;

   insert = YES;
   last = ids;
   did = ids->next;
   while (insert && did != NULL && strlen(did->entry) &&
          strcmp(did->entry, seqname) <= 0)
   {
      if (strcmp(seqname, did->entry) == 0)
      {
          insert = NO;
          return(did);
      }
      last = did;
      did = did->next;
   }
   if (insert)
   {
      new = makedbid();
      strcpy(new->entry, seqname);
      new->found = NO;		/* flag => new id */
      /*  insert new in front of did  */
      new->next = did;
      last->next = new;
      if (did != NULL)
      {
         new->prior = did->prior;
         did->prior = new;
      }
      return(new);
   }
   else
   {     return(NULL);    }

}  /* end of insert_id */
/*====================================================================================*/
void free_ids(ids)
struct db_id *ids;
{
   struct db_id *did, *old;

   did = ids->next;
   while (did != NULL)
   {
      old = did;
      did = did->next;
      free(old);
   }
   ids->next = ids->prior = NULL;
} /* end of free_ids  */

/*======================================================================
	Read the repeats.dat file
======================================================================*/
int read_repeats()
{
   int nrep;
   FILE *frep;
   char line[MAXLINE] ;

   nrep = 0;
   MaxRepeat = 0;

   /*   Look in current directory first */
   frep=fopen("repeats.dat", "r");
/*
   if (frep == NULL)
   {
      sprintf(fname, "%srepeats.dat", DatDir);
      frep=fopen(fname, "r");
   }
*/

   if (frep != NULL)
   {
      while (nrep < MAXGROUP && 
             !feof(frep) && fgets(line, MAXLINE, frep) != NULL)
      {
         if (line[0] != '>' && line[0] != '#')
         {
            sscanf(line, "%s %d", Repeats[nrep].ac, &Repeats[nrep].num);
            if (Repeats[nrep].num < 0) Repeats[nrep].num = 0;
            if (Repeats[nrep].num > MaxRepeat) MaxRepeat = Repeats[nrep].num;
            nrep++;
         }
      }
   }
   return(nrep);
}  /* end of read_repeats */
/*=========================================================================
	Look up number of repeats for ac     
	Assuming that absence => no repeats
==========================================================================*/
int get_repeats(fam)
char *fam;
{
   int j;

   j = 0;
   /*   Assumes repeats.dat is sorted by ac     */
   while (j < NRepeat && strcmp(Repeats[j].ac, fam) <= 0) j++;
   if (j > 0 && strcmp(Repeats[j-1].ac, fam) == 0)
	return(Repeats[j-1].num);
   else return(0);
} /* end of get_repeats  */
blimps-3.9/blimps/lisblk.c000064400001460000012000000132100774312250000160550ustar00jorjastaff00000400000027/*=======================================================================
(C) Copyright 1995-2000, Fred Hutchinson Cancer Research Center          
        lisblk.c  reads a .lis file & a .blk file, determines which
	   sequences from .blk are in .lis & writes out a new .lis
	   file with the block sequences flagged to .lsb file in current
	   directory.

	   lisblk  
		   	= file containing list of sequences in
				  PROTOMAT format (.lis or .lst file).
                                  Assumes this file has LENGTH= for
                                  each sequence.
				= block; if "none", looks for a block
				  with same name as  file.
*/
/*-----------------------------------------------------------------------
   8/1/95   J. Henikoff.   From select.c
   6/25/00  Changed to use blimps routines
========================================================================*/
#define EXTERN
#include 

/*------------------Routines here------------------------------*/
int flag_ids();
int write_lis();
/*----------------- Routines from protomat.c---------------------*/
struct db_id *makedbid();
int get_ids();
struct db_id *check_entry();
struct split_name *split_names();

char Pros[FNAMELEN];
char Title[MAXLINE];

/*======================================================================*/
void main(argc, argv)
int argc;
char *argv[];
{
   FILE *flis, *fblk, *fout;
   char blkfile[FNAMELEN], lisfile[FNAMELEN], outfile[FNAMELEN];
   int lisseq, blkseq, i, done, nout;
   struct db_id *ids;
   struct split_name *lissplit;
   Block *block;

   printf("\nLISBLK: (C) Copyright 1995-2000,");
   printf(" Fred Hutchinson Cancer Research Center");

/*------------- arg 1:  .lis file -------------------------------*/
   if (argc > 1)
      strcpy(lisfile, argv[1]);
   else
   {
      printf("\nEnter name of file containing list of sequences: ");
      gets(lisfile);
   }
   if ( (flis=fopen(lisfile, "r")) == NULL)
   {
      printf("\nCannot open file %s", lisfile);
      exit(-1);
   }
   lissplit = split_names(lisfile);
/*------------- arg 2:  .blk file -------------------------------*/
/*   Look for lisfile.blk then lisfileA.blk     */
   fblk = NULL;  blkfile[0] = '\0';
   if (argc > 2)
      strcpy(blkfile, argv[2]);
   else
   {
      printf("\nEnter name of block file: ");
      gets(blkfile);
   }

   if ((fblk=fopen(blkfile, "r")) == NULL)
   {
      done = NO;  i = strlen(blkfile)-1;
      while (!done && i >=0)
      {
         if (blkfile[i] == '.')
         {  blkfile[i] = '\0'; done=YES; }
         i--;
      }
      strcat(blkfile, "A.blk");
      if ((fblk=fopen(blkfile, "r")) == NULL)
      {
	    printf("\nEnter name of block file: ");
	    gets(blkfile);
      }
   }
   if (fblk == NULL)
      if ((fblk=fopen(blkfile, "r")) == NULL)
      {
	 printf("\nCannot open file %s\n", blkfile);
	 exit(-1);
      }
/*---------------  Get the sequences in the .lis file -----------------*/
   ids = makedbid();
   printf("\nReading %s...", lisfile);
/*-------------  First line of extract file may have a title ----------*/
   fgets(Title, MAXLINE, flis);
   if (Title[0] != '>')
   { rewind(flis); Title[0] = '\0'; }
/*------------Second line may have a directory name --------------*/
   Pros[0] = '\0';
   fgets(Pros, MAXLINE, flis);
   if (strstr(Pros, "/") == NULL)
   {  rewind(flis); Pros[0] = '\0'; }

/*>>>>>>> why isn't ids getting updated here <<<<<<<*/
   lisseq = get_ids(flis, ids);
   printf("\n  %d sequences in %s", lisseq, lisfile);
   fclose(flis);

/*--------------- Compare with sequences in the .blk file -------------*/
   printf ("\nReading %s...", blkfile);
   block = read_a_block(fblk);
   if (block != NULL)
   {
       blkseq = flag_ids(block, ids);
       printf(" %d sequences from %s\n  were found in %s\n",
	   blkseq, lisfile, blkfile);
   }
   else
   {
      printf("No block found in %s\n", blkfile);
   }
   fclose(fblk);


/*--------------- Open the new output list file -----------------------*/
/*-----------  Make the .lsb file in the current directory----------*/
   outfile[0] = '\0';
   strncat(outfile, lisfile+lissplit->dir_len, lissplit->name_len);
   outfile[lissplit->name_len] = '\0';
   strcat(outfile, ".lsb");
   if ( (fout=fopen(outfile, "w+t")) == NULL)
   {
      printf("\nCannot open file %s\n", outfile);
      exit(-1);
   }
   if (strlen(Title)) fprintf(fout, "%s", Title);
   if (strlen(Pros))  fprintf(fout, "%s", Pros);
   nout = write_lis(fout, ids);
   printf("%d sequences written to %s\n", nout, outfile);

   fclose(fout);

   printf("\n");
   exit(0);
}  /*  end of main */
/*================================================================*/
int flag_ids(block, ids)
Block *block;
struct db_id *ids;
{
   struct db_id *did;
   int s, nfound;

   nfound = 0;
   for (s=0; s < block->num_sequences; s++)
   {
      did = check_entry(ids, block->sequences[s].name);
      if (did != NULL) did->block = YES;
      nfound++;
   }
   return(nfound);
} /* end of flag_ids */
/*========================================================================
==========================================================================*/
int write_lis(flis, ids)
FILE *flis;
struct db_id *ids;
{
   struct db_id *id;
   int nlis;

   nlis = 0;
   id = ids->next;
   while (id != NULL)
   {
       nlis += 1;
       fprintf(flis, "%-12s", id->entry);
       if (strlen(id->ps)) fprintf(flis, "  PS=%s", id->ps);
       if (id->len > 0 ) fprintf(flis, "  LENGTH=%-6d", id->len);
       if (id->frag)     fprintf(flis, "  FRAGMENT");
       if (id->block)    fprintf(flis, "  BLOCK");
       if (id->lst)      fprintf(flis, "  LST");
       fprintf(flis, "\n");
       id = id->next;
   }
   return(nlis);
}  /* end of write_lis */
blimps-3.9/blimps/lists.c000064400001460000012000000072020774312250000157370ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* lists.c: definitions and functions for various ordered lists */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

/*	system headers not in global.h  */
/*	blimps library headers not in global.h */
#include 
#include 	/* includes sequences.h  */
#ifndef NO_MATRIX
#include 	/* includes pattern.h */
#endif
/*	headers in current directory */
#include "lists.h"
#include "blimps.h"
#ifndef NO_SCORES
#include "scores.h"
#endif


/*
 * Exported variables and data structures
 */

ScoreList    Scores;
ScoreList    PrintScores;
MatrixList   Matrices;
BlockList    Blocks;
SequenceList Sequences;

int MinScoreOfList = -1;	/* the minimum score of the score list */


/*
 * Local variables and data structures
 */


/*
 * Function definitions
 */


/* 
 * initialize_lists
 *   initializes the lists.
 *   Parameters: none
 *   Error codes:
 */

void initialize_lists()
{
#ifndef NO_SCORES
  Scores      = NewSL(score_comparison,     free_score, ALLOW_DUPLICATES);
  PrintScores = NewSL(neg_score_comparison, free_score, ALLOW_DUPLICATES);
#endif
#ifndef NO_MATRIX
  Matrices   = NewSL(matrix_comparison,    NULL, ALLOW_DUPLICATES);
#endif
  Blocks      = NewSL(block_comparison,     NULL, ALLOW_DUPLICATES);
  Sequences   = NewSL(sequence_comparison,  NULL, ALLOW_DUPLICATES);
}




/*
 * Score List functions
 *
 */
#ifndef NO_SCORES

/*
 * insert_in_score_list
 *   Inserts the score entry into the score list and makes sure that the 
 *   number of elements n the list are fewer than the NumberToReport if there
 *   is a limit.
 *   Parameters:
 *     Score score: the score entry.
 *   Return codes: the same as InsertSL.
 *   Error codes: none
 */

int insert_in_score_list(score)
     Score *score;
{
  int ret_value;

  ret_value = InsertSL(Scores, score);
  if (NumberToReport >= 0) {
    DoForSL(Scores, limit_Scores_list_size, NULL);
  }
  return ret_value;
}


/* 
 * limit_Scores_list_size
 *   Used in insert_in_score_list to limit the size of the score list.
 *   Parameters: 
 *     Score *score: the score list entry
 *     void *arg: unused, here to match the procedure call in DoForSL
 *   Return codes: SL_DELETE if the list is too big, SL_QUIT otherwise.
 *   Error codes: none
 */

int limit_Scores_list_size(score, arg)
     Score *score;
     void *arg;  /* not used */
{
/*>>> Seems to cause memory problems?
  if (NumInSL(Scores) > NumberToReport &&
      SavedScoresFlag && score->score > 1000 && NumberToReport < 4990)
  {		NumberToReport += 10;    }
*/

  if (NumInSL(Scores) > NumberToReport) {
    return SL_DELETE;
  }
  else {
    MinScoreOfList = score->score;
    return SL_QUIT; /* done limiting size, stop the DoForSL */
  }
}


/* 
 * enter_score_into_print_scores
 *   Places the score from Scores into PrintScores.  PrintScores is a reverse
 *   ordered list so that the printing comes out with the largest score
 *   first.
 *   Parameters:
 *     Score *score: the score list entry
 *     void *arg: unused, here to match the procedure call in DoForSL
 *   Return code: SL_CONTINUE always.
 *   Error codes: none
 */

int enter_score_into_print_scores(score, arg)
     Score *score;
     void *arg;
{
  InsertSL(PrintScores, score);
  return SL_CONTINUE;
}

#endif








/* Change log information follows. */
/* 
 Changes since version 3.2.5:
 3/3/99 Corrected spelling of Matrices.
        Note: SavedScoresFlag changes to limit_Scores_list_size() were removed,
	      see comments there.
 */
ct to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* lists.c: definitions and functions for various ordered lists */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

/*	system headers not in global.h  */
/*	blimps library headers not in global.h */
#include 
#include 	/* includes sequences.hblimps-3.9/blimps/mablock.c000064400001460000012000000751271054325706000162260ustar00jorjastaff00000400000027/* see mablockprob.in - decides on MSF format now */
/* MABLOCK Copyright 1999-2003 Fred Hutchinson Cancer Research Center
   Read a file of multiple alignmentss in fasta format or clustalw format 
   and carve out blocks at least MinWidth wide. clustalw format alignments
   must have the word "CLUSTAL" on the first non-blank line.
   Recognizes when input file is already in blocks format.

   NOTES: Requires version 3.2.6 or higher of BLIMPS libraries.

   mablock    [ ]
	Puts blocks in output_file.blks & sequences in output_file.seqs
--------------------------------------------------------------------
11/16/97  J. Henikoff
11/25/97  MAXWIDTH of output block = 55
12/26/97  Check input file for blocks format first
12/30/97  Modified insert_blist() if > 26 blocks in list
 1/ 2/98  Modified try_clustal() to look out for lines with asterisks
 3/18/98  Modified find_blocks() to NOT treat B,Z,X as gaps
 5/13/98  Try MSF format.
 1/15/99  Increased MAXLEN for Prodom 99.1
 1/26/99  Edit sequence names for clustalw; 1st 10 chars unique, 
		don't start with P1; (see makelis.c)
 2/16/99  Clustal or CLUSTAL on 1st non-blank line => clustal format
 6/20/99  Longer sequence names
12/17/99  Longer ACs
 1/ 8/01  Wider blocks (MAXWIDTH -> EXTRA_LARGE_BUFF)
 1/ 9/01  Added MaxWidth & output_fasta(), put temp files in output dir
 7/ 5/01  Fix problem with msf format when seq names right-justified
12/18/02  Accomodate "STOCKHOLM" format (like CLUSTAL)
 4/30/03  Read until > (FASTA), CLUSTAL, STOCKHOLM or // (MSF)
 8/19/03  Fix "distance from previous block" format error
12/23/06  Longer sequence names
====================================================================*/

#define EXTERN
#define MAXNAME 80	/* Maximum file name length */
#define MINWIDTH 10	/* Minimum block width */
#define MAXWIDTH 55	/* Maximum block width */
#define MAXSEQ 400	/* Maximum number of sequences */
#define MAXLEN 800	/* Max line length for clustal format */
#define SNAMELEN 20	/* Max sequence name length */

#include 
/*	Tried following for basename() & dirname(), didn't work
#include 
	See /usr/man/man3g/
*/

/*  List of blocks structure:
    First entry has no block, just nblock, nseq, totwidth & minseq,
    other entries in list have pointers to the blocks, minprev & seqprev
*/
struct blocks_list {		/* list of blocks for a family */
   int nblock;				/* number of blocks in family */
   int nseq;				/* number of sequences in blocks */
   int totwidth;			/* total width of blocks in list  */
   int minseq;				/* sequence most like consensus */
   int minprev;				/* min distance from previous block*/
   int seqprev;				/* previous distance for minseq */
   int *consensus;			/* consensus for this block */
   Block *block;
   struct blocks_list *next;
};

struct seqseq {			/* reorder sequences */
   int seq;
   int pos;
};

int try_clustal();
int try_msf();
struct blocks_list *find_blocks();
Block *make_block();
struct blocks_list *make_blist();
void insert_blist();
void free_blist();
void fasta_seqs();
void order_seq();
void fix_names();
void output_blocks();
void output_fasta();

int MinWidth;		/* Minimum block width */
int MaxWidth;		/* Maximum block width */
char OutName[MAXNAME];
char Block_AC[MAXNAME];
char Block_ID[MAXNAME];
char Block_DE[MAXNAME];
double frequency[MATRIX_AA_WIDTH];    /* for frequency.c */

/*=======================================================================*/
/*
 * main
 *   controls flow of program
 *   Parameters: argc, argv
 *   Error codes:
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
   FILE *ifp, *bfp, *sfp;
   Sequence *seqs[MAXSEQ];
   char ctemp[MAXNAME], bdbname[MAXNAME], outtype[10], *ptr;
   int db_type, seq_type, nseq, i, bflag, ftype;
   struct blocks_list *blocks;
   Block *block;

   ErrorLevelReport = 4;	/* BLIMPS error level */

   if (argc < 4)
   {
      printf("MABLOCK: Copyright 2001 Fred Hutchinson Cancer Research");
      printf(" Center\nUSAGE: mablock     \n");
      printf("    = file of fasta or clustal multiple alignments\n");
      printf("             Clustal format must have CLUSTAL on first non-blank line\n");
      printf("      = output file of blocks\n");
      printf("             Puts blocks in out.blks & sequences in out.seqs\n");
      printf("      = output type, B=blocks, F=fasta\n");
      printf("    = minimum ungapped width to define a block\n");
      printf("    = maximum block width\n");
   }
/* ------------1st arg = blocks database -------------------------------*/
   if (argc > 1)
      strcpy(bdbname, argv[1]);
   else
   {
      printf("\nEnter name of blocks database: ");
      gets(bdbname);
   }
   if ( (ifp=fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbname);
      exit(-1);
   }
   /*  should be smarter about this!  */
   strcpy(ctemp, bdbname);
   ptr = strrchr(ctemp, '/'); /* find the last slash */
   if (ptr != NULL) strcpy(Block_AC, ptr); 
   else             strcpy(Block_AC, bdbname); 
   if (strlen(Block_AC) > MAXAC-1)
        Block_AC[MAXAC-1] = '\0';	/* leave one char for A-Z */
   else if (strlen(Block_AC) < MINAC)
   {
      for (i=strlen(Block_AC); i < MINAC; i++) Block_AC[i] = 'x';
      Block_AC[MINAC] = '\0';
   }
   for (i=0; i 2)
      strcpy(OutName, argv[2]);
   else
   {
      printf("\nEnter name of output file: ");
      gets(OutName);
   }
   strcpy(ctemp, OutName); strcat(ctemp, ".blks");
   if ( (bfp=fopen(ctemp, "w")) == NULL)
   {
      printf("\nCannot open file %s\n", ctemp);
      exit(-1);
   }
   strcpy(ctemp, OutName); strcat(ctemp, ".seqs");
   if ( (sfp=fopen(ctemp, "w")) == NULL)
   {
      printf("\nCannot open file %s\n", ctemp);
      exit(-1);
   }
/* ------------3rd arg = output type  -----------------------------------*/
   sprintf(outtype, "B"); ftype = 0;
   if (argc > 3) {  strcpy(outtype, argv[3]);  }
   else
   {
      printf("\nEnter type of output file [B=blocks|F=fasta]: ");
      gets(outtype);
   }
   if (outtype[0] == 'F' || outtype[0] == 'f') ftype = 1;
/* ------------4th arg = optional min trimming size--------------------*/
   MinWidth = MINWIDTH;
   if (argc > 4) MinWidth = atoi(argv[4]);
   if (MinWidth < 4 || MinWidth > EXTRA_LARGE_BUFF)
	 MinWidth = MINWIDTH;

/* ------------5th arg = optional max trimming size---------------------*/
   MaxWidth = MAXWIDTH;
   if (argc > 5) MaxWidth = atoi(argv[5]);
   if (MaxWidth < 3 || MaxWidth > EXTRA_LARGE_BUFF) 
	MaxWidth = MAXWIDTH;

/*=====================================================================*/
   /*  1. Is input already blocks?  2. Is it a file of sequences?
    3. Is it CLUSTAL/STOCKHOLM format? */
   /*-----------------------------------------------------------------*/
   blocks = NULL;
   nseq = 0;
   /*   Check first for input file of blocks */
   bflag = FALSE;
   while ( (block = read_a_block(ifp)) != NULL)
   {
      bflag = TRUE;
      if (blocks == NULL) blocks = make_blist();
      insert_blist(blocks, block);
   /*-----------Now should read blocks to fill seqs[], see code in
          blalign:fasta_seqs()  */
   }

   if (!bflag)
   {
      rewind(ifp);

      /*-----------------------------------------------------------------*/
      /*   Check next for input file of sequences & assume are aligned */
      db_type = type_dbs(ifp, DbInfo);
      /* shouldn't send seq_type_dbs() a negative value of db_type,
	 but need to preserve if for next paragraph */
      seq_type = UNKNOWN_SEQ;
      seq_type = seq_type_dbs(ifp, DbInfo, db_type, seq_type);
      if (seq_type == NA_SEQ)
      {
         printf("WARNING: Sequences appear to be DNA but will be treated");
         printf(" as protein\n");
         seq_type = AA_SEQ;
      }
      rewind(ifp);
   
      /*-----------------------------------------------------------------*/
      /*   First read all the sequences into memory                    */
      if (db_type >= 0)
      {
         while ( nseq < MAXSEQ &&
             (seqs[nseq] = read_a_sequence(ifp, db_type, seq_type)) != NULL)
         {
            nseq++;
         }
      }
      else
      {
         nseq = try_clustal(ifp, seqs);
         if (nseq <= 0)
         {  nseq = try_msf(ifp, seqs);    }
      }
      fix_names(nseq, seqs);

      /*  Now look for ungapped regions in all the sequences  */
      if (nseq > 0)
      {
         /*>>>>> compute an array of column scores first <<<<<*/
         blocks = find_blocks(nseq, seqs);
      }
   }  /*  end of not blocks input */
   fclose(ifp);
  

   /*-----------------------Output results now ----------------------*/
/*
   printf("%s:  %d sequences read, ", OutName, nseq);
*/
   if (nseq == MAXSEQ)
   { printf("WARNING: Maximum number of sequences = %d\n", nseq); }
   if (nseq > 0)
   {
      for (i=0; inblock, MinWidth, MaxWidth );
      printf("Output written to %s.blks and %s.seqs\n", OutName, OutName);
   }
   else
   {
      printf("no blocks found with minimum width %d\n",
              MinWidth );
   }
   fclose(bfp);

   exit(0);

}  /* end of main */
/*========================================================================
	Find ungapped stretches at least MinWidth long in all sequences
        Treating all characters other than the 20 real aas (1-20) and
	B (21), Z (22), X (23) as gaps
	Gap character == '-' (0)
        Arbitrarily ends at block when width reaches MAXWIDTH; need to
        split blocks more elegantly, perhaps based on a column score.
        Means have to pre-compute an array of column scores from seqs[].
========================================================================*/
struct blocks_list *find_blocks(nseq, seqs)
int nseq;
Sequence *seqs[MAXSEQ];
{
   struct blocks_list *blocks;
   Block *block;
   int length, s, pos, spos, width, firstpos;

   blocks = make_blist();

   length = seqs[0]->length;
   for (s=1; slength < length)
      {
         length = seqs[s]->length;
         fprintf(stderr,
             "WARNING: sequence segments are of different lengths\n");
         fprintf(stderr, "%s %d : %s %d\n", 
   	     seqs[0]->name, seqs[0]->length, seqs[s]->name, seqs[s]->length);
       
      }
   }

   width = firstpos = 0;
   for (pos=0; pos < length; pos++)
   {
      spos = 0;
      for (s=0; s< nseq; s++)
         if (seqs[s]->sequence[pos] > 0 &&
             seqs[s]->sequence[pos] < 24 )
               spos++;
      if (spos == nseq) { width++; }
      /*   This pos has a gap, did we find a block ? */
      if ( spos < nseq || (spos == nseq && width == MaxWidth) )
      {
         if (width >= MinWidth)
         /*    Make a block starting at firstpos  */
         {
            block = make_block(width, firstpos, nseq, seqs);
            insert_blist(blocks, block);
         }
         firstpos = pos + 1;
         width = 0;
      }
   } /* end of sequence position */

   /*   Final block may run to end of sequences */
   if (width >= MinWidth)
   /*    Make a block starting at firstpos  */
   {
      block = make_block(width, firstpos, nseq, seqs);
      insert_blist(blocks, block);
   }

   return(blocks);

}  /*  end of find_blocks */
/*========================================================================
 Try clustal format, which has multiple lines per sequence with the
 sequence name in the first 16 columns of each line.
 Writes each set of sequence segments out to a temporary file, then
 reads them back in & appends them to sequence array.
 Assumes each set of segments is separarated by at least one blank line.
 Assumes each line of a set contains the sequence name, whitespace, residues:

CLUSTAL W(1.60) multiple sequence alignment

JC2395          NVSDVNLNK---YIWRTAEKMK---ICDAKKFARQHKIPESKIDEIEHNSPQDAAE----
KPEL_DROME      MAIRLLPLPVRAQLCAHLDAL-----DVWQQLATAVKLYPDQVEQISSQKQRGRS-----
FASA_MOUSE      NASNLSLSK---YIPRIAEDMT---IQEAKKFARENNIKEGKIDEIMHDSIQDTAE----

JC2395          -------------------------QKIQLLQCWYQSHGKT--GACQALIQGLRKANRCD
KPEL_DROME      -------------------------ASNEFLNIWGGQYN----HTVQTLFALFKKLKLHN
FASA_MOUSE      -------------------------QKVQLLLCWYQSHGKS--DAYQDLIKGLKKAECRR

JC2395          IAEEIQAM
KPEL_DROME      AMRLIKDY
FASA_MOUSE      TLDKFQDM

============================================================================*/
int try_clustal(ifp, seqs)
FILE *ifp;
Sequence *seqs[MAXSEQ];
{
   FILE *tmp;
   Sequence *tmp_seq;
   int nseq, this_seq, i, my_pid, db_type, seq_type;
   char line[MAXLEN], tmp_name[MAXNAME], *name, *residues;

   nseq = 0; seqs[0] = NULL;

   /*  Look for the word clustal on the first non-blank line, if find it,
	skip to next non-blank line and begin  */
   while (!feof(ifp) && fgets(line, MAXLEN, ifp) != NULL &&
           strstr(line, "CLUSTAL") == NULL &&
           strstr(line, "STOCKHOLM") == NULL)
		;
   if (strstr(line, "CLUSTAL") == NULL && strstr(line, "Clustal") == NULL &&
       strstr(line, "STOCKHOLM") == NULL && strstr(line, "Stockholm") == NULL)
   {
      rewind(ifp);
      return(nseq);
   }
   else
   {
      fprintf(stderr, "Trying CLUSTAL/STOCKHOLM format.\n");
      fgets(line, MAXLEN, ifp);
   }

   /*  Read sequences until the next blank line, or until a line
       with blanks at the start
	then start over and add to existing sequences, etc.  */
   my_pid = getpid();
   sprintf(tmp_name, "%s.%d", OutName, my_pid);
   tmp=fopen(tmp_name, "w");
   while (!feof(ifp))
   {
      /*   Write a set of sequence segments to a temp file */
      /*  NOTE: Blank lines from netscape can be "^M\n\0", len=3 */
      while (!feof(ifp) && fgets(line, MAXLEN, ifp) != NULL &&
           strlen(line) > (int) 3 )
      {
         if (line[0] != ' ')        /* some lines of asterisks, etc */
         {
            name = strtok(line, " \t");
            residues = strtok(NULL, " \t\r\n");
/*printf("%s %s\n", name, residues); */
            if (tmp != NULL)
            {
               if (name != NULL && residues != NULL)
               {
                   fprintf(tmp, ">%s\n", name);
		   fprintf(tmp, "%s\n", residues);
               }
               else
               {   fprintf(stderr,"ERROR reading Clustal file\n%s", line);  }
            }
         }
      } /* end while */
      /*   Encountered a blank line or eof */
      fclose(tmp);
      if ( (tmp = fopen(tmp_name, "r")) != NULL)
      {
         db_type = type_dbs(tmp, DbInfo);
         seq_type = UNKNOWN_SEQ;
         seq_type = seq_type_dbs(tmp, DbInfo, db_type, seq_type);
         if (seq_type == NA_SEQ)
         {
            printf("WARNING: Sequences appear to be DNA but will be treated");
            printf(" as protein\n");
            seq_type = AA_SEQ;
         }
         if (seqs[0] == NULL)
         {
         /*   initialize sequences */
            nseq = 0;
            if (db_type >= 0)
            {
               while ( nseq < MAXSEQ &&
                   (seqs[nseq] = read_a_sequence(tmp, db_type, seq_type)) != NULL)
               {
                  nseq++;
               }
            }
         }
         else
         /*     add on to existing sequences */
         {
            this_seq = 0;
            if (db_type >= 0)
            {
               while ( this_seq < MAXSEQ &&
                   (tmp_seq = read_a_sequence(tmp, db_type, seq_type)) != NULL)
               {
                  if (seqs[this_seq] != NULL &&
                      strcmp(seqs[this_seq]->name, tmp_seq->name) == 0 )
                  {
                     if ((seqs[this_seq]->length + tmp_seq->length) >
                          seqs[this_seq]->max_length)
                              resize_sequence(seqs[this_seq]);
                     for (i=0; ilength; i++)
                     {
                        seqs[this_seq]->sequence[ seqs[this_seq]->length++ ] =
                          tmp_seq->sequence[i];
                     }
                  }
                  this_seq++;
                  free_sequence(tmp_seq);
               }
            }
         }
         fclose(tmp);
      }
      tmp=fopen(tmp_name, "w");
   }

   sprintf(line, "\\rm %s", tmp_name);
   system(line);

   return(nseq);
}  /*  end of try_clustal   */
/*============================================================================
MSF format:  Comments until alignment begins after "//" line:

//

            1                                                   50
P09254-1    .....KRQED AGYDICVPYN LYLKR..... NEFIKIVLPI IRDWDLQHPS
A37470-1    .TFAPKRDED AGYDIAMPYT AVL....... APGENLHVRL PVAYAADAHA
Q00030-2    DYFAPKRDED AGYDISAQTN ATI....... EPDESYFVEL PIVFSSSNPA
P28892-1    .....KRVED AGYDISAPED ATI....... DPDESHFVDL PIVFANSNPA
P10234-1    .....KREED AGFDIVVRRP VTV.P..... ANGTTVVQPS LRMLHADAGP
CONSENSUS

seq names can be right or left-justified!
============================================================================*/
int try_msf(ifp, seqs)
FILE *ifp;
Sequence *seqs[MAXSEQ];
{
   FILE *tmp;
   Sequence *tmp_seq;
   int nseq, this_seq, i, my_pid, db_type, seq_type, allnumbers;
   char line[MAXLEN], tmp_name[30], *name, *residues;

   nseq = 0; seqs[0] = NULL;
   fprintf(stderr, "Trying  MSF format.\n");

   /*  Look for "//"     */
   while (!feof(ifp) && fgets(line, MAXLEN, ifp) != NULL &&
           strncmp(line, "//", 2) != 0)
		;
   /*  Didn't find "//"  */
   if (feof(ifp)) { rewind(ifp); }

   /*  Read sequences until the next blank line, or until a line
       with blanks at the start
	then start over and add to existing sequences, etc.  */
   /* Have to change this; now seq names are right-justified so */
   my_pid = getpid();
   sprintf(tmp_name, "mablock.%d", my_pid);
   tmp=fopen(tmp_name, "w");
   while (!feof(ifp))
   {
      /*   Write a set of sequence segments to a temp file */
      /*  NOTE: Blank lines from netscape can be "^M\n\0", len=3 */
      while (!feof(ifp) && fgets(line, MAXLEN, ifp) != NULL &&
             line[0] != '\n' && line[0] != '\r' )
      {
         /* some lines of numbers, etc */
         allnumbers = 1; i=0;
         while(allnumbers && i%s\n", name);
		   fprintf(tmp, "%s\n", residues);
               }
               else
               {   fprintf(stderr,"ERROR reading MSF file\n%s", line);  }
            }
         }
      } /* end while */
      /*   Encountered a blank line or eof */
      fclose(tmp);
      if ( (tmp = fopen(tmp_name, "r")) != NULL)
      {
         db_type = type_dbs(tmp, DbInfo);
         seq_type = UNKNOWN_SEQ;
         seq_type = seq_type_dbs(tmp, DbInfo, db_type, seq_type);
         if (seq_type == NA_SEQ)
         {
            printf("WARNING: Sequences appear to be DNA but will be treated");
            printf(" as protein\n");
            seq_type = AA_SEQ;
         }
         if (seqs[0] == NULL)
         {
         /*   initialize sequences */
            nseq = 0;
            if (db_type >= 0)
            {
               while ( nseq < MAXSEQ &&
                   (seqs[nseq] = read_a_sequence(tmp, db_type, seq_type)) != NULL)
               {
                  nseq++;
               }
            }
         }
         else
         /*     add on to existing sequences */
         {
            this_seq = 0;
            if (db_type >= 0)
            {
               while ( this_seq < MAXSEQ &&
                   (tmp_seq = read_a_sequence(tmp, db_type, seq_type)) != NULL)
               {
                  if (seqs[this_seq] != NULL &&
                      strcmp(seqs[this_seq]->name, tmp_seq->name) == 0 )
                  {
                     if ((seqs[this_seq]->length + tmp_seq->length) >
                          seqs[this_seq]->max_length)
                              resize_sequence(seqs[this_seq]);
                     for (i=0; ilength; i++)
                     {
                        seqs[this_seq]->sequence[ seqs[this_seq]->length++ ] =
                          tmp_seq->sequence[i];
                     }
                  }
                  this_seq++;
                  free_sequence(tmp_seq);
               }
            }
         }
         fclose(tmp);
      }
      tmp=fopen(tmp_name, "w");
   }

   sprintf(line, "\\rm %s", tmp_name);
   system(line);

   return(nseq);
}  /*  end of try_msf   */
/*========================================================================
========================================================================*/
Block *make_block(width, firstpos, nseq, seqs)
int width, firstpos, nseq;
Sequence *seqs[MAXSEQ];
{
   Block *block;
   int bpos, spos, s;

   block = new_block(width, nseq);
   
   for (s=0; s < nseq; s++)
   {
      strcpy(block->sequences[s].name, seqs[s]->name);
      block->sequences[s].position = firstpos;
      block->sequences[s].weight = 100.0;
      bpos = 0;
      for (spos = firstpos; spos < firstpos + width; spos++)
          block->sequences[s].sequence[bpos++] = seqs[s]->sequence[spos];
   } /* end of sequence s */

   pb_weights(block);

/*   weights are now fp, re-normalize them so max=100 or output block
	as fp ... */
/*	calibrate block now?
	what about ID, AC, DE?
*/

   return(block);
}  /*  end of make_block */

/*=======================================================================
     routines for a list of blocks
========================================================================*/
struct blocks_list *make_blist()
{
   struct blocks_list *new;
   
   new = (struct blocks_list *) malloc (sizeof(struct blocks_list));
   new->nblock = new->nseq = new->totwidth = new->minprev = 0;
   new->minseq = new->seqprev = 0;
   new->consensus = NULL;
   new->block = NULL;
   new->next = NULL;

   return(new);
}  /* end of make_blist */

void insert_blist(blist, block)
struct blocks_list *blist;
Block *block;
{
   struct blocks_list *cur;
   char ctemp[MAXNAME];
   int i, prev, minprev, maxprev;

   /*------ Accumulate totals in header record ------*/
   blist->nblock += 1;
   blist->nseq = block->num_sequences;
   blist->totwidth += block->width;

   /*--- Insert a new record for the current block at the end of the list ---*/
   cur = blist;
   while (cur->next != NULL)
      cur = cur->next;

   /*------ Fill in some of the block information -------*/
   strcpy(block->id, Block_ID);
   strcpy(block->de, Block_DE);
   strcpy(block->motif, "UNK");
   sprintf(block->bl, "UNK motif; width=%d; seqs=%d;",
          block->width, block->num_sequences);
   strcpy(ctemp, Block_AC);
   if      (blist->nblock ==  1) strcat(ctemp, "A");
   else if (blist->nblock ==  2) strcat(ctemp, "B");
   else if (blist->nblock ==  3) strcat(ctemp, "C");
   else if (blist->nblock ==  4) strcat(ctemp, "D");
   else if (blist->nblock ==  5) strcat(ctemp, "E");
   else if (blist->nblock ==  6) strcat(ctemp, "F");
   else if (blist->nblock ==  7) strcat(ctemp, "G");
   else if (blist->nblock ==  8) strcat(ctemp, "H");
   else if (blist->nblock ==  9) strcat(ctemp, "I");
   else if (blist->nblock == 10) strcat(ctemp, "J");
   else if (blist->nblock == 11) strcat(ctemp, "K");
   else if (blist->nblock == 12) strcat(ctemp, "L");
   else if (blist->nblock == 13) strcat(ctemp, "M");
   else if (blist->nblock == 14) strcat(ctemp, "N");
   else if (blist->nblock == 15) strcat(ctemp, "O");
   else if (blist->nblock == 16) strcat(ctemp, "P");
   else if (blist->nblock == 17) strcat(ctemp, "Q");
   else if (blist->nblock == 18) strcat(ctemp, "R");
   else if (blist->nblock == 19) strcat(ctemp, "S");
   else if (blist->nblock == 20) strcat(ctemp, "T");
   else if (blist->nblock == 21) strcat(ctemp, "U");
   else if (blist->nblock == 22) strcat(ctemp, "V");
   else if (blist->nblock == 23) strcat(ctemp, "W");
   else if (blist->nblock == 24) strcat(ctemp, "X");
   else if (blist->nblock == 25) strcat(ctemp, "Y");
   else if (blist->nblock == 26) strcat(ctemp, "Z");
   else strcat(ctemp, "*");

   minprev = 99999; maxprev = -99999;
   for (i=0; inum_sequences; i++)
   {
      /* NOTE: In general can't assume sequences are in
         same order in all the blocks, but should work
         in this program */
      if (blist->nblock > 1)
         prev = block->sequences[i].position -
             cur->block->sequences[i].position -
             cur->block->width;
      else
         prev = block->sequences[i].position;
      if (prev < minprev) minprev = prev;
      if (prev > maxprev) maxprev = prev;
   }
   if (minprev < 0) minprev = 0;

   sprintf(block->ac, "%s; distance from previous block=(%d,%d)",
           ctemp, minprev, maxprev);

   cur->next = make_blist();
   cur->next->consensus = (int *) malloc(block->width * sizeof(int));
   cur->next->block = block;
   cur->next->minprev = minprev;

}  /* end of insert_blist */

void free_blist(blist)
struct blocks_list *blist;
{
   struct blocks_list *cur, *last;

   cur = last = blist;
   while (cur->next != NULL)
   {
      last = cur;  cur = cur->next;
   }
   if (cur != blist)
   {
      if (cur->consensus != NULL) free(cur->consensus);
      free(cur);
      last->next = NULL;
      free_blist(last);
   }
   else free(blist);

}  /* end of free_blist */
/*==================================================================
      Puts the portion of the sequences in blocks into seqs[] array
====================================================================*/
void fasta_seqs(sseq, blist, seqs)
struct seqseq *sseq;
struct blocks_list *blist;
Sequence *seqs[MAXSEQ];
{
   int nseq, seq, seq1, pos, curpos;
   struct blocks_list *bcur;
   Block *b;

   nseq = blist->nseq;

/*>>>>>>>> See code in try_clustal(): write seqs out & then read them
  back in with read_a_sequence() <<<<<<*/
   for (seq=0; seq < nseq; seq++)
   {
      printf(">%20s          from blocks\n",
              blist->next->block->sequences[seq].name);
      curpos = 0;
      bcur = blist->next;
      while (bcur != NULL && bcur->block != NULL)
      {
         b = bcur->block;
         order_seq(sseq, blist->next->block, b);
         seq1 = sseq[seq].seq;
         printf("%5d ", b->sequences[seq1].position);
         for (pos=0; pos < b->width; pos++)
            printf("%c", aa_btoa[b->residues[seq1][pos]]);
         printf("\n");
         bcur = bcur->next;
      } /* end of blocks */
   }   /*  end of a sequence  */
}   /* end of fasta_seqs */
/*=======================================================================*/
/*  Sequences may not be in the same order both blocks. If not, then
    set sseq[s1] = s2  where
    b1->sequences[s1].name == b2->sequences[s2].name
=========================================================================*/
void order_seq(sseq, b1, b2)
struct seqseq *sseq;
Block *b1, *b2;
{
   int nseq, i1, i2;

   nseq = b1->num_sequences;
   if (b2->num_sequences < nseq) nseq = b2->num_sequences;
   for (i1 = 0; i1 < nseq; i1++)
   {
      if (b1 == b2) sseq[i1].seq = i1;
      else
      {
         sseq[i1].seq = -1;
         i2 = 0;
         while (sseq[i1].seq < 0 && i2 < nseq)
         {
            if (strcmp(b1->sequences[i1].name, b2->sequences[i2].name) == 0)
               sseq[i1].seq = i2;
            i2++;
         }
      }
   }
}  /*  end of order_seq */
/*======================================================================
   Fix up the sequence names
=======================================================================*/
void fix_names(nseq, seqs)
int nseq;
Sequence *seqs[MAXSEQ];
{
  Boolean done;
  int i, s, len, mlen;
  char ctemp[80];

  for (s=0; s < nseq; s++)
  {
    /*   Get rid of leading "P1;"    */
    if (strncmp(seqs[s]->name, "P1;", 3) == 0)
    {
        if ((int) strlen(seqs[s]->name) > 15) seqs[s]->name[15] = '\0';
        strcpy(ctemp, seqs[s]->name);
        strcpy(seqs[s]->name, ctemp+3);
    }
    if ((int) strlen(seqs[s]->name) > SNAMELEN)
        seqs[s]->name[SNAMELEN] = '\0';	/* ensure ony 20 characters long */

    /*  Check for duplicate sequence names here */
    i = s-1; done = FALSE;
    while (!done && i >= 0)
    {
       if (strcmp(seqs[s]->name, seqs[i]->name) == 0)
       {
          printf("Non-unique sequence name: %s\n", seqs[s]->name);
/*
          printf("First 20 characters of sequence name must be unique.\n");
*/
          strcpy(ctemp, seqs[s]->name);
          len = strlen(seqs[s]->name);
          mlen = 9 - (int) log10((double) s);	/* #digits in s*/
          if (len > mlen) ctemp[mlen] = '\0';
          sprintf(seqs[s]->name, "%s%d", ctemp, s);
          seqs[s]->name[SNAMELEN] = '\0';
          printf("Modified name to %s\n", seqs[s]->name);
          done = TRUE;
      } /* end of non-unique name */
      i--;
    }
  }  /* end of for s */
}  /*  end of fix_names */
/*==========================================================================
	Output blocks in blocks format
==========================================================================*/
void output_blocks(blocks, bfp)
struct blocks_list *blocks;
FILE *bfp;
{
   struct blocks_list *bcur;

   if (blocks != NULL)
   {
      bcur = blocks;
      while (bcur->next != NULL)
      {
             /* Have to make weights integer to use INT_OUTPUT  */
             output_block_s(bcur->next->block, bfp, FLOAT_OUTPUT);
          bcur = bcur->next;
      }
   }

}   /* end of output_blocks */
/*==========================================================================
	Output blocks in fasta format
==========================================================================*/
void output_fasta(blocks, bfp)
struct blocks_list *blocks;
FILE *bfp;
{
   struct blocks_list *bcur;
   Block *block;
   int seq, pos, nout;

   if (blocks != NULL)
   {
      for (seq = 0; seq < blocks->nseq; seq++)
      {
         nout = 0;
         bcur = blocks;
         while (bcur->next != NULL)
         {
            block = bcur->next->block;
            if (nout == 0)
            {
               fprintf(bfp, ">%s\n", block->sequences[seq].name);
            }
            for (pos=0; pos < block->width; pos++)
            {
                  fprintf(bfp, "%c", aa_btoa[block->residues[seq][pos]]);
            }
            fprintf(bfp, "\n");
            nout++;
            bcur = bcur->next;
         }
      }  /* end of sequence */
   }


}   /* end of output_fasta */
           }
                  }
                  this_seq++;
                  free_sequence(tmp_seq);
               }
            }
         }
         fclose(tmp);
      }
      tmp=fopen(tmp_name, "w");
   }

   sprintf(line, "\\rm %s", tmp_name);
   system(line);

   return(nseq);
}  /*  end of try_msf   */
/*========================================================================
==================================blimps-3.9/blimps/makeblockmap.c000064400001460000012000000567440774312250000172460ustar00jorjastaff00000400000027/*    makeblockmap.c  create a block map description from 
                      block families in a blocks DB
      makeblockmap   []

      written by Shmuel Pietrokovski.

April 97. Changes made by Ross Morgan-Linial :

          A note printed out that the reported sequence lengths are 
          actually the position of the end of the 'farthest' block on 
          the sequence.

          The 'pseudo' sequence length is taken from position of the 
          'farthest' block - not necessarily the last one.

Apr/May 97. Changes by Shmuel Pietrokovski :

          Block sequence segments scanned for gaps to get correct end 
          coordinate of the block region.

          Using procedure getargs to get arguments. Default input and 
          output as stdin/stdout. removed procedure print_map.

January 98. Changes by Shmuel Pietrokovski :

          Block overlap will not cause program to quit. User is notified 
          and start position of the C' block is modified to follow the end
          of the N' block. 

6/14/99 Change map to start with ">" instead of "#MAP#.
6/23/99 Add correct_lengths code: read in .lis file containing sequence
	names & lengths
2/ 2/00 Allow longer ACs for block_family name
4/ 9/03 It was still sometimes assuming block family name was 7
====================================================================*/

#define EXTERN

#include 
#include "blockmap.h"

#define INP_DFLT_FNAME "stdin"
#define INP_DFLT        stdin
#define OUT_DFLT_FNAME "stdout"
#define OUT_DFLT        stdout
#define DFLT_SRC_FAM_NAME ""

#define USAGE "A program to create block map description(s) from block family(ies) data:\n%s blocks-input_file_name [output_file_name] [-Fblock_family_name] [-Lsequence_length_file]\n"

#define GET_HELP "((input now expected from screen; CTRL-C to quit))\n\n"

#define DEFAULTS "Defaults: in-\"%s\" out-\"%s\" block_family_name-\"%s\"\n\n"

#define COMMENTS "Comments: \"-\" instead of an input/output file name => stdin/stdout\n           The order of the arguments is not important but the\n           first name is for the input file and the second for the output.\n          block_family_name = \"\" : all block families in input\n\n"

/*  routines from protomat.o */
struct db_id *makedbid();
int get_ids();

/*
 * Local variables and data structures
 */

int check_block_fam() ;
blocks_map *makemap() ;
void write_a_map() ;
void free_map() ;
void getargs() ;

/*=======================================================================*/
/*
 * main
 *   controls flow of program
 *   Parameters: argc, argv
 *   Error codes:
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE  *bfp=INP_DFLT, *ofp=OUT_DFLT ;
  FILE *lfp;
  char  bdbname[MAXNAME]=INP_DFLT_FNAME, outname[MAXNAME]=OUT_DFLT_FNAME ;
  char lisname[MAXNAME];
  char  src_fam_name[MAXNAME]=DFLT_SRC_FAM_NAME;
  Block *block, *block_1, **block_fam, **tmp_ptr ;
  int  i1, blocks_num, seqs_num , nlis, aclen;
  int  allocated_blocks = BLOCKS_ALLOC, prcssd_maps = 0, unprcssd_maps = 0 ;
  char family_name[8] ;
  blocks_map *map ;
  struct db_id *ids;

  if (argc == 1) /* show usage and what defaults are used */
     {
     fprintf(stderr, USAGE, argv[0]) ;
     fprintf(stderr, DEFAULTS, bdbname, outname, src_fam_name) ;
     fprintf(stderr, COMMENTS);
     fprintf(stderr, GET_HELP) ;
     }
  else
     getargs(argc,argv,bdbname,outname,src_fam_name,lisname) ;

/* open files */
/* Input */
  if (strcmp(bdbname,INP_DFLT_FNAME) !=0 && (bfp=fopen(bdbname, "r")) == NULL)
     {
     fprintf(stderr, "Cannot open input file %s\n", bdbname);
     exit(-1);
     }
  lfp = NULL;
  if (strlen(lisname) && (lfp=fopen(lisname, "r")) == NULL)
     {
     fprintf(stderr, "Cannot open input file %s\n", lisname);
     }

/* output */
  if (strcmp(outname,OUT_DFLT_FNAME) !=0 && (ofp=fopen(outname, "w")) == NULL)
     {
     fprintf(stderr, "Cannot open output file %s\n", outname);
     exit(-1);
     }

/*-----------------------------------------------------------------*/
  fprintf(stderr, "Input file \"%s\" processed by program \"%s\"\n",
               bdbname, argv[0]) ;

  if (lfp == NULL)
  {
     ids = NULL;
     fprintf(stderr, "Note: The sequence lengths shown are the 'right-most' sequence positions found in the blocks.\n");
  }
  else   /* read in the sequence names & lengths */
  {
      ids = makedbid();
if (ids == NULL) printf("Unable to allocate ids\n");
      nlis = get_ids(lfp, ids);
      fclose(lfp);
  }

/*-----------------------------------------------------------------*/
/* allocate memory for blocks family array - 
   more would be reallocated if needed */
  block_fam = (Block **) calloc(allocated_blocks, sizeof(Block *)) ;

/* read first block in DB */
  if ((block_1 = read_a_block(bfp)) == NULL)
     {
     fprintf(stderr, "Error ! Input file %s does not contain any blocks.\n",
            bdbname) ;
     exit(-2) ;
     }

  block_fam[0] = block_1 ;
  aclen = strlen(block_fam[0]->number) - 1; 
  if (block_fam[0]->number[(int) strlen(block_fam[0]->number)-1] != 'A')
  {   aclen++;  }
  blocks_num = 1 ;

/* read all blocks of blocks DB */
  while ((block = read_a_block(bfp)) != NULL)
     {
     if (strncmp(block->number, block_1->number, aclen) == 0)
        {
        block_fam[blocks_num++] = block ;

                      /* check if more elements needed in block family array */
        if (blocks_num == allocated_blocks)                    /* reallocate */
	   {
           allocated_blocks += BLOCKS_ALLOC ;
           tmp_ptr = (Block **)
                     realloc(block_fam, allocated_blocks*sizeof(Block *)) ;
           block_fam = tmp_ptr ;
	   }
        }
     else              /* all blocks belonging to 1st block's family read in */
        {

        if ( (int)strlen(src_fam_name) == 0 || 
            ((int) strlen(src_fam_name) > 0 && 
             strncmp(src_fam_name,block_1->number, aclen) == 0))
	   {
/* check that the blocks are in consecutive order and 
   how many different sequences they contain */

           if (check_block_fam(block_fam, blocks_num, &seqs_num) != OK) 
              exit (-3) ;

/*           sprintf(family_name, "%s",block_1->number) ; */
           strncmp(family_name, block_1->number, aclen);
           family_name[aclen] = '\0';

           if ((map = makemap(block_fam, blocks_num, seqs_num, ids)) != NULL)
	      {
              write_a_map(map, ofp) ;
              free_map(map) ;
              prcssd_maps++ ;
              }
           else
              { 
              fprintf(stderr,"Couldn't make a block map for block family %s.\n",
                     family_name) ;
              unprcssd_maps++ ;
	      }
           }
                          /* free memory allocated to block structures array */
        for(i1=0; i1 0 && 
       strncmp(src_fam_name,block_1->number, aclen) == 0))
     {
/* check that the blocks are in consecutive order and 
   how many different sequences they contain */
        
     if (check_block_fam(block_fam, blocks_num, &seqs_num) != OK) exit (-3) ;

/*     sprintf(family_name, "%.7s",block_1->number) ; */
     strncmp(family_name, block_1->number, aclen);
     family_name[aclen] = '\0';

     if ((map = makemap(block_fam, blocks_num, seqs_num, ids)) != NULL)
        {
        write_a_map(map, ofp) ;
        free_map(map) ;
        prcssd_maps++ ;
	}
     else 
        {
        fprintf(stderr,"Couldn't make a block map for block family %s.\n\n", 
               family_name) ;
        unprcssd_maps++ ;
        }
     }

                          /* free memory allocated to block structures array */
  for(i1=0; i1 0)
     fprintf(stderr,"\nCouldn't find or process block family %s !\n", src_fam_name) ;
  else
     {
     fprintf(stderr,"\n%d block family(ies) processed into maps.", prcssd_maps) ;
     if (unprcssd_maps > 0) 
        fprintf(stderr,"\n%d block family(ies) could not be processed.", unprcssd_maps) ;
     fprintf(stderr,"\nOutput in file %s.\n", outname) ;
     }

  exit(0);

}  /* end of main */


/* check that the blocks are in consecutive order and 
   how many different sequences they contain */

int check_block_fam(block_fam, blocks_num, seqs_num)
Block *block_fam[] ;
int   blocks_num, *seqs_num ;
{
   int i1, i2, i3, i4 ;

/* is the first block's has family suffix A ? */
   if (block_fam[0]->number[(int) strlen(block_fam[0]->number)-1] != 'A')
      {
      fprintf(stderr,"Warning ! The name of the first block in family %s\n",
             block_fam[0]->number) ;
      fprintf(stderr,"does not end with an \"A\".\n") ;
      }

/* does the suffix of each block follow the suffix of the preceding block ? */

   for(i1=1; i1number[(int) strlen(block_fam[i1]->number)-1] -
          block_fam[i1-1]->number[(int) strlen(block_fam[i1-1]->number)-1]
          != 1) 
         {
         fprintf(stderr,
            "Error ! Block %s is not the block expected to follow (by name)\n",
                block_fam[i1]->number ) ;
         fprintf(stderr,"block %s.\n", block_fam[i1-1]->number) ;
         return(ERROR) ;
	 }


   *seqs_num = block_fam[0]->num_sequences ;

/* in case some blocks include sequences not found in the first block : */
/* this is not allowed in the Blocks DB, where each sequence must contain
   all the blocks, but this is possible in general */

   for(i1=1; i1num_sequences; i2++) 
         {
                 /* compare sequence name to all the ones in previous blocks */
      /* this is inefficient but avoids the need to store the sequence names */
         for(i3=0; i3num_sequences &&
                      strcmp(block_fam[i1]->sequences[i2].name,
                             block_fam[i3]->sequences[i4].name) != 0; i4++) ;

         /* if the sequence name was equal to any sequence name in THIS block 
            no need to check any other blocks */
            if (i4 < block_fam[i3]->num_sequences) break ;
            }

 /* check if no break occurred i.e. sequence name was different from all 
     those it was compared to */
         if (i3 == i1) (*seqs_num)++ ;
         }

   for(i1=0; i1num_sequences == *seqs_num; 
       i1++) ;
   if (i1 != blocks_num)
      fprintf(stderr,
          "Note - Not all sequences in family %s contain all the blocks.\n",
             block_fam[0]->number) ;

   return(OK) ;

} /* end of check_block_fam */

blocks_map *makemap(block_fam, blocks_num, seqs_num, ids)
Block *block_fam[] ;
int blocks_num, seqs_num ;
struct db_id *ids;
{
   blocks_map *map ;
   int i1, i2, i3, i4, gaps ;
   char *blk_sfx ;
   struct db_id *did;


/* allocate memory to blocks_map structure */

                                                 /* memory for map structure */
  map = (blocks_map *) malloc(sizeof(blocks_map)) ;

                                    /* memory for sequences in map structure */
  map->seq_map = (sequence_map *) calloc(seqs_num, sizeof(sequence_map)) ;

                          /* memory for blocks in sequences in map structure */
  for(i1=0; i1seq_map[i1].blocks = 
                        (block_pos *) calloc(blocks_num, sizeof(block_pos)) ;
 
/* allocate memory to block suffices array */

  blk_sfx = (char *) calloc(blocks_num, sizeof(char)) ;

  sprintf(map->block_family, "%s", block_fam[0]->family) ;

  strncpy(map->description, block_fam[0]->de, SMALL_BUFF_LENGTH) ;

  strncpy(map->id, get_token(block_fam[0]->id), SMALL_BUFF_LENGTH) ;

                                      /* strip possible ";" at end of string */
  if (map->id[(int) strlen(map->id)-1] == ';')
     map->id[(int) strlen(map->id)-1] = '\0' ;

  map->num_seqs = seqs_num ;

  map->tot_num_blocks = blocks_num ;

/* get block suffices */
  for (i1=0; i1number[(int) strlen(block_fam[i1]->number)-1] ;

      if (!isalpha(blk_sfx[i1]) && blocks_num == 1) blk_sfx[i1] = 'A' ;
      }

/* get sequence names */
  for (i1=0; i1num_sequences; i1++) 
      strncpy(map->seq_map[i1].seq_name, block_fam[0]->sequences[i1].name, 
              SMALL_BUFF_LENGTH) ;

/* If not all blocks contain all sequences it is possible that the first block
   doesn't have all the sequence names. If so keep looking for them in the
   rest of the blocks. */
  if (block_fam[0]->num_sequences < seqs_num) 
     {
     i1 = block_fam[0]->num_sequences ;

     for(i2=1; i2num_sequences; i3++) 
	    {
               /* compare sequence name to all the ones in the map structure */
            for(i4=0; i4sequences[i3].name,
                       map->seq_map[i4].seq_name) != 0; i4++) ;

          /* is sequence name equal to any sequence name in map structure ? */
            if (i4 == i1) strncpy(map->seq_map[i1++].seq_name,
                                  block_fam[i2]->sequences[i3].name,
                                  SMALL_BUFF_LENGTH) ;
	    }

     if (i1 != seqs_num) /* not all sequence found */
        {
        fprintf(stderr,"Error ! Couldn't find all %d sequences.\n", seqs_num) ;
        free_map(map) ;
        free(blk_sfx) ;
        return(NULL) ;
	}
     }
/** sort sequence names - makes it easier to compare different  maps of same sequences **/

/* for each sequence get the suffices and positions of all blocks in it */

  for(i1=0; i1seq_map[i1].num_blocks = 0 ;
     for(i2=0; i2seq_map[i1].seq_name, 
                      block_fam[i2]->sequences[i3].name) == 0) break ;
        if (i3 == seqs_num) 
           fprintf(stderr,
              "Note - Sequence %s in family %s does not contain block %c.\n",
                  map->seq_map[i1].seq_name, map->block_family, blk_sfx[i2]) ;
        else
           {
           map->seq_map[i1].blocks[map->seq_map[i1].num_blocks].code = 
                                     blk_sfx[i2] ;

/* check if first block starts before position 1. 
   Do it here so that the sequence can be examined if this is so */
           if (map->seq_map[i1].num_blocks == 0 &&
               block_fam[i2]->sequences[i3].position < 1) 
	       {
                                     /* this is OK only if the aa < 1 are Xs */
               for(i4=0; i4<(1-block_fam[i2]->sequences[i3].position) && 
                   block_fam[i2]->sequences[i3].sequence[i4] == aa_atob['X'];
                   i4++) ;
               if (i4 != 1 - block_fam[i2]->sequences[i3].position)
		  {
                  fprintf(stderr,
                   "Note, first block (%c %d-%d) in sequence %s of family %s\n\
begins BEFORE the first aa of the sequence !\n",
                         map->seq_map[i1].blocks[0].code,
                         block_fam[i2]->sequences[i3].position,
                         block_fam[i2]->sequences[i3].position +
                         block_fam[i2]->sequences[i3].length - 1,
                         map->seq_map[i1].seq_name, map->block_family) ;
/* This was not made an error because of the inteins - they are "imbeded"
   inside other proteins and their first and last blocks include aa in this
   flanking protein sequence 
                  free_map(map) ;
                  free(blk_sfx) ;
                  return(NULL) ;
*/
  	          }
/*
               else
*/
                   /* the begining of the block is missing from the sequence */
               map->seq_map[i1].blocks[map->seq_map[i1].num_blocks].start = 1 ;
	       }
           else
               map->seq_map[i1].blocks[map->seq_map[i1].num_blocks].start = 
                                     block_fam[i2]->sequences[i3].position ;

                      /* check how many gaps (if at all) are in the sequence
                         segment in this block */
                      /* this will be used to adjust the length of the block */

           for(i4=0, gaps=0; i4sequences[i3].length; i4++)
              if (block_fam[i2]->sequences[i3].sequence[i4] == aa_atob['-']) gaps++;



/*if (gaps !=0 )
printf("%d gaps in block %c of %s\n", 
gaps, map->seq_map[i1].blocks[map->seq_map[i1].num_blocks].code, map->seq_map[i1].seq_name) ;*/

           /* find end of block position, taking into account possible gaps. */

           map->seq_map[i1].blocks[map->seq_map[i1].num_blocks].end = 
                                     block_fam[i2]->sequences[i3].position +
                                     block_fam[i2]->sequences[i3].length - 1 - gaps ;

           map->seq_map[i1].num_blocks++ ;
           }
        }
     }

/* sequence lengths are unknown 
   use end of fartherest block in each sequence as the sequence length */

  for (i1=0; i1seq_map[i1].seq_len = 0;
    /*  first get right-most block end  */
    for (i2 = 0; i2 < map->seq_map[i1].num_blocks; i2++)
      if (map->seq_map[i1].blocks[i2].end > map->seq_map[i1].seq_len)
      	 map->seq_map[i1].seq_len = map->seq_map[i1].blocks[i2].end;

    /*  then see if the .lis file has a longer length for this sequence */
    if (ids != NULL) did = ids->next;
    else             did = NULL;
    while (did != NULL && strcmp(did->entry, map->seq_map[i1].seq_name) != 0)
    {   did = did->next; }
    if (did != NULL && strcmp(did->entry, map->seq_map[i1].seq_name) == 0 &&
        did->len > map->seq_map[i1].seq_len )
    {   map->seq_map[i1].seq_len = did->len; }
  }

/* find length of longest sequence */
  map->max_seq_len = 0 ;
  for (i1=0; i1seq_map[i1].seq_len > map->max_seq_len)
         map->max_seq_len = map->seq_map[i1].seq_len ;

/* check for each sequence that the blocks follow one another, do not overlap
   and are within the sequence boundaries */

  for (i1=0; i1seq_map[i1].blocks[map->seq_map[i1].num_blocks-1].end >
          map->seq_map[i1].seq_len)
         {
         fprintf(stderr,"Error ! Last block (%c, %d-%d) in sequence %s of family %s\n\
is out of bounds.\n",
                map->seq_map[i1].blocks[map->seq_map[i1].num_blocks-1].code,
                map->seq_map[i1].blocks[map->seq_map[i1].num_blocks-1].start,
                map->seq_map[i1].blocks[map->seq_map[i1].num_blocks-1].end,
                map->seq_map[i1].seq_name, map->block_family) ;
         free_map(map) ;
         free(blk_sfx) ;
         return(NULL) ;
         }

      for(i2=1; i2 < map->seq_map[i1].num_blocks; i2++)
      {
	 if (map->seq_map[i1].blocks[i2].start <= 
             map->seq_map[i1].blocks[i2-1].end)
         {
            if (map->seq_map[i1].blocks[i2].end <= 
             map->seq_map[i1].blocks[i2-1].start)
            {  fprintf(stderr,
           "Note - Block %c PRECEDES block %c in sequence %s of family %s.\n",
                      map->seq_map[i1].blocks[i2-1].code, 
                      map->seq_map[i1].blocks[i2].code, 
                      map->seq_map[i1].seq_name, map->block_family) ;
            }
            else 
            /* blocks overlap */
            {
      fprintf(stderr,"Note - Blocks %c (%d-%d) and %c (%d-%d) in sequence %s\n\
of family %s overlap.\n", 
                map->seq_map[i1].blocks[i2-1].code, 
                map->seq_map[i1].blocks[i2-1].start,
                map->seq_map[i1].blocks[i2-1].end,
                map->seq_map[i1].blocks[i2].code, 
                map->seq_map[i1].blocks[i2].start,
                map->seq_map[i1].blocks[i2].end,
                map->seq_map[i1].seq_name, map->block_family) ;
     map->seq_map[i1].blocks[i2].start = map->seq_map[i1].blocks[i2-1].end + 1;
            }
         }
      } /* end of i2 block */

   }  /* end of i1 seq */

  free(blk_sfx) ;
  return(map) ;
}   /* end of makemap  */

/* free memory allocated to blocks_map structure */
void free_map(map) 
blocks_map *map ;
{
  int i1 ;

  for(i1=0; i1num_seqs; i1++) free(map->seq_map[i1].blocks) ; 
   
  free(map->seq_map) ;

  free(map) ;

} /* end of free_map */

/* write out a block map */
void write_a_map(map, ofp) 
blocks_map *map ;
FILE *ofp ;
{
  int i1, i2 ;

/*
  fprintf(ofp, "#MAP# ") ;
*/
  fprintf(ofp, ">%s %d %d %d %s\n%s\n",
          map->block_family, map->tot_num_blocks, map->num_seqs, 
          map->max_seq_len, map->id, map->description);

  for(i1=0; i1num_seqs; i1++)
     {
     fprintf(ofp, "%s %d %d\n",
             map->seq_map[i1].seq_name, map->seq_map[i1].seq_len,
             map->seq_map[i1].num_blocks) ;

     for(i2=0; i2seq_map[i1].num_blocks; i2++)
        fprintf(ofp, "%c %d %d\n", map->seq_map[i1].blocks[i2].code, 
                                   map->seq_map[i1].blocks[i2].start, 
                                   map->seq_map[i1].blocks[i2].end) ;
     }

  fprintf(ofp, "//\n") ;
  fflush(ofp) ;

} /* end of write_a_map */

/*****************************************************************************
 * get input and output file names and other program parameters.
 *
 * All parameters, except explicit input and output file names, 
 * should be preceded by a "-".
 * A sole "-" (implicitly) specifies a default for a file name.
 * The first explicit or implicit file name will be assigned to the input file
 * and the second to the output file.
 *****************************************************************************/

void getargs(argc,argv,inpfname,outfname,fam_name, lisname)
int    argc;
char   *argv[];
char   inpfname[], outfname[], fam_name[], lisname[];
{
   int i1 ;
   int fnames=0 ;
   char *chr_ptr ;

   inpfname[0] = outfname[0] = fam_name[0] = lisname[0] = '\0';

   for(i1=1; i1sequences[blimps-3.9/blimps/makelis.c000064400001460000012000000320611054325723000162300ustar00jorjastaff00000400000027/*     ~ptest/src/makelis.c   for blockmaker email server
       Read the sequences in the mail message & convert them
       into fasta format for motifj & gibbsj using blimps routines

	   makelis name return
	
	where name is from "name.in" which contains the
	mail message, "return" is the return address.
        Expects the full mail message to be in "name.in" (gets Subject
        line and sequences from the body).

	Writes name.seqlen (for block maps), name.lis, name.pros,
		name.warn & name.err: processmail mail will quit
		if name.err is non-empty.

=========================================================================
 3/11/95  Since motifj no longer requires the sequences in separate files,
          modified this to dump them all into one file   JGH
 4/ 2/95  Edit sequences and change all "-" or "*" to "X" for gibbsj, which 
	  chokes on dashes (added edit_seq() ).
 6/22/95  Don't change "*" to "X", caused problem with TC1 seqs for gibbsj
 8/ 7/97  Added .seqlen output file
10/15/97  Get sequences directly from the .in file (don't use readseq or
          the .seq file from processmail any more). Fix up non-unique
          sequence names. Warning if sequences appear to be DNA.
10/23/97  Removed warnings - writing to stderr causes processmail to quit.
10/25/97  Added .warn file
 1/12/99  If sequence names start ">P1;" change to just ">" because
	  clustalw will assume PIR format otherwise.
 6/20/99  Sequence name from 10 to 18; need to get rid of leading spaces
	  between fields on title line (eg seq->info)
 6/ 5/00  ACLEN from 7 to 9
 7/15/01  Don't run protomat.csh if DNA seqs (write to ErrP not WarnP)
 5/15/02  SNAMELEN issue; motifj really uses SNAMELEN-1; changed it from
		18 to 17 here to be safe, but this isn't really right
12/23/06 Increased sequence name length
========================================================================*/
#define EXTERN
#define XNAMELEN 19
#define ACLEN 9

/*	Include files from $BLIMPS_DIR/include  */
#include 
/*	Include files from $BLIMPS_DIR/blimps  */
#include "blimps.h"
#include "license.h"
#include "blimps-mem.h"
#include "config.h"
#include "scores.h"
#include "scoring.h"		/* for alignments_done and scores_done */
#include "lists.h"

Boolean SavedScoresFlag;		/* not used, blimps kludge */


/*	Local routines */
int make_lis();
void edit_seq();
void get_seqs();
int read_seqs();

/*	Global variables */
char SequenceFile[LARGE_BUFF_LENGTH];
char LisFile[LARGE_BUFF_LENGTH], ProFile[LARGE_BUFF_LENGTH];
char LenFile[LARGE_BUFF_LENGTH];
char ErrFile[LARGE_BUFF_LENGTH];
FILE *LisFileP, *LenFileP, *ProFileP, *ErrP, *WarnP;

char Path[LARGE_BUFF_LENGTH];
char Process[LARGE_BUFF_LENGTH];

char User[LARGE_BUFF_LENGTH];
char Return[LARGE_BUFF_LENGTH];

char BlockName[LARGE_BUFF_LENGTH];

char SubjectLine[LARGE_BUFF_LENGTH];
char TruncSubjectLine[LARGE_BUFF_LENGTH];
char DELine[LARGE_BUFF_LENGTH];

int Count = 0;

int NumberToReport;		/* needed for lists.c */
/*	Following are needed to scores.c , not really used */
int SearchType, SequenceMatrixScoringMethod;

/*=========================================================================*/
int main(argc, argv)
     int argc;
     char *argv[];		/* arg[1] path name + process name */
				/* arg[2] return address */
{
  int i, str_length;

  FILE *mailfp;

  ErrorLevelReport = SERIOUS_ERR_LVL; /* report only serious and higher */
  /*  Have to use stderr because the blimps routines write to it, so
      make it a named file. Any write to .err causes processmail to
      quit, non-fatal messages are written to .warn later    */
  sprintf(ErrFile, "%s.err", argv[1]);
  ErrP = freopen(ErrFile, "a", stderr);

  initialize_lists();

  strncpy(Path, argv[1], LARGE_BUFF_LENGTH);

  /*------------------------------------------------------------------------------*/
  /*  All this code is to construct the first line of the .lis file for protomat:
       format is ">AC     ;ID ;DE ;;$", here AC = 1st 8 chars of Subject line,
	ID = complete Subject line, DE = from first sequence info */

  str_length = (int) strlen(Path);
  str_length--;
  while ((Path[str_length] != '/') &&
	 (str_length >= 0)) {
    str_length--;
  }

  strncpy(Process, Path+str_length+1, LARGE_BUFF_LENGTH);
  Path[str_length+1] = '\0';

  strncpy(User, argv[2], LARGE_BUFF_LENGTH);
  str_length = (int) strlen(User);
  str_length--;
  while ((User[str_length] != '@') &&
	 (str_length >= 0)) {
    str_length--;
  }

  if (str_length < 0) {
    sprintf(Return, " ");	/* the space is so that the header is */
				/* built right */
  }
  else {
    strncpy(Return, User+str_length+1, LARGE_BUFF_LENGTH);
    User[str_length] = '\0';
  }

  strncpy(BlockName, User, LARGE_BUFF_LENGTH);
  BlockName[ACLEN] = ' ';
  BlockName[ACLEN+1] = '\0';
  str_length = 0;
  for (i=0; i 20) {
	sprintf(SubjectLine, "%19s...", SubjectLine);
      }
    }
  }
  strncpy(TruncSubjectLine, SubjectLine, LARGE_BUFF_LENGTH);
  TruncSubjectLine[ACLEN] = ' ';
  TruncSubjectLine[ACLEN+1] = '\0';
  str_length = 0;
  for (i=0; i%s;%s;%s;;$\n", TruncSubjectLine, SubjectLine, DELine);
  }
  else {
    fprintf(LisFileP, ">%s;%s;%s;;$\n", BlockName, argv[2], DELine);
  }
  fprintf(LisFileP, "%s\n", Path);

  /*  Executes make_lis for each sequence in the list of sequences */
  DoForSL(Sequences, make_lis, NULL);

  if (Count < 3)
    fprintf(stderr, "Only %d sequence found, need at least 3\n", Count);
  fclose(LisFileP); fclose(LenFileP); fclose(ProFileP);
  exit(0);
}  /* end of main */

/*========================================================================
    Fixes up the sequence name, writes the .lis, .seqlen & .pros files
=========================================================================*/
int make_lis(seq, arg)
     Sequence *seq;
     void *arg;   /* Not used */
{
  char seqname[LARGE_BUFF_LENGTH];

  strncpy(seqname, seq->name, XNAMELEN);
  if (strcmp(seqname, "\0") == 0) {
    sprintf(seqname, "%s_%d", Process, Count);
  }
  seqname[XNAMELEN] = '\0';		/* ensure ony 20 characters long */

  fprintf(LisFileP, "%s\tLENGTH=%d\n", seqname, seq->length);
  fprintf(LenFileP, "%s\t%d\n", seqname, seq->length);

  output_sequence(seq, ProFileP);

  Count++;

  return SL_CONTINUE;
} /* end of make_lis */

/*=========================================================================
    Change "-" to "X" for gibbsj so it doesn't choke
	X is 23, - is 0, * is 24
===========================================================================*/
void edit_seq(seq)
Sequence *seq;
{
   int i;

   for (i=0; i < seq->length; i++)
      if (seq->type == AA_SEQ && seq->sequence[i] == 0)
	  seq->sequence[i] = 23;
}   /* end of edit_seq */

/*=======================================================================
     Open the .in file and skip to the first blank line. The sequences
     are assumed to start following the first blank line.
     Problems if the first non-blank line following the first blank line
	begins with white space ...
=========================================================================*/
void get_seqs(seq_file)
     char *seq_file;
{
  long fpos;
  char line[LARGE_BUFF_LENGTH];
  int nseq;

  /* put the sequence file in the memory */
  insert_file(seq_file, SEQUENCE_FILES);

  SequenceFiles.fp = fopen(SequenceFiles.file_names[0], "r");
  
  /*  read to first blank line, then set start of sequences to next line */
  if (SequenceFiles.fp != NULL) 
  {
    /*  Read to first blank line and mark it  */
    while(!feof(SequenceFiles.fp) && 
          fgets(line, sizeof(line), SequenceFiles.fp) != NULL &&
                strlen(line) > 1 )
/*>>>>DEBUG
                  printf("%d %s", (int) strlen(line), line);
DEBUG<<<<*/
			;
    fpos = ftell(SequenceFiles.fp);

    /* determine sequence database db_type and seq_type */
    /*  type_dbs() reads one line and then rewinds .fp  */
    SequenceFiles.db_type = type_dbs(SequenceFiles.fp, DbInfo);
    fseek(SequenceFiles.fp, fpos, 0);

    if (SequenceFiles.db_type < 0 || SequenceFiles.db_type >= MAXDB)
    {
      /* unknown database type */
      sprintf(ErrorBuffer, 
              "Unknown sequence format.  Known formats are:");
      ErrorReport(SERIOUS_ERR_LVL);
      sprintf(ErrorBuffer,
              "Fasta, GenBank, PIR, Swiss Prot, and GCG.");
      ErrorReport(SERIOUS_ERR_LVL);
      sprintf(ErrorBuffer,
              "Trying with Fasta format.\n");
      ErrorReport(SERIOUS_ERR_LVL);
      SequenceFiles.db_type = FASTA;
    }
    SequenceFiles.seq_type = seq_type_dbs(SequenceFiles.fp, DbInfo,
            SequenceFiles.db_type, UNKNOWN_SEQ);
    fseek(SequenceFiles.fp, fpos, 0);

    if (SequenceFiles.seq_type == NA_SEQ) 
    {
      fprintf(ErrP, 
         "Sequences appear to be DNA: Block Maker is designed for protein.");
    }

    /*   Now read the sequences   */
    nseq =
     read_seqs(SequenceFiles.fp, SequenceFiles.db_type, SequenceFiles.seq_type);
  }  /* end of good input file  */

  else 
  {
    sprintf(ErrorBuffer, "Unable to read sequence file: %s ",
            SequenceFiles.file_names[0]);
    ErrorReport(SERIOUS_ERR_LVL);
    sprintf(ErrorBuffer, "to determine the type of database\n");
    ErrorReport(SERIOUS_ERR_LVL);
  }
} /* end of get_seqs */

/*======================================================================
   Read the sequences into a list
=======================================================================*/
int read_seqs(fp, db_type, seq_type)
FILE *fp;
int db_type, seq_type;
{
  Sequence *seq;
  Boolean first_seq = TRUE;
  int i, itemp, nseq;
  char ctemp[80];

  nseq = 0;
  while((seq = read_a_sequence(fp, db_type, seq_type)) != NULL)
  {
    /*   Get rid of leading "P1;"    */
    if (strncmp(seq->name, "P1;", 3) == 0)
    {
        if ((int) strlen(seq->name) > XNAMELEN) seq->name[XNAMELEN] = '\0';
        strcpy(ctemp, seq->name);
        strcpy(seq->name, ctemp+3);
    }

    /*  Get rid of leading spaces */
    itemp = strspn(seq->name, " ");
    if (itemp > 0)
    {
      strcpy(ctemp, seq->name);
      strcpy(seq->name, ctemp+itemp);
    }

    if ((int) strlen(seq->name) > XNAMELEN)
        seq->name[XNAMELEN] = '\0';		/* ensure ony 20 characters long */

    /*  Get rid of leading spaces */
    itemp = strspn(seq->info, " ");
    if (itemp > 0)
    {
      strcpy(ctemp, seq->info);
      strcpy(seq->info, ctemp+itemp);
    }

    if (first_seq) {
      first_seq = FALSE;
      /* read the DE line stuff */
      if ((int)strlen(seq->info) <= (60-ACLEN)) {
	sprintf(DELine, "%s family", seq->info);
      }
      else {
	strncpy(Buffer, seq->info, 50);
	Buffer[50] = '\0';
	sprintf(DELine, "%s... family", Buffer);
      }
    }
    nseq++;

  /*  Check for duplicate sequence names here & append an error to
      stderr if not unique */
    if (SearchSL(Sequences, seq) != NULL) 
    {
     fprintf(WarnP, "Non-unique sequence name: %s\n", seq->name);
     fprintf(WarnP, "First 20 characters of sequence name must be unique.\n");
     if (strlen(seq->name) < XNAMELEN)  /*  Try using other info */
     { 
        strcpy(seq->name, seq->info);
        seq->name[XNAMELEN] = '\n';
        for (i=0; i< XNAMELEN; i++) if (seq->name[i] == ' ') seq->name[i] = '_';
     }
     i = strlen(seq->name);
     while (i >= 0 && SearchSL(Sequences, seq) != NULL) 
     {
        strcpy(ctemp, seq->name);
        ctemp[i] = '\0';
        sprintf(seq->name, "%s%d", ctemp, nseq);
        seq->name[XNAMELEN] = '\0';
        i--;
     }
     fprintf(WarnP, "Modified name to %s\n", seq->name);
    } /* end of non-unique name */

    edit_seq(seq);		/* Change gap characters, etc. */
    InsertSL(Sequences, seq);

  }  /* end of sequence file */
  return(nseq);
}  /*  end of read_seqs */
blimps-3.9/blimps/makelogob.c000064400001460000012000003033600774312250000165450ustar00jorjastaff00000400000027/*=======================================================================
    www/src/makelogob.c
    Version of makelogo.c for use with getblock function of the blocks
    WWW server. Modified to accept an argument which it uses as a suffix
    for input files symvec.suffix colors.suffix and makelogop.suffix 
    (created by matrix_logo program) and output file logo.suffix  (JGH)
	Requires p2clib 
2/16/95 Jorja Henikoff
Feb 27, 95 - modified to use colors.suffix (instead of colors) SP 
4/1/95  Added Adobe PostScript structuring comments to avoid problems
        with some browsers (%% lines). Also increased maxstring from
        150 to 1500 to accomodate global alignments.   JGH
2/2/00  Never print the right-hand bar (look for endline & barends)
=========================================================================*/
/* Output from p2c, the Pascal-to-C translator */
/* From input file "makelogo.p" */

/* function labs (long [?] absolute number) changed to abs, since labs was not 
   available on math library in howard.fhcrc.org . */ 

#include "p2c.h"

/* makelogo: make a graphical `sequence logo' for aligned sequences
  by Thomas Schneider
  NCI/FCRDC Bldg 469. Room 144
  P.O. Box B
  Frederick, MD  21702-1201
  (301) 846-5581 (-5532 for messages)
  (301) 846-5598 fax
  network address: toms@ncifcrf.gov

module libraries required: delman, prgmods */

/* end of program */

/* begin module version */

#define version         7.64
/* of makelogo.p 1994 July 8
origin 1990 Feb 28 from rsgra */
/* end module version */

/* begin module describe.makelogo */
/*
name
   makelogo: make a graphical `sequence logo' for aligned sequences

synopsis
   makelogo(symvec: in, makelogop: in, colors: in, marks: in,
            wave: in, logo: out, output: out)

files
   symvec: A "symbol vector" file from the alpro or dalvec program.
     If the file is empty, the alphabet is printed.  This allows one
     to determine the correction factors described below.
     If the error bars have a negative size, they are not displayed.
     This allows the sites program to control the display when it
     would not be appropriate.
     If the number of a symbol is negative in symvec, then the
     symbol will be rotated 180 degrees before being printed.
     The absolute value is used by makelogo to determine the height.
     This allows statistical tests which find rare symbols to be
     significant to show that the symbol is rare by having
     it up side down.  Notice that ACGT are all easy to distinguish
     from their upside down versions, but unfortunately this is not always
     true for protein sequences.

   makelogop: parameters to control the program.
     line 1: contains the lowest to highest range of the binding
             site to do the logo graph. (FROM to TO range)
     line 2: bar: sequence coordinate before which to print a vertical bar
             NOTE: the vertical bar takes up a small amount of horizontal space.
             This will offset the logo from that point on by a tiny amount.
     line 3: xcorner and ycorner.  This is the coordinate of the
             lower left hand corner of the logo (in cm).
             These should be real numbers.
     line 4: rotation: angle in degrees to rotate the logo.  Warning:
             rotations other than by factors of 90 degrees may produce
             incorrect logos because character scaling depends on the
             orientation of the characters.  (Essentially, it's a design
             fault of PostScript.)
     line 5: charwidth: (real, > 0) the width of the logo characters, in cm
     line 6: barheight barwidth: (real, > 0) height of the vertical bar, in cm,
             and its width, in cm.
     line 7: barbits: (real) The height of the vertical bar, in bits, is given
             by the absolute value of barbits.  If barbits is positive, an
             "I-beam" will appear at the top of the symbol stack.  The I-beam
             indicates one standard deviation of the stack height, based
             entirely on how small the sample of sequences is.  If the value of
             barbits is negative, the I-beam is not displayed.  Not knowing how
             big the sampling effects are can fool one, so one should usually
             have the I-beam, even if it is ugly.
                WARNING: it is not known how to calculate the error for data
             derived from a dirty DNA synthesis experiment (see Schneider1989,
             reference given below).  In that case the error could be
             calculated (in program sites) from the number of sequences, so
             that the error bar would be an underestimate of the variation.
             Unfortunately, when I tried this, people interpreted the error bar
             as the size they saw, so this does not work well visually.
             Therefore when data come from the sites program, the I-beam is
             suppressed.
                The combination of barheight and barbits determines the size of
             the logo in bits per centimeter.  Both must be specified even if
             no vertical bar is desired.
     line 8: Ibeamfraction: real. The fraction of the vertical part of the
             Ibeam to draw.  When it is 1, the Ibeam is normal.  When it is
             zero, no vertical line is drawn.  At 0.1, only 10 percent of the
             top half and 10 percent of the bottom half of the Ibeam is drawn,
             for a total of 10 percent of the entire ibeam.  More precisely,
             this number is the fraction of a standard deviation to draw.
             Negative values will reverse the direction of the part drawn,
             making a 'thumbtack'.  (Note:  if this parameter is missing, as in
             old makelogop files, the program will ignore it.)  I thank Shmuel
             Pietrokovski (Structural Biology department, Weizmann Institute of
             Science, 76100 Rehovot - ISRAEL, bppietro@dapsas1.weizmann.ac.il)
             for suggesting this method, and for the code to do it.  See
             further description below.
     line 9: barends: if the first character on the line is a 'b', then bars
             are put before and after each line, in addition to the other bar.
             The first bar on each line is labeled with tic marks and
             the number of bits.  If you don't want this, you can remove
             the call to maketic in the logo.
    line 10: showingbox: if the first character on the line is an 's',
             then show a dashed box around each character.
    line 11: outline: If the first character is 'o' then the characters show
             up in outline form.  Otherwise, they are solid.
    line 12: caps: if the first letter is 'c' then alphabetic
             characters are converted to capital form.
    line 13: stacksperline: number of character stacks per line output.
             A "stack" is a vertical set of characters.  A "line" is a series
             of stacks.  One may have several lines per page (next parameter).
             Special note: This value is used to do the centering of strings.
             For a range of -23 to +19, you have to set it to (19)-(-23)+1 = 43
             to get your title centered correctly.  You can get the program to
             tell you the number '43' by setting stacksperline very large, in
             which case it realizes there is something wrong and does the
             calculation.
    line 14: linesperpage: number of lines per page output
    line 15: linemove: line separation relative to the barheight
    line 16: numbering: if the first letter is 'n' then each stack is
             numbered.  Otherwise, the number is suppressed as a PostScript
             comment.  This allows you to modify the logo file by hand to
             reinstate numbering for only the positions you want by removing
             the percent (%) symbol from in front of the calls to makenumber.
    line 17: shrinking: (real)  Factor by which to shrink the characters.  If
             shrinking <= 0 or shrinking >= 1 then the characters exactly fit
             into the dashed box.  If shrinking > 0 and shrinking < 1, the
             characters are shrunk inside the dashed box.  To use this feature,
             the parameter showningbox be on, so that the user does not create
             a logo whose height is misleading.
    line 18: strings: the number of user defined strings to follow.  Each
             string definition takes up two lines.  The first is the (x,y)
             coordinate of the string, the second is the string itself.  The
             coordinates are in centimeters relative to the coordinate
             transforms performed above.  (This way, the title position stays
             the same relative to the logo.)
    line 19: (x,y,s) coordinates of first user defined string (if strings >= 1)
             followed by the factor by which to scale the string.  A factor
             of 1 means no scaling.  In addition, if the x coordinate is
             negative, then the string is centered by using the string
             width, the stacksperline and charwidth.
    line 20: the first user defined string (if strings >= 1)
    line 21: (x,y,s) coordinates of second user defined string (if strings >= 2)
    line 22: the second user defined string (if strings >= 2)
             (etc. for the remaining strings.)
    The remainder of the file is ignored and may contain comments.

   colors: Defines the color of each character printed.
     Any number of lines that begin with an asterisk [*] can be used
     as comments to identify the file or portions of the file.
     Put into the file one line for each character that is to
     have a color other than black.  The line must contain:
                    character red green blue
     The last three parameters are real values between 0 and 1 (inclusive).
     The values depend on the PostScript interpreter, but 0 means black
     and a value of 1 means the most bright.
     To assign the asterisk a color, proceed it with a backslash [as \*].
     To assign the backslash a color, proceed it with a backslash [as \\].
     If the file is empty, the logo is made in black and white and the lower
     half of the I-beam error bar is made white so that when it is inside the
     letters it is visible.

   marks: an empty file means no marks are made.  Otherwise, a series
     of lines containing four pieces of data that define marks to be placed
     over the output:
        mark: o means open circle, f means filled circle.
        base coordinate: a real number that determines the center of the mark
        bits coordinate: a real number that determines the position of the
           mark in bits.
        scale: a positive real number by which to scale the mark.
     The symbols must be in increasing order of position in the site.

   wave: Define a cosine wave over the graph.  Empty file means no cosine
     wave, otherwise the parameters of the wave are given one per line:
       extreme: char;  h or l, the extreme high or low point on the curve
          defined by the wavelocation and wavebit
       wavelocation: real; the location in bases of the extreme
       wavebit: real; the location in bits of the extreme
       waveamplitude: real; the amplitude of the wave in bits
       wavelength: real; the wave length of the wave in bases
       dash: real; the size of dashes in cm.  Zero or negative means no dashes
       thickness: real; thickness of the wave in cm.  Zero or negative
          means the value defaults to PostScript line thickness.

   logo: the output file, a PostScript program to display the logo.

   output: messages to the user

description
   The makelogo program generates a `sequence logo' for a set of aligned
   sequences.  A full description is in the documentation paper.  The input is
   an `symvec', or symbol-vector that contains the information at each
   position and the numbers of each symbol.  The output is in the graphics
   language PostScript.

   The program now indicates the small sample error in the logo by a small
   'I-beam' overlayed on the top of the logo.  Although the user may
   turn this off to make pretty logos, I strongly recommend use of it
   to avoid being fooled by small amounts of data.

   Making A Logo As Part of Another Figure
   ---------------------------------------

   The normal logo file is designed to stand by itself.  However, it is often
   desirable to incorporate the logo as part of another figure.  The difficulty
   is that the stand-alone logo PostScript program will erase the page (which
   wipes out any previous figure drawing) and show the page (which prints the
   page right after the logo).  To prevent these actions, the lines of
   PostScript code which do this have comments that contain the word REMOVE.
   All you have to do is remove these lines and your logo will be able to fit
   into your figure.  In Unix this can be easily done by:

   grep -v REMOVE logo > logo.ps

   If you do this, then it is advisable to do the erasepage and the
   showpage yourself.  A convenient way to do this is to have several
   files that contain postscript commands, and to use a shell script
   to concatenate them together:

   cat start.ps logo.ps end.ps > myfigure.ps

   If you have a large number of logos together in one figure, you can reduce
   the size of the final figure by another trick.  Logo files begin with a
   header which is the same from one figure to the next assuming you don't
   change colors/letter combinations.  So the first logo in the figure must
   contain this header, but later ones don't really need it.  You can remove
   the header material by using the censor program:

   censor < logo.ps > logo.no.header.ps

   Playing with Ibeams
   -------------------
   Shmuel Pietrokovski (bppietro@dapsas1.weizmann.ac.il) suggested that the
   middle of the Ibeams be removable so that it doesn't get in the way of
   logos.  That is, a normal Ibeam looks like:

   -----
     |
     |
     |
     |
     |
     |
   -----

   This is sitting on the top of the sequence logo stack of letters.  This is
   obtained by setting the Ibeamfraction to 1.0.  Shmuel suggested that there be
   a parameter to remove the vertical part or to have it partway:

   -----
     |
     |


     |
     |
   -----

   This is obtained by setting the Ibeamfraction to 0.6.  Setting Ibeamfraction
   to -1.0, puts the vertical parts OUTSIDE the bars.  This way one can read
   one standard deviation of the stack and also have a mark at (for example) 2
   standard deviations out at the tips of the thumb tacks:

     |
     |
   -----


   -----
     |
     |

author
   Thomas D. Schneider
   National Cancer Institute
   Laboratory of Mathematical Biology
   NCI/FCRDC Bldg 469. Room 144
   P.O. Box B
   Frederick, MD  21702-1201
   (301) 846-5581 (-5532 for messages)
   email: toms@ncifcrf.gov

examples
   makelogop parameters:

-15 2      FROM to TO range to make the logo over
1          sequence coordinate before which to put a bar on the logo
15 2       (xcorner, ycorner) lower left hand corner of the logo (in cm)
90         rotation: angle to rotate the graph
1.0        charwidth: (real, > 0) the width of the logo characters, in cm
10 0.1     barheight, barwidth: (real, > 0) height of vertical bar, in cm
2          barbits: (real) height of the vertical bar, in bits; < 0: no I-beam
no bars    barends: if 'b' put bars before and after each line
show       showingbox: if 's' show a dashed box around each character
no outline outline: if 'o' make each character as an outline
100        stacksperline: number of character stacks per line output
1          linesperpage: number of lines per page output
1.1        linemove: line separation relative to the barheight
numbers    numbering: if the first letter is 'n' then each stack is numbered
1          shrinking: factor by which to shrink characters inside dashed box
2          strings: the number of user defined strings to follow
2 14 1     coordinates of the first string (in cm)
First TITLE
3 13 1     coordinates of the second string (in cm)
SECOND TITLE

   colors:
* Color scheme for logos of DNA (for the makelogo program).
* color order is red-green-blue
*
* green:
A 0 1 0
a 0 1 0
*
* blue:
C 0 0 1
c 0 0 1
*
* red:
T 1 0 0
t 1 0 0
*
* orange:
G 1 0.7 0
g 1 0.7 0

   wave:
l        extreme: char; h or l, the high or low extreme to be defined
2        wavelocation: real; the location in bases of the extreme
1.0      wavebit: real; the location in bits of the extreme
0.5      waveamplitude: real; the amplitude of the wave in bits
10.4     wavelength: real; the wave length of the wave in bases
0        dash: real; the size of dashes in cm.  dash <= 0 means no dashes
0.1      thickness: real; thickness of the wave in cm. <=0: default.

  A test symvec is provided with the program, file 'symvec.demo', to be run with
  'colors.demo' and 'makelogop.demo'.

documentation
   Description of Logos:
@article{Schneider.Stephens.Logo,
author = "T. D. Schneider
 and R. M. Stephens",
title = "Sequence Logos: A New Way to Display Consensus Sequences",
journal = "Nucl. Acids Res.",
volume = "18",
pages = "6097-6100",
year = "1990"}

   The Blue Book:
@book{PostScriptTutorial1985,
author = "{Adobe Systems Incorporated}",
title = "PostScript Language Tutorial and Cookbook",
publisher = "Addison-Wesley Publishing Company",
address = "Reading, Massachusetts",
callnumber = "QA76.73.P67P68",
isbn = "0-201-10179-3",
year = "1985"}

   The Red Book:
@book{PostScriptManual1985,
author = "{Adobe Systems Incorporated}",
title = "PostScript Language Reference Manual",
publisher = "Addison-Wesley Publishing Company",
address = "Reading, Massachusetts",
callnumber = "QA76.73.P67P67",
isbn = "0-201-10174-2",
year = "1985"}

   Dirty DNA synthesis experiments:
@article{Schneider1989,
author = "T. D. Schneider
 and G. D. Stormo",
title = "Excess Information at Bacteriophage {T7} Genomic Promoters
Detected by a Random Cloning Technique",
year = "1989",
journal = "Nucl. Acids Res.",
volume = "17",
pages = "659-674"}

see also
   rsgra.p, rseq.p, dalvec.p, alpro.p, sites.p, censor.p

bugs
   Some chi-logo (upside down characters) do not display on OpenWindows,
   but do print ok on the Apple LaserWriter IIntx.  The reason is completely
   obscure.

   A bug in NeWS 1.1 is that characters that are scaled too small are
   forced to be big.  This messes up the logo and can be confusing.
   Another bug in NeWS 1.1 prevents one from using the outline, but
   the dashed boxes will show up.
   Sometimes displaying a logo in NeWS 1.1 on a Sun 4 will cause an 'illegal
   instruction', after which one is thrown completely off the computer.  The
   source of this is not known, since it is not repeatable.
   The first two bugs are resolved under OpenWindows 2; the third has not
   been observed.
   These NeWS bugs do not apply to the Apple LaserWriter IIntx,
   which prints everything correctly.

technical notes
   Unfortunately PostScript fonts are not exactly the same height.  Thus if A
   and T are the standard, then C and G hang above and below the line.
   This has been solved in this version of makelogo.  As a consequence,
   the user never need to determine any character sizes empirically, and
   the logos should work on any PostScript printer.

   Special thanks go to the following people for their help in solving this
   problem:

   Kevin Andresen [kevina@apple.com]
   "The problem facing you is that, while the PostScript language is more or
   less standard, the font shapes depend on the designer, type vendor, or
   language implementation.  The fonts used in NeWS are not exactly the same
   as those from Adobe, which are not the same as those from Bitstream, which
   are not the same as the original lead type, etc.  (This is an
   industry-wide issue.)  One way to compensate for this in PostScript is to
   use the charpath and pathbbox operators and scale appropriately."

   He provided a program, which I then rewrote and generalized.  That version
   almost worked, but not quite.  This was solved by:

   finlay@Eng.Sun.COM (John Finlay) who said:
   "It would appear that the calculation of the pathbbox for characters varies
   with the scale of the characters (I don't know why exactly but would
   speculate that there's probably some weirdness with the font hints and
   scaling).  I modified your postscript to iterate once on the size and
   recalculate the pathbbox at the scaled size.  Seems to printout OK (inside
   the boxes) on a LWI, LWII and in NeWS2.0 (though NeWS still seems to get the
   wide slightly wrong)."

   shiva@well.sf.ca.us (Kenneth Porter) was also involved and actively
   interested.  My apologies if I have forgotten someone else who contributed.

   The letter I and the vertical bar (|) are treated specially since in the
   Helvetica-Bold font they are rectangles and would completely fill the
   character space.  In addition, the letter I is centered by makelogo.

   Thanks go to Joe Mack for suggesting numbering and titles (strings) and to
   Pete Lemkin and Wojciech Kasprzak for pointing out that the shrink option
   would be helpful.  Thanks to Jeff Haemer for pointing out that the
   PostScript program should begin with '%!', and for suggesting that
   the string fonts should be different from the logos themselves.

   MISSING LOGO LETTER PROBLEM

   The OpenWindows PostScript on a Sun workstation will mess up displaying a
   stack of letters if the vertical movement is too small.  The result is that
   the letters above that point are missing.  This occurs if there is a highly
   conserved base and very few other bases.  The result is a huge gap where the
   highly conserved base should be.  Other printers do fine, so this is a
   problem with the Sun implementation of PostScript (will they ever get it
   right???).  If you don't have this window system, set the constant
   gooddisplay to true.  If you do want the logos to show up properly on the
   screen, use false.  Unfortunately, this will mean that the vertical
   translation for the small letters won't be done, so the display will be very
   slightly wrong.

*/
/* end module describe.makelogo */

/* begin module makelogo.const */

#define infofield       8
    /* size of field for printing information in bits */
#define infodecim       5
    /* number of decimal places for printing information */

#define nfield          4
    /* size of field for printing n, the number of sites */
#define mapmax          26
    /* the maximum number of symbols that can be sorted */

#define pwid            8
    /* width in character places to print PostScript numbers */
#define pdec            5   /* decimal places to print PostScript numbers */
#define pdecolor        4
/* decimal places for color descriptions (5 WILL CAUSE
                 NeWS 1.1 TO BOMB) */

#define pnum            100000L
    /* 10^pdec for testing when something will round to zero */

#define protecting      true
/* protect the user against PostScript requirements
   in user defined strings.  */

#define gooddisplay     false   /* see technical notes for explanation. */

/* end module makelogo.const */

/* begin module interact.const */

#define maxstring       1500   /* the maximum string */


/* end module interact.const version = 4.09; (@ of prgmod.p 1990 May 18 */


/* begin module interact.type */

typedef struct string {
  /* a string of characters */
  Char letters[maxstring];   /* the letters in the string */
  long length;   /* the number of characters in the string */
  long current;   /* the letter we are working on */
} string;

/* end module interact.type version = 4.09; (@ of prgmod.p 1990 May 18 */

/* begin module makelogo.type */
/* types for sorting the symbols */
typedef char position;

typedef struct place {
  Char b;   /* the symbol */
  /* the number of symbols */
  long n;
} place;

/* type for making a list of strings */

typedef struct strings {
  string astring;
  double x;   /* x coordinate of the string */
  double y;   /* y coordinate of the string */
  double s;   /* scale factor */
  struct strings *next;
} strings;

/* end module makelogo.type */

/* begin module rsgra.type */
/* to link several wave definitions together */

typedef struct waveparam {
  /* parameters to define a cosine wave */
  /* define a cosine wave: */
  Char extreme;   /* h or l, the high or low extreme to be defined */
  double wavelocation;   /* the location in bases of the extreme */
  double wavebit;   /* the location in bits of the extreme */
  double waveamplitude;   /* the amplitude of the wave in bits */
  double wavelength;   /* the wave length of the wave in bases */
  double dash;   /* the size of dashes in cm.  dash <= 0 means no dashes */
  double thickness;   /* thickness of the wave in cm.  <= 0 means default */
  struct waveparam *next;   /* the next wave */
} waveparam;

/* end module rsgra.type */


/* begin module makelogo.var */
Static _TEXT symvec;   /* output of alpro program */
Static _TEXT makelogop;   /* parameters to control the program */
Static _TEXT colors;   /* color definitions */
Static _TEXT marks;   /* locations of marks on the logo */
Static _TEXT wave;   /* cosine wave definition */
Static _TEXT logo;   /* output of program */

/* the storage for sorting the symbols */
Static place map[mapmax];


Static jmp_buf _JL1;


/* end module makelogo.var */

/* begin module halt */
Static Void halt()
{
  /* stop the program.  the procedure performs a goto to the end of the
     program.  you must have a label:
        label 1;
     declared, and also the end of the program must have this label:
        1: end.
     examples are in the module libraries.
     this is the only goto in the delila system. */
  printf(" program halt.\n");
  longjmp(_JL1, 1);
}


/* end module halt version = 4.09; (@ of prgmod.p 1990 May 18 */

/* begin module interact.clearstring */
Static Void clearstring(ribbon)
string *ribbon;
{
  /* empty the string */
  long index;   /* to the ribbon */

  for (index = 0; index < maxstring; index++)
    ribbon->letters[index] = ' ';
  ribbon->length = 0;
  ribbon->current = 0;
}  /* clearstring */


/* end module interact.clearstring version = 4.09; (@ of prgmod.p 1990 May 18 */

/* begin module interact.getstring */
Static Void getstring(afile, buffer, gotten)
_TEXT *afile;
string *buffer;
boolean *gotten;
{
  /* get a string from a file not using string calls.  this lets one
obtain lines from a file without interactive prompts */
  long index;   /* of buffer */

  clearstring(buffer);
  if (BUFEOF(afile->f)) {
    *gotten = false;
    return;
  }
  index = 0;
  while (!P_eoln(afile->f) && index < maxstring) {
    index++;
    buffer->letters[index - 1] = getc(afile->f);
    if (buffer->letters[index - 1] == '\n')
      buffer->letters[index - 1] = ' ';
  }

  if (!P_eoln(afile->f)) {
    printf(" getstring: a line exceeds maximum string size (%ld)\n",
	   (long)maxstring);
    halt();
  }

  buffer->length = index;
  buffer->current = 1;
  fscanf(afile->f, "%*[^\n]");
  getc(afile->f);
  *gotten = true;
}  /* getstring */


/* end module interact.getstring version = 4.09; (@ of prgmod.p 1990 May 18 */

/* begin module interact.writestring */
Static Void writestring(tofile, s)
_TEXT *tofile;
string *s;
{
  /* write the string s to file tofile, no writeln */
  long i;   /* index to s */
  long FORLIM;

  FORLIM = s->length;
  for (i = 0; i < FORLIM; i++)
    putc(s->letters[i], tofile->f);
}  /* writestring */


/* end module interact.writestring version = 4.09; (@ of prgmod.p 1990 May 18 */

Static boolean lessthan(a, b)
position a, b;
{
  /* see quicksort */
  /* the abs function makes sure upside down
     letters are still sorted the right way! */
  return (abs(map[a - 1].n) < abs(map[b - 1].n));
}


Static Void swap_(a, b)
position a, b;
{
  /* see quicksort */
  Char holdb;
  long holdn;

  holdn = map[a - 1].n;
  map[a - 1].n = map[b - 1].n;
  map[b - 1].n = holdn;

  holdb = map[a - 1].b;
  map[a - 1].b = map[b - 1].b;
  map[b - 1].b = holdb;

  /*;write(output,'a=',a:1,', b=',b:1); print (@ for testing */
}


/* begin module quicksort */

Static Void quicksort(left, right)
position left, right;
{
  /* quick sort a list between positions left and right, into ascending order.
     a position is simply a scalar of the form 0..max.
     the array to be sorted is dimensioned 1..max.
(the difference in the ranges is important to the correct operation
of the sort...)
     two external routines are used:
        function lessthan(a, b: position): boolean is a generalized test for
            value-at-a < value-at-b.
        procedure swap(a, b: position) switches the items at positions a and b.
     since these routines are external, the procedure is general.

     this procedure taken from the book
     'algorithms + data structures = programs' by niklaus wirth,
     prentice-hall, inc., englewood cliffs, n.j.(1976), pp. 76-82 */
  position lower, upper;   /* the positions looked at currently */
  position center;   /* the rough center of the region being sorted */

  lower = left;
  center = (left + right) / 2;
  upper = right;

  do {
    while (lessthan(lower, center))
      lower++;
    while (lessthan(center, upper))
      upper--;

    if (lower <= upper) {
      /* keep track of the center through the map: */
      if (lower == center)
	center = upper;
      else if (upper == center)
	center = lower;
      swap_(lower, upper);
      lower++;
      upper--;
    }
  } while (lower <= upper);

  if (left < upper)
    quicksort(left, upper);
  if (lower < right)
    quicksort(lower, right);
}


/* end module quicksort version = 4.09; (@ of prgmod.p 1990 May 18 */

/* begin module copyaline */
Static Void copyaline(fin, fout)
_TEXT *fin, *fout;
{
  /* copy a line from file fin to file fout */
  while (!P_eoln(fin->f)) {
    putc(P_peek(fin->f), fout->f);
    getc(fin->f);
  }
  fscanf(fin->f, "%*[^\n]");
  getc(fin->f);
  putc('\n', fout->f);
}  /* copyaline */


/* end module copyaline version = 4.09; (@ of prgmod.p 1990 May 18 */

/* ********************************************************************** */
/* begin module rsgra.readwaveparameters */
Static Void readwaveparameters(afile, w)
_TEXT *afile;
waveparam **w;
{
  /* read from afile the wave parameters w */
  waveparam *p;   /* one of the definitions of a cosine wave */

  if (*afile->name != '\0') {
    if (afile->f != NULL)
      afile->f = freopen(afile->name, "r", afile->f);
    else
      afile->f = fopen(afile->name, "r");
  } else
    rewind(afile->f);
  if (afile->f == NULL)
    _EscIO(FileNotFound);
  RESETBUF(afile->f, Char);
  if (BUFEOF(afile->f)) {
    *w = NULL;
    return;
  }
  *w = (waveparam *)Malloc(sizeof(waveparam));
  p = *w;
  while (!BUFEOF(afile->f)) {
    fscanf(afile->f, "%c%*[^\n]", &p->extreme);
    getc(afile->f);
    if (p->extreme == '\n')
      p->extreme = ' ';
    fscanf(afile->f, "%lg%*[^\n]", &p->wavelocation);
    getc(afile->f);
    fscanf(afile->f, "%lg%*[^\n]", &p->wavebit);
    getc(afile->f);
    fscanf(afile->f, "%lg%*[^\n]", &p->waveamplitude);
    getc(afile->f);
    fscanf(afile->f, "%lg%*[^\n]", &p->wavelength);
    getc(afile->f);

    /* one may skip the dash and thickness parameters
       of the last wave definition.  This allows
       backwards compatability, but should not be
       used in general. */
    if (BUFEOF(afile->f)) {
      p->dash = 0.0;
      p->thickness = 0.0;
    } else {
      fscanf(afile->f, "%lg%*[^\n]", &p->dash);
      getc(afile->f);
      if (BUFEOF(afile->f))
	p->thickness = 0.0;
      else {
	fscanf(afile->f, "%lg%*[^\n]", &p->thickness);
	getc(afile->f);
      }
    }
    if (!BUFEOF(afile->f)) {
      p->next = (waveparam *)Malloc(sizeof(waveparam));
      p = p->next;
    } else
      p->next = NULL;
  }
}


/* end module rsgra.readwaveparameters */
/* ********************************************************************** */

/* begin module makelogo.protectpostscript */
Static Void protectpostscript(afile, c)
_TEXT *afile;
Char c;
{
  /* Special characters must be protected against!  Put out a protective
backslash for character c which would otherwise destroy the PostScript
interpreter.  The parenthesis is used in PostScript to indicate the bounds of a
string, while the percent is the comment character.  The backslash also needs
protection, since it is the escape to indicate that the next character is part
of the string. */
  if (c == '\\' || c == '%' || c == ')' || c == '(')
    putc('\\', afile->f);
}


/* end module makelogo.protectpostscript */

/* begin module makelogo.postscriptstring */
Static Void postscriptstring(tofile, s)
_TEXT *tofile;
string *s;
{
  /* write the string s to file tofile, no writeln.  Protect the user
by blocking postscript specific characters. */
  long i;   /* index to s */
  long FORLIM;

  putc('(', tofile->f);
  if (protecting) {
    FORLIM = s->length;
    for (i = 0; i < FORLIM; i++) {
      protectpostscript(tofile, s->letters[i]);
      putc(s->letters[i], tofile->f);
    }
  } else
    writestring(tofile, s);
  putc(')', tofile->f);
}  /* postscriptstring */


/* end module makelogo.postscriptstring */

/* ********************************************************************** */
/* ********************************************************************** */

/* begin module makelogo.truth */
Static Void truth(f, b)
_TEXT *f;
boolean b;
{
  /* write the true-false value of b to file f */
  if (b)
    fprintf(f->f, "true");
  else
    fprintf(f->f, "false");
}


/* Local variables for startpostscript: */
struct LOC_startpostscript {
  _TEXT *l, *colors;
  long lowest, highest, bar;
  double xcorner, ycorner, rotation, charwidth, barheight, barwidth, barbits,
	 Ibeamfraction;
  boolean barends, showingbox, outline, caps;
  long stacksperline, linesperpage;
  double linemove;
  boolean numbering, shrinking;
  double shrink;
  strings *thestrings;
  boolean HalfWhiteIbeam;
  Char symbol;   /* a symbol to which to assign a color */
  strings *stringspot;   /* current spot in thestrings */
  long stringnumber;   /* count of the strings written */
  double red, green, blue;   /* color definitions */
} ;

Local Void p1(LINK)
struct LOC_startpostscript *LINK;
{
  fprintf(LINK->l->f, "%%\n");
  fprintf(LINK->l->f, "%% logo from %ld to %ld\n",
	  LINK->lowest, LINK->highest);
  fprintf(LINK->l->f, "%%%%EndComments\n\n");

  fprintf(LINK->l->f,
	  "/cmfactor 72 2.54 div def %% defines points -> cm conversion\n");
  fprintf(LINK->l->f,
	  "/cm {cmfactor mul} bind def %% defines centimeters\n\n");

  fprintf(LINK->l->f, "%% user defined parameters\n");
  fprintf(LINK->l->f, "/lowest %ld def\n", LINK->lowest);
  fprintf(LINK->l->f, "/highest %ld def\n", LINK->highest);
  fprintf(LINK->l->f, "/bar %ld def\n", LINK->bar);
  fprintf(LINK->l->f, "/xcorner %*.*f cm def\n", pwid, pdec, LINK->xcorner);
  fprintf(LINK->l->f, "/ycorner %*.*f cm def\n", pwid, pdec, LINK->ycorner);
  fprintf(LINK->l->f, "/rotation %*.*f def %% degrees\n",
	  pwid, pdec, LINK->rotation);
  fprintf(LINK->l->f, "/charwidth %*.*f cm def\n",
	  pwid, pdec, LINK->charwidth);
  fprintf(LINK->l->f, "/barheight %*.*f cm def\n",
	  pwid, pdec, LINK->barheight);
  fprintf(LINK->l->f, "/barwidth %*.*f cm def\n", pwid, pdec, LINK->barwidth);
  fprintf(LINK->l->f, "/barbits %*.*f def %% bits\n",
	  pwid, pdec, LINK->barbits);
  fprintf(LINK->l->f, "/Ibeamfraction %*.*f def\n",
	  pwid, pdec, LINK->Ibeamfraction);
  fprintf(LINK->l->f, "/barends ");
  truth(LINK->l, LINK->barends);
  fprintf(LINK->l->f, " def\n");
  fprintf(LINK->l->f, "/showingbox ");
  truth(LINK->l, LINK->showingbox);
  fprintf(LINK->l->f, " def\n");
  fprintf(LINK->l->f, "/outline ");
  truth(LINK->l, LINK->outline);
  fprintf(LINK->l->f, " def\n");
  fprintf(LINK->l->f, "/caps ");
  truth(LINK->l, LINK->caps);
  fprintf(LINK->l->f, " def\n");
  fprintf(LINK->l->f, "/stacksperline %ld def\n", LINK->stacksperline);
  fprintf(LINK->l->f, "/linesperpage %ld def\n", LINK->linesperpage);
  fprintf(LINK->l->f, "/linemove %*.*f def\n", pwid, pdec, LINK->linemove);
  fprintf(LINK->l->f, "/numbering ");
  truth(LINK->l, LINK->numbering);
  fprintf(LINK->l->f, " def\n");
  fprintf(LINK->l->f, "/shrinking ");
  truth(LINK->l, LINK->shrinking);
  fprintf(LINK->l->f, " def\n");
  fprintf(LINK->l->f, "/shrink %*.*f def\n", pwid, pdec, LINK->shrink);
  fprintf(LINK->l->f, "/HalfWhiteIbeam ");
  truth(LINK->l, LINK->HalfWhiteIbeam);
  fprintf(LINK->l->f, " def\n\n");

  fprintf(LINK->l->f, "/knirhs 1 shrink sub 2 div def\n");
  fprintf(LINK->l->f, "/charwidth4 charwidth 4 div def\n");
  fprintf(LINK->l->f, "/charwidth2 charwidth 2 div def\n\n");

  if (LINK->outline) {
    fprintf(LINK->l->f,
      "%% Since outlining goes around the inner edge of the character\n");
    fprintf(LINK->l->f,
	    "%% make the thickness of the character bigger to compensate.\n");
    fprintf(LINK->l->f, "/setthelinewidth {2 setlinewidth} def\n");
  } else
    fprintf(LINK->l->f, "/setthelinewidth {1 setlinewidth} def\n");
  fprintf(LINK->l->f, "setthelinewidth %% set to normal linewidth\n\n");

  fprintf(LINK->l->f, "%% Set up the font size for the graphics\n");
  fprintf(LINK->l->f, "/fontsize charwidth def\n\n");

}

Local Void p2(LINK)
struct LOC_startpostscript *LINK;
{
  putc('%', LINK->l->f);
  fprintf(LINK->l->f,
	  "(*[[ This special comment allows deletion of the repeated\n");
  fprintf(LINK->l->f,
	  "%% procedures when several logos are concatenated together\n");
  fprintf(LINK->l->f, "%% See the censor program.\n\n");

  fprintf(LINK->l->f, "/charparams { %% char charparams => uy ux ly lx\n");
  fprintf(LINK->l->f,
	  "%% takes a single character and returns the coordinates that\n");
  fprintf(LINK->l->f, "%% defines the outer bounds of where the ink goes\n");
  fprintf(LINK->l->f, "  gsave\n");
  fprintf(LINK->l->f, "    newpath\n");
  fprintf(LINK->l->f, "    0 0 moveto\n");
  fprintf(LINK->l->f,
	  "    %% take the character off the stack and use it here:\n");
  fprintf(LINK->l->f, "    true charpath \n");
  fprintf(LINK->l->f, "    flattenpath \n");
  fprintf(LINK->l->f,
    "    pathbbox %% compute bounding box of 1 pt. char => lx ly ux uy\n");
  fprintf(LINK->l->f, "    %% the path is here, but toss it away ...\n");
  fprintf(LINK->l->f, "  grestore\n");
  fprintf(LINK->l->f, "  /uy exch def\n");
  fprintf(LINK->l->f, "  /ux exch def\n");
  fprintf(LINK->l->f, "  /ly exch def\n");
  fprintf(LINK->l->f, "  /lx exch def\n");
  /*
writeln(l,'%     % print the parameters to the user:');
writeln(l,'%     (lx) lx (ly) ly (ux) ux (uy) uy pstack');
writeln(l,'%     clear % clean up the stack, having printed all that');
*/
  fprintf(LINK->l->f, "} bind def\n\n");

  fprintf(LINK->l->f, "/dashbox { %% xsize ysize dashbox -\n");
  fprintf(LINK->l->f, "%% draw a dashed box of xsize by ysize (in points)\n");
  fprintf(LINK->l->f, "  /ysize exch def %% the y size of the box\n");
  fprintf(LINK->l->f, "  /xsize exch def %% the x size of the box\n");
  fprintf(LINK->l->f, "  1 setlinewidth\n");
  fprintf(LINK->l->f, "  gsave\n");
  fprintf(LINK->l->f,
	  "    %% Define the width of the dashed lines for boxes:\n");
  fprintf(LINK->l->f, "    newpath\n");
  fprintf(LINK->l->f, "    0 0 moveto\n");
  fprintf(LINK->l->f, "    xsize 0 lineto\n");
  fprintf(LINK->l->f, "    xsize ysize lineto\n");
  fprintf(LINK->l->f, "    0 ysize lineto\n");
  fprintf(LINK->l->f, "    0 0 lineto\n");
  fprintf(LINK->l->f, "    [3] 0 setdash\n");
  fprintf(LINK->l->f, "    stroke\n");
  fprintf(LINK->l->f, "  grestore\n");
  fprintf(LINK->l->f, "  setthelinewidth\n");
  fprintf(LINK->l->f, "} bind def\n\n");

  fprintf(LINK->l->f, "/boxshow { %% xsize ysize char boxshow\n");
  fprintf(LINK->l->f,
	  "%% show the character with a box around it, sizes in points\n");
  fprintf(LINK->l->f, "gsave\n");
  fprintf(LINK->l->f, "  /tc exch def %% define the character\n");
  fprintf(LINK->l->f, "  /ysize exch def %% the y size of the character\n");
  fprintf(LINK->l->f, "  /xsize exch def %% the x size of the character\n");
  fprintf(LINK->l->f, "  /xmulfactor 1 def /ymulfactor 1 def\n\n");

  fprintf(LINK->l->f,
	  "  %% if ysize is negative, make everything upside down!\n");
  fprintf(LINK->l->f, "  ysize 0 lt {\n");
  fprintf(LINK->l->f, "    %% put ysize normal in this orientation\n");
  fprintf(LINK->l->f, "    /ysize ysize abs def\n");
  fprintf(LINK->l->f, "    xsize ysize translate\n");
  fprintf(LINK->l->f, "    180 rotate\n");
  fprintf(LINK->l->f, "  } if\n\n");

  fprintf(LINK->l->f,
	  "  %% Don't show the box if it is a vertical bar, otherwise do.\n");
  fprintf(LINK->l->f,
	  "  showingbox {tc (|) ne {xsize ysize dashbox} if} if\n\n");

  fprintf(LINK->l->f, "  shrinking {tc (|) ne {\n");
  fprintf(LINK->l->f, "    xsize knirhs mul ysize knirhs mul translate\n");
  fprintf(LINK->l->f, "    shrink shrink scale\n");
  fprintf(LINK->l->f, "  } if} if\n\n");

  fprintf(LINK->l->f, "  2 {\n");
  fprintf(LINK->l->f, "    gsave\n");
  fprintf(LINK->l->f, "    xmulfactor ymulfactor scale\n");
  fprintf(LINK->l->f, "    tc charparams\n");
  fprintf(LINK->l->f, "    grestore\n\n");

  /* NOTE:  The following if statements in the next two sections make sure that
the size of the character has not gone to zero.  This apparently can happen
under OpenWindows, but not NeWS the Apple laserwriter or Freedom of the Press
Tektronix colorquick conversion. */

  fprintf(LINK->l->f, "    ysize %% desired size of character in points\n");
  fprintf(LINK->l->f, "    uy ly sub %% height of character in points\n");
  fprintf(LINK->l->f, "    dup 0.0 ne {\n");
  fprintf(LINK->l->f,
	  "      div %% factor by which to scale up the character\n");
  fprintf(LINK->l->f, "      /ymulfactor exch def\n");
  fprintf(LINK->l->f, "    } %% end if\n");
  fprintf(LINK->l->f, "    {pop pop}\n");
      /* remove the stuff from the stack and go on */
  fprintf(LINK->l->f, "    ifelse\n\n");
  fprintf(LINK->l->f, "    xsize %% desired size of character in points\n");
  fprintf(LINK->l->f, "    ux lx sub %% width of character in points\n");
  fprintf(LINK->l->f, "    dup 0.0 ne {\n");
  fprintf(LINK->l->f,
	  "      div %% factor by which to scale up the character\n");
  fprintf(LINK->l->f, "      /xmulfactor exch def\n");
  fprintf(LINK->l->f, "    } %% end if\n");
  fprintf(LINK->l->f, "    {pop pop}\n");
  fprintf(LINK->l->f, "    ifelse\n");
  fprintf(LINK->l->f, "  } repeat\n\n");

  /* The letter I must be specially centered in the Helvetica-Bold font.
We also account for the width of the character itself, so it should be centered
perfectly. */
  fprintf(LINK->l->f,
	  "  %% Adjust horizontal position if the symbol is an I\n");
  fprintf(LINK->l->f,
    "  tc (I) eq {charwidth 2 div %% half of requested character width\n");
  fprintf(LINK->l->f,
	  "             ux lx sub 2 div %% half of the actual character\n");
  fprintf(LINK->l->f, "                sub      0 translate} if\n");
  fprintf(LINK->l->f, "  %% Avoid x scaling for I\n");
  fprintf(LINK->l->f, "  tc (I) eq {/xmulfactor 1 def} if\n\n");

  fprintf(LINK->l->f, "  /xmove xmulfactor lx mul neg def\n");
  fprintf(LINK->l->f, "  /ymove ymulfactor ly mul neg def\n\n");

  fprintf(LINK->l->f, "  newpath\n");
  fprintf(LINK->l->f, "  xmove ymove moveto\n");
  fprintf(LINK->l->f, "  xmulfactor ymulfactor scale\n\n");

  if (LINK->outline) {
    fprintf(LINK->l->f, "  %% Outline characters:\n");
    /* get the character's path: */
    fprintf(LINK->l->f, "  tc true charpath\n");
    /* erase the center of the character (seems necessary to do!) */
    fprintf(LINK->l->f, "  gsave 1 setgray fill grestore\n");
    /* clip everything outside the character to prevent characters
       from overlapping each other (!) and then stroke the edge.
       Thus only the part of the stroke that reaches into the CENTER
       of the character becomes black and so the character size does
       not change even though it is an outline. */
    fprintf(LINK->l->f, "  clip stroke\n");
    printf("\nWARNING: Outlined characters will not display at all under NeWS\n");
    printf("but will print fine on an Apple LaserWriter IIntx\n\n");
  } else
    fprintf(LINK->l->f, "  tc show\n");

  fprintf(LINK->l->f, "grestore\n");
  fprintf(LINK->l->f, "} def\n\n");

  fprintf(LINK->l->f, "/numchar{ %% charheight character numchar\n");
  fprintf(LINK->l->f, "%% Make a character of given height in cm,\n");
  fprintf(LINK->l->f, "%% then move vertically by that amount\n");
  fprintf(LINK->l->f, "  gsave\n");
  fprintf(LINK->l->f, "    /char exch def\n");
  fprintf(LINK->l->f, "    /charheight exch cm def\n");

  /* set up the color statements */
  if (*LINK->colors->name != '\0') {
    if (LINK->colors->f != NULL)
      LINK->colors->f = freopen(LINK->colors->name, "r", LINK->colors->f);
    else
      LINK->colors->f = fopen(LINK->colors->name, "r");
  } else
    rewind(LINK->colors->f);
  if (LINK->colors->f == NULL)
    _EscIO(FileNotFound);
  RESETBUF(LINK->colors->f, Char);
  while (!BUFEOF(LINK->colors->f)) {
    if (P_peek(LINK->colors->f) == '*') {  /* skip comment lines */
      fscanf(LINK->colors->f, "%*[^\n]");
      getc(LINK->colors->f);
      continue;
    }
    /* implement the backslash protection scheme: */
    if (P_peek(LINK->colors->f) == '\\')
      getc(LINK->colors->f);
    fscanf(LINK->colors->f, "%c%lg%lg%lg%*[^\n]", &LINK->symbol, &LINK->red,
	   &LINK->green, &LINK->blue);
    getc(LINK->colors->f);
    if (LINK->symbol == '\n')
      LINK->symbol = ' ';
    fprintf(LINK->l->f, "    char (");
    protectpostscript(LINK->l, LINK->symbol);
    fprintf(LINK->l->f, "%c) eq {", LINK->symbol);
    if (LINK->red == 1.0 || LINK->red == 0.0)
      fprintf(LINK->l->f, "%ld", (long)floor(LINK->red + 0.5));
    else
      fprintf(LINK->l->f, "%*.*f", pwid, pdecolor, LINK->red);
    putc(' ', LINK->l->f);
    if (LINK->green == 1.0 || LINK->green == 0.0)
      fprintf(LINK->l->f, "%ld", (long)floor(LINK->green + 0.5));
    else
      fprintf(LINK->l->f, "%*.*f", pwid, pdecolor, LINK->green);
    putc(' ', LINK->l->f);
    if (LINK->blue == 1.0 || LINK->blue == 0.0)
      fprintf(LINK->l->f, "%ld", (long)floor(LINK->blue + 0.5));
    else
      fprintf(LINK->l->f, "%*.*f", pwid, pdecolor, LINK->blue);
    fprintf(LINK->l->f, " setrgbcolor} if\n");
  }

  /* note: adding the following text is sufficient to cause
the converter to C to bomb with a segmentation fault!
writeln(l,'    % note: charwidth and charheight');
writeln(l,'    %  have already been converted to points');
*/

  fprintf(LINK->l->f, "    charwidth charheight char boxshow\n");
  fprintf(LINK->l->f, "  grestore\n");

  /*
writeln(l,'  % the abs in the translation function below',
            ' handles negative heights');
  */

  /* The if statements ask if the character height is greater than
one point.  If it is, the display should be ok.  If not, some
displays mess up, notably OpenWindows (!).  Force the character
to be 1 point high just to be safe.  I hate bad implementations
of PostScript! */

  if (gooddisplay)
    fprintf(LINK->l->f, "  0 charheight abs translate\n");
  else
    fprintf(LINK->l->f,
	    "  charheight abs 1 gt {0 charheight abs translate} if\n");

  fprintf(LINK->l->f, "} bind def\n\n");   /* numchar */

}

Local Void p3(LINK)
struct LOC_startpostscript *LINK;
{
  fprintf(LINK->l->f, "/Ibar{\n");
  fprintf(LINK->l->f, "%% make a horizontal bar\n");
  fprintf(LINK->l->f, "gsave\n");
  fprintf(LINK->l->f, "  newpath\n");
  fprintf(LINK->l->f, "    charwidth4 neg 0 moveto\n");
  fprintf(LINK->l->f, "    charwidth4 0 lineto\n");
  fprintf(LINK->l->f, "  stroke\n");
  fprintf(LINK->l->f, "grestore\n");
  fprintf(LINK->l->f, "} bind def\n\n");   /* Ibar */

  fprintf(LINK->l->f, "/Ibeam{ %% height Ibeam\n");
  fprintf(LINK->l->f, "%% Make an Ibeam of twice the given height, in cm\n");
  fprintf(LINK->l->f, "  /height exch cm def\n");
  fprintf(LINK->l->f, "  /heightDRAW height Ibeamfraction mul def\n");
  fprintf(LINK->l->f, "  1 setlinewidth\n");
  fprintf(LINK->l->f, "     HalfWhiteIbeam outline not and\n");
  fprintf(LINK->l->f, "     {0.75 setgray} %% grey on bottom\n");
  fprintf(LINK->l->f, "     {0 setgray} %% black on bottom\n");
  fprintf(LINK->l->f, "  ifelse\n");
  fprintf(LINK->l->f, "  gsave\n");
  fprintf(LINK->l->f, "    charwidth2 height neg translate\n");
  fprintf(LINK->l->f, "    Ibar\n");
  fprintf(LINK->l->f, "    newpath\n");
  fprintf(LINK->l->f, "      0 0 moveto\n");
  fprintf(LINK->l->f, "      0 heightDRAW rlineto\n");
  fprintf(LINK->l->f, "    stroke\n");
  fprintf(LINK->l->f, "    0 setgray %% black on top\n");
  fprintf(LINK->l->f, "    newpath\n");
  fprintf(LINK->l->f, "      0 height moveto\n");
  fprintf(LINK->l->f, "      0 height rmoveto\n");
  fprintf(LINK->l->f, "      currentpoint translate\n");
  fprintf(LINK->l->f, "    Ibar\n");
  fprintf(LINK->l->f, "    newpath\n");
  fprintf(LINK->l->f, "      0 0 moveto\n");
  fprintf(LINK->l->f, "      0 heightDRAW neg rlineto\n");
  fprintf(LINK->l->f, "      currentpoint translate\n");
  fprintf(LINK->l->f, "    stroke\n");
  fprintf(LINK->l->f, "  grestore\n");
  fprintf(LINK->l->f, "  setthelinewidth\n");
  fprintf(LINK->l->f, "} bind def\n\n");   /* Ibeam */

  /* The original simple Ibeam
writeln(l,'/Ibeam{ % height Ibeam');
writeln(l,'% Make an Ibeam of twice the given height, in cm');
writeln(l,'  /height exch cm def');
writeln(l,'  1 setlinewidth');
writeln(l,'  0 setgray % black');
writeln(l,'  gsave');
writeln(l,'    charwidth2 height neg translate');
writeln(l,'    Ibar');
writeln(l,'    newpath');
writeln(l,'      0 0 moveto');
writeln(l,'      0 height 2 mul lineto');
writeln(l,'      currentpoint translate');
writeln(l,'    stroke');
writeln(l,'    Ibar');
writeln(l,'  grestore');
writeln(l,'  setthelinewidth');
writeln(l,'} bind def'); (# Ibeam #)
writeln(l);
*/

  fprintf(LINK->l->f, "/makenumber { %% number makenumber\n");
  fprintf(LINK->l->f, "%% make the number\n");
  fprintf(LINK->l->f, "gsave\n");
  fprintf(LINK->l->f, "  shift %% shift to the other side of the stack\n");
  fprintf(LINK->l->f, "  90 rotate %% rotate so the number fits\n");
  fprintf(LINK->l->f,
	  "  dup stringwidth pop %% find the length of the number\n");
  fprintf(LINK->l->f, "  neg %% prepare for move\n");
  fprintf(LINK->l->f,
	  "  charwidth (0) charparams uy ly sub %% height of numbers\n");
  fprintf(LINK->l->f, "  sub 2 div %%\n");
  fprintf(LINK->l->f, "  moveto %% move back to provide space\n");
  fprintf(LINK->l->f, "  show\n");
  fprintf(LINK->l->f, "grestore\n");
  fprintf(LINK->l->f, "} bind def\n\n");   /* makenumber */

  fprintf(LINK->l->f, "/shift{ %% move to the next horizontal position\n");
  fprintf(LINK->l->f, "charwidth 0 translate\n");
  fprintf(LINK->l->f, "} bind def\n\n");

  fprintf(LINK->l->f, "/makebar { %% make a vertical bar and shift\n");
  fprintf(LINK->l->f, "   barwidth barheight (|) boxshow\n");
  fprintf(LINK->l->f, "   barwidth 0 translate\n");
  fprintf(LINK->l->f, "} def\n\n");

  fprintf(LINK->l->f, "%% definitions for maketic\n");
  fprintf(LINK->l->f, "/str 10 string def %% string to hold number\n");
  fprintf(LINK->l->f, "%% points of movement between tic marks:\n");
  fprintf(LINK->l->f, "%% (abs protects against barbits being negative)\n");
  fprintf(LINK->l->f, "/ticmovement barheight barbits abs div def\n\n");
  fprintf(LINK->l->f, "/maketic { %% make tic marks and numbers\n");
  fprintf(LINK->l->f, "gsave\n");
  fprintf(LINK->l->f, "  %% initial increment limit proc for\n");
  fprintf(LINK->l->f, "  0 1 barbits abs cvi\n");
  fprintf(LINK->l->f, "  {/loopnumber exch def\n\n");
  fprintf(LINK->l->f,
	  "    %% convert the number coming from the loop to a string\n");
  fprintf(LINK->l->f, "    %% and find its width\n");
  fprintf(LINK->l->f, "    loopnumber 10 str cvrs\n");
  fprintf(LINK->l->f,
	  "    /stringnumber exch def %% string representing the number\n\n");
  fprintf(LINK->l->f, "    stringnumber stringwidth pop\n");
  fprintf(LINK->l->f,
	  "    /numberwidth exch def %% width of number to show\n\n");
  fprintf(LINK->l->f, "    /halfnumberheight\n");
  fprintf(LINK->l->f, "      stringnumber charparams %% capture sizes\n");
  fprintf(LINK->l->f, "      uy ly sub 2 div\n");
  fprintf(LINK->l->f, "    def\n\n");
  fprintf(LINK->l->f, "    numberwidth 2 mul %% move back two digits\n");
  fprintf(LINK->l->f,
	  "    neg loopnumber ticmovement mul %% shift on y axis\n");
  fprintf(LINK->l->f, "    halfnumberheight sub %% down half the digit\n\n");
  fprintf(LINK->l->f, "    moveto %% move back the width of the string\n\n");
  fprintf(LINK->l->f, "    stringnumber show\n\n");
  fprintf(LINK->l->f, "    %% now show the tic mark\n");
  fprintf(LINK->l->f, "    0 halfnumberheight rmoveto %% shift up again\n");
  fprintf(LINK->l->f, "    numberwidth 0 rlineto\n");
  fprintf(LINK->l->f, "    stroke\n");
  /* note: the following two lines are separated to avoid a
problem with the p2c Pascal to C translator */
  fprintf(LINK->l->f, "  }");
  fprintf(LINK->l->f, " for\n");
  fprintf(LINK->l->f, "  grestore\n");

  /*
writeln(l,'% at this point numberwidth says how far back to go.  do that');
*/
  /* put the word 'bits' on the left */
  fprintf(LINK->l->f, "  gsave\n");
  fprintf(LINK->l->f, "    /labelstring (bits) def\n");
  fprintf(LINK->l->f, "    numberwidth neg 2.5 mul\n");
      /* x coordinate to start writing */
  fprintf(LINK->l->f, "    barheight\n");   /* height of bar */
  fprintf(LINK->l->f, "    labelstring stringwidth pop\n");
      /* length of string */
  fprintf(LINK->l->f, "    sub 2 div\n");
      /* y coordinate to start writing */
  fprintf(LINK->l->f, "    translate\n");
  fprintf(LINK->l->f, "    90 rotate\n");
  fprintf(LINK->l->f, "    0 0 moveto\n");
  fprintf(LINK->l->f, "    labelstring show\n");
      /* x coordinate to start writing */
  fprintf(LINK->l->f, "  grestore\n");

  fprintf(LINK->l->f, "} def\n");

}

Local Void p4(LINK)
struct LOC_startpostscript *LINK;
{
  fprintf(LINK->l->f, "\n/degpercycle 360 def\n");
  fprintf(LINK->l->f, " \n");
  fprintf(LINK->l->f, "/cosine {%%    amplitude  phase  wavelength  base\n");
  fprintf(LINK->l->f,
	  "%%             xmin ymin xmax ymax step dash thickness\n");
  fprintf(LINK->l->f, "%%             cosine -\n");
  fprintf(LINK->l->f, "%% draws a cosine wave with the given parameters:\n");
  fprintf(LINK->l->f, "%% amplitude (points): height of the wave\n");
  fprintf(LINK->l->f, "%% phase (points): starting point of the wave\n");
  fprintf(LINK->l->f, "%% wavelength (points): length from crest to crest\n");
  fprintf(LINK->l->f, "%% base (points): lowest point of the curve\n");
  fprintf(LINK->l->f,
	  "%% xmin ymin xmax ymax (points): region in which to draw\n");
  fprintf(LINK->l->f, "%% step steps for drawing a cosine wave\n");
  fprintf(LINK->l->f,
    "%% dash if greater than zero, size of dashes of the wave (points)\n");
  fprintf(LINK->l->f,
	  "%% thickness if greater than zero, thickness of wave (points)\n\n");
  fprintf(LINK->l->f, "  /thickness exch def\n");
  fprintf(LINK->l->f, "  /dash exch def\n");
  fprintf(LINK->l->f, "  /step exch def\n");
  fprintf(LINK->l->f, "  /ymax exch def\n");
  fprintf(LINK->l->f, "  /xmax exch def\n");
  fprintf(LINK->l->f, "  /ymin exch def\n");
  fprintf(LINK->l->f, "  /xmin exch def\n");
  fprintf(LINK->l->f, "  /base exch def\n");
  fprintf(LINK->l->f, "  /wavelength exch def\n");
  fprintf(LINK->l->f, "  /phase exch def\n");
  fprintf(LINK->l->f, "  /amplitude exch def\n");
  fprintf(LINK->l->f,
	  "  %% fun := amplitude*cos( ((-y-phase)/wavelength)*360) + base\n");
  fprintf(LINK->l->f,
	  "  /fun {phase sub wavelength div degpercycle mul cos\n");
  fprintf(LINK->l->f, "           amplitude mul base add} def\n\n");
  fprintf(LINK->l->f, "  gsave\n");
  fprintf(LINK->l->f, "    /originallinewidth currentlinewidth def\n");
  fprintf(LINK->l->f, "    thickness 0 gt {thickness setlinewidth} if\n");
  fprintf(LINK->l->f, "    /c currentlinewidth def\n");
  fprintf(LINK->l->f, "%%   Make the curve fit into the region specified\n");
  fprintf(LINK->l->f, "    newpath\n");
  fprintf(LINK->l->f, "    xmin ymin c sub moveto\n");
  fprintf(LINK->l->f, "    xmax ymin c sub lineto\n");
  fprintf(LINK->l->f, "    xmax ymax c add lineto\n");
  fprintf(LINK->l->f, "    xmin ymax c add lineto\n");
  fprintf(LINK->l->f, "    closepath\n");
  fprintf(LINK->l->f, "    clip\n\n");   /* stroke'); */
  fprintf(LINK->l->f, "    newpath\n");
  fprintf(LINK->l->f, "    xmin dup fun moveto\n");
  fprintf(LINK->l->f,
	  "    xmin step xmax { %% loop from xmin by step to xmax\n");
  fprintf(LINK->l->f, "      dup fun lineto } for\n");
  fprintf(LINK->l->f,
	  "    dash 0 gt {[dash cvi] 0 setdash} if %% turn dash on\n");
  fprintf(LINK->l->f, "    stroke\n\n");
  fprintf(LINK->l->f, "    originallinewidth setlinewidth\n");
  fprintf(LINK->l->f, "  grestore\n");
  fprintf(LINK->l->f, "} bind def\n\n");

  /* example test:
% amplitude  phase  wavelength  base:
   -2.50000 cm  6.40000 cm  8.48000 cm  7.50000 cm
% xmin ymin xmax ymax step:
   -4.80000 cm  0.00000 cm 17.60000 cm 50.50000 cm 1
    0.5 cm 0.1 cosine
  */

  fprintf(LINK->l->f, "/circle { %% x y radius circle - (path)\n");
  fprintf(LINK->l->f, "newpath 0 360 arc closepath} bind def\n\n");

  fprintf(LINK->l->f,
    "%% The following special comment allows deletion of the repeated\n");
  fprintf(LINK->l->f,
	  "%% procedures when several logos are concatenated together\n");
  fprintf(LINK->l->f, "%% See the censor program.\n");
  fprintf(LINK->l->f, "%%]]%%*)\n\n");

  fprintf(LINK->l->f, "/startpage { %% start a page\n");
  fprintf(LINK->l->f, "  %% set the font used in the title strings\n");
  fprintf(LINK->l->f, "  /Times-Bold findfont fontsize scalefont setfont\n");
  fprintf(LINK->l->f, "  gsave\n");
  fprintf(LINK->l->f,
	  "  erasepage %% REMOVE FOR PACKAGING INTO ANOTHER FIGURE\n");
  fprintf(LINK->l->f, "  xcorner ycorner translate\n");
  fprintf(LINK->l->f, "  rotation rotate\n");

}

Local Void p5(LINK)
struct LOC_startpostscript *LINK;
{
  _TEXT TEMP;

  if (LINK->thestrings == NULL)
    return;

  fprintf(LINK->l->f, "  %% create the user defined strings\n");
  LINK->stringspot = LINK->thestrings;
  LINK->stringnumber = 0;
  while (LINK->stringspot != NULL) {
    fprintf(LINK->l->f, "  gsave\n");
    if (LINK->stringspot->x < 0) {
      LINK->stringnumber++;
      fprintf(LINK->l->f, "    %% string number %ld\n", LINK->stringnumber);
      fprintf(LINK->l->f, "    %% center the string\n");
      fprintf(LINK->l->f, "    /stringscale %*.*f def\n",
	      pwid, pdec, LINK->stringspot->s);
      fprintf(LINK->l->f, "    ");
      postscriptstring(LINK->l, &LINK->stringspot->astring);
      fprintf(LINK->l->f,
	      "\n    stringwidth pop stringscale mul neg stacksperline\n");
      /* the string is actually going to be bigger than this, so multiply
         it up by the stringscalefactor */

      /* check if the user will be fooled by the loss of the string */
      if (LINK->stacksperline > (LINK->highest - LINK->lowest) * 2) {
	printf("\nWARNING: if you don't see centered string number %ld:\n",
	       LINK->stringnumber);
	printf("    \"");
	TEMP.f = stdout;
	*TEMP.name = '\0';
	writestring(&TEMP, &LINK->stringspot->astring);
	printf("\"\n");
	printf(
	  "it may be off the page because stacksperline is large (%ld) relative to the\n",
	  LINK->stacksperline);
	printf(
	  "FROM-TO range (%ld to %ld) and centering is based on stacks-per-line.  To\n",
	  LINK->lowest, LINK->highest);
	printf("solve this, reduce parameter stacksperline to FROM-TO+1 = %ld\n\n",
	       LINK->highest - LINK->lowest + 1);
      }

      fprintf(LINK->l->f, "    charwidth mul add 2 div\n");
      fprintf(LINK->l->f, "    %*.*f cm moveto\n",
	      pwid, pdec, LINK->stringspot->y);
    } else {
      fprintf(LINK->l->f, "    /stringscale %*.*f def\n",
	      pwid, pdec, LINK->stringspot->s);
      fprintf(LINK->l->f, "    %*.*f cm %*.*f cm moveto\n",
	      pwid, pdec, LINK->stringspot->x, pwid, pdec,
	      LINK->stringspot->y);
    }
    fprintf(LINK->l->f, "    stringscale stringscale scale\n");
    fprintf(LINK->l->f, "    ");
    postscriptstring(LINK->l, &LINK->stringspot->astring);
    fprintf(LINK->l->f, " show\n");
    fprintf(LINK->l->f, "    %%\n");
    LINK->stringspot = LINK->stringspot->next;
    fprintf(LINK->l->f, "  grestore\n");
  }
}

Local Void p6(LINK)
struct LOC_startpostscript *LINK;
{
  /* no obnoxious messages for now:
(* create obnoxious message to keep the user straight and true... *)
if sitesused then begin
writeln(l,
'gsave /stringscale  0.80000 def 0.00000 cm -2.00000 cm moveto % OBNOXIOUS');
writeln(l, 'stringscale stringscale scale % OBNOXIOUS');
writeln(l,
            '(\(Note: error bars show an UNDERESTIMATE of the true variation\))',
            ' % OBNOXIOUS');
writeln(l, 'show grestore % OBNOXIOUS');
end;
  */

  fprintf(LINK->l->f, "  %% now move up to the top of the top line:\n");
  fprintf(LINK->l->f,
	  "  0 linesperpage linemove barheight mul mul translate\n\n");
  fprintf(LINK->l->f, "  %% set the font used in the logos\n");
  fprintf(LINK->l->f,
	  "  /Helvetica-Bold findfont fontsize scalefont setfont\n");
  fprintf(LINK->l->f, "} def\n\n");

  fprintf(LINK->l->f,
	  "%%(*[[ This special comment allows deletion of the repeated\n");
  fprintf(LINK->l->f,
	  "%% procedures when several logos are concatenated together\n");
  fprintf(LINK->l->f, "%% See the censor program.\n\n");

  fprintf(LINK->l->f, "/endpage { %% end a page\n");
  fprintf(LINK->l->f, "  grestore\n");
  fprintf(LINK->l->f,
	  "  showpage %% REMOVE FOR PACKAGING INTO ANOTHER FIGURE\n");
  fprintf(LINK->l->f, "} def\n\n");

  fprintf(LINK->l->f, "/startline{ %% start a line\n");
  fprintf(LINK->l->f, "%% move down to the bottom of the line:\n");
  fprintf(LINK->l->f, "  0 linemove barheight mul neg translate\n");
  fprintf(LINK->l->f, "  gsave\n");
  if (LINK->barends) {
    fprintf(LINK->l->f, "  maketic\n");
    fprintf(LINK->l->f, "  makebar\n");
  }
  fprintf(LINK->l->f, "} def\n\n");

  fprintf(LINK->l->f, "/endline{ %% end a line\n");
/*>>>>>>>>   Never print the right-hand bar
  if (LINK->barends)
    fprintf(LINK->l->f, "  makebar\n");
*/
  fprintf(LINK->l->f, "  grestore\n");
  fprintf(LINK->l->f, "} def\n\n");
  fprintf(LINK->l->f,
    "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n");
  fprintf(LINK->l->f,
    "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% End of procedures %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n");
  fprintf(LINK->l->f,
    "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n\n");

  fprintf(LINK->l->f,
    "%% The following special comment allows deletion of the repeated\n");
  fprintf(LINK->l->f,
	  "%% procedures when several logos are concatenated together\n");
  fprintf(LINK->l->f, "%% See the censor program.\n");
  fprintf(LINK->l->f, "%%]]%%*)\n\n");

}


/* end module makelogo.truth */

/* begin module makelogo.startpostscript */
Static Void startpostscript(l_, colors_, lowest_, highest_, bar_, xcorner_,
  ycorner_, rotation_, charwidth_, barheight_, barwidth_, barbits_,
  Ibeamfraction_, barends_, showingbox_, outline_, caps_, stacksperline_,
  linesperpage_, linemove_, numbering_, shrinking_, shrink_, thestrings_,
  HalfWhiteIbeam_)
_TEXT *l_, *colors_;
long lowest_, highest_, bar_;
double xcorner_, ycorner_, rotation_, charwidth_, barheight_, barwidth_,
       barbits_, Ibeamfraction_;
boolean barends_, showingbox_, outline_, caps_;
long stacksperline_, linesperpage_;
double linemove_;
boolean numbering_, shrinking_;
double shrink_;
strings *thestrings_;
boolean HalfWhiteIbeam_;
{
  /* not in use now:
                            sitesused: boolean);
  */
  /* start the PostScript definitions to file l.
This routine is broken up into a number of separate procedures
to allow translation into C by the p2c program.  If this is not
done, then apparently p2c's memory for literal strings fills up,
and one gets errors like 'segmentation fault'. */
  struct LOC_startpostscript V;

  V.l = l_;
  V.colors = colors_;
  V.lowest = lowest_;
  V.highest = highest_;
  V.bar = bar_;
  V.xcorner = xcorner_;
  V.ycorner = ycorner_;
  V.rotation = rotation_;
  V.charwidth = charwidth_;
  V.barheight = barheight_;
  V.barwidth = barwidth_;
  V.barbits = barbits_;
  V.Ibeamfraction = Ibeamfraction_;
  V.barends = barends_;
  V.showingbox = showingbox_;
  V.outline = outline_;
  V.caps = caps_;
  V.stacksperline = stacksperline_;
  V.linesperpage = linesperpage_;
  V.linemove = linemove_;
  V.numbering = numbering_;
  V.shrinking = shrinking_;
  V.shrink = shrink_;
  V.thestrings = thestrings_;
  V.HalfWhiteIbeam = HalfWhiteIbeam_;
  p1(&V);
  p2(&V);
  p3(&V);
  p4(&V);
  p5(&V);
  p6(&V);
}


/* end module makelogo.startpostscript */

/* ********************************************************************** */
/* ********************************************************************** */

/* begin module capitalize */
Static Char capitalize(c)
Char c;
{
  /* convert the character c to upper case */
  long n;   /* c is the n'th letter of the alphabet */

  n = c;

  if (n >= 'a' && n <= 'z')
    c = _toupper(n);

  return c;
}


/* end module capitalize version = 4.09; (@ of prgmod.p 1990 May 18 */

/* begin module skipblanks */
Static Void skipblanks(thefile)
_TEXT *thefile;
{
  /* skip over blanks until a non-blank, or end of line, is found */
  while ((P_peek(thefile->f) == ' ') & (!P_eoln(thefile->f)))
    getc(thefile->f);
}


Static Void skipnonblanks(thefile)
_TEXT *thefile;
{
  /* skip over nonblanks until a blank, or end of line, is found */
  while ((P_peek(thefile->f) != ' ') & (!P_eoln(thefile->f)))
    getc(thefile->f);
}


/* end module skipblanks version = 2.63; (@ of dops.p 1991 November 2 */

/* begin module softnumbertest */
Static boolean softnumbertest(f)
_TEXT *f;
{
  /* test that a number follows, but don't die if there is none */
  skipblanks(f);
  if (P_peek(f->f) != '9' && P_peek(f->f) != '8' && P_peek(f->f) != '7' &&
      P_peek(f->f) != '6' && P_peek(f->f) != '5' && P_peek(f->f) != '4' &&
      P_peek(f->f) != '3' && P_peek(f->f) != '2' && P_peek(f->f) != '1' &&
      P_peek(f->f) != '0' && P_peek(f->f) != '+' && P_peek(f->f) != '-') {
    /* we can't do this because it would wreck reading parameters
          bar(output,'-');
          writeln(output,'NOTE: in the parameter file,',
            ' another number is now allowed for on this line:');
          copyaline(f,output);
    */
    return false;
  } else
    return true;
}


/* end module softnumbertest */

/* begin module makelogo.readparameters */
Static Void readparameters(theplace, lowest, highest, bar, xcorner, ycorner,
			   rotation, charwidth, barheight, barwidth, barbits,
			   Ibeamfraction, barends, showingbox, outline, caps,
			   stacksperline, linesperpage, linemove, numbering,
			   shrinking, shrink, thestrings)
_TEXT *theplace;
long *lowest, *highest, *bar;
double *xcorner, *ycorner, *rotation, *charwidth, *barheight, *barwidth,
       *barbits, *Ibeamfraction;
boolean *barends, *showingbox, *outline, *caps;
long *stacksperline, *linesperpage;
double *linemove;
boolean *numbering, *shrinking;
double *shrink;
strings **thestrings;
{
  /* read in the parameters from the place */
  boolean gotten;   /* if true, we got a user defined string */
  long numberstrings;   /* the number of strings to read from theplace */
  long n;   /* index to numberstrings */
  strings *stringspot;   /* current spot in thestrings */

  if (*theplace->name != '\0') {
    if (theplace->f != NULL)
      theplace->f = freopen(theplace->name, "r", theplace->f);
    else
      theplace->f = fopen(theplace->name, "r");
  } else
    rewind(theplace->f);
  if (theplace->f == NULL)
    _EscIO(FileNotFound);
  RESETBUF(theplace->f, Char);
  if (!BUFEOF(theplace->f)) {
    fscanf(theplace->f, "%ld%ld%*[^\n]", lowest, highest);
    getc(theplace->f);
  } else {
    printf("missing all parameters\n");
    halt();
  }

  if (!BUFEOF(theplace->f)) {
    fscanf(theplace->f, "%ld%*[^\n]", bar);
    getc(theplace->f);
  } else {
    printf("missing bar coordinate parameter\n");
    halt();
  }

  if (!BUFEOF(theplace->f)) {
    fscanf(theplace->f, "%lg%lg%*[^\n]", xcorner, ycorner);
    getc(theplace->f);
  } else {
    printf("missing corner coordinate parameters\n");
    halt();
  }

  if (!BUFEOF(theplace->f)) {
    fscanf(theplace->f, "%lg%*[^\n]", rotation);
    getc(theplace->f);
  } else {
    printf("missing rotation parameter\n");
    halt();
  }
  if ((long)floor(*rotation + 0.5) % 90 != 0) {
    printf("\nWARNING: rotations that are not multiples of\n");
    printf("of 90 degrees are likely to be scaled\n");
    printf("incorrectly, due to a PostScript limitation.\n");
    printf("See the description of the pathbbox function\n");
    printf("in the Red book.\n\n");
  }
/* p2c: makelogo.p, line 1569:
 * Note: Using % for possibly-negative arguments [317] */

  if (!BUFEOF(theplace->f)) {
    fscanf(theplace->f, "%lg%*[^\n]", charwidth);
    getc(theplace->f);
  } else {
    printf("missing charwidth parameter\n");
    halt();
  }
  if (*charwidth <= 0.0) {
    printf("charwidth parameter must be > 0 cm\n");
    halt();
  }

  if (!BUFEOF(theplace->f)) {
    fscanf(theplace->f, "%lg%lg%*[^\n]", barheight, barwidth);
    getc(theplace->f);
  } else {
    printf("missing barheight and barwidth parameters\n");
    halt();
  }
  if (*barheight <= 0.0) {
    printf("barheight parameter must be > 0 cm\n");
    halt();
  }
  if (*barwidth <= 0.0) {
    printf("barwidth parameter must be > 0 cm\n");
    halt();
  }

  if (!BUFEOF(theplace->f)) {
    fscanf(theplace->f, "%lg%*[^\n]", barbits);
    getc(theplace->f);
  } else {
    printf("missing barbits parameter\n");
    halt();
  }
  if (*barbits < 0.0) {
    printf(
      "\nWARNING: are you SURE you don't want to show the variation due to a small\n");
    printf("number of samples (i.e. the I-beam error bars)?\n\n");
  } else {
    printf("Reminder: the I-beam error bars show the\n");
    printf("variation of the entire stack not just the highest\n");
    printf("symbol, even though it may look like that.\n");
  }
  if (*barbits == 0.0) {
    printf("barbits parameter must not be zero\n");
    halt();
  }

  /* slip in a new parameter, but do it softly.  That is,
     if the user has a number, the parameter is there and read,
     but if it is not a number, just go on to the next */
  if (softnumbertest(theplace)) {
    fscanf(theplace->f, "%lg%*[^\n]", Ibeamfraction);
    getc(theplace->f);
    /* Although we could do checks on this, it's fun, and perhaps
       useful to allow the user to put in weird numbers here.  */
  } else
    *Ibeamfraction = 1.0;

  if (!BUFEOF(theplace->f)) {
    if (P_peek(theplace->f) == 'b')
      *barends = true;
    else
      *barends = false;
    fscanf(theplace->f, "%*[^\n]");
    getc(theplace->f);
  } else {
    printf("barends parameter is missing\n");
    halt();
  }

  if (!BUFEOF(theplace->f)) {
    if (P_peek(theplace->f) == 's')
      *showingbox = true;
    else
      *showingbox = false;
    fscanf(theplace->f, "%*[^\n]");
    getc(theplace->f);
  } else {
    printf("showingbox parameter is missing\n");
    halt();
  }

  if (!BUFEOF(theplace->f)) {
    if (P_peek(theplace->f) == 'o')
      *outline = true;
    else
      *outline = false;
    fscanf(theplace->f, "%*[^\n]");
    getc(theplace->f);
  } else {
    printf("outline parameter is missing\n");
    halt();
  }

  if (!BUFEOF(theplace->f)) {
    if (P_peek(theplace->f) == 'c')
      *caps = true;
    else
      *caps = false;
    fscanf(theplace->f, "%*[^\n]");
    getc(theplace->f);
  } else {
    printf("caps parameter is missing\n");
    halt();
  }

  if (!BUFEOF(theplace->f)) {
    fscanf(theplace->f, "%ld%*[^\n]", stacksperline);
    getc(theplace->f);
  } else {
    printf("stacksperline parameter is missing\n");
    halt();
  }
  if (*stacksperline <= 0) {
    printf("stacksperline parameter must be positive\n");
    halt();
  }

  if (!BUFEOF(theplace->f)) {
    fscanf(theplace->f, "%ld%*[^\n]", linesperpage);
    getc(theplace->f);
  } else {
    printf("linesperpage parameter is missing\n");
    halt();
  }
  if (*linesperpage <= 0) {
    printf("linesperpage parameter must be positive\n");
    halt();
  }

  if (!BUFEOF(theplace->f)) {
    fscanf(theplace->f, "%lg%*[^\n]", linemove);
    getc(theplace->f);
  } else {
    printf("linemove parameter is missing\n");
    halt();
  }
  if (*linemove <= 0) {
    printf("linemove parameter must be positive\n");
    halt();
  }

  if (!BUFEOF(theplace->f)) {
    if (P_peek(theplace->f) == 'n')
      *numbering = true;
    else
      *numbering = false;
    fscanf(theplace->f, "%*[^\n]");
    getc(theplace->f);
  } else {
    printf("numbering parameters are missing\n");
    halt();
  }

  if (!BUFEOF(theplace->f)) {
    fscanf(theplace->f, "%lg%*[^\n]", shrink);
    getc(theplace->f);
  } else {
    printf("shrink parameter is missing\n");
    halt();
  }
  if (*shrink > 1.0) {
    printf("Shrink parameter must be less than or equal to 1.\n");
    printf("This way, you won't create a misleading logo\n");
    printf("which has an apparent height larger than it should.\n");
  }
  if (*shrink > 0.0 && *shrink < 1.0 && !*showingbox) {
    printf("Shrinking can only be done when showing the dashed box.\n");
    printf("This way, you won't create a misleading logo\n");
    printf("which has an apparent height smaller than it should.\n");
  }
  if (!*showingbox || *shrink <= 0.0 || *shrink >= 1.0)
    *shrinking = false;
  else
    *shrinking = true;

  if (!BUFEOF(theplace->f)) {
    fscanf(theplace->f, "%ld%*[^\n]", &numberstrings);
    getc(theplace->f);
  } else {
    printf("number of user defined strings must be given\n");
    halt();
  }
  if (numberstrings <= 0) {
    *thestrings = NULL;
    return;
  }

  *thestrings = (strings *)Malloc(sizeof(strings));
  stringspot = *thestrings;
  for (n = 1; n <= numberstrings; n++) {
    if (BUFEOF(theplace->f)) {
      printf("missing a user defined string coordinate\n");
      halt();
    }
    fscanf(theplace->f, "%lg%lg%lg%*[^\n]", &stringspot->x, &stringspot->y,
	   &stringspot->s);
    getc(theplace->f);
    getstring(theplace, &stringspot->astring, &gotten);
    if (!gotten) {
      printf("missing a user defined string\n");
      halt();
    }
    if (n < numberstrings) {
      stringspot->next = (strings *)Malloc(sizeof(strings));
      stringspot = stringspot->next;
    } else
      stringspot->next = NULL;
  }
}


/* end module makelogo.readparameters */

/* begin module makelogo.warnifsitesused */
Static Void warnifsitesused(symvec, fout, sitesused)
_TEXT *symvec, *fout;
boolean *sitesused;
{
  /* 'warn [the user about error bars] if [the] sites [program] was used
[to create the symvec].' */
  Char a, b, c, d, e, f, g;   /* a simple way to do a string */

  *sitesused = false;
  if (*symvec->name != '\0') {
    if (symvec->f != NULL)
      symvec->f = freopen(symvec->name, "r", symvec->f);
    else
      symvec->f = fopen(symvec->name, "r");
  } else
    rewind(symvec->f);
  if (symvec->f == NULL)
    _EscIO(FileNotFound);
  RESETBUF(symvec->f, Char);
  if (BUFEOF(symvec->f))
    return;
  fscanf(symvec->f, "%*[^\n]");
  getc(symvec->f);   /* skip first line ('* dalvec') */
  if (BUFEOF(symvec->f))  /* determine prior program name */
    return;
  /* check that the string '* sites' exists */
  /* *   s i t e s */
  a = getc(symvec->f);
  b = getc(symvec->f);
  c = getc(symvec->f);
  d = getc(symvec->f);
  e = getc(symvec->f);
  f = getc(symvec->f);
  g = getc(symvec->f);
  if (a == '\n')
    a = ' ';
  if (b == '\n')
    b = ' ';
  if (c == '\n')
    c = ' ';
  if (d == '\n')
    d = ' ';
  if (e == '\n')
    e = ' ';
  if (f == '\n')
    f = ' ';
  if (g == '\n')
    g = ' ';
  if (a != '*' || b != ' ' || c != 's' || d != 'i' || e != 't' || f != 'e' ||
      g != 's')
    return;
  fprintf(fout->f,
    "******************************************************************************\n");
  fprintf(fout->f,
    "* NOTE: since the data come from the sites program, the error bar is not     *\n");
  fprintf(fout->f,
    "* printed on the sequence logo.                                              *\n");
  fprintf(fout->f,
    "******************************************************************************\n");

  /* no more obnoxious messages:
              writeln(fout);
              writeln(fout,'To remove the obnoxious message from your logo,');
              writeln(fout,'delete lines that have the word OBNOXIOUS on them.');
              writeln(fout);
  */

  *sitesused = true;
}


/* the value of the threshold is a guess right now! */

#define threshold       0.00001


/* end module makelogo.warnifsitesused */

/* begin module makelogo.makesymbol */
Static Void makesymbol(afile, height, caps, c)
_TEXT *afile;
double height;
boolean caps;
Char c;
{
  /* write the instructions for the symbol c with height h to file afile.
The move by the amount `height' vertically afterward is done in numchar. */
  if (fabs(height) <= threshold)
    return;
  fprintf(afile->f, "%*.*f (", pwid, pdec, height);
  protectpostscript(afile, c);
  if (caps)
    fputc(capitalize(c), afile->f);
  else
    putc(c, afile->f);
  fprintf(afile->f, ") numchar\n");
}

#undef threshold


/* end module makelogo.makesymbol */

/* begin module makelogo.Ibeam */
Static Void Ibeam(afile, height)
_TEXT *afile;
double height;
{
  /* write the instructions for making an I beam with height (in cm) to file
afile.  Return to the original coordinate afterwards */
  fprintf(afile->f, "%*.*f Ibeam\n", pwid, pdec, height);
}


/* end module makelogo.Ibeam */

/* begin module makelogo.summary */
Static Void summary(f, c, rstotal, varhnb, thefrom, theto)
_TEXT *f;
Char c;
double rstotal, varhnb;
long thefrom, theto;
{
  /* write summary information to file f.  Start each line with character c. */
  if (c != ' ')
    fprintf(f->f, "%c ", c);
  fprintf(f->f, "Rs total is %*.*f", infofield, infodecim, rstotal);
  if (varhnb >= 0)
    fprintf(f->f, " +/- %*.*f bits", infofield, infodecim, sqrt(varhnb));
  else
    fprintf(f->f, " bits (sample error not known)");
  fprintf(f->f, " in the range from %ld to %ld\n", thefrom, theto);
}


/* end module makelogo.summary */

/* begin module makelogo.makenumber */
Static Void makenumber(l, number)
_TEXT *l;
long number;
{
  /* write the PostScript instructions for forming the number in file l */
  fprintf(l->f, "(%ld ) makenumber\n", number);
}


/* end module makelogo.makenumber */

/* begin module makelogo.cosine */
Static Void cosine(afile, amplitude, phase, wavelength, base, xmin, ymin,
		   xmax, ymax, step, dash, thickness)
_TEXT *afile;
double amplitude, phase, wavelength, base, xmin, ymin, xmax, ymax;
long step;
double dash, thickness;
{
  /* write the cosine wave out to afile as defined by the parameters */
  fprintf(afile->f, "%% amplitude  phase  wavelength  base:\n");
  fprintf(afile->f, " %*.*f cm %*.*f cm %*.*f cm %*.*f cm\n",
	  pwid, pdec, amplitude, pwid, pdec, phase, pwid, pdec, wavelength,
	  pwid, pdec, base);
  fprintf(afile->f, "%% xmin ymin xmax ymax step:\n");
  fprintf(afile->f, " %*.*f cm %*.*f cm %*.*f cm %*.*f cm %ld\n",
	  pwid, pdec, xmin, pwid, pdec, ymin, pwid, pdec, xmax, pwid, pdec,
	  ymax, step);
  fprintf(afile->f, "%% dash thickness:\n");
  fprintf(afile->f, " %*.*f cm", pwid, pdec, dash);
  fprintf(afile->f, " %*.*f cm cosine\n", pwid, pdec, thickness);
}


/* end module makelogo.cosine */

/* begin module makelogo.getmark */
Static Void getmark(marks, marksymbol, markbase, markbits, markscale,
		    nextmark)
_TEXT *marks;
Char *marksymbol;
double *markbase, *markbits, *markscale;
long *nextmark;
{
  /* Obtain the information for placing the next mark (markbase,markbits),
its kind (marksymbol) and the integer location (nextmark) */
  if (BUFEOF(marks->f)) {
    *nextmark = LONG_MAX;
    return;
  }
  fscanf(marks->f, "%c%lg%lg%lg%*[^\n]", marksymbol, markbase, markbits,
	 markscale);
  getc(marks->f);
  if (*marksymbol == '\n')
    *marksymbol = ' ';
  if (*marksymbol != 'f' && *marksymbol != 'o') {
    printf("mark symbol in file marks must be one of: \"of\"\n");
    halt();
  }
  if (*markscale <= 0.0) {
    printf("mark scale must be positive\n");
    halt();
  }
  *nextmark = (long)(*markbase);
}


/* end module makelogo.getmark */

/* begin module makelogo.circle */
Static Void circle(f, x, y, radius, fill)
_TEXT *f;
double x, y, radius;
boolean fill;
{
  /* write a circle to file f at (x, y), of given radius and fill it if
"fill" is true */
  fprintf(f->f, " %*.*f cm %*.*f cm %*.*f cm circle\n",
	  pwid, pdec, x, pwid, pdec, y, pwid, pdec, radius);
  if (fill)
    fprintf(f->f, " fill\n");
  else
    fprintf(f->f, " stroke\n");
}


/* Local variables for themain: */
struct LOC_themain {
  _TEXT *logo;
  double barheight;
      /* (real, > 0) height of the vertical bar, in centimeters */
  double charwidth;
      /* (real, > 0) the width of the logo characters, in cm */
  double cmperbit;   /* conversion of bits to centimeters */
  long position_;   /* a location in the aligned sequence (true coordinate) */
  /* true if the sites program was used to create the
     data.  This determines whether an obnoxious warning should be put
     into the logo ... */
  long stacknumber;
  waveparam *wp;   /* wave parameters that define cosine waves */
} ;

Local Void docosinewave(LINK)
struct LOC_themain *LINK;
{
  /* overlay a cosine wave as specified by the parameters */
  double xscale, yscale;   /* converstion factors for x and y for the wave */
  double xmin, ymin;
      /* lower left corner the wave could be in, for the wave */
  double xmax, ymax;
      /* upper right corner the wave could be in, for the wave */
  waveparam *thiswave;   /* the wave we are currently printing */
  waveparam *WITH;

  thiswave = LINK->wp;
  while (thiswave != NULL) {
    WITH = thiswave;
    xscale = LINK->charwidth;
    yscale = LINK->cmperbit;
    xmin = (LINK->position_ - LINK->stacknumber + 1) * xscale;
	/* position */
    xmax = (LINK->position_ + 1) * xscale;   /* position */
    ymin = 0.0;   /* bits */
    ymax = WITH->waveamplitude + LINK->barheight * yscale;   /* bits */
    /* move back to the zero on the plot! */
    fprintf(LINK->logo->f, "gsave\n");
    fprintf(LINK->logo->f, " %*.*f cm 0 translate\n",
	    pwid, pdec, -(LINK->position_ + 1) * LINK->charwidth);
    if (WITH->extreme == 'h')   /* high center point cosine wave */
      cosine(LINK->logo, yscale * WITH->waveamplitude,
	     xscale * (WITH->wavelocation + 0.5), xscale * WITH->wavelength,
	     yscale * (WITH->wavebit - WITH->waveamplitude), xmin, ymin, xmax,
	     ymax, 1L, WITH->dash, WITH->thickness);
    else   /* low center point cosine wave */
      cosine(LINK->logo, -yscale * WITH->waveamplitude,
	     xscale * (WITH->wavelocation + 0.5), xscale * WITH->wavelength,
	     yscale * (WITH->wavebit + WITH->waveamplitude), xmin, ymin, xmax,
	     ymax, 1L, WITH->dash, WITH->thickness);
    /* amplitude */
    /* phase */
    /* the half of a base is to make it put the
       extreme in the middle of the character rather
       than between characters */
    /* wavelength (cm) */
    /* base (cm) */
    /* limiting box (cm) */
    /* step is in points */
    /* dash is in cm */
    /* thickness is in cm */
    /* thickness is in cm */
    fprintf(LINK->logo->f, "grestore\n");
    thiswave = thiswave->next;
  }

  /* step is in points */
  /* dash is in cm */
}


/* end module makelogo.circle */

/* begin module themain */
Static Void themain(symvec, makelogop, colors, marks, wave, logo_)
_TEXT *symvec, *makelogop, *colors, *marks, *wave, *logo_;
{
  /* the main procedure of the program */
  struct LOC_themain V;
  long actualsymbols;
  /* the sum of the actual number of symbols found in
    symvec, as opposed to nl, the number that is SUPPOSED to be there */
  long b;   /* index to a symbol */
  long bar;   /* location before which to print the bar */
  double barbits;
  /* (real) height of the vertical bar, in bits.  If negative,
     then the I-beam will not be displayed */
  boolean barends;   /* put a | before and after each line? */
  double barwidth;
      /* (real, > 0) width of the vertical bar, in centimeters */
  boolean caps;   /* if true, capitalize the logo */
  long stacksperline;   /* the number of characters per line output */
  boolean chilogo;   /* if true, this is a chilogo */
  boolean dobeam;   /* true means we are going to write the Ibeam */
  boolean dostack;   /* true means we are going to write a stack of letters */
  double fbl;   /* frequency of symbol b at position l */
  boolean HalfWhiteIbeam;
  /* true means that no colors are defined in the
     colors so the I-beam error bar is made white when inside the letters */
  long highest;   /* the coordinate of the highest symbol to graph in logo */
  double Ibeamfraction;
  /* The fraction of the Ibeam to draw.  When it is 1,
     the Ibeam is normal.  When it is zero, no vertical line is drawn. At 0.1,
     only 10 percent of the top and bottom parts of the Ibeam are drawn. */
  Char letter;   /* a letter in the alphabet test */
  long l;   /* predicted coordinate */
  double linemove;   /* line separation relative to the barheight */
  long linenumber;   /* number of lines of logo printed so far */
  long linesperpage;   /* the number of lines per page output */
  long lowest;   /* the coordinate of the lowest symbol to graph in logo */
  Char marksymbol;   /* a symbol to mark on the logo */
  double markbase;   /* location in bases of the marksymbol */
  double markbits;   /* location in bits of the marksymbol */
  double markscale;
      /* factor by which to change the size of the marksymbol */
  long nextmark;   /* the position to place the next mark */
  long nl;   /* number of symbols at position l */
  boolean numbering;   /* if true, numbers are made below the logo */
  boolean outline;   /* if true, characters are made in outline */
  long page;   /* page number we are beginning to write out */
  long previousposition;   /* the previous value of position */
  double radius;   /* radius of a circle mark */
  double rotation;   /* angle in degrees to rotate the figure */
  double rsl;   /* information at position l */
  double rsvar;   /* variance of information at position l */
  double rstotal;   /* sum of the rsl for the whole logo */
  double varhnb;   /* variance of rstotal for the whole logo */
  boolean showingbox;   /* if true, show a box around each character */
  double shrink;   /* the factor by which to shrink symbols */
  boolean shrinking;   /* whether or not to shrink */
  boolean sitesused;
  /* the number of the stack of symbols.  Unlike the
     position variable, it begins at 1.  It is used to decide when to break
     the logo onto the next line */
  long symbols;   /* number of symbols possible */
  strings *thestrings;   /* set of user defined strings */
  double x;   /* an x coordinate on the logo */
  double xcorner;
      /* the lower left corner of the x-axis on the paper (cm) */
  double y;   /*  a y coordinate on the logo */
  double ycorner;
      /* the lower left corner of the y-axis on the paper (cm) */
  _TEXT TEMP;

  V.logo = logo_;
  printf("makelogo %4.2f\n", version);

  readparameters(makelogop, &lowest, &highest, &bar, &xcorner, &ycorner,
		 &rotation, &V.charwidth, &V.barheight, &barwidth, &barbits,
		 &Ibeamfraction, &barends, &showingbox, &outline, &caps,
		 &stacksperline, &linesperpage, &linemove, &numbering,
		 &shrinking, &shrink, &thestrings);
  readwaveparameters(wave, &V.wp);

  TEMP.f = stdout;
  *TEMP.name = '\0';
  warnifsitesused(symvec, &TEMP, &sitesused);

  V.cmperbit = V.barheight / fabs(barbits);   /* converts bits to cm */

  if (*marks->name != '\0') {
    if (marks->f != NULL)
      marks->f = freopen(marks->name, "r", marks->f);
    else
      marks->f = fopen(marks->name, "r");
  } else
    rewind(marks->f);
  if (marks->f == NULL)
    _EscIO(FileNotFound);
  RESETBUF(marks->f, Char);
  getmark(marks, &marksymbol, &markbase, &markbits, &markscale, &nextmark);

  if (*colors->name != '\0') {
    if (colors->f != NULL)
      colors->f = freopen(colors->name, "r", colors->f);
    else
      colors->f = fopen(colors->name, "r");
  } else
    rewind(colors->f);
  if (colors->f == NULL)
    _EscIO(FileNotFound);
  RESETBUF(colors->f, Char);
  if (BUFEOF(colors->f) && !outline) {
    printf("Half-White Ibeams are used because the symbols are solid black.\n");
    HalfWhiteIbeam = true;
  } else
    HalfWhiteIbeam = false;

  if (*symvec->name != '\0') {
    if (symvec->f != NULL)
      symvec->f = freopen(symvec->name, "r", symvec->f);
    else
      symvec->f = fopen(symvec->name, "r");
  } else
    rewind(symvec->f);
  if (symvec->f == NULL)
    _EscIO(FileNotFound);
  RESETBUF(symvec->f, Char);
  if (*V.logo->name != '\0') {
    if (V.logo->f != NULL)
      V.logo->f = freopen(V.logo->name, "w", V.logo->f);
    else
      V.logo->f = fopen(V.logo->name, "w");
  } else {
    if (V.logo->f != NULL)
      rewind(V.logo->f);
    else
      V.logo->f = tmpfile();
  }
  if (V.logo->f == NULL)
    _EscIO(FileNotFound);
  SETUPBUF(V.logo->f, Char);
  fprintf(V.logo->f, "%%!PS-Adobe-\n");   /* Minimally conforming */
  fprintf(V.logo->f, "%%%%Title: makelogo %4.2f\n", version);
  if (!BUFEOF(symvec->f)) {
    while (P_peek(symvec->f) == '*') {
      fprintf(V.logo->f, "%% ");
      copyaline(symvec, V.logo);
    }
    fscanf(symvec->f, "%ld%*[^\n]", &symbols);
    getc(symvec->f);
    printf("%ld symbols.\n", symbols);
  }
  page = 0;
  startpostscript(V.logo, colors, lowest, highest, bar, xcorner, ycorner,
		  rotation, V.charwidth, V.barheight, barwidth, barbits,
		  Ibeamfraction, barends, showingbox, outline, caps,
		  stacksperline, linesperpage, linemove, numbering, shrinking,
		  shrink, thestrings, HalfWhiteIbeam);
  /* not in use:
                          sitesused);
  */

  if (BUFEOF(symvec->f)) {  /* do an alphabetic test logo */
    printf("Alphabet Logo\n");
    fprintf(V.logo->f, "%% Alphabet Logo\n");
    fprintf(V.logo->f, "startpage startline\n");
    if (barends)
      fprintf(V.logo->f, "makebar\n");
    fprintf(V.logo->f, "%% find out how high the bar is in centimeters:\n");
    fprintf(V.logo->f, "/barincm barheight cmfactor div def\n");
    for (b = 'A'; b <= 'Z'; b++) {
      V.position_ = b + 1 - 'A';
      if (V.position_ == bar)
	fprintf(V.logo->f, "makebar\n");
      if (V.position_ >= lowest && V.position_ <= highest) {
	if (numbering)
	  makenumber(V.logo, V.position_);
	if (!caps)
	  letter = _tolower(b);
	else
	  letter = (Char)b;
	fprintf(V.logo->f, "  gsave barincm (%c) numchar grestore shift\n",
		letter);
      }
    }
    if (barends)
      fprintf(V.logo->f, "makebar\n");
    fprintf(V.logo->f, "endline endpage\n");
    return;
  }
  /* the main loop; read through the symvec, sort the characters and then
     create the graphic.  The program assumes that the header of symvec has
     been skipped and that symbols is read in already */
  rstotal = 0.0;
  varhnb = 0.0;
  linenumber = 0;   /* trigger start of a page */
  l = lowest;
  V.position_ = lowest;
  chilogo = false;
  while (!BUFEOF(symvec->f)) {
    previousposition = V.position_;   /* keep track of previous position */
    fscanf(symvec->f, "%ld%ld%lg%lg%*[^\n]", &V.position_, &nl, &rsl, &rsvar);
    getc(symvec->f);

    /* read through the symbols and see if they are really all there.
    This check is useful when someone writes a symvec themselves. */
    actualsymbols = 0;
    for (b = 0; b < symbols; b++) {
      while (P_peek(symvec->f) == ' ')   /* skip leading blanks */
	getc(symvec->f);
      fscanf(symvec->f, "%c%ld%*[^\n]", &map[b].b, &map[b].n);
      getc(symvec->f);
      if (map[b].b == '\n')
	map[b].b = ' ';
      if (map[b].n < 0) {
	if (!chilogo) {
	  chilogo = true;
	  printf("This is a Chilogo! - Upside down letterswill be produced\n");
	}
      }
      if (chilogo)
	actualsymbols += abs(map[b].n);
      else
	actualsymbols += map[b].n;
    }
    if (!chilogo && nl != actualsymbols ||
	chilogo && abs(nl - actualsymbols) > 1.5) {
      printf("\nTHE SYMVEC FILE IS BAD!\n");
      printf("At position %ld the sum of symbols found is %ld\n",
	     V.position_, actualsymbols);
      printf("But the noted number is %ld\n", nl);
      halt();
    }
    /* in the case of the chilogo, the sum of rounded numbers
       may be off by 1 */

    /* create the PostScript code for this stack of symbols */
    if (V.position_ < lowest || V.position_ > highest)
      continue;

    rstotal += rsl;
    varhnb += rsvar;

    /* put the symbols into order of their frequency */
    quicksort(1, (int)symbols);

    /* track the line number */
    if (linenumber == 0) {
      fprintf(V.logo->f, "%%%%Page:? ?\n");    /* don't specify page # */
      fprintf(V.logo->f, "\nstartpage\n");

      page++;
      if (page > 1)
	printf("writing page %ld\n", page);

      V.stacknumber = 0;   /* trigger line to start */
    }

    /* track the number of stacks on the line */
    if (V.stacknumber == 0) {
      linenumber++;
      fprintf(V.logo->f, "startline %% line number %ld\n", linenumber);
    }
    V.stacknumber++;

    if (V.position_ == bar) {
      if (!barends || V.stacknumber != 1) {
	fprintf(V.logo->f, "%% before coordinate %ld: make the bar\n",
		V.position_);
	fprintf(V.logo->f, "makebar\n");
      }
    }

    fprintf(V.logo->f, "%% at coordinate %ld\n", V.position_);

    /* allow user to unearth the call to makenumber by hand */
    if (!numbering)
      fprintf(V.logo->f, "%% ");
    makenumber(V.logo, V.position_);

    /* avoid plotting tiny Rs values at all (PostScript blows up
       on the Apple LaserWriter - and no plot comes out.) */
    if ((long)floor(pnum * rsl * V.cmperbit + 0.5) > 0.0)
      dostack = true;
    else
      dostack = false;

    /* if rsvar is negative, this indicates that the
       sample variation is unknown.  (see the sites.p program) */
    dobeam = false;
    if (rsvar >= 0.0) {
      if (barbits > 0.0)
	dobeam = true;
    } else if (!sitesused) {
      printf("WARNING: negative Rs variation found in symvec,\n");
      printf("but the data are not from the sites program\n");
      printf("possible program or data error.\n");
    }

    if (dostack || dobeam)
      fprintf(V.logo->f, "gsave\n");
    if (dostack) {
      for (b = 0; b < symbols; b++) {
	/* draw one character in the stack of characters */
	fbl = (double)map[b].n / nl;
	makesymbol(V.logo,
	  (double)((long)floor(pnum * fbl * rsl * V.cmperbit + 0.5)) /
	  ((pnum < 0) ? -pnum : pnum), caps, map[b].b);
	/* note: the abs(pnum) makes sure that the sign of pnum
	   DOES get passed to makesymbol, so that upside down
	   symbols can be printed! */
      }
    }
    if (dobeam && !sitesused)
      Ibeam(V.logo, sqrt(rsvar) * V.cmperbit);
    if (dostack || dobeam)
      fprintf(V.logo->f, "grestore\n");

    /* make the appropriate marks within this base interval */
    if (V.position_ >= nextmark) {
      do {
	if (V.position_ == nextmark) {
	  fprintf(V.logo->f, "gsave\n");
	  x = (markbase - nextmark + 0.5) * V.charwidth;
	  y = markbits * V.cmperbit;
	  if (marksymbol == 'o' || marksymbol == 'f') {
	    radius = markscale * V.charwidth / 2.0;
	    switch (marksymbol) {

	    case 'f':
	      circle(V.logo, x, y, radius, true);
	      break;

	    case 'o':
	      circle(V.logo, x, y, radius, false);
	      break;
	    }
	  }
	  fprintf(V.logo->f, "grestore\n");
	}
	/* do the mark */
	/*
writeln(output,marksymbol,' ',markbase:5:3,
	                          ' ',markbits:5:3,' ',markscale:5:3,' ',nextmark:5);
	*/
	/* get the next one */
	getmark(marks, &marksymbol, &markbase, &markbits, &markscale,
		&nextmark);
      } while (V.position_ >= nextmark);
    }

    fprintf(V.logo->f, "shift\n");   /* move away from this stack */
    if (V.stacknumber == stacksperline || V.position_ == highest)
      docosinewave(&V);

    if (linenumber == linesperpage && V.stacknumber == stacksperline)
    {  /* complete the page */
      if (highest == bar - 1) {
	if (!barends) {
	  fprintf(V.logo->f,
		  "%% bar at end of logo: make the bar before position %ld\n",
		  V.position_);
	  fprintf(V.logo->f, "makebar\n");
	}
	/* or (stacknumber <> 1) residue from main call */
      }

      fprintf(V.logo->f, "endline\n");
      V.stacknumber = 0;   /* trigger for restarting the line */
      fprintf(V.logo->f, "endpage\n");
      linenumber = 0;   /* trigger for restarting the page */
    }


    if (V.stacknumber == stacksperline) {  /* complete the line */
      fprintf(V.logo->f, "endline\n");
      V.stacknumber = 0;   /* trigger for restarting the line */
    }

    /* check the coordinate system */
    while (l != V.position_ && l <= highest) {
      printf("\nWARNING: symvec does not contain data for position %ld\n", l);
      if (l == 0 && lowest < 0 && highest > 0 && V.position_ == 1 &&
	  previousposition == -1) {
	printf("It seems that you don't have a zero coordinate.\n");
	printf(
	  "\"... the invention, probably by the Hindus, of the digit zero has been\n");
	printf(
	  "described as one of the greatest importance in the history of mathematics.\"\n");
	printf("--- Encyclopaedia Britannica (1:1175, 1982)\n");
	printf("Please use a zero!\n");
	if (*V.logo->name != '\0') {
	  if (V.logo->f != NULL)
	    V.logo->f = freopen(V.logo->name, "w", V.logo->f);
	  else
	    V.logo->f = fopen(V.logo->name, "w");
	} else {
	  if (V.logo->f != NULL)
	    rewind(V.logo->f);
	  else
	    V.logo->f = tmpfile();
	}
	if (V.logo->f == NULL)
	  _EscIO(FileNotFound);
	SETUPBUF(V.logo->f, Char);
	halt();
      }
      putchar('\n');
      l++;   /* predict the next position */
    }
    l++;   /* predict the next position */
  }

  if (V.position_ < highest) {
    printf("\nWARNING: Highest position requested was not found in symvec\n\n");
    /* in this case, the cosine wave was not done above, so do it now */
    if (V.stacknumber != 0)
      docosinewave(&V);
  }

  /* make sure that the end line and page is done! */
  if (V.stacknumber != 0)
    fprintf(V.logo->f, "endline\n");
  if (linenumber != 0)
    fprintf(V.logo->f, "endpage\n");

  summary(V.logo, '%', rstotal, varhnb, lowest, highest);
  TEMP.f = stdout;
  *TEMP.name = '\0';
  summary(&TEMP, ' ', rstotal, varhnb, lowest, highest);


  /* do the regular logo */
}


/* end module themain */

main(argc, argv)
int argc;
Char *argv[];
{
  PASCAL_MAIN(argc, argv);
  if (setjmp(_JL1))
    goto _L1;
  logo.f = NULL;
  strcpy(logo.name, "logo");
  wave.f = NULL;
  strcpy(wave.name, "wave");
  marks.f = NULL;
  strcpy(marks.name, "marks");
  colors.f = NULL;
  strcpy(colors.name, "colors");
  makelogop.f = NULL;
  strcpy(makelogop.name, "makelogop");
  symvec.f = NULL;
  strcpy(symvec.name, "symvec");
  /*   Look for input file name suffix   JGH*/
   if(argc > 1)
   {
      strcat(logo.name, "."); strcat(logo.name, argv[1]);
      strcat(symvec.name, "."); strcat(symvec.name, argv[1]);
      strcat(makelogop.name, "."); strcat(makelogop.name, argv[1]);
      strcat(colors.name, "."); strcat(colors.name, argv[1]);  /*SP*/
   }

  themain(&symvec, &makelogop, &colors, &marks, &wave, &logo);
_L1:
  if (symvec.f != NULL)
    fclose(symvec.f);
  if (makelogop.f != NULL)
    fclose(makelogop.f);
  if (colors.f != NULL)
    fclose(colors.f);
  if (marks.f != NULL)
    fclose(marks.f);
  if (wave.f != NULL)
    fclose(wave.f);
  if (logo.f != NULL)
    fclose(logo.f);
  exit(EXIT_SUCCESS);
}



/* End. */
on);
  if (!BUFEOF(symvec->f)) {
    while (P_peek(symvec->f) == '*') {
      fprintf(V.logo->f, "%% ");
      copyaline(symvec, V.logo);
    }
    fscanf(symvec->f, "%ld%*[^\n]", &symbols);
    getc(symvec->f);
    printf("%ld symbols.\n", symbols);
  }
  page = 0;
  stablimps-3.9/blimps/matrix.c000064400001460000012000000507570774312250000161220ustar00jorjastaff00000400000027/* (C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* matrix.c: matrix manipulation functions */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

/*	system headers not in global.h   */
/*	blimps library headers */
#include 
#include 	/* includes sequences.h, output.h */
#include 	/* includes pattern.h */
#include 

/*
 * Exported variables and data structures
 */

/*
 * Local variables and data structures
 */

#define MATRIX_LENGTH_INCREASE_SIZE 80 /* the default length of the matrix */
				       /* and the size to increase by if */
				       /* more room is needed (doubtful) */

/*
 * Function definitions
 */

static Boolean read_matrix_header();
static void read_matrix_body();
static void resize_matrix();

/*
 * read_a_matrix
 *   reads a matrix from the data base and returns a pointer to the new
 *   matrix data structure
 *   Parameters:  
 *     FILE *mfp: a pointer to the database file with the matrix.
 *   Error codes: NULL if a matrix was not read
 */

Matrix *read_a_matrix (mfp)
     FILE *mfp;			/* matrix file pointer */
{
  Matrix *matrix;


  /* get the matrix file pointer */
/*  mfp = get_file(MATRIX_FILES);*/
  if (mfp == NULL) {
    /* no more data to read into matricies */
    matrix = NULL;
    return matrix;
  }

  /* allocate space for a new matrix */
  CheckMem(
	   matrix = (Matrix *) malloc(sizeof(Matrix))
	   );

  /* set the max size of the length */
  matrix->max_length = 0;

  matrix->block = NULL;	/* there is no block */

  /* read header */
  if (read_matrix_header(mfp, matrix) == FALSE) {
    free(matrix);
    return NULL;
  }

  /* read body */
  read_matrix_body(mfp, matrix); 

  /* set the patterns to NULL */
  matrix->patterns = NULL;

  /* return matrix */
  return matrix;
}  /* end of read_a_matrix() */


/*
 * read_matrix_header
 *   Reads the header information for the matrix.
 *   Parameters:
 *     FILE *mfp:      the matrix file pointer. 
 *     Matrix *matrix: the matrix to put the data in.
 *   Error Codes: FALSE if the matrix could not be read, TRUE otherwise
 */

static Boolean read_matrix_header(mfp, matrix)
     FILE *mfp;
     Matrix *matrix;
{
  char *buf2, *buf3;

  /* scan for either ID, AC, DE, MA */
  fgets(Buffer, LARGE_BUFF_LENGTH, mfp);

  while ( !(((Buffer[0] == 'I') && (Buffer[1] == 'D')) ||  /* ID */
	    ((Buffer[0] == 'A') && (Buffer[1] == 'C')) ||  /* AC */
	    ((Buffer[0] == 'D') && (Buffer[1] == 'E')) ||  /* DE */
	    ((Buffer[0] == 'M') && (Buffer[1] == 'A')))    /* MA */
	 && !feof(mfp) ) { 
    fgets(Buffer, LARGE_BUFF_LENGTH, mfp);
  }

  /* if we reached the end of the file, then there was no matrix */
  if (feof(mfp)) {
    return FALSE;			/* it did not read the matrix */
  }

  /* read ID if it exists */
  if ((Buffer[0] == 'I') && (Buffer[1] == 'D')) {
    buf2 = &Buffer[2];		/* Eat the ID at the beginining */
    buf2 = eat_whitespace(buf2); /* get a pointer to the string after ID */
    remove_trailing_whitespace(buf2); /* remove the \n at the end of the line */
    strncpy(matrix->id, buf2, SMALL_BUFF_LENGTH); /* copy the string into the matrix entry */
    fgets(Buffer, LARGE_BUFF_LENGTH, mfp);	/* read the next line */
  }
  else { /* no ID field, raise error */
    matrix->id[0] = '\0';	/* make sure string is empty */
    sprintf(ErrorBuffer, "Error in matrix file format.  No ID line.\n");
    ErrorReport(WARNING_ERR_LVL);
  }

  /* read AC if it exists */
  if ((Buffer[0] == 'A') && (Buffer[1] == 'C')) {
    buf2 = &Buffer[2];		/* Eat the AC at the beginining */
    buf2 = eat_whitespace(buf2); /* get a pointer to the string after AC */
    remove_trailing_whitespace(buf2); /* remove the \n at the end of the line */
    strncpy(matrix->ac, buf2, SMALL_BUFF_LENGTH); /* copy the string into the matrix entry */
    buf2 = get_token(buf2);	/* get the number */
    if (buf2[strlen(buf2)-1] == ';') {
      /* remove the ';' at the end of the number */
      buf2[strlen(buf2)-1] = '\0'; 
    }
    strncpy(matrix->number, buf2, NUMBER_WIDTH); /* copy the string into the matrix entry */
    fgets(Buffer, LARGE_BUFF_LENGTH, mfp);	/* read the next line */
  }
  else { /* no AC field, raise error */
    matrix->ac[0] = '\0';	/* make sure string is empty */
    matrix->number[0] = '\0';	/* make sure string is empty */
    sprintf(ErrorBuffer, "Error in matrix file format.  No AC line.\n");
    ErrorReport(WARNING_ERR_LVL);
  }

  /* read DE if it exists */
  if ((Buffer[0] == 'D') && (Buffer[1] == 'E')) {
    buf2 = &Buffer[2];		/* Eat the DE at the beginining */
    buf2 = eat_whitespace(buf2); /* get a pointer to the string after DE */
    remove_trailing_whitespace(buf2); /* remove the \n at the end of the line */
    strncpy(matrix->de, buf2, DESC_WIDTH); /* copy the string into the matrix entry */
    fgets(Buffer, LARGE_BUFF_LENGTH, mfp); /* read the next line */
  }
  else { /* no DE field, raise error */
    matrix->de[0] = '\0';	/* make sure string is empty */
    sprintf(ErrorBuffer, "Error in matrix file format.  No DE line.\n");
    ErrorReport(WARNING_ERR_LVL);
  }
  
  /* read MA if it does not exist raise an error */
  if ((Buffer[0] == 'M') && (Buffer[1] == 'A')) {
    buf2 = &Buffer[2];		/* Eat the MA at the beginining */
    buf2 = eat_whitespace(buf2); /* get a pointer to the string after MA */
    remove_trailing_whitespace(buf2); /* remove the \n at the end of */
					     /* the line */
    strncpy(matrix->ma, buf2, SMALL_BUFF_LENGTH);	/* copy the string into the matrix entry */
    
    /* scan and process the MA line */
    /* find the motif */
    buf3 = strstr(Buffer, "motif");
    if (buf3!=NULL) {
      buf3 -= 4;		/* move back to the motif type */
      sscanf(buf3, "%s", matrix->motif);
    }
    else {
      matrix->motif[0] = '\0';
    }

    /* find the width */
    buf3 = strstr(Buffer, "width=");
    if (buf3!=NULL) {
      sscanf(buf3, "width=%d;", &(matrix->width));
    }
    else {
      /* report an error, it is serious if the width is not set */
      sprintf(ErrorBuffer, "No width field for matrix %s", matrix->number);
      ErrorReport(SERIOUS_ERR_LVL);
      sprintf(ErrorBuffer, "Setting width to zero\n");
      ErrorReport(SERIOUS_ERR_LVL);
      matrix->width = 0;
    }

    /* find the seqs */
    buf3 = strstr(Buffer, "seqs=");
    if (buf3!=NULL) {
      sscanf(buf3, "seqs=%d", &(matrix->num_sequences));
      if (matrix->num_sequences < 0) { /* incase the number is there but is <1 */
	matrix->num_sequences = 0;
      }
    }
    else {
      matrix->num_sequences = 0;
    }
    
    /* find the 99.5% */
    buf3 = strstr(Buffer, "99.5%=");
    if (buf3!=NULL) {
      sscanf(buf3, "99.5%%=%d;", &(matrix->percentile));
    }
    else {
      matrix->percentile = 0;
    }

    /* find the strength */
    buf3 = strstr(Buffer, "strength=");
    if (buf3!=NULL) {
      sscanf(buf3, "strength=%d", &(matrix->strength));
    }
    else {
      matrix->strength = 0;
    }
  }
  else { /* no MA field, raise error */
    matrix->ma[0] = '\0';	/* make sure the MA string is empty */
    matrix->motif[0] = '\0';	/* make sure the motif string is empty */
    matrix->width = 0;		/* make sure the width is small */
    matrix->percentile = 0;	
    matrix->strength = 0;	
    matrix->num_sequences = 0;	
    matrix->max_length = 0;	
    sprintf(ErrorBuffer, "Error in matrix file format.  No MA line.");
    ErrorReport(SERIOUS_ERR_LVL);
    sprintf(ErrorBuffer, "Attempting to set values to be able to continue.");
    ErrorReport(SERIOUS_ERR_LVL);
    sprintf(ErrorBuffer, "The first column of the matrix will be missed.\n");
    ErrorReport(SERIOUS_ERR_LVL);
  }

  return TRUE;
}

/*
 * read_matrix_body
 *   Reads the body information of the matrix.
 *   Parameters:
 *     FILE *mfp:      the matrix file pointer. 
 *     Matrix *matrix: the matrix to put the data in.
 *   Error Codes: needed
 */

static void read_matrix_body(mfp, matrix)
     FILE *mfp;
     Matrix *matrix;
{
  int aa, len;
  float dtemp;
  char c;
  char *num_buf;
  
  if (matrix->width <= 0) {
    matrix->max_length = MATRIX_LENGTH_INCREASE_SIZE;
  }
  else {
    matrix->max_length = matrix->width;
  }
  
  /* allocate space for the weights arrays */
    CheckMem(
	matrix->weights[0] = (MatType *) calloc(matrix->width*MATRIX_AA_WIDTH,
						sizeof(MatType))
	   );

  /* setup the array of pointers, remember weights is an array of arrays */
  for (aa=0; aaweights[aa] = matrix->weights[0] + aa*matrix->width;
  }

  /*
   * read in the matrix values
   */
  
  len = 0;

  /* skip the letters */
  fgets(Buffer, LARGE_BUFF_LENGTH, mfp);

  /* read in the numbers */
  while (fgets(Buffer, LARGE_BUFF_LENGTH, mfp) &&
	 !blank_line(Buffer) &&
	 !((Buffer[0] == '/') && (Buffer[1] == '/'))) {

    if (len > matrix->max_length) {
      resize_matrix(matrix);
    }

    num_buf = get_token(Buffer);
    /*  NOTE:  Assumes matrix is in integer format !  */
    for (c='A'; c<='Z'; c++) {
      if ((c != 'J') && (c != 'O') && (c != 'U')) {
	sscanf(num_buf, "%f", &dtemp);
        matrix->weights[aa_atob[c]][len] = (MatType) dtemp;
	num_buf = get_token(NULL);
	/* do not try to catch long lines by reading in more.  Do this */
	/* only if code has been added to take care of the possibility of */
	/* splitting a number in half. */
	/* no more tokens left, so get the next line */
	/*
	if (num_buf == NULL) {	
	  fgets(Buffer, LARGE_BUFF_LENGTH, mfp);
	  num_buf = get_token(Buffer);
	}
        */
      }
    }
    c = '*';
    sscanf(num_buf, "%f", &dtemp);
    matrix->weights[aa_atob[c]][len] = (MatType) dtemp;
    num_buf = get_token(NULL);
    /* do not try to catch long lines by reading in more.  Do this */
    /* only if code has been added to take care of the possibility of */
    /* splitting a number in half. */
    /* no more tokens left, so get the next line */
    /*
    if (num_buf == NULL) {	
      fgets(Buffer, LARGE_BUFF_LENGTH, mfp);
      num_buf = get_token(Buffer);
    }
    */
    c = '-';
    sscanf(num_buf, "%f", &dtemp);
    matrix->weights[aa_atob[c]][len] = (MatType) dtemp;

    len++;
  }
}  /* end of read_matrix_body */


/*
 * new_matrix
 *   allocates space for a matrix of length len, sets up the data structure
 *   and returns a pointer to the Matrix.
 *   Parameters:
 *     int len: the length of the sequence/matrix
 *   Error codes:
 */

Matrix *new_matrix(len) 
     int len;
{
  int aa;
  Matrix *matrix;

  /* get the space for the Matrix data structure */
  CheckMem(
	   matrix = (Matrix *) malloc(sizeof(Matrix))
	   );

  /* initialize */
  matrix->block = NULL;
  matrix->id[0] = matrix->ac[0] = matrix->de[0] = '\0';
  sprintf(matrix->ma, "width=%d;", len);
  matrix->number[0] = matrix->motif[0] = '\0';
  matrix->width = matrix->max_length = len;
  matrix->num_sequences = 0;
  matrix->percentile = matrix->strength = matrix->undefined = 0;
  matrix->patterns = NULL;
  matrix->undefined_ptr = NULL;

  /* allocate the space for the matrix weights */
  CheckMem(
	matrix->weights[0] = (MatType *) calloc(matrix->width*MATRIX_AA_WIDTH,
						sizeof(MatType))
	   );

  /* setup the array of pointers, remember weights is an array of arrays */
  for (aa=0; aaweights[aa] = matrix->weights[0] + aa*matrix->width;
  }

  return matrix;
}  /* end of new_matrix */


/* 
 * resize_matrix
 *   Increases the memory for the storage of the matrix weights in a matrix.
 *   Parameter:
 *     Matrix *matrix: the matrix to resize
 *   Error codes: none
 */

static void resize_matrix(matrix)
     Matrix *matrix;
{
  /* remember to allocate new space and then to copy over. */
  /* matrix.weights is an array of arrays */
  fprintf(stderr, "resize_matrix() not finished.  Exiting.\n");
  exit(1000);
}


  
/* 
 * free_matrix
 *   Deletes the matrix and the sub elements.
 *   Parameters: 
 *     Matrix *matrix: the matrix to free
 *   Return code: none
 *   Error code: none
 */

void free_matrix(matrix) 
     Matrix *matrix;
{
  if (matrix->patterns != NULL) {
    free(matrix->patterns);
  }
  free(matrix->weights[0]);
  free(matrix);
}


/*
 * matrix_comparison
 *   Compares two matricies.   It compares by the value in the block->id
 *   field if it exists.
 *   Parameters:
 *     MatrixListEntry a, b: the entries to compare
 *   Return codes:  a return value < 0 if a < b, a return value = 0 if a == b,
 *                  and a return value > 0 if a > b
 *   Error codes: none
 */

int matrix_comparison(a, b)
     Matrix *a, *b;
{
  return (int) (strcmp(a->number, b->number));
}




/*
 * Matrix printing.
 */

/*
 * print_matrix
 *   Prints a Matrix data structure.  Primarily for debugging purposes.
 *   Parameters: 
 *     Matrix *matrix:  the matrix to print
 *   Error Codes: none
 */

void print_matrix(matrix)
     Matrix *matrix;
{
  int pos;
  int low, high;
  char c;

#define MATRIX_PRINT_WIDTH 18

  high = MATRIX_PRINT_WIDTH;
  for (low=0; 
       lowwidth; 
       low = (high+=MATRIX_PRINT_WIDTH) - MATRIX_PRINT_WIDTH) {



  printf("\n");

  if (matrix->width > 99) {
    printf("  |");
    for (pos=low; poswidth; pos++) {
      if (pos > 99) {
	printf("% 4d", pos%100);
      }
      else {
	printf("    ");
      }
    }
  }

  printf("\n");
  if (matrix->width > 9) {
    printf("  |");
    for (pos=low; poswidth; pos++) {
      if (pos > 9) {
	printf("% 4d", (pos-((pos/100)*100)) / 10);
      }
      else {
	printf("    ");
      }
    }
  }
  
  printf("\n");
  printf("  |");
  for (pos=low; poswidth; pos++) {
    printf("% 4d", (pos-((pos/10)*10)));
  }
  
  printf("\n");
  printf("--+");
  for (pos=low; poswidth; pos++) {
    printf("----");
  }

  printf("\n");
  
 
  for (c='A'; c<='Z'; c++) {
    printf("%c |", c);
    for (pos=low; poswidth; pos++) {
      printf("% 6.4f", matrix->weights[aa_atob[c]][pos]);
    }
    printf("\n");
  }
  c = '*';
  printf("%c |", c);
  for (pos=low; poswidth; pos++) {
    printf("% 6.4f", matrix->weights[aa_atob[c]][pos]);
  }
  printf("\n");
  c = '-';
  printf("%c |", c);
  for (pos=low; poswidth; pos++) {
    printf("% 6.4f", matrix->weights[aa_atob[c]][pos]);
  }
  printf("\n");

  }

}

/* 
 * output_matrix
 *   Outputs a matrix data structure to the given file.
 *   Parameters: 
 *     Matrix *matrix: the matrix to output
 *     FILE   *omfp:   the output matrix file pointer
 *   Return code: none
 *   Error code: none
 */

void output_matrix(matrix, omfp)
     Matrix *matrix;
     FILE *omfp;
{
  output_matrix_st(matrix, omfp, INT_OUTPUT, AA_SEQ);
}


/* 
 * output_matrix_s
 *   Outputs a matrix data structure to the given file with the 
 *   specified style of data.
 *   Parameters: 
 *     Matrix *matrix: the matrix to output
 *     FILE   *omfp:   the output matrix file pointer
 *     int    style:   the kind of output (INT_OUTPUT, FLOAT_OUTPUT)
 *   Return code: none
 *   Error code: none
 */

void output_matrix_s(matrix, omfp, style)
     Matrix *matrix;
     FILE *omfp;
     int style;
{
  char c;
  int l;

  if (style == INT_OUTPUT) {
    fprintf(omfp, "ID   %s\n", matrix->id);
    fprintf(omfp, "AC   %s\n", matrix->ac);
    fprintf(omfp, "DE   %s\n", matrix->de);
    fprintf(omfp, "MA   %s\n", matrix->ma);
    
    fprintf(omfp, " ");
    for (c='A'; c <= 'Z'; c++) {
      if ((c != 'J') && (c != 'O') && (c != 'U')) {
	fprintf(omfp, " %c  ", c);
      }
    }
    fprintf(omfp, " *  ");
    fprintf(omfp, " -\n");
    
    for (l=0; lwidth; l++) {
      for (c='A'; c <= 'Z'; c++) {
	if ((c != 'J') && (c != 'O') && (c != 'U')) {
	  fprintf(omfp, "%3d ", (int) round(matrix->weights[aa_atob[c]][l]));
	}
      }
      fprintf(omfp, "%3d ", (int) round(matrix->weights[aa_atob['*']][l]));
      fprintf(omfp, "%3d\n", (int) round(matrix->weights[aa_atob['-']][l]));
    }  
    
    fprintf(omfp, "//\n");
  }
  else if (style == FLOAT_OUTPUT) {
    fprintf(omfp, "ID   %s\n", matrix->id);
    fprintf(omfp, "AC   %s\n", matrix->ac);
    fprintf(omfp, "DE   %s\n", matrix->de);
    fprintf(omfp, "MA   %s\n", matrix->ma);
    
    fprintf(omfp, " ");
    for (c='A'; c <= 'Z'; c++) {
      if ((c != 'J') && (c != 'O') && (c != 'U')) {
	fprintf(omfp, " %c  ", c);
      }
    }
    fprintf(omfp, " *  ");
    fprintf(omfp, " -\n");
    
    for (l=0; lwidth; l++) {
      for (c='A'; c <= 'Z'; c++) {
	if ((c != 'J') && (c != 'O') && (c != 'U')) {
	  fprintf(omfp, "% 6.4f ", matrix->weights[aa_atob[c]][l]);
	}
      }
      fprintf(omfp, "% 6.4f ", matrix->weights[aa_atob['*']][l]);
      fprintf(omfp, "% 6.4f\n", matrix->weights[aa_atob['-']][l]);
    }  
    
    fprintf(omfp, "//\n");
  } 
  else { /* unknown */
    sprintf(ErrorBuffer, 
	    "Unknown output type: %d, using integer output\n", style);
    ErrorReport(WARNING_ERR_LVL);
    output_matrix_s(matrix, omfp, INT_OUTPUT);
  }
}  /*  end of output_matrix_s() */


/* 
 * output_matrix_st
 *   Outputs a matrix data structure to the given file with the 
 *   specified style of data. NA_SEQ => only ouput ACTG columns.
 *   Parameters: 
 *     Matrix *matrix: the matrix to output
 *     FILE   *omfp:   the output matrix file pointer
 *     int    style:   the kind of output (INT_OUTPUT, FLOAT_OUTPUT)
 *     int    type:    matrix type (AA_SEQ, NA_SEQ)
 *   Return code: none
 *   Error code: none
 */

void output_matrix_st(matrix, omfp, style, type)
     Matrix *matrix;
     FILE *omfp;
     int style, type;
{
  char c;
  int l;

  if ( (style != INT_OUTPUT) && (style != FLOAT_OUTPUT) )
  {
    sprintf(ErrorBuffer, 
	    "Unknown output style: %d, using integer output\n", style);
    ErrorReport(WARNING_ERR_LVL);
    style = INT_OUTPUT;
  }
  if ( (type != AA_SEQ) && (type != NA_SEQ) )
  {
    sprintf(ErrorBuffer, 
	    "Unknown sequence type: %d, using amino acid\n", type);
    ErrorReport(WARNING_ERR_LVL);
    type = AA_SEQ;
  }

  fprintf(omfp, "ID   %s\n", matrix->id);
  fprintf(omfp, "AC   %s\n", matrix->ac);
  fprintf(omfp, "DE   %s\n", matrix->de);
  fprintf(omfp, "MA   %s\n", matrix->ma);
  
  if (type == AA_SEQ)
  {
    for (c='A'; c <= 'Z'; c++) {
      if ((c != 'J') && (c != 'O') && (c != 'U'))
      {
         if (style == FLOAT_OUTPUT) fprintf(omfp, "    %c     ", c);
         else fprintf(omfp, "  %c ", c);
      }
    }
    if (style == FLOAT_OUTPUT) fprintf(omfp, "    *         -\n");
    else                       fprintf(omfp, "  *   -\n");
  }
  else
  {
     if (style == FLOAT_OUTPUT)
        fprintf(omfp, "    A         C         G         T\n");
     else
        fprintf(omfp, "  A   C   G   T\n");
  }

  if (style == INT_OUTPUT) {
    for (l=0; lwidth; l++) {
      if (type == AA_SEQ)
      {
         for (c='A'; c <= 'Z'; c++) {
	   if ((c != 'J') && (c != 'O') && (c != 'U')) {
	     fprintf(omfp, "%3d ", (int) round(matrix->weights[aa_atob[c]][l]));
	   }
         }
         fprintf(omfp, "%3d ", (int) round(matrix->weights[aa_atob['*']][l]));
         fprintf(omfp, "%3d\n", (int) round(matrix->weights[aa_atob['-']][l]));
      }
      else
      {
         for (c='A'; c <= 'T'; c++) {
	   if ((c == 'A') || (c == 'C') || (c == 'G') || (c == 'T')) {
	     fprintf(omfp, "%3d ", (int) round(matrix->weights[aa_atob[c]][l]));
           }
         }
         fprintf(omfp, "\n");
      }  
    } /*  end of for l */
  }   /* end of INT_OUTPUT */

  else if (style == FLOAT_OUTPUT) {
    for (l=0; lwidth; l++) {
      if (type == AA_SEQ)
      {
         for (c='A'; c <= 'Z'; c++) {
      	   if ((c != 'J') && (c != 'O') && (c != 'U')) {
	     fprintf(omfp, "% 9.4f ", matrix->weights[aa_atob[c]][l]);
	   }
         }
         fprintf(omfp, "% 9.4f ", matrix->weights[aa_atob['*']][l]);
         fprintf(omfp, "% 9.4f\n", matrix->weights[aa_atob['-']][l]);
      }
      else
      {
         for (c='A'; c <= 'T'; c++) {
	   if ((c == 'A') || (c == 'C') || (c == 'G') || (c == 'T')) {
	     fprintf(omfp, "% 9.4f ", matrix->weights[aa_atob[c]][l]);
           }
         }
         fprintf(omfp, "\n");
      }
    }  
    
  }  /*  end of FLOAT */ 
  fprintf(omfp, "//\n");
}  /*  end of output_matrix_st */

/* Change log information follows. */
/*
  Changes since version 3.3.2:
   6/ 7/00 Put width in matrix->ma in new_matrix()
  Changes since version 3.1:
   2/14/97 Added output_matrix_st()
  11/18/96 Changed new_matrix() to initialize fields.  JGH
  Changes since version 3.0.0:
  4/11/96  Changed read_matrix_body() to sscanf with %f instead of %d. JGH
  3/25/96  Changed MatType for matrix->weights from int to double. JGH
             Still assumes input matrix is integer & still exports integers.
*/

trix *) malloc(siblimps-3.9/blimps/matrix_logob.c000064400001460000012000000522610774312250000172740ustar00jorjastaff00000400000027/*----------------------------------------------------------------------------o
 Copyright 1995-8 Fred Hutchinson Cancer Research Center
 www/src/matrix_logob.c
 Version of matrix_logo.c for use with the getblock function 
 of the blocks WWW server.
	Use:  matrix_logob   
		blocksdb = name of blocks db, "-" => read stdin
		blockac = block AC number in blocksdb or "-" for all blocks
		suffix = suffix for outfile files
 Transform a block's matrix (PSSM) into the format read by the Tom Schneider's
 makelogo program (file symvec, usually made by program alpro), create and copy 
 all files needed by makelogo program and create a sequence-logo with that
 program. 
 
 The names of the variables for calculating the information are taken from
 Tom Schneider's alpro program.

* set_defaults from config.c by Bill Alford

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

TO DO:

Aug '98 - Change suffix2. This variable has to be unique for each processed
          block. Currently suffix2 is made up of the suffix variable and the 
          block name. This is not robust since we have no control on the block
          name. It may contain special unix characters that can cause problems 
          when file names including suffix2 are passed to the system (problem
          adressed in Aug 98). The block names themselves might not be unique 
          and hence suffix2 won't be unique.
          A possible solution is to make suffix2 a running variable, perhaps,
          the nblock variable.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Jan. 1995 Written by Shmuel Pietrokovski
Feb. 1995 Modified by Jorja Henikoff for blocks WWW server (JGH)
2/14/95  Write files named makelogop.arg[1] & symvec.argv[1].
         Read blocks from stdin instead of bdbname.
	 If only Prosite group name in argv[2], takes the first block
	 found for that group (eg BL00094 => BL00094A).
         Don't execute viewer.
         Same character size for all blocks, only rotate those > 45 wide.
2/16/95  Center logo on the page.
2/17/95  If db file name = "-" read stdin. Suffix is arg 3.
3/31/95  Changed to execute makelogob for each block in the input file.
12/3/95  Changed to use load_frequencies() & block_to_matrix() 
         from blimps-3.0.0
May 20 96 Modified procedure write_makelogop to position the logos in the top 
          of the page and the plcae the logo cation closer to the logo. This
          will make it easier to join logos together. SP

 7/24/96 Modified for Blimps 3.1; matrix->weights are now type double
 3/24/97 Modified name of logo.* file to be logo.suffixAC 
 3/26/97 Detect whether input is BLOCK or MATRIX
 7/30/98 version 1.3 Procedure write_symvec:
         Small sample correction (variable e) and variance (variable avarhnb)
         are calculted separately for each column using the actual number of
         specified residues: gaps, unspecified residues, termination codons etc.
         are not counted, only the 20 aa, B (Asp or Asn) and Z (Glu or Gln).
         A number of print commands for debug mode added, use debug value (4th
         argument) > 2 to see each block column, actual number of residues and
         small sample correction calculations of each column. 

         When the input is of a matrix type warning messages are generated by 
         the program when it first tries to read the input as a block.

 8/17/98 version 1.35 fixing problem with use of suffix2. 
         Single quoted ('...') to strings with the suffix2 variable that are
         passed to the system. Suffix2 is made up of the suffix parameter
         and the block name. The block name can potentially include 
         unix-system special characters (&, $ etc.) which with out the quotes
         would be interpted as unix directives. SP.

11/27/98 Don't rotate wide blocks; reduce size so 55 wide fits on 8.5" page
12/ 4/98 Check for "; MATRIX" instead of just "MATRIX" on ID line (see
	 PR00138, PR00234) to determine input type.
         
-----------------------------------------------------------------------------*/

#define EXTERN
#define SEEK_SET 0 	/* for fseek() */
#define MAXNAME 80	/* Maximum file name length */
#define OK    0
#define YES  1
#define NO   0
#define ERROR 1

#define AAs 20
#define infofield 8        /* size of field for printing information in bits */
#define infodecim 5     /* number of decimal places for printing information */
#define nfield 4        /* size of field for printing n, the number of sites */

#define SEARCH_TYPE_UNSET  -1

#include 
#include 
#include 

/* variables set by the configuration file in blimps program */

int StrandsToSearch;
int NumberToReport;
int SearchType;
int GeneticCodeInitializer;
int SiteSpecificScoringMatrixType;
int BlockToMatrixConversionMethod; /* default method is two */
int SequenceMatrixScoringMethod;   /* default method is zero */

extern
Matrix *block_to_matrix() ;


/*
 * Local variables and data structures
 */

int    getargs() ;
void   set_defaults() ;
void   write_symvec();
void   write_makelogop();
void   view_logo();
int    dbg_lvl ;
int    isblock ;

/*=======================================================================*/
/*
 * main 
 *   controls flow of program
 *   Parameters: argc, argv
 *   Error codes:
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
   FILE       *bfp, *out ;
   Block      *block ;
   Matrix     *matrix ;
   int	      itemp, nblock, done, all;
   long	      bfp_pos;
   char       bdbname[MAXNAME], suffix[MAXNAME], outname[MAXNAME] ;
   char       blockAC[MAXNAME], blockID[MAXNAME], version[32], line[160] ;
   char       logodir[MAXNAME], suffix2[MAXNAME], blockAC2[MAXNAME];
   char       symvec[MAXNAME], makelogop[MAXNAME], colors[MAXNAME];

   struct stat status ;

   strcpy(version,"1.35") ;					/*JGH*/
   strcpy(logodir, "./") ;					/*JGH*/

   dbg_lvl = 0 ;		/* debugging level */

                                    /* getting input and output file names */
   if (getargs(argc,argv,bdbname,suffix,&bfp,blockAC) != OK) exit(ERROR) ; 
   strcpy(suffix2, suffix);   /* may be different if more than one block */

   set_defaults();                      /*set the blimps default values */
                 /* load the frequencies for converting blocks to matrices */
   load_frequencies("default.amino.frq");

   /* create and check the presence of files needed by program makelogo */
   /* If file colors.suffix doesn't exist copy file colors to that name SP */

   sprintf(colors, "colors.%s", suffix);
   if (stat(colors, &status) < 0) 
      {
         sprintf(line, "cp %s/colors %s", logodir, colors) ; 
         system(line) ;

      }

                         /* create empty wave and marks files 
                            if they do not exist in the present directory */
   if (stat("wave", &status) < 0) system("touch wave") ;
   if (stat("marks", &status) < 0) system("touch marks") ;



   /* If partial name is given, take all blocks with partial name    JGH*/
   /* If the name is "-" process all the blocks                         */
   nblock = 0;
   done = all = NO;
   if ( strcmp(blockAC, "-") == 0 ) { all = YES; blockAC[0] = '\0'; }
   strcpy(blockAC2, blockAC);
   bfp_pos = ftell(bfp);
   while ((block = read_a_block(bfp)) != NULL && (all || !done))
   {
      if ( all ||
           (strcmp(block->number,blockAC) == 0) ||
            ( strlen(blockAC) < strlen(block->number) &&
              strncmp(blockAC, block->number, (int) strlen(blockAC)) == 0) )
      {
         nblock++;
         strcpy(suffix2, suffix);
         itemp = (int) strlen(block->number) - strlen(blockAC);
         if ( itemp > 0 )
         {
             strcpy(blockAC2, block->number);
             strncat(suffix2, block->number + strlen(blockAC), itemp);
             suffix2[ (int) strlen(suffix) + itemp ] = '\0';

/* Single-quote the suffix strings to avoid problems from the possible
   occurrence of unix-system special characters (&, $ etc.) in them 
   SP */
             sprintf(line, "cp \'colors.%s\' \'colors.%s\'", suffix, suffix2);
             system(line);
         }
         else if (!all) done = YES;
		 /* just get the ID, not the BLOCK key word*/
         sscanf(block->id, "%s %*s", blockID) ;

         /*   Have we been looking at a matrix?   */
         if (strstr(block->id, "; MATRIX"))
         {
         isblock = 0 ; /* input data is NOT a block */
printf("MATRIX input\n");
            fseek(bfp, bfp_pos, SEEK_SET);	/* rewind input */
            matrix = read_a_matrix(bfp);
         }
         else
         {
         isblock = 1 ; /* input data is a block */
            /*   Convert a block to a matrix  */
            /*  Use method #2; values b/w 0 and 100 that add to 100 in each
                column of the alignment */
            matrix = block_to_matrix(block, 2);
         }

         /*   Open symvec output file   */
         strcpy(symvec, "symvec");
         if (strlen(suffix2))
         {  strcat(symvec, "."); strcat(symvec, suffix2); }
         if ( (out=fopen(symvec, "w")) == NULL)
         {
            printf("\nCannot open file %s\n", symvec);
            exit(ERROR);
         }

         fprintf(out, "* %s %s\n", argv[0], version) ;
         fprintf(out, "* PSSM of block %s (%s) from file %s.\n",
	      blockAC2, blockID, bdbname) ;	
         write_symvec(out, matrix);
         fclose(out) ;                                 /* close file symvec */


                  /* create file makelogop - the makelogo parameter file */
         strcpy(makelogop, "makelogop");
         if (strlen(suffix2))
         {   strcat(makelogop, "."); strcat(makelogop, suffix2);  }
         if ( (out=fopen(makelogop, "w")) == NULL) 
         {
            printf("\nCannot open file %s\n", makelogop) ;
            exit(ERROR) ;
         }

         write_makelogop(out, matrix);
         fprintf(out, "PSSM of %s (%s) %d sequences.\n", 
	      blockAC2, blockID, matrix->num_sequences) ;   
         fclose(out) ;                             /* close file makelogop */


                /* run program makelogo to generate file logo 
                   containing the postscript represenation of the matrix */
/* Single-quote the suffix2 string to avoid problems from the possible
   occurrence of unix-system special characters (&, $ etc.) in that string 
   SP */
         sprintf(line, "%s/makelogob \'%s\' > /dev/null", logodir, suffix2) ; 
         system(line) ;
         sprintf(outname, "logo.%s", suffix2);
/*
         view_logo(outname); 
*/
         free_block(block); free_matrix(matrix);

         /*   Remove all the intermediate files   */
/* Single-quote the suffix2 string to avoid problems from the possible
   occurrence of unix-system special characters (&, $ etc.) in that string 
   SP */
/* Disable intermediate file removal on WWW server version of program.
   Shell running the program removes these files.

         sprintf(line, "rm \'colors.%s\' \'symvec.%s\' \'makelogop.%s\'",
                        suffix2, suffix2, suffix2);

         system(line);
*/
      }   /* end of if it's a block we want to process */
      bfp_pos = ftell(bfp);
   }  /* end of input file */

   fclose(bfp) ;                             /* close blocks database file */

   if (nblock == 0)                  /* No block with name blockAC found */
      {
      printf("No block with name %s found in file %s !\n", blockAC, bdbname) ; 
      exit(ERROR) ;
      }

   exit(0);

}  /* end of main */

/****************************************************************************
 * get input file names and other program parameters interactively
 * or from command line. 
 ****************************************************************************/
int getargs(argc,argv,bdbname,suffix,bfp,blockAC)

int   argc;
char  *argv[];
char  bdbname[MAXNAME], suffix[MAXNAME], blockAC[];
FILE  **bfp ;
{

   if (argc < 4)
   {
      printf("MATRIX_LOGOB: Copyright 1995-8 Fred Hutchinson Cancer ");
      printf("Research Center\n");
      printf("USAGE: matrix_logob blocks|pssms AC|- suffix\n");
      printf("   pssms must be in blimps format and consist of values ");
      printf("betwen 0 and 100\n    which sum to 100 in each column.\n");
      printf("These files must be in the current directory:\n");
      printf("   makelogob, colors, default.amino.frq\n");
   }

/* ------------1st arg = block file 1 ------------------------------------*/
   if (argc > 1) strcpy(bdbname, argv[1]);
   else                               
      {
      printf("\nEnter name of BLOCK or MATRIX file: ");
      gets(bdbname);
      }

   /*   Read stdin if the filename starts with '-'   */
   if (!strlen(bdbname) || bdbname[0] == '-')  *bfp = stdin;
   else if ( (*bfp=fopen(bdbname, "r")) == NULL)
      {
      printf("\nCannot open file \"%s\"\n", bdbname);
      return(ERROR);
      }

/* ------------block accession --------------------------------------------*/
   if (argc > 2) strcpy(blockAC, argv[2]);
   else                                   /* get input file(s) interactively */
      {
      printf("\nEnter AC in %s or - to make logos for all: ", bdbname);
      gets(blockAC);
      }

/* ------------3rd arg = file name suffix ------------------------------JGH*/
   suffix[0] = '\0';
   if (argc > 3) strcpy(suffix, argv[3]);
   else
      {
      printf("\nEnter file name suffix: ");
      gets(suffix);
      printf("Logos will be written to logo.%s\n", suffix);
      }

/* ------------last arg = debug level (unprompted) ------------------------*/

   if (argc > 4) dbg_lvl = atoi(argv[argc-1]) ;			/*JGH*/

   return(OK) ;

}  /* end of getargs */


/****************************************************************************
 * set the default values for some of the variables.
 ****************************************************************************/

void set_defaults()
{

  GeneticCodeInitializer = 0;           /* the standard genetic code */

  StrandsToSearch = 2;          /* == 2 if want to search both strands */
  NumberToReport  = 0;          /* <0 means all, 0 means judge, */
                                /* >0 means use that number */
  SearchType      = SEARCH_TYPE_UNSET;

  BlockToMatrixConversionMethod = 2; /* Patmat method is two */
  SequenceMatrixScoringMethod   = 0; /* default method is zero */

  ErrorLevelReport = WARNING_ERR_LVL;

}

/*=======================================================================*/
void write_symvec(out, matrix)
FILE *out;
Matrix *matrix;
{
   double ln2, e, r, hmax, ntrue, avarhnb, dtemp;
   int aa, pos, seq, num_residues;

   fprintf(out, "* position, samples, information, variance\n");
   fprintf(out, "%d number of symbols\n", AAs);

  
   ln2 = log(2.0) ;
   hmax = log((double) AAs) ;

/* print debug output headers */
   if (dbg_lvl > 1) 
      {
      printf("col") ;
      for(aa=1; aa < AAs+1; aa++) printf("   %c", aa_btoa[aa]) ;
      printf("   info.  sum") ;
      if (dbg_lvl > 2) 
         printf("     residues   #_of_specified_residues/#_of_seqs   e   var") ;
      printf("\n") ;
      }

   for(pos=0; pos < matrix->width; pos++)
      {
/* if input is a block, count actual number of residues in each column. 
   Including the 20 aa ('residues' matrix values 1-20) 
   and B (Asp or Asn, value 21) and Z (Glu or Gln, value 22) 
   Excluding gaps (-, value 0) unidentified aa (X, value 23) and 
   stop codon (*, value 24). */

      num_residues = matrix->num_sequences ;

      if (isblock)
         for(seq=0; seq < matrix->num_sequences; seq++) 
            if (matrix->block->residues[seq][pos] < 1 ||
                matrix->block->residues[seq][pos] > 22) num_residues-- ; 

                                /* correction factor for small sample size */
      e = (AAs-1) / ((double) 2 * ln2 * num_residues) ; 

      avarhnb = e * e ;

      r = hmax ;
      for(aa=1, ntrue=0.; aa < AAs+1; aa++) 
	ntrue += (double) round( matrix->weights[aa][pos] ) ;

      for(aa=1; aa < AAs+1; aa++) 
                    /* start loop at 1 and end at AAs+1 because aa values 
                      at the weight matrix start at 1, 0 is the gap value */
      	 {
         if (matrix->weights[aa][pos] > 0)
            {
            dtemp = (double) matrix->weights[aa][pos] / ntrue;
            r += dtemp * log(dtemp);
            }
	 }

      r /= ln2 ;                                       /* convert to bits */
      r -= e ;                     /* a correction for small sample sizes */

      fprintf(out, "%*ld %*.0lf %*.*f % .1E\n",
              nfield, pos+1, infofield, ntrue, infofield, infodecim,
	      r, avarhnb);

      for(aa=1; aa < AAs+1; aa++) 
         fprintf(out, "%c %4d\n", aa_btoa[aa],
                 round(matrix->weights[aa][pos]) ) ;

      if (dbg_lvl > 1) 
/* print PSSM values, their info value and the values sum for this column */
	 {
         printf("%2d|", pos+1) ;
         for(aa=1; aa < AAs+1; aa++) 
            printf(" %3d", round(matrix->weights[aa][pos])) ;
         printf("  %6.3f  %3.0f", r, ntrue) ;

         if (dbg_lvl > 2) 
/* print block column, number of specified residues and sample correction values */
	    {
            printf("     ") ;
            for(seq=0; seq < matrix->num_sequences; seq++) 
               printf("%c", aa_btoa[matrix->block->residues[seq][pos]]); 
            printf("  %2d/%d %6.3f %6.3f", 
                   num_residues, matrix->num_sequences, e, avarhnb) ;
            }
         printf("\n") ;
         }

      }

   if (dbg_lvl > 1) 
      printf("\nsmall sample correction (e) : %6.3f, variance (avarhnb) : %6.3f\n(these are are actually the values for the last column and will be different for the other columns if they contain a different number of unspecified residues - gaps, Xs, etc.)\n",
	     e, avarhnb) ;
}   /*  end of write_symvec */

/*=================================================*/
void write_makelogop(out, matrix)
FILE *out;
Matrix *matrix;
{
   double legendsize;

                /* FROM to TO range to of the logo showing all the block */
   fprintf(out, "1 %d\n", matrix->width) ; 

   fprintf(out, "1\n") ;   /* put the vertical bar before first position */

   /* lower left hand corner of the logo (in cm), landscape coordinates */ 
   /*  Rotate wide blocks     JGH*/
/*
   if ( matrix->width > 44) 
   {
      fprintf(out, "12 26\n") ;

      fprintf(out, "-90\n");
   }
   else
*/
   {
      /* Change the corner depending on block width to center it JGH*/
      /* Width = 44 => x = 1, width = 0 => x = 11 (page about 21cm wide) */
      /*xcorner = (double) 11.0 - 10.0 * matrix->width / 44.0; SP */

      fprintf(out, "1 20\n"); /* corner *//*modified from '"%.2f 10\n", xcorner' SP */
      fprintf(out, "0\n") ;             /* rotation: angle to rotate the graph */
   }
      {
      fprintf(out, "0.365\n") ; /* width of the logo characters, in cm */
      fprintf(out, "5.48 0.1\n") ; /* height and width of the vertical bar*/
      legendsize = 1.0 ;
      }
/*
   else
      {
      fprintf(out, "0.454\n") ;   
      fprintf(out, "6.82 0.1\n") ;
      legendsize = 1.0 ;
      }
*/

                 /* height of the vertical bar, in bits; < 0: no I-beams */
   fprintf(out, "-4\n") ;

   fprintf(out, "1\n") ;     /* Ibeamfraction: fraction of Ibeam to draw */

               /* if begins with 'b' put bars before and after each line */
   fprintf(out, "bars on\n") ;

           /* if begins with 's' show a dashed box around each character */
   fprintf(out, "-\n") ;

                 /* if begins with 'o' draw each character as an outline */
   fprintf(out, "no outline\n") ;

                    /* if begins with 'c' sequence letters in upper case */
   fprintf(out, "capitals\n") ;

   fprintf(out, "55\n") ; /* maximal number of character stacks per line */

   fprintf(out, "1\n") ;              /* number of lines per page output */

   fprintf(out, "1.5\n") ; /* lines separation relative to the barheight */

   fprintf(out, "numbers\n") ;  /* if begins with 'n' then number stacks */

   fprintf(out, "1.0\n") ;              /* shrinking factor inside boxes */

   fprintf(out, "1\n") ;     /* number of user defined strings following */

                    /* coordinates of string 1 (in cm) and relative size */
                                   /* modified from "0.0 -3.0 %.2f\n" SP */
   fprintf(out, "0.0 -1.5 %.2f\n", legendsize) ; 
}  /* end of write_makelogop */
/*=====================================================================*/
void view_logo(outname)
char *outname;
{
   char       PSviewer[MAXNAME], PSviewer_opt[MAXNAME] ;
   char       PSprint[MAXNAME], ans[2] , line[80] ;

   strcpy(PSviewer, "pageview") ;
   strcpy(PSviewer_opt, "-left") ;       
   strcpy(PSprint, "lpr") ;
   ans[0] = 'V' ;

   while (toupper(ans[0]) == 'V')
      {
      printf("\nThe created sequence-logo file (%s) is a PostScript file.\n", 
	     outname) ;
      printf("  (V to view logo with program %s (%s %s %s))\n",
	     PSviewer, PSviewer, PSviewer_opt, outname) ;
      printf("     after viewing you can also choose to print,\n") ;
      printf("   P to print logo (%s %s).)\n", PSprint, outname) ;

      gets(ans) ;

      switch (toupper(ans[0]))
	 {
         case 'V' :
            sprintf(line, "%s %s %s", PSviewer, PSviewer_opt, outname) ; 
            system(line) ;
            break ;
         case 'P' :
            sprintf(line, "%s %s", PSprint, outname) ; 
            system(line) ;
            printf("\nFile %s sent to printer.\n", outname) ;
            break ;
	 }
      }

}   /* end of view_logo  */
 */
      {
      printf("No block with name %s found in file %s !\n", blockAC, bdbname) ; 
      exit(ERROR) ;
      }

   exit(0);

}  /* end of main */

/****************************************************************************
 * get input file names and other program parameters interactively
 * or from command line. 
 *******blimps-3.9/blimps/memory.c000064400001460000012000000036700774312250000161160ustar00jorjastaff00000400000027/* (C) Copyright 1993-9, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* memory.c: Memory management functions. */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

/*	system headers not in global.h  */
/*	blimps library headers not in global.h */
#include 

/*
 * Exported variables and data structures
 */

/*
 * Local variables and data structures
 */

static Boolean (*RecFunc)() = NULL;

/*
 * Function definitions
 */

/*
 * reclaim_space
 *   Tries to reclaim some of the allocated memory.  It tries to
 *   reclaim the memory the program used using the function specified in 
 *   init_reclaim_space().
 *   NOTE: The reclaiming function must have the same return and error codes
 *         as below!
 *   Parameters: none
 *   Return codes: TRUE if it was able to get free some space, FALSE
 *                 if not.
 *   Error codes:  FALSE if it unable to get space.
 */

Boolean reclaim_space()
{
  if (RecFunc == NULL) {
    sprintf(ErrorBuffer, "Reclaim space function is not defined.  No memory will be reclaimed.\n");
    ErrorReport(WARNING_ERR_LVL);
    return FALSE;
  }
  else {
    return (*RecFunc)();
  }
}
  


/*
 * init_reclaim_space
 *   Sets up the reclaim_space function to call the passed function.
 *   Parameters:
 *     Boolean (*rec_func)(): The reclaiming function.
 *   Return codes: none.
 *   Error codes: none.
 */

void init_reclaim_space(rec_func) 
     Boolean (*rec_func)();
{
  if (rec_func == NULL) {
    sprintf(ErrorBuffer, "Reclaim space function is not defined.  No memory will be reclaimed.\n");
    ErrorReport(WARNING_ERR_LVL);
  }
  RecFunc = rec_func;
}





/* Change log information follows. */
/* 
 * Revision 2.2010  1995/07/28  23:47:14  billa
 * Added new convert method and pattern matching and minor updates merged.
 *
 */

blimps-3.9/blimps/narrow.c000064400001460000012000000525500774312250000161170ustar00jorjastaff00000400000027/*>>> change to use block_to_matrix(block, 9)  <<<<*/
/*  Copyright 2000 Fred Hutchinson Cancer Research Center
	Implements procedures developed by Jon Cooper & Jim Smothers
    Read a block or a file of frequencies
	narrow  
    Make a log-odds matrix in mast or blimps format as follows:
	For col=c, amino acid=a:
	w_ac = log_2[p_ca/p_a]
		If f_ac > 0, p_ca = f_ca => w_ac = log_2[f_ca/p_a]
		If f_ac = 0, p_ca = p_a/1000 => w_ac = log_2[1000]
		f_ac = sequence-weighted frequencies, 0 <= f_ac <= 1
			if block has no sequence weights, use equal weights
		p_a = background frequences, 0 <= p_a <= 1

	This model approximates no pseudo-counts.

	Mast file is assumed to look like this:
ALPHABET= ARND...
log-odds matrix: alength=  w= 
nw*na numbers
		or
ARND...
nw*na numbers
----------------------------------------------------------------------*/

#define EXTERN
#define AASALL 26
#define MAXWIDTH 400
#define TOTREAL 10000	/* Total number of presumed real counts if freqs in */
#define PERREAL 10000.0	/* Total number of pseudo per real if block in */

#include 

struct working {	/* Working information for one column */
  double cnt[AASALL];		/* Sequence-weighted counts */
  double totcnt;
  double raw[AASALL];		/* unweighted counts */
  double totraw;
  double reg[AASALL];		/*  pseudo counts */
  double totreg;
};

struct work_pssm {		/* Working PSSM area */
  double value[MAXWIDTH][AASALL];
  double sum[MAXWIDTH];
};


/*		Duplicate static routines in convert.c    */
struct working *make_col();
struct work_pssm *make_pssm();
void counts();
void positive_matrix();
void compute_BZX();
void output_mast_matrix();
void pseudo_alts();
int count_residues();

/*	Routines for this program */
Matrix *make_matrix();
void dummy_counts();
void dummy_pseudos();
void positive100_matrix();

int TotReal;
/*====================================================================*/
int main(argc, argv)
int argc;
char *argv[];
{
   FILE *chk, *fout;
   char chkname[80], ctemp[80], line[MAXLINE], *ptr, *ptr1;
   Matrix *pssm, *matrix;
   Block *block;
   int s, pos, aa, alpha[MATRIX_AA_WIDTH], width, alength, itemp, okay, type;
   int mast, nlines;
   double dtemp, dmin, dmax;

   ErrorLevelReport = 3;	/* only serious errors, set to 5 for none */

   if (argc < 3)
   {
      printf("COPYRIGHT 2000 Fred Hutchinson Cancer Research Center\n");
      printf("USAGE:  narrow  \n");
      printf("		file_type = B|F|W	B=block, F=frequencies, W=weights\n");
      printf("					F or W in MAST format\n");
      printf("Writes a positive PSSM to stdout in BLIMPS format\n");
   }
   /*------------1st arg =  type ----------------------------*/
   type = 0;	/* 0=> block, 1=>freqs 2=>weights in MAST format */
   if (argc > 1)
      strcpy(ctemp, argv[1]);
   else
   {
      printf("\nEnter type of input file (Block|Frequencies|Weights): ");
      gets(ctemp);
   }
   if (ctemp[0] == 'F' || ctemp[0] == 'f') type = 1; 
   else if (ctemp[0] == 'W' || ctemp[0] == 'w') type = 2; 

   /*------------2nd arg = input file--------------------*/
   if (argc > 2)
      strcpy(chkname, argv[2]);
   else
   {
      printf("\nEnter name of input file: ");
      gets(chkname);
   }
   if ( (chk=fopen(chkname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", chkname);
      exit(-1);
   }

   /*----------------------------------------------------------------------*/
   frq_qij();	/* Sets Qij, RTot and frequency[] to default values */
   RTot = 1.0;
   TotReal = TOTREAL;

   for (aa=0; aa < MATRIX_AA_WIDTH; aa++) alpha[aa] = -1;
   alength = width = pos = 0;
   dmin = 9999999.99;
   dmax = -9999999.99;
   pssm = matrix = NULL;
   block = NULL;
   okay = mast = NO;

   
   if (type == 0)
   {
      block = read_a_block(chk);
      if (block == NULL)
      {
         printf("ERROR:No block found in file %s\n", chkname);
	 printf("Please verify input format type\n");
         exit(-1);
      }
      width = block->width;
      for (s=0; s< block->num_sequences; s++) 
	block->sequences[s].weight = 100.0; 
   }
   else		/* read the frequencies or weights into a pssm */
   {
      /*  see if input file is in mast format  */
      mast = NO; nlines = 0;
      while (!mast && !feof(chk) && fgets(line, MAXLINE, chk) != NULL )
      {
         if (strncmp(line, "ALPHABET", 7) == 0) mast = YES;
         nlines++;
      }
      rewind(chk);

      if (mast)
      {
         while (!okay && !feof(chk) && fgets(line, MAXLINE, chk) != NULL )
         {
            if (strncmp(line, "ALPHABET", 7) == 0)
            {
	      ptr = strtok(line, " ");
              if (ptr != NULL)
              {
		ptr = strtok(NULL, " \r\t\n");
		if (ptr != NULL) alength = (long) strlen(ptr);
		else alength = 0;
              }
              if (alength == 0)
              {
		printf("\nProblem finding ALPHABET in %s\n", chkname);
		exit(-1);
              }
	      for (itemp=0; itemp= 0 && aa < MATRIX_AA_WIDTH) alpha[itemp] = aa;
	      }
            }   /* end of ALPHABET */

            /* alength= %d w= %d  */
            if ( (strncmp(line, "log-odds", 8) == 0) ||
                 (strncmp(line, "frequency", 9) == 0)  )
            {
	      ptr1 = strstr(line, "alength=");
              if (ptr1 != NULL)
              {
		sscanf(ptr1, "alength= %d w=%d", &itemp, &width);
		if (itemp != alength)
		{
		   printf("\nALPHABET length (%d) not alength (%d)\n", 
				alength, itemp);
		   exit(-1);
		}
              }
              if (width == 0)
              {
		printf("\nProblem finding width in %s\n", chkname);
		exit(-1);
              }
	      else
	      {
                okay = YES;
	      }
            }  /* end of log-odds */
         }      /* end of while */
      }  /* end of if mast format  */
      else
      {
		printf("Not sure about the format of %s,", chkname);
		printf(" assuming first line contains alphabet\n");
		width = nlines - 1;
		fgets(line, MAXLINE, chk);
		ptr = strtok(line, " \r\t\n");
		if (ptr != NULL) alength = (long) strlen(ptr);
		else alength = 0;
	      for (itemp=0; itemp= 0 && aa < MATRIX_AA_WIDTH) alpha[itemp] = aa;
	      }
              if (width > 0 && alength > 0)  okay = YES;
      }  /* end of not-mast input  */

      /*  Now have width and alphabet; read the weights next */
      if (okay)
      { 
	pssm = new_matrix( (int) width);
	pssm->width = width;
	strcpy(pssm->id, "WEIGHTS");
	strcpy(pssm->ac, "WEIGHTS");
	strcpy(pssm->de, chkname);
	sprintf(pssm->ma, "width=%d;", width);
         while (pos < width && !feof(chk) && fgets(line, MAXLINE, chk) != NULL )
         {
	    ptr = strtok(line, " \t\r\n");
            for (aa=0; aa < alength; aa++)
            {
		if (ptr != NULL)
		{
			dtemp = atof(ptr);
			pssm->weights[ alpha[aa] ][pos] = dtemp;
			if (dtemp < dmin) dmin = dtemp;
			if (dtemp > dmax) dmax = dtemp;
			ptr = strtok(NULL, " \t\r\n");
		}
		else
		{
			printf("\nProblem finding value for pos=%d aa=%c\n",
				pos, aa_btoa[aa]);
		}
            }
	    pos++;
	}
        if (type == 1 && dmin < 0.0)
        {
           printf("ERROR: Negative frequencies read\n");
	   printf("Please verify input format type\n");
           exit(-1);
        }
        if (type > 0 && dmin == 0.0 && dmax == 0.0)
        {
           printf("ERROR: All values read as zero\n");
	   printf("Please verify input format type\n");
           exit(-1);
        }
      } /* end of okay */
      else
      {
	printf("Could not find alphabet or width in %s\n", chkname);
        exit(-1);
      }
   }  /* end of non-zero (non-block) input type */ 

   /*----------------------------------------------------------------------*/
   /*>>>>  what scale? 0=> nats  <<<<*/
   switch(type)
   {
      case 0:  /* block was input; pssm is NULL */
         matrix = make_matrix(block, pssm, 0);
      break;

      case 1:	/* frequencies were input */
         /*  Print the frequencies */
/*>>>>  need to check that freqs add to 1.0 in each column 
         output_matrix_st(pssm, stdout, FLOAT_OUTPUT, AA_SEQ);
<<<<*/
	 /* Create a dummy block for make_matrix() */
         block = new_block( (int) width, 0);
         block->width = width;
         strcpy(block->id, "FREQS");
         strcpy(block->ac, "FREQS");
         strcpy(block->de, chkname);
         sprintf(block->bl, "seqs=%d; width=%d;", TotReal, width);
         block->num_sequences = 0;
	 /*  Create the matrix with almost no pseudo counts */
         matrix = make_matrix(block, pssm, 0);
      break;

      case 2:		/* weights were input */
		matrix = pssm;
      break;

      default:
      break;
   } /* end of switch(type) */

   /*  Print the nat matrix in mast format */
   sprintf(ctemp, "%s.mast", chkname);
   if ( (fout=fopen(ctemp, "w")) == NULL)
   {
      printf("\nCannot open file %s\n", ctemp);
      output_mast_matrix(matrix, stdout);
   }
   else
   { 
      output_mast_matrix(matrix, fout);
      fclose(fout);
   }
   /*  Normalize weights to add to 100 in each position */
   positive100_matrix(matrix);
   /*  Print the weights in Blimps format */
   sprintf(ctemp, "%s.blimps", chkname);
   if ( (fout=fopen(ctemp, "w")) == NULL)
   {
      printf("\nCannot open file %s\n", ctemp);
      output_matrix_st(matrix, stdout, FLOAT_OUTPUT, AA_SEQ);
   }
   else
   { 
      output_matrix_st(matrix, fout, FLOAT_OUTPUT, AA_SEQ);
      fclose(fout);
   }

   exit(0);
}  /* end of main */
/*==========================================================================
    Make a log-odds matrix with as few pseudo-counts as possible
	Expects global variables RTot, Qij, and frequency[]
	RTot  = dummy number of real counts if frequencies entered
	If just frequencies entered, block->num_sequences = 0 and
		frequencies are in colfreqs
===========================================================================*/
Matrix *make_matrix(block, colfreqs, scale)
     Block *block;
     Matrix *colfreqs;
     int scale;
{
  double factor, dtemp, epsilon;
  int pos, aa;
  struct working *col;
  struct work_pssm *work;
  Matrix *matrix;

  matrix = new_matrix( (int) block->width);
  matrix->width = block->width;
  strcpy(matrix->id, block->id);
  strcpy(matrix->ac, block->ac);
  strcpy(matrix->de, block->de);
  strcpy(matrix->ma, block->bl);

  factor = 1.0;
  if (scale > 0 && scale < 10) factor = (double) scale / log(2.0);
  col = make_col();
  work = make_pssm();
  
  /*--------------  Do one position at a time -------------------*/
  for (pos = 0; pos < block->width; pos++) 
  {
    /*-------- count the number of each aa in this position ------------*/
    /*  Might have frequencies already           */
    if (colfreqs == NULL) counts(block, col, pos);
    /* col->cnt[aa] = n_ca = TotReal * f_ca  */
    else dummy_counts(colfreqs, col, TotReal, pos); 
    
    /*-------- determine total number of pseudo-counts in column ------*/
    epsilon = 1.0;
    
    /*---------- get the pseudo counts -------------------------------*/
    if (colfreqs == NULL)
    { 
/*
        epsilon = RTot * (double) count_residues(col);
*/
        /* if a block was input, use 1 pseudo-count per 100 counts */
        epsilon = (double) col->totcnt / PERREAL;
        pseudo_alts(col, Qij, epsilon);
    }
    /* col->reg[aa] = b_ca = epsilon * p_a  */
    else  dummy_pseudos(col, epsilon);
    
    /*---------   Fill in the matrix entries --------------------*/
    work->sum[pos] = 0.0;
    for (aa=1; aa < AAS; aa++)
    {
       work->value[pos][aa] = col->cnt[aa] + col->reg[aa];
       if ( (col->totcnt + col->totreg) > 0.0)
             work->value[pos][aa] /= (col->totcnt + col->totreg);
    
       /*     Odds ratios  */
       if (frequency[aa] > 0.0)
          work->value[pos][aa] /= frequency[aa];

       /*   take the log of the odds ratio  */
       if (work->value[pos][aa] > 0.0) 
          work->value[pos][aa] = log(work->value[pos][aa]);
 
       work->sum[pos] += work->value[pos][aa];

       /*  scale the matrix  */
       dtemp = factor * work->value[pos][aa];
       matrix->weights[aa][pos] = dtemp;

     }  /* end of aa */

/*>>>>??? this is what blimps does
     compute_BZX(matrix, pos); 
*/
  }  /*  end of for pos */

  /*------ Now make the final scores; make log scores non-neg    */
  /*       by subtracting the min. value for all positions ----- */
/*>>>>??? this is what blimps does
  if (!scale) positive_matrix(work, matrix);
*/
  
  free(col);
  free(work);
  return(matrix);
}  /* end of make_matrix */
/*==================================================================*/
void dummy_counts(colfreqs, col, totreal, pos)
Matrix *colfreqs;
struct working *col;
int totreal, pos;
{
   int aa;

   col->totcnt = totreal;
   for (aa=0; aacnt[aa] = 0.0;
   for (aa=1; aa < AAS; aa++) col->cnt[aa] = totreal * colfreqs->weights[aa][pos];

}  /* end of dummy_counts */
/*==================================================================*/
void dummy_pseudos(col, totpseudo)
struct working *col;
double totpseudo;
{
   int aa;

   col->totreg = totpseudo;
   for (aa=0; aareg[aa] = 0.0;
   for (aa=1; aa < AAS; aa++) col->reg[aa] = totpseudo * frequency[aa];

}  /* end of dummy_pseudos */
/*==================================================================*/
struct working *make_col()
{
  struct working *col;
  int aa;
  
  CheckMem(
	   col = (struct working *) malloc(sizeof(struct working))
	   );
  
  col->totcnt = col->totreg = 0.0;
  for (aa=0; aa < AASALL; aa++) {
    col->cnt[aa] = col->reg[aa] = 0.0;
  }

  return col;
}  /* end of make_col */


/*=====================================================================*/
struct work_pssm *make_pssm()
{
  struct work_pssm *pssm;
  int pos, aa;
  
  CheckMem(
	   pssm = (struct work_pssm *) malloc(sizeof(struct work_pssm))
	   );

  for (pos = 0; pos < MAXWIDTH; pos++) {
    pssm->sum[pos] = 0.0;
    for (aa=0; aa < AASALL; aa++) {
      pssm->value[pos][aa] = 0.0;
    }
  }

  return pssm;
}  /* end of make_pssm */
/*======================================================================
>>>> What to do with Xs? 
======================================================================*/
void counts(block, col, pos)
     Block *block;
     struct working *col;
     int pos;
{
  int seq, aa, aa1;

  col->totcnt = col->totraw = col->totreg = 0.0;
  for (aa = 0; aa < AASALL; aa++) { 
    col->cnt[aa] = col->raw[aa] = col->reg[aa] = 0.0;
  }

  /*  Only count the real 20 aas, combine B(21) with D & Z(22) with E  */
  for (seq = 0; seq < block->num_sequences; seq++) {
    aa = block->residues[seq][pos];
    if (aa == 21) aa = 4;			/* combine B with D */
    if (aa == 22) aa = 7;			/* combine Z with E */
    if (aa >= 1 && aa < AAS) {
      col->cnt[aa] += block->sequences[seq].weight;
      col->totcnt += block->sequences[seq].weight;
      col->raw[aa] += 1.0;
      col->totraw += 1.0;
    }
    else  
    {
/*>>>>   Want to just ignore the count ???  <<<< */
      /* If not one of the basic aas, divide the count among them */
      for (aa1 = 1; aa1 < AAS; aa1++)
      {
         col->cnt[aa1] += (block->sequences[seq].weight / 20.0);
         col->raw[aa1] += (1.0 / 20.0) ;
      }
      col->totcnt += block->sequences[seq].weight;
      col->totraw += 1.0;
    }
  }
}  /* end of counts */
/*=========================================================================
      Adds negative minval to give all positive matrix,
      then multiplies by 99/maxval to give scores ranging from 0 to 99 
      NOTE: Not 0 to 100 because "output_matrix" routine might not leave
	    enough space.
===========================================================================*/
void positive_matrix(pssm, matrix)
     struct work_pssm *pssm;
     Matrix *matrix;
{
  int pos, aa;
  double factor, maxval, minval, dtemp;

  minval = 9999.9;
  maxval = -9999.9;
  for (pos = 0; pos < matrix->width; pos++) {
    for (aa=1; aa < AAS; aa++) {
      if (pssm->value[pos][aa] < minval) minval = pssm->value[pos][aa];
      if (pssm->value[pos][aa] > maxval) maxval = pssm->value[pos][aa];
    }
  }
   
  if (minval < 0.0) {
    factor = 99.0 / (maxval - minval);
  }
  else {
    factor = 99.0 / maxval;
  }
  if (factor < 1.0) {
    factor = 1.0;
  }
  for (pos = 0; pos < matrix->width; pos++) {
    for (aa=1; aa < AAS; aa++) {
      if (minval < 0.0) {
	dtemp = factor * (pssm->value[pos][aa] - minval);
      }
      else {
	dtemp = factor * pssm->value[pos][aa];
      }
      matrix->weights[aa][pos] = (MatType) dtemp;
    }
    compute_BZX(matrix, pos);
  }  /*  end of for pos */
}  /* end of positive_matrix */
/*=========================================================================
	Normalize 20 aa weights to add to 100 in every column
===========================================================================*/
void positive100_matrix(matrix)
Matrix *matrix;
{
  int pos, aa;
  double maxval, minval, dtemp;

  minval = 9999.9;
  maxval = -9999.9;
  for (pos=0; pos < matrix->width; pos++)
  {
     for (aa=1; aa <= 20; aa++) 
     {
      if (matrix->weights[aa][pos] < minval) minval = matrix->weights[aa][pos];
      if (matrix->weights[aa][pos] > maxval) maxval = matrix->weights[aa][pos];
     }
  }
   
  /* make all weights positive */
  if (minval < 0)
  {
     for (pos=0; pos < matrix->width; pos++)
     {
        for (aa=1; aa <= 20; aa++)
        { matrix->weights[aa][pos] = matrix->weights[aa][pos] - minval; }
     }
  }

  /* make weights sum to 100.0 in each position */
  for (pos=0; pos < matrix->width; pos++)
  {
     dtemp = 0.0;
     for (aa=1; aa <= 20; aa++) 
     { dtemp += matrix->weights[aa][pos]; }
     /*  if all weights = minval to start, dtemp will be zero */
     if (dtemp > 0.0)
     {
        for (aa=1; aa <= 20; aa++) 
        { matrix->weights[aa][pos] = 100.0 * matrix->weights[aa][pos] / dtemp; }
     }

     compute_BZX(matrix, pos);
  }

}  /* end of positive100_matrix */


/*========================================================================
	Computes scores for B, Z, X, -(gap) and *(stop) in a column
	of a PSSM using other scores in the column
	Assumes global frequency[]
==========================================================================*/
void compute_BZX(matrix, col)
Matrix *matrix;
int col;
{
  int aa;
  double dmean, dmin;
  double part_D;		/* the partition of D for B. */
				/* = freq[D] / ( freq[D] + freq[N] ) */
  double part_N;		/* the partition of N for B. */
				/* = freq[N] / ( freq[D] + freq[N] ) */
  double part_E;		/* the partition of E for Z. */
				/* = freq[E] / ( freq[E] + freq[Q] ) */
  double part_Q;		/* the partition of Q for Z. */
				/* = freq[Q] / ( freq[E] + freq[Q] ) */
  /*
   * find the partitions of D, N, E, and Q for B and Z
   */
  part_D = frequency[aa_atob['D']] / 
    ( frequency[aa_atob['D']] + frequency[aa_atob['N']] );
  part_N = frequency[aa_atob['N']] / 
    ( frequency[aa_atob['D']] + frequency[aa_atob['N']] );
  part_E = frequency[aa_atob['E']] / 
    ( frequency[aa_atob['E']] + frequency[aa_atob['Q']] );
  part_Q = frequency[aa_atob['Q']] / 
    ( frequency[aa_atob['E']] + frequency[aa_atob['Q']] );

    /* fill in the matrix for B, Z, X, gap, stop and non */
    matrix->weights[aa_atob['B']][col] = 
      (part_D * matrix->weights[aa_atob['D']][col] +
       part_N * matrix->weights[aa_atob['N']][col]);
    matrix->weights[aa_atob['Z']][col] =
      (part_E * matrix->weights[aa_atob['E']][col] +
       part_Q * matrix->weights[aa_atob['Q']][col]);

    /*   X or unk gets the weighted average score; - and * get the min score */
    dmin = 999.99;
    dmean = 0.0;
    for (aa=1; aa<20; aa++)
    {
       dmean += frequency[aa] * matrix->weights[aa][col];
       if (matrix->weights[aa][col] < dmin) dmin = matrix->weights[aa][col];
    }
    matrix->weights[aa_atob['X']][col] = dmean;
    matrix->weights[aa_atob[25]][col] = dmean;		/* unknown res */
    matrix->weights[aa_atob['-']][col] = dmin;
    if (dmin > 0.0) matrix->weights[aa_atob['*']][col] = 0.0;
    else            matrix->weights[aa_atob['*']][col] = dmin;

}  /* end of compute_BZX */
/*=======================================================================
    0- 1A 2R 3N 4D 5C 6Q 7E 8G 9H 10I 11L 12K 13M 14F 15P 16S 17T 18W 19Y
   20V 21B 22Z 23X 24* 25J,O,U 
========================================================================*/
void output_mast_matrix(matrix, ofp)
Matrix *matrix;
FILE *ofp;
{
   int pos, aa;

   fprintf(ofp, "ALPHABET= ARNDCQEGHILKMFPSTWYVBZX\n");
   fprintf(ofp, "log-odds matrix: alength= 23 w= %d\n", matrix->width);
   for (pos=0; pos < matrix->width; pos++)
   {
      /*  Force U == X */
      matrix->weights[25][pos] = matrix->weights[23][pos];
      for (aa=1; aa <= 23; aa++)
      {
         fprintf(ofp, "% 6.3f ", matrix->weights[aa][pos]);
      }
      fprintf(ofp, "\n");
   }

}  /* end of output_mast_matrix */
/*=======================================================================*/
void pseudo_alts(col, qij, epsilon)
     struct working *col;
     struct float_qij *qij;
     double epsilon;
{
  int aa, row;
  
  /*---------- get the pseudo counts -------------------------------*/
  for (aa=1; aa < AAS; aa++) {
    col->reg[aa] = 0.0;
    for (row = 1; row < AAS; row++) {
      col->reg[aa] += (col->cnt[row] * qij->value[aa][row] / qij->marg[row]);
    }
    col->reg[aa] *= epsilon;
    if (col->totcnt > 0.0) col->reg[aa] /= col->totcnt;
    col->totreg += col->reg[aa];
  }
}  /* end of pseudo_alts */
/*=====================================================================*/
int count_residues(col)
     struct working *col;
{
  int aa, nr;

  nr = 0;
  for (aa = 1; aa < AAS; aa++) {
    if (col->cnt[aa] > 0.0) nr++;
  }

  return nr;
}  /*  end of count_residues */

+ col->reg[aa];
       if ( (col->totcnt + col->totreg) > 0.0)
             work->value[pos][aa] /= (col->totcnt + col->totreg);
    
       /*     Oddsblimps-3.9/blimps/oligo_melt.c000064400001460000012000000221650774312250000167400ustar00jorjastaff00000400000027/* COPYRIGHT 1997 Fred Hutchinson Cancer Research Center, Seattle, WA, USA
   oligo_melt.c:  Calculate various melting point temperatures for an oligo.
     oligo_melt  
==========================================================================
12/30/97 1.
 1/13/98 1. Print reverse.
 3/28/98 1. Don't print reverse. References.
 11/20/99 1. Added SantaLucia
*/

#define EXTERN

#include 

#define is_res(x) (x==aa_atob['A'] || x==aa_atob['C'] || x== aa_atob['G'] ||   \
                x==aa_atob['T']) ? TRUE : FALSE
/*	Clamp temperate: a = AT content, g = GC content of clamp region */
#define suggs(a,g) (3.0 + 2.0 * a + 4.0 * g)

double freier();
double rychlik();
void compute_thermo();
void santalucia();
void print_reverse();

/*---------------------- Global variables ----------------------------*/
char Version[12] = "11/20/99.1";		/* Version date */

double Koncentration = 50;		/* salt in mM units */
double Concentration = 50;		/* DNA concentration in nM */
/* Primer3's Conc = 50nM while Nar's = 0.1nM */

/*  Breslauer, et al entropy & enthalpy for nearest neighbors, order is
     AA AC AG AT CA CC CG CT    GA GC GG GT TA TC TG TT          */
double Bres_Enthalpy[16]  = {  9.1,  6.5,  7.8,  8.6,  5.8, 11.0, 11.9,  7.8,
                              5.6, 11.1, 11.0,  6.5,  6.0,  5.6,  5.8,  9.1 };
double Bres_Entropy[16] = { 24.0, 17.3, 20.8, 23.9, 12.9, 26.6, 27.8, 20.8,
                             13.5, 26.7, 26.6, 17.3, 16.9, 13.5, 12.9, 24.0 };
/*  SantaLucia, et al entropy & enthalpy for nearest neighbors, order is
     AA AC AG AT CA CC CG CT    GA GC GG GT TA TC TG TT          */
double SaLu_Enthalpy[16]  = {  7.9,  8.4,  7.8,  7.2,  8.5,  8.0, 10.6,  7.8,
                              8.2,  9.8,  8.0,  8.4,  7.2,  8.2,  8.5,  7.9 };
double SaLu_Entropy[16] = { 22.2, 22.4, 21.0, 20.4, 22.7, 19.9, 27.2, 21.0,
                             22.2, 24.4, 19.9, 22.4, 21.3, 22.2, 22.7, 22.2 };
/*=======================================================================*/
/*
 * main
 *   controls flow of program
 *   Parameters: argc, argv
 *   Error codes:
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
   FILE  *inpf=stdin;
   char fname[80];
   Sequence *seq;
   int db_type, seq_type, num_at, num_gc;
   double entropy, enthalpy, salt, suggs_temp, nar_temp, primer3_temp;

   ErrorLevelReport = 2;		/* suppress BLIMPS errors */

   if (argc < 2)
   {
      printf("OLIGO_MELT %s\n", Version);
      printf("COPYRIGHT 1997, Fred Hutchinson Cancer Research");
      printf(" Center, Seattle, WA, USA\n");
      printf("\nUSAGE:  oligo_melt  [DNA conc in nM]\n");
   }

   /*--------------------------1st arg = sequence file ------------*/
   if (argc > 1) strcpy(fname, argv[1]);
   else
   {
      printf("Enter name of file containing oligos: ");
      gets(fname);
   }
   if (!strlen(fname) ) inpf = stdin;
   else if ((inpf=fopen(fname, "r")) == NULL)
   {
      printf("Cannot open %s\n", fname);
      exit(-1);
   }
   /*--------------------------2nd arg = concentration ------------*/
   if (argc > 2) Concentration = atof(argv[2]);

   /*  Assumes Koncentration is in mM = 10-3 */
   salt = 16.6 * ( log10(Koncentration) + log10(0.001) );

   db_type = type_dbs(inpf, DbInfo);
   seq_type = seq_type_dbs(inpf, DbInfo, db_type);
   if (seq_type != NA_SEQ)
   {
	seq_type = NA_SEQ;	/*  degen residues will be ignored */
   }

   printf("\nEstimated melting temperatures of non-degenerate clamp region (C=%.2fnM):\n",
        Concentration);
   while ((seq = read_a_sequence(inpf, db_type, seq_type)) != NULL)
   {
      printf("\n-----------------------------------------------------------\n");
      output_sequence(seq, stdout);

      /*  Using Breslauer's entropy & enthalpy  */
      compute_thermo(seq, &entropy, &enthalpy, &num_at, &num_gc);
      suggs_temp = suggs(num_at, num_gc);
      nar_temp =  freier(entropy, enthalpy);
      primer3_temp = nar_temp + salt;
      printf("Length=%d, clamp=%d\n", seq->length, seq->undefined);

      printf("\n---Using Breslauer's entropy=-%.1f & enthalpy=-%.1f\n",
		entropy, enthalpy);
      printf("AT/GC=%.1f, NAR=%.1f, PRIMER3=%.1f\n",
              suggs_temp, nar_temp, primer3_temp);

      /*  Using SantaLucia's entropy & enthalpy  */
      santalucia(seq, &entropy, &enthalpy, &num_at, &num_gc);
      suggs_temp = suggs(num_at, num_gc);
      nar_temp =  freier(entropy, enthalpy);
      primer3_temp = nar_temp + salt;

      printf("---Using SantaLucia's entropy=-%.1f & enthalpy=-%.1f\n",
		entropy, enthalpy);
      printf("AT/GC=%.1f, NAR=%.1f, PRIMER3=%.1f\n",
             suggs_temp, nar_temp, primer3_temp);


/*
      print_reverse(seq);
*/
      free_sequence(seq);
   }

   fclose(inpf);

   printf("\n-----------------------------------------------------------\n");
   printf("References:\n");
   printf("Entropy/Enthalpy: Table 2 from Breslauer, et al, (1986) PNAS 83:3746-3750\n");
   printf("Entropy/Enthalpy: Table 2 from SantaLucia, (1998) PNAS 95:1460-1465\n");
   printf("AT/GC: Suggs, et al, (1981) ICN-UCLA Symp.Dev.Biol. 23:683-693\n");
   printf("NAR: Eqn [2] from Freier, et al, (1986) PNAS 83:9373-9377\n");
   printf("PRIMER3: Eqn (ii) from Rychlik, et al, (1990) NAR 18:6409-6412\n");

   exit(0);
}  /* end of main */

/*=================================================================
    Equation [2] from Freier, et al, PNAS 83:9373-9377
=================================================================*/
double freier(entropy, enthalpy)
double entropy, enthalpy;
{
   double tm, top, bot;

   top = 0.0 - 1000.0 * enthalpy;
   /*   Assumes concentration is given in nM units  */
   bot = 1.987 * (log(Concentration/4.0) + log(0.000000001));
   bot -= entropy;
   if (bot < 0.0)
      tm = top / bot - 273.15;
   else
      tm = 0.0;

   return(tm);
}  /* end of freier */
/*=================================================================
    Equation [] from Rychlik, et al (1990), NAR 18:6409
	Ta = 0.3Tm_primer + 0.7Tm_product - 14.9
=================================================================*/
double rychlik(entropy, enthalpy)
double entropy, enthalpy;
{
   double tm_primer, tm_prod, salt, ta;

   /*  Assumes Koncentration is in mM = 10-3 */
   salt = 16.6 * ( log10(Koncentration) + log10(0.001) );
   tm_primer = freier(entropy, enthalpy) + salt;

   return(tm_primer);
}  /* end of rychlik */
/*=================================================================
   Compute entropy & enthalpy for an oligo clamp
	clamp_last is the 5' end, clamp_first is the 3' end
	Compute from the 5' to the 3' end
   strand > 0: 5' clamp_last, clamp_first, core_last, core_first 3'
   strand < 0: 3' core_first, core_last, clamp_first, clamp_last 5'
=================================================================*/
void compute_thermo(seq, entropy, enthalpy, nat, ngc)
Sequence *seq;
double *entropy, *enthalpy;
int *nat, *ngc;
{
   int pos, prev_res, res, bi;

   *nat = *ngc = 0;
   *entropy = 10.8;  *enthalpy = 0.0;
   res = prev_res = -99;
   /*	Assumes seq is loaded 5' to 3' and stops at first degen. res */
   pos = 0;
   while (pos < seq->length &&
          seq->sequence[pos] >= 0 && seq->sequence[pos] < 4)
   {
      res = seq->sequence[pos];
      if (res == 0 || res == 3) *nat += 1;
      if (res == 1 || res == 2) *ngc += 1;
      if (prev_res >= 0 && prev_res < 4) 
      {
         bi = prev_res * 4 + res;
         *entropy += Bres_Entropy[bi]; 
         *enthalpy += Bres_Enthalpy[bi];
      }
      prev_res = res;
      pos++;
   }  
   seq->undefined = pos;		/* clamp+nondegen core */
}   /* end of compute_thermo */
/*=================================================================
   Compute entropy & enthalpy for an oligo clamp
	clamp_last is the 5' end, clamp_first is the 3' end
	Compute from the 5' to the 3' end
   strand > 0: 5' clamp_last, clamp_first, core_last, core_first 3'
   strand < 0: 3' core_first, core_last, clamp_first, clamp_last 5'
=================================================================*/
void santalucia(seq, entropy, enthalpy, nat, ngc)
Sequence *seq;
double *entropy, *enthalpy;
int *nat, *ngc;
{
   int pos, prev_res, res, bi;

   *nat = *ngc = 0;
   *entropy = 10.8;  *enthalpy = 0.0;
   res = prev_res = -99;
   /*	Assumes seq is loaded 5' to 3' and stops at first degen. res */
   pos = 0;
   while (pos < seq->length &&
          seq->sequence[pos] >= 0 && seq->sequence[pos] < 4)
   {
      res = seq->sequence[pos];
      if (res == 0 || res == 3) *nat += 1;
      if (res == 1 || res == 2) *ngc += 1;
      if (prev_res >= 0 && prev_res < 4) 
      {
         bi = prev_res * 4 + res;
         *entropy += SaLu_Entropy[bi]; 
         *enthalpy += SaLu_Enthalpy[bi];
      }
      prev_res = res;
      pos++;
   }  
   seq->undefined = pos;		/* clamp+nondegen core */
}   /* end of santalucia */
/*=====================================================================*/
/*=====================================================================*/
void print_reverse(seq)
Sequence *seq;
{
   int pos;

   printf("\nOligo in reverse order:\n");
   for (pos = seq->length-1; pos >= 0; pos--)
   {
      printf("%c", nt_btoa[ seq->sequence[pos] ]);
      if (pos%60 == 0) printf("\n");
   }
   printf("\n");
}  /* end of  print_reverse */
blimps-3.9/blimps/options.c000064400001460000012000000135300774312250000162750ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* options.c: */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#define EXTERN

/*	system headers not in global.h */
/*	blimps library headers */
#include 
#include 	/* requires global.h ! */

char **OptionsARGV = NULL;
int OptionsARGC = 0;



/* 
 * get_option_args
 *  This retrieves the desired option arguments from the OptionsARGV
 *  array.  This is the function to use to retrieve options for any of
 *  the sub-algorithms (algorithms that are optional and not used
 *  generally).
 *  The options/arguments are accessed from the returned pointer.
 *  NOTE: there is no argument quoting yet.  All arguments are
 *    whitespace delimited.
 *  To identify which algorithm a set of arguments belongs to the
 *  arguments need to be prefixed and postfixed with a key.  For
 *  example (the colon is needed):
 *    OP Alt: arg0 arg1 arg2 arg3 :Alt
 *
 *  NOTE: The key is case INsensitive.  Also, if there is no
 *    terminating key the rest of the arguments are included in the
 *    returned argc.
 *  In the above example the returned value for argc would be 4 and
 *  the argv vector would start at arg0.
 *  WARNING: all of the following arguments after the key region are
 *    STILL accessible.  Only the address of the first arg is set.  No
 *    memory is duplicated.
 *  IMPORTANT NOTE: This does NOT follow the standard argc/argv
 *    conventions in main().  The argv[0] is the first ARGUMENT.
 *  Parameters:
 *    char *key:        the key (case INsensitive)
 *    int *argc_ptr:    a pointer to where to place argc.
 *    char ***argv_ptr: a pointer to where to place the argv address.
 *                      (remember argv is accessed as an array of char
 *                      ptrs.  An array of char ptrs is of type char **.  
 *                      so this is just a pointer to the place to put
 *                      the "array")
 *  Return Codes: returns TRUE if it can find the key region, FALSE
 *                otherwise
 *  Error Codes:  See above and argc is set to -1 and argv is set to NULL
 *
 *  Calling example:
 *    int argc;
 *    char **argv;  -- this can NOT be an array
 *    int result;
 *
 *    result = get_option_args("mykey", & argc, & argv); -- pass the addresses!
 *    if (result == TRUE) {
 *      printf("Got them\n");
 *    }
 *    else {
 *      printf("Could not find the args\n");
 *      -- error handling stuff here -- 
 *    }
 */

#define KEYCHAR ':'

Boolean 
get_option_args(key, argc_ptr, argv_ptr)
     char *key;
     int *argc_ptr;
     char ***argv_ptr;
{
  int x, start, stop;
  int keylen;

  keylen = strlen(key);
  x = 0;
  while ((x < OptionsARGC) &&
	 ! ((strncasecmp(OptionsARGV[x], key, keylen) == 0) &&
	    (OptionsARGV[x][keylen] == KEYCHAR))) {
    x++;
  }

  if (x >= OptionsARGC) {
    *argc_ptr = -1;
    *argv_ptr = NULL;
    return FALSE;
  } 

  start = x;
	 
  while ((x < OptionsARGC) &&
	 ! ((strncasecmp(&(OptionsARGV[x][1]), key, keylen) == 0) &&
	    (OptionsARGV[x][0] == KEYCHAR))) {
    x++;
  }

  stop = x;

  *argc_ptr = stop - start - 1;

/* debug stuff
printf("Start= %d, stop = %d\n", start, stop);
printf("OptionsARGV[start]= %s\n", OptionsARGV[start]);
*/

  *argv_ptr = &(OptionsARGV[start+1]);

  return TRUE;

}



/* 
 * insert_into_options
 *   Inserts the tokens in string into the options array for later
 *   retreival. 
 *   NOTE, get_token() is the function called to parse the tokens.  If
 *     a parse is in progress just pass in NULL, this will get passed
 *     to get_token() the first time, retreiving the next token.
 *   Parameters:
 *     char  *string: the string of tokens whitespace delimited
 *   Return codes: none
 *   Error codes: none
 */

void
insert_into_options(string)
     char *string;
{
  int x;
  char ** argv;
  int argc;
  int max_arg;
  char *tmp;
  char **tmp_argv;

  int cgt; /* whether a call to get token has been done with the string yet */
  cgt = 0;

  /* allocate a temporary argv */
  CheckMem(
	   argv = (char **) malloc(sizeof(char *) * 5)	/* allocate 5 ptrs */
	   );

  max_arg=5;
  argc = 0;

  /* fill it */
  while ( (tmp = ((cgt) ?
		  (get_token(NULL)) :
		  ((cgt=1), (get_token(string))) )) != NULL) {
    /* increase if needed */
    if (argc >= max_arg) {
      CheckMem(
	       tmp_argv = (char **) realloc(argv, sizeof(char *) * (max_arg+5))
	       );
      argv = tmp_argv;
      max_arg = max_arg+5;
    }

    /* allocate space for the duplicate string and put it in the array */
    CheckMem(
	     argv[argc] = strdup(tmp)
	     );
    argc++;
  }

  /* do NOT need check if the OptionsARG[VC] are already used since */
  /* realloc acts like malloc if the pointer was NULL */
  /* WRONG!!! Some systems do not have realloc like this. :P */
  
  /* (re)allocate enough space for the new argv */
  if (OptionsARGV == NULL) {
    CheckMem(
	     tmp_argv = (char **) malloc(sizeof(char *) * (OptionsARGC+argc))
	     );
  }
  else {
    CheckMem(
	     tmp_argv = (char **) realloc(OptionsARGV, 
					  sizeof(char *) * (OptionsARGC+argc))
	     );
  }
  OptionsARGV = tmp_argv;
  
  /* add the new args to OptionsARGV */
  for (x=0; x
#endif


#define Isspace(c)  isspace(c)      /* or "((c) == ' ')" if preferred */




int P_argc;
char **P_argv;

short P_escapecode;
int P_ioresult;

long EXCP_LINE;    /* Used by Pascal workstation system */

Anyptr __MallocTemp__;

__p2c_jmp_buf *__top_jb;




void PASCAL_MAIN(argc, argv)
int argc;
char **argv;
{
    P_argc = argc;
    P_argv = argv;
    __top_jb = NULL;

#ifdef LOCAL_INIT
    LOCAL_INIT();
#endif
}





/* In case your system lacks these... */

long my_labs(x)
long x;
{
    return((x > 0) ? x : -x);
}


#ifdef __STDC__
Anyptr my_memmove(Anyptr d, Const Anyptr s, size_t n)
#else
Anyptr my_memmove(d, s, n)
Anyptr d, s;
register int n;
#endif
{
    register char *dd = (char *)d, *ss = (char *)s;
    if (dd < ss || dd - ss >= n) {
	memcpy(dd, ss, n);
    } else if (n > 0) {
	dd += n;
	ss += n;
	while (n-- > 0)
	    *--dd = *--ss;
    }
    return d;
}


#ifdef __STDC__
Anyptr my_memcpy(Anyptr d, Const Anyptr s, size_t n)
#else
Anyptr my_memcpy(d, s, n)
Anyptr d, s;
register int n;
#endif
{
    register char *ss = (char *)s, *dd = (char *)d;
    while (n-- > 0)
	*dd++ = *ss++;
    return d;
}

#ifdef __STDC__
int my_memcmp(Const Anyptr s1, Const Anyptr s2, size_t n)
#else
int my_memcmp(s1, s2, n)
Anyptr s1, s2;
register int n;
#endif
{
    register char *a = (char *)s1, *b = (char *)s2;
    register int i;
    while (n-- > 0)
	if ((i = (*a++) - (*b++)) != 0)
	    return i;
    return 0;
}

#ifdef __STDC__
Anyptr my_memset(Anyptr d, int c, size_t n)
#else
Anyptr my_memset(d, c, n)
Anyptr d;
register int c;
register int n;
#endif
{
    register char *dd = (char *)d;
    while (n-- > 0)
	*dd++ = c;
    return d;
}


int my_toupper(c)
int c;
{
    if (islower(c))
	return _toupper(c);
    else
	return c;
}


int my_tolower(c)
int c;
{
    if (isupper(c))
	return _tolower(c);
    else
	return c;
}




long ipow(a, b)
long a, b;
{
    long v;

    if (a == 0 || a == 1)
	return a;
    if (a == -1)
	return (b & 1) ? -1 : 1;
    if (b < 0)
	return 0;
    if (a == 2)
	return 1L << b;
    v = (b & 1) ? a : 1;
    while ((b >>= 1) > 0) {
	a *= a;
	if (b & 1)
	    v *= a;
    }
    return v;
}




/* Common string functions: */

/* Store in "ret" the substring of length "len" starting from "pos" (1-based).
   Store a shorter or null string if out-of-range.  Return "ret". */

char *strsub(ret, s, pos, len)
register char *ret, *s;
register int pos, len;
{
    register char *s2;

    if (--pos < 0 || len <= 0) {
        *ret = 0;
        return ret;
    }
    while (pos > 0) {
        if (!*s++) {
            *ret = 0;
            return ret;
        }
        pos--;
    }
    s2 = ret;
    while (--len >= 0) {
        if (!(*s2++ = *s++))
            return ret;
    }
    *s2 = 0;
    return ret;
}


/* Return the index of the first occurrence of "pat" as a substring of "s",
   starting at index "pos" (1-based).  Result is 1-based, 0 if not found. */

int strpos2(s, pat, pos)
char *s;
register char *pat;
register int pos;
{
    register char *cp, ch;
    register int slen;

    if (--pos < 0)
        return 0;
    slen = strlen(s) - pos;
    cp = s + pos;
    if (!(ch = *pat++))
        return 0;
    pos = strlen(pat);
    slen -= pos;
    while (--slen >= 0) {
        if (*cp++ == ch && !strncmp(cp, pat, pos))
            return cp - s;
    }
    return 0;
}


/* Case-insensitive version of strcmp. */

int strcicmp(s1, s2)
register char *s1, *s2;
{
    register unsigned char c1, c2;

    while (*s1) {
	if (*s1++ != *s2++) {
	    if (!s2[-1])
		return 1;
	    c1 = toupper(s1[-1]);
	    c2 = toupper(s2[-1]);
	    if (c1 != c2)
		return c1 - c2;
	}
    }
    if (*s2)
	return -1;
    return 0;
}




/* HP and Turbo Pascal string functions: */

/* Trim blanks at left end of string. */

char *strltrim(s)
register char *s;
{
    while (Isspace(*s++)) ;
    return s - 1;
}


/* Trim blanks at right end of string. */

char *strrtrim(s)
register char *s;
{
    register char *s2 = s;

    if (!*s)
	return s;
    while (*++s2) ;
    while (s2 > s && Isspace(*--s2))
        *s2 = 0;
    return s;
}


/* Store in "ret" "num" copies of string "s".  Return "ret". */

char *strrpt(ret, s, num)
char *ret;
register char *s;
register int num;
{
    register char *s2 = ret;
    register char *s1;

    while (--num >= 0) {
        s1 = s;
        while ((*s2++ = *s1++)) ;
        s2--;
    }
    return ret;
}


/* Store in "ret" string "s" with enough pad chars added to reach "size". */

char *strpad(ret, s, padchar, num)
char *ret;
register char *s;
register int padchar, num;
{
    register char *d = ret;

    if (s == d) {
	while (*d++) ;
    } else {
	while ((*d++ = *s++)) ;
    }
    num -= (--d - ret);
    while (--num >= 0)
	*d++ = padchar;
    *d = 0;
    return ret;
}


/* Copy the substring of length "len" from index "spos" of "s" (1-based)
   to index "dpos" of "d", lengthening "d" if necessary.  Length and
   indices must be in-range. */

void strmove(len, s, spos, d, dpos)
register char *s, *d;
register int len, spos, dpos;
{
    s += spos - 1;
    d += dpos - 1;
    while (*d && --len >= 0)
	*d++ = *s++;
    if (len > 0) {
	while (--len >= 0)
	    *d++ = *s++;
	*d = 0;
    }
}


/* Delete the substring of length "len" at index "pos" from "s".
   Delete less if out-of-range. */

void strdelete(s, pos, len)
register char *s;
register int pos, len;
{
    register int slen;

    if (--pos < 0)
        return;
    slen = strlen(s) - pos;
    if (slen <= 0)
        return;
    s += pos;
    if (slen <= len) {
        *s = 0;
        return;
    }
    while ((*s = s[len])) s++;
}


/* Insert string "src" at index "pos" of "dst". */

void strinsert(src, dst, pos)
register char *src, *dst;
register int pos;
{
    register int slen, dlen;

    if (--pos < 0)
        return;
    dlen = strlen(dst);
    dst += dlen;
    dlen -= pos;
    if (dlen <= 0) {
        strcpy(dst, src);
        return;
    }
    slen = strlen(src);
    do {
        dst[slen] = *dst;
        --dst;
    } while (--dlen >= 0);
    dst++;
    while (--slen >= 0)
        *dst++ = *src++;
}




/* File functions */

/* Peek at next character of input stream; return EOF at end-of-file. */

int P_peek(f)
FILE *f;
{
    int ch;

    ch = getc(f);
    if (ch == EOF)
	return EOF;
    ungetc(ch, f);
    return (ch == '\n') ? ' ' : ch;
}


/* Check if at end of file, using Pascal "eof" semantics.  End-of-file for
   stdin is broken; remove the special case for it to be broken in a
   different way. */

int P_eof(f)
FILE *f;
{
    register int ch;

    if (feof(f))
	return 1;
    if (f == stdin)
	return 0;    /* not safe to look-ahead on the keyboard! */
    ch = getc(f);
    if (ch == EOF)
	return 1;
    ungetc(ch, f);
    return 0;
}


/* Check if at end of line (or end of entire file). */

int P_eoln(f)
FILE *f;
{
    register int ch;

    ch = getc(f);
    if (ch == EOF)
        return 1;
    ungetc(ch, f);
    return (ch == '\n');
}


/* Read a packed array of characters from a file. */

Void P_readpaoc(f, s, len)
FILE *f;
char *s;
int len;
{
    int ch;

    for (;;) {
	if (len <= 0)
	    return;
	ch = getc(f);
	if (ch == EOF || ch == '\n')
	    break;
	*s++ = ch;
	--len;
    }
    while (--len >= 0)
	*s++ = ' ';
    if (ch != EOF)
	ungetc(ch, f);
}

Void P_readlnpaoc(f, s, len)
FILE *f;
char *s;
int len;
{
    int ch;

    for (;;) {
	ch = getc(f);
	if (ch == EOF || ch == '\n')
	    break;
	if (len > 0) {
	    *s++ = ch;
	    --len;
	}
    }
    while (--len >= 0)
	*s++ = ' ';
}


/* Compute maximum legal "seek" index in file (0-based). */

long P_maxpos(f)
FILE *f;
{
    long savepos = ftell(f);
    long val;

    if (fseek(f, 0L, SEEK_END))
        return -1;
    val = ftell(f);
    if (fseek(f, savepos, SEEK_SET))
        return -1;
    return val;
}


/* Use packed array of char for a file name. */

Char *P_trimname(fn, len)
register Char *fn;
register int len;
{
    static Char fnbuf[256];
    register Char *cp = fnbuf;
    
    while (--len >= 0 && *fn && !isspace(*fn))
	*cp++ = *fn++;
    *cp = 0;
    return fnbuf;
}




/* Pascal's "memavail" doesn't make much sense in Unix with virtual memory.
   We fix memory size as 10Meg as a reasonable compromise. */

long memavail()
{
    return 10000000;            /* worry about this later! */
}

long maxavail()
{
    return memavail();
}




/* Sets are stored as an array of longs.  S[0] is the size of the set;
   S[N] is the N'th 32-bit chunk of the set.  S[0] equals the maximum
   I such that S[I] is nonzero.  S[0] is zero for an empty set.  Within
   each long, bits are packed from lsb to msb.  The first bit of the
   set is the element with ordinal value 0.  (Thus, for a "set of 5..99",
   the lowest five bits of the first long are unused and always zero.) */

/* (Sets with 32 or fewer elements are normally stored as plain longs.) */

long *P_setunion(d, s1, s2)         /* d := s1 + s2 */
register long *d, *s1, *s2;
{
    long *dbase = d++;
    register int sz1 = *s1++, sz2 = *s2++;
    while (sz1 > 0 && sz2 > 0) {
        *d++ = *s1++ | *s2++;
	sz1--, sz2--;
    }
    while (--sz1 >= 0)
	*d++ = *s1++;
    while (--sz2 >= 0)
	*d++ = *s2++;
    *dbase = d - dbase - 1;
    return dbase;
}


long *P_setint(d, s1, s2)           /* d := s1 * s2 */
register long *d, *s1, *s2;
{
    long *dbase = d++;
    register int sz1 = *s1++, sz2 = *s2++;
    while (--sz1 >= 0 && --sz2 >= 0)
        *d++ = *s1++ & *s2++;
    while (--d > dbase && !*d) ;
    *dbase = d - dbase;
    return dbase;
}


long *P_setdiff(d, s1, s2)          /* d := s1 - s2 */
register long *d, *s1, *s2;
{
    long *dbase = d++;
    register int sz1 = *s1++, sz2 = *s2++;
    while (--sz1 >= 0 && --sz2 >= 0)
        *d++ = *s1++ & ~*s2++;
    if (sz1 >= 0) {
        while (sz1-- >= 0)
            *d++ = *s1++;
    }
    while (--d > dbase && !*d) ;
    *dbase = d - dbase;
    return dbase;
}


long *P_setxor(d, s1, s2)         /* d := s1 / s2 */
register long *d, *s1, *s2;
{
    long *dbase = d++;
    register int sz1 = *s1++, sz2 = *s2++;
    while (sz1 > 0 && sz2 > 0) {
        *d++ = *s1++ ^ *s2++;
	sz1--, sz2--;
    }
    while (--sz1 >= 0)
	*d++ = *s1++;
    while (--sz2 >= 0)
	*d++ = *s2++;
    while (--d > dbase && !*d) ;
    *dbase = d - dbase;
    return dbase;
}


int P_inset(val, s)                 /* val IN s */
register unsigned val;
register long *s;
{
    register int bit;
    bit = val % SETBITS;
    val /= SETBITS;
    if (val < *s++ && ((1L< size) {
        s += size;
        while (val > size)
            *++s = 0, size++;
        *sbase = size;
    } else
        s += val;
    *s |= 1L< (int)v2)
	return sbase;
    b1 = v1 % SETBITS;
    v1 /= SETBITS;
    b2 = v2 % SETBITS;
    v2 /= SETBITS;
    size = *s;
    v1++;
    if (++v2 > size) {
        while (v2 > size)
            s[++size] = 0;
        s[v2] = 0;
        *s = v2;
    }
    s += v1;
    if (v1 == v2) {
        *s |= (~((-2L)<<(b2-b1))) << b1;
    } else {
        *s++ |= (-1L) << b1;
        while (++v1 < v2)
            *s++ = -1;
        *s |= ~((-2L) << b2);
    }
    return sbase;
}


long *P_remset(s, val)              /* s := s - [val] */
register long *s;
register unsigned val;
{
    register int bit;
    bit = val % SETBITS;
    val /= SETBITS;
    if (++val <= *s) {
	if (!(s[val] &= ~(1L<= 0) {
        if (*s1++ != *s2++)
            return 0;
    }
    return 1;
}


int P_subset(s1, s2)                /* s1 <= s2 */
register long *s1, *s2;
{
    register int sz1 = *s1++, sz2 = *s2++;
    if (sz1 > sz2)
        return 0;
    while (--sz1 >= 0) {
        if (*s1++ & ~*s2++)
            return 0;
    }
    return 1;
}


long *P_setcpy(d, s)                /* d := s */
register long *d, *s;
{
    register long *save_d = d;

#ifdef SETCPY_MEMCPY
    memcpy(d, s, (*s + 1) * sizeof(long));
#else
    register int i = *s + 1;
    while (--i >= 0)
        *d++ = *s++;
#endif
    return save_d;
}


/* s is a "smallset", i.e., a 32-bit or less set stored
   directly in a long. */

long *P_expset(d, s)                /* d := s */
register long *d;
register long s;
{
    if (s) {
	d[1] = s;
	*d = 1;
    } else
        *d = 0;
    return d;
}


long P_packset(s)                   /* convert s to a small-set */
register long *s;
{
    if (*s++)
        return *s;
    else
        return 0;
}





/* Oregon Software Pascal extensions, courtesy of William Bader */

int P_getcmdline(l, h, line)
int l, h;
Char *line;
{
    int i, len;
    char *s;
    
    h = h - l + 1;
    len = 0;
    for(i = 1; i < P_argc; i++) {
	s = P_argv[i];
	while (*s) {
	    if (len >= h) return len;
	    line[len++] = *s++;
	}
	if (len >= h) return len;
	line[len++] = ' ';
    }
    return len;
}

Void TimeStamp(Day, Month, Year, Hour, Min, Sec)
int *Day, *Month, *Year, *Hour, *Min, *Sec;
{
#ifndef NO_TIME
    struct tm *tm;
    long clock;

    time(&clock);
    tm = localtime(&clock);
    *Day = tm->tm_mday;
    *Month = tm->tm_mon + 1;		/* Jan = 0 */
    *Year = tm->tm_year;
    if (*Year < 1900)
	*Year += 1900;     /* year since 1900 */
    *Hour = tm->tm_hour;
    *Min = tm->tm_min;
    *Sec = tm->tm_sec;
#endif
}

Void VAXdate(s)
char *s;
{
    long clock;
    char *c;
    int i;
    static int where[] = {8, 9, 0, 4, 5, 6, 0, 20, 21, 22, 23};

    time(&clock);
    c = ctime(&clock);
    for (i = 0; i < 11; i++)
	s[i] = my_toupper(c[where[i]]);
    s[2] = '-';
    s[6] = '-';
}

Void VAXtime(s)
char *s;
{
    long clock;
    char *c;
    int i;

    time(&clock);
    c = ctime(&clock);
    for (i = 0; i < 8; i++)
	s[i] = c[i+11];
    s[8] = '.';
    s[9] = '0';
    s[10] = '0';
}




/* SUN Berkeley Pascal extensions */

Void P_sun_argv(s, len, n)
register char *s;
register int len, n;
{
    register char *cp;

    if ((unsigned)n < P_argc)
	cp = P_argv[n];
    else
	cp = "";
    while (*cp && --len >= 0)
	*s++ = *cp++;
    while (--len >= 0)
	*s++ = ' ';
}




int _OutMem()
{
    return _Escape(-2);
}

int _CaseCheck()
{
    return _Escape(-9);
}

int _NilCheck()
{
    return _Escape(-3);
}





/* The following is suitable for the HP Pascal operating system.
   It might want to be revised when emulating another system. */

char *_ShowEscape(buf, code, ior, prefix)
char *buf, *prefix;
int code, ior;
{
    char *bufp;

    if (prefix && *prefix) {
        strcpy(buf, prefix);
	strcat(buf, ": ");
        bufp = buf + strlen(buf);
    } else {
        bufp = buf;
    }
    if (code == -10) {
        sprintf(bufp, "Pascal system I/O error %d", ior);
        switch (ior) {
            case 3:
                strcat(buf, " (illegal I/O request)");
                break;
            case 7:
                strcat(buf, " (bad file name)");
                break;
            case FileNotFound:   /*10*/
                strcat(buf, " (file not found)");
                break;
            case FileNotOpen:    /*13*/
                strcat(buf, " (file not open)");
                break;
            case BadInputFormat: /*14*/
                strcat(buf, " (bad input format)");
                break;
            case 24:
                strcat(buf, " (not open for reading)");
                break;
            case 25:
                strcat(buf, " (not open for writing)");
                break;
            case 26:
                strcat(buf, " (not open for direct access)");
                break;
            case 28:
                strcat(buf, " (string subscript out of range)");
                break;
            case EndOfFile:      /*30*/
                strcat(buf, " (end-of-file)");
                break;
            case FileWriteError: /*38*/
		strcat(buf, " (file write error)");
		break;
        }
    } else {
        sprintf(bufp, "Pascal system error %d", code);
        switch (code) {
            case -2:
                strcat(buf, " (out of memory)");
                break;
            case -3:
                strcat(buf, " (reference to NIL pointer)");
                break;
            case -4:
                strcat(buf, " (integer overflow)");
                break;
            case -5:
                strcat(buf, " (divide by zero)");
                break;
            case -6:
                strcat(buf, " (real math overflow)");
                break;
            case -8:
                strcat(buf, " (value range error)");
                break;
            case -9:
                strcat(buf, " (CASE value range error)");
                break;
            case -12:
                strcat(buf, " (bus error)");
                break;
            case -20:
                strcat(buf, " (stopped by user)");
                break;
        }
    }
    return buf;
}


int _Escape(code)
int code;
{
    char buf[100];

    P_escapecode = code;
    if (__top_jb) {
	__p2c_jmp_buf *jb = __top_jb;
	__top_jb = jb->next;
	longjmp(jb->jbuf, 1);
    }
    if (code == 0)
        exit(EXIT_SUCCESS);
    if (code == -1)
        exit(EXIT_FAILURE);
    fprintf(stderr, "%s\n", _ShowEscape(buf, P_escapecode, P_ioresult, ""));
    exit(EXIT_FAILURE);
}

int _EscIO(code)
int code;
{
    P_ioresult = code;
    return _Escape(-10);
}




/* End. */



s = ftell(f);
    long val;

    if (fseek(f, 0L, SEEK_END))
        return -1;
    val = ftell(f);
    if (fseek(f, savepos, SEEK_SET))
        return -1;
    return val;
}


/* Use packed array of char for a fileblimps-3.9/blimps/papssm.c000064400001460000012000002243171016337716500161250ustar00jorjastaff00000400000027/*    papssm.c     blpssm.c with a PA option
         blpssm  

	 must contain:
	BL	blocks database to make PSSMs from (input)
	EX	PSSM database output file
	OU      observed frequencies output file
	FR	frequency file
        GR	substitution matrix for Gribskov ratios
	GQ	qij matrix for Gribskov
	DI	Dirichlet mixtures file for pseudo counts
  	AL	R qij matrix file for Altschul pseudo counts (AL = RC + AQ)
	AQ	qij matrix file for Altschul pseudo counts
	RC	R => tot. # pseudos = R x #residues 
	BC	B = total number of pseudos in a column
	ST	min max qij   Multiple entries for Steve's method
	CL	substitution matrix file for pseudo counts
	GI	make simple background pseudo counts like Gibbs does
        LO	use natural log scores (DI, CL or GI only)
	BR	get counts using Bill Bruno's method instead of seq wts
	HY	hybrid counts; nseq from Bruno, counts from seq wts
	HC	% hybrid counts; nseq from % clumping, counts from seq wts
	NN	YES => set all real counts to zero
	PA	min_score  pattern_output_file
	FP	Output matrix in floating point format

	If DI or CL, must have FR
	If just FR, makes usual PATMAT PSSM
--------------------------------------------------------------------
 6/30/94 J. Henikoff 
 7/ 2/94 Added log option for make_diri()
 7/ 4/94 Changed log calculations to make a positive PSSM by
         subtracting the min. log value for the entire matrix
         from every entry in the matrix, rather than doing each
         position separately.
 7/ 7/94 Changed load_subst() to make matrix non-neg. if nec.
         Added make_clav()  CL option
 7/11/94 Added make_gribs() GR option
 8/10/94 Added make_gibbs()  GI option, simple pseudo counts like Gibbs
         Cleaned up code
         Changed from 0,AASALL to 1,AAS for all but make_gribs()
 8/18/94 Added load_qij()
 8/29/94 Added make_gribq() GQ option - doesn't work, scaling problem
 8/31/94 Added counts_bruno() BR option.
 9/ 4/94 Multiply final matrices to give score range b/w 0 and 99 (final).
 9/ 7/94 Make sure multiplying by a number >= 1.0.
 9/15/94 Added counts_hybrid() HY option.
	 Added counts_clumps() HC option.
 9/26/94 Added Steve's elaboration of Altschul's method
10/31/94 Changed make_matrix() to add seqs= to matrix->ma if not in block
-------------------Added to /howard/local/bin----------------------------
12/ 7/94 Also outputs the observed frequencies, with pseudo counts.
 1/16/95 Changed pseudo-count count from sqrt(n) to 1/n for GI & AL
 1/18/95 Changed pseudo-count count from 1/n to column entropy for GI & AL,
         added compute_entropy()
	 Changed pseudo-count count from entropy to #residues for GI & AL,
         added count_residues()
 1/28/95 Modified Steve's method; use a different substitution matrix
         for every column of a block, not just for every block.
	 Added ratio_counts(), make_steves()
 1/30/95 Fixed problem with too many FILEs in make_steves(). 
	 NOTE: This routine is currently very inefficient, reads qij
         file over for each column!
 2/ 8/95 Changed pseudo_count count from #residues to RTot x # residues for
	 GI, AL, ST
 2/ 8/95 Changed pseudo_alts() to use unweighted counts for pseudo
         counts (not sequence-weighted). Counts are still seq-wted
	 Modified struct working, counts(), pseudo_alts().
 2/15/95 Changed pseudo_alts() back to use weighted counts.
 2/19/95 Made RTot a parameter on the AL option
 2/19/95 Added bruno_rind() & changed counts_bruno() to use Bruno's
         new rind program.
 2/26/95 Initialized col stuff in counts_bruno().
 3/20/95 Changed default RTOT from 1.0 to 5.0; applies to make_gibbs() also.
 3/30/95 Changed make_gibbs() back to use sqrt(N).
         Changed make_gribs() to rescale between 0 and 99; added positive_matrix()
 4/ 6/95 Added free_block() & also freed other data structures.
 4/ 8/95 Changed all counting routines so B->D, Z->E and only the 20
         real aas are counted. Therefore, column counts may not add to
	 the number of sequences if a column contains "-" or "X".
 4/12/95 Changed Gribskov to score B,Z,X,- & x like the other methods.
 5/28/95 Added PA option, PA lines to PSSM
 6/29/95 Write PA lines to a separate file
 7/ 7/95 Fixed problem in add_patterns() when only one pattern.
 7/12/95 Fixed problem in make_col() initialization.
 8/30/95 Added AQ, RC, BC and NN parameters (AL = RC + AQ)
	 Added BTot variable = total # pseudos in a column
 9/11/95 Changed GQ, make_gribq() to use log-odds 
10/ 2/95 Changed strnicmp() to strncasecmp()
 4/24/96 Initialized matrix->patterns in make_matrix() - caused abort with
	 prints.cf input file.
 7/ 4/96 Updated Bruno counts for new version of rind program.
 9/19/96 Added option for floating point output (FP, FloatPt);
	 matrices aren't re-scaled at all in this case.
 11/25/97 Increased MAXWIDTH from 60 to 200 for Bork's groups
 12/25/04 Increased MAXNSEQ from 700 to 1000; use blocksprogs.h
====================================================================*/

#define BLPSSM_C_
#define EXTERN

#include 
#include "blimps.h"

#define FNAMELEN 80
#define AAS 21
#define AASALL 26
/* 0- 1A 2R 3N 4D 5C 6Q 7E 8G 9H 10I 11L 12K 13M 14F 15P 16S 17T 18W 19Y
   20V 21B 22Z 23X 24* 25J,O,U */
#define MAXCOMP 40			/* Max. # of Dirichlet components */
#define MAXWIDTH 200			/* Max. block width */
#define MAXNSEQ 1000			/* Max. # seqs in a block */
#define MAXMAT 10			/* Max. #matrices for Steve's method*/
#define PATCUT 90			/* Default pattern cutoff score */
#define RTOT 5.0			/* Total #pseudos in col  = RTOT * R*/
#define BTOT 25.0			/* Total # pseudos in col */
#define PI 3.141592654
/*   INDEX & INDEXCOL compute the sequential indices for the lower half of an
     nxn symmetric matrix given row & column coordinates.  Lower half has
     n(n-1)/2 entries; col=0,n-2 and row=col+1,n-1; col has n-col-1 rows.
     Index runs from 0 to n(n-1)/2 - 1 down columns with
     (index=0)==(col=0,row=1) and (index=n(n-1)/2-1)==(col=n-2,row=n-1).  */
#define INDEXCOL(n, col)    ( col*n - (col*(col+1))/2 )
#define INDEX(n, col, row)  ( col*n - (col*(col+3))/2 - 1 + row )

/*-----------------------------------------------------------------------*/
/*    Structure for pairs of sequences.  From protomat.h                 */
/*     pair should be allocated as an array, & the number of the         */
/*     sequences forming the pair inferred from the array index.         */
/*-----------------------------------------------------------------------*/

struct dirichlet {	/* Dirichlet mixture information */
   int ncomp;		/* number of components */
   double q[MAXCOMP];
   double altot[MAXCOMP];
   double alpha[MAXCOMP][AAS];
};

struct clump_work {
   int cluster[MAXNSEQ], ncluster[MAXNSEQ], nclus[MAXNSEQ];
};

struct working {	/* Working information for one column */
   double cnt[AASALL];		/* Sequence-weighted counts */
   double totcnt;
   double raw[AASALL];		/* unweighted counts */
   double totraw;
   double probn[MAXCOMP];
   double probj[MAXCOMP];
   double reg[AASALL];		/*  pseudo counts */
   double totreg;
};

struct work_pssm {		/* Working PSSM area */
   double value[MAXWIDTH][AASALL];
   double sum[MAXWIDTH];
};

struct steve {
   double nmin, nmax;		/* min & max diag/off-diag ratio for col */
   char qijname[FNAMELEN];
};

int read_cf();
int load_frequencies();
double read_freq();
void load_subst();
double nrgamma();
double addlogs();
void normalize();
struct working *make_col();
struct work_pssm *make_pssm();
struct dirichlet *load_diri2();
Matrix *make_matrix();
Matrix *make_diri();
Matrix *make_gribs();
Matrix *make_gribq();
Matrix *make_clav();
Matrix *make_alts();
Matrix *make_patmat();
Matrix *make_gibbs();
Matrix *make_steves();
FILE *steves_qij();
void counts();
void counts_hybrid();
void counts_clumps();
int clump_seqs();
void pseudo_diric();
void pseudo_clav();
void pseudo_alts();
void pseudo_gibbs();
double compute_entropy();
int count_residues();
double ratio_counts();
void fillin();
void final();
void compute_BZX();
void positive_matrix();
void add_patterns();
/*     Bill Bruno's rind program   */
struct work_pssm *bruno_rind();
void counts_bruno();

/*-------------global variables ----------------------------------------*/
FILE *Fbl, *Fex, *Fou, *Ffr, *Fal, *Fdi, *Fcl, *Fgr, *Fgq;  /* files */
FILE *Fpa;
int LogScores;				/* take natural log of scores */
struct steve *Steve[MAXMAT];			/* Steve's parameters */
int BrunoCounts;			/* use Bill Bruno's counts */
int HybridCounts;			/* use hybrid counts */
int ClumpCounts;			/* use hybrid clump counts */
int NoCounts;				/* don't use actual counts */
int FloatPt;				/* floating point output */
int ClumpTot;				/* # of clumps in block */
int PatternCutoff;			/* pattern cutoff score */
double RTot;				/* B_c = RTot * # residues */
double BTot;				/* B_c = BTot = Total pseudos */
/*    Dirichlet stuff */
double LCof = 2.50662827465;	/* sqrt(2*PI)  */
double Cof[6] = {76.18009173, -86.50532033, 24.01409822, -1.231739516,
                  0.120858003e-2, -0.536382e-5};
double Log2;
/*     Bruno stuff */
/*   blimps[aa] == bruno[ Bruno_Order[aa] ]     */
int Bruno_Order[AASALL] = {1, 21, 5, 4, 7, 14, 8, 9, 10, 23, 12, 11, 13,
        3, 23, 15, 6, 2, 16, 17, 23, 20, 18, 23, 19, 22};

/*=====================================================================
 * main
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
   FILE *cfp;
   Block *block;
   int type;
   char bdbname[FNAMELEN], pssmname[FNAMELEN], cfname[FNAMELEN];
   char freqname[FNAMELEN], diriname[FNAMELEN];
   double freqs[AASALL], subst[AASALL][AASALL];
   struct dirichlet *diric;
   struct float_qij *qij;
   Matrix *matrix, *obs_freqs;

   Log2 = log(2.0);
/* ------------1st arg = configuration file ----------------------------*/
   if (argc > 1)
      strcpy(cfname, argv[1]);
   else
   {
      printf("\nEnter name of configuration file: ");
      gets(cfname);
   }
   if ( (cfp=fopen(cfname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", cfname);
      exit(-1);
   }
   type = read_cf(cfp);
   if (type <= 0)
   {
      printf("\nConfiguration file errors\n");
      exit(-1);
   }
   else
   {
      switch(type)
      {
         case 1:
            printf("Using PATMAT algorithm...\n");
            break;
        case 2:		/* Gribskov profile */
           printf("Using Gribskov algorithm...\n");
           break;
        case 3:		/* Altschul's pseudo-counts */
           printf("Using Altschul's pseudo-counts...\n");
           break;
        case 4:		/* Claverie's pseudo-counts */
	   printf("Using Claverie pseudo-counts...\n");
           break;
        case 5:		/* Dirichlet pseudo-counts */
           printf("Using Dirichlet pseudo-counts\n");
           break;
        case 6:		/* simple background pseudo-counts */
           printf("Using background pseudo-counts (like Gibbs)\n");
           break;
        case 7:		/* Gribskov profile with qij */
           printf("Using Gribskov algorithm with qij...\n");
           break;
 	case 8:		/* Steve's method */
	   printf("Using Steve's method...\n");
	   printf("WARNING: Parameters are not checked for validity!\n");
           break;
        default:
           break;
      }
   }

/*----------------------------------------------------------------------*/
  if (Ffr != NULL) load_frequencies(Ffr, freqs);
  if (type == 2) load_subst(Fgr, subst);
  if (type == 3) qij = load_qij(Fal);
  if (type == 4) load_subst(Fcl, subst);
  if (type == 5) diric = load_diri2(Fdi);
  if (type == 7) qij = load_qij(Fgq);

  while ((block = read_a_block(Fbl)) != NULL)
  {
     normalize(block);
     if (ClumpCounts) ClumpTot = clump_seqs(block);
     if (Fou != NULL) obs_freqs = make_matrix(block);
     switch (type)
     {
        case 1:		/* Patmat odds ratios */
           matrix = make_patmat(block, freqs, obs_freqs);
           break;
        case 2:		/* Gribskov profile */
           matrix = make_gribs(block, subst, obs_freqs);
           break;
        case 3:		/* Altschul's pseudo-counts */
           matrix = make_alts(block, freqs, qij, obs_freqs); 
           break;
        case 4:		/* Claverie's pseudo-counts */
           matrix = make_clav(block, freqs, subst, obs_freqs);
           break;
        case 5:		/* Dirichlet pseudo-counts */
           matrix = make_diri(block, freqs, diric, obs_freqs);
           break;
        case 6:		/* simple background pseudo-counts */
           matrix = make_gibbs(block, freqs, obs_freqs);
           break;
        case 7:		/* Gribskov profile with qij */
           matrix = make_gribq(block, qij, obs_freqs);
           break;
	case 8:		/* Steve's method */
	   matrix = make_steves(block, freqs, obs_freqs);
	   break;
        default:
           break;
     }
     if (matrix != NULL)
     {
        if (!FloatPt) output_matrix(matrix, Fex);
        else          output_matrix_s(matrix, Fex, 1); /* FLOAT_OUTPUT == 1 */
        if (PatternCutoff && Fpa != NULL)  add_patterns(matrix, Fpa);
        free_matrix(matrix);
     }
     if (obs_freqs != NULL)
     {
        output_matrix(obs_freqs, Fou);
        free_matrix(obs_freqs);
     }
     free_block(block);
  }
   
  fclose(Fbl); fclose(Fex);
  if (Fpa != NULL) fclose(Fpa);
  if (Fou != NULL) fclose(Fou);
  exit(0);

}  /* end of main */
/*=======================================================================*/
int read_cf(cfp)
FILE *cfp;
{
   int type, gibbs, nsteve;
   char line[MAXLINE], keyword[20], *ptr;
   char blname[FNAMELEN], exname[FNAMELEN], frname[FNAMELEN];
   char alname[FNAMELEN], diname[FNAMELEN], clname[FNAMELEN];
   char grname[FNAMELEN], gqname[FNAMELEN], ouname[FNAMELEN];
   char paname[FNAMELEN];

   type = 0;
   gibbs = FALSE;
   Fbl = Fex = Fpa = Fou = Ffr = Fal = Fdi = Fcl = Fgr = Fgq = NULL;
   for (nsteve = 0; nsteve < MAXMAT; nsteve++) Steve[nsteve] = NULL;
   nsteve = 0;
   BTot = RTot = -1;
   LogScores = BrunoCounts = HybridCounts = ClumpCounts = NoCounts = FALSE;
   FloatPt = FALSE;
   PatternCutoff = 0;
   while (!feof(cfp) && fgets(line, MAXLINE, cfp) != NULL)
   {
      ptr = strtok(line, " \t\r\n");
      if (ptr != NULL && ptr[0] != ';')
      {
         strcpy(keyword,ptr);
         ptr = strtok(NULL, " \t\r\n;");
         if (ptr != NULL)
         {
            if (strncasecmp(keyword, "BL", 2) == 0)
            {
               strcpy(blname, ptr);
               if ( (Fbl = fopen(blname, "r")) == NULL)
                  printf("\nCannot open BL file %s\n", blname);
            }
            else if (strncasecmp(keyword, "EX", 2) == 0)
            {
               strcpy(exname, ptr);
               if ( (Fex = fopen(exname, "w")) == NULL)
                  printf("\nCannot open EX file %s\n", exname);
            }
            else if (strncasecmp(keyword, "OU", 2) == 0)
            {
               strcpy(ouname, ptr);
               if ( (Fou = fopen(ouname, "w")) == NULL)
                  printf("\nCannot open OU file %s\n", ouname);
            }
            else if (strncasecmp(keyword, "FR", 2) == 0)
            {
               strcpy(frname, ptr);
               if ( (Ffr = fopen(frname, "r")) == NULL)
                  printf("\nCannot open FR file %s\n", frname);
            }
            else if (strncasecmp(keyword, "AL", 2) == 0)
            {
               RTot = atof(ptr);
	       if (RTot < 0.0) RTot = RTOT;
	       ptr = strtok(NULL, " \t\r\n");
               strcpy(alname, ptr);
               if ( (Fal = fopen(alname, "r")) == NULL)
                  printf("\nCannot open AL file %s\n", alname);
            }
            else if (strncasecmp(keyword, "RC", 2) == 0)
            {
               RTot = atof(ptr);
	       if (RTot < 0.0) RTot = RTOT;
            }
            else if (strncasecmp(keyword, "BC", 2) == 0)
            {
               BTot = atof(ptr);
	       if (BTot < 0.0) BTot = BTOT;
            }
            else if (strncasecmp(keyword, "AQ", 2) == 0)
            {
               strcpy(alname, ptr);
               if ( (Fal = fopen(alname, "r")) == NULL)
                  printf("\nCannot open AQ file %s\n", alname);
            }
            else if (strncasecmp(keyword, "ST", 2) == 0)
            {
               if (Steve[nsteve] == NULL)
	   Steve[nsteve] = (struct steve *) malloc(sizeof(struct steve));
	       if (Steve[nsteve] == NULL)
               {
                   printf("\nread_cf: OUT OF MEMORY\n");
                   exit(-1);
               }
               Steve[nsteve]->nmin = atof(ptr);
               ptr = strtok(NULL, " \t\r\n");
               Steve[nsteve]->nmax = atof(ptr);
               ptr = strtok(NULL, " \t\r\n");
	       strcpy(Steve[nsteve]->qijname, ptr);
               nsteve++;
            }
            else if (strncasecmp(keyword, "GR", 2) == 0)
            {
               strcpy(grname, ptr);
               if ( (Fgr = fopen(grname, "r")) == NULL)
                  printf("\nCannot open GR file %s\n", grname);
            }
            else if (strncasecmp(keyword, "GQ", 2) == 0)
            {
               strcpy(gqname, ptr);
               if ( (Fgq = fopen(gqname, "r")) == NULL)
                  printf("\nCannot open GQ file %s\n", gqname);
            }
            else if (strncasecmp(keyword, "DI", 2) == 0)
            {
               strcpy(diname, ptr);
               if ( (Fdi = fopen(diname, "r")) == NULL)
                  printf("\nCannot open DI file %s\n", diname);
            }
            else if (strncasecmp(keyword, "CL", 2) == 0)
            {
               strcpy(clname, ptr);
               if ( (Fcl = fopen(clname, "r")) == NULL)
                  printf("\nCannot open CL file %s\n", clname);
            }
            else if (strncasecmp(keyword, "LO", 2) == 0)
            {
                if (ptr[0] == 'y' || ptr[0] == 'Y' ||
                    ptr[0] == 't' || ptr[0] == 'T')
		LogScores = TRUE;
            }
            else if (strncasecmp(keyword, "BR", 2) == 0)
            {
                if (ptr[0] == 'y' || ptr[0] == 'Y' ||
                    ptr[0] == 't' || ptr[0] == 'T')
		BrunoCounts = TRUE;
            }
            else if (strncasecmp(keyword, "HY", 2) == 0)
            {
                if (ptr[0] == 'y' || ptr[0] == 'Y' ||
                    ptr[0] == 't' || ptr[0] == 'T')
		HybridCounts = TRUE;
            }
            else if (strncasecmp(keyword, "NN", 2) == 0)
            {
                if (ptr[0] == 'y' || ptr[0] == 'Y' ||
                    ptr[0] == 't' || ptr[0] == 'T')
		NoCounts = TRUE;
            }
            else if (strncasecmp(keyword, "FP", 2) == 0)
            {
                if (ptr[0] == 'y' || ptr[0] == 'Y' ||
                    ptr[0] == 't' || ptr[0] == 'T')
		FloatPt = TRUE;
            }
            else if (strncasecmp(keyword, "HC", 2) == 0)
            {
		ClumpCounts = atoi(ptr);
		if (ClumpCounts < 0 || ClumpCounts > 100) ClumpCounts = 0;
            }
            else if (strncasecmp(keyword, "GI", 2) == 0)
            {
               gibbs = TRUE;
            }
            else if (strncasecmp(keyword, "PA", 2) == 0)
            {
		PatternCutoff = atoi(ptr);
		if (PatternCutoff < 0 || PatternCutoff > 100)
			 PatternCutoff = PATCUT;
	        ptr = strtok(NULL, " \t\r\n");
                strcpy(paname, ptr);
                if ( (Fpa = fopen(paname, "w")) == NULL)
                  printf("\nCannot open PA file %s\n", paname);
            }
         }   /* end of if ptr */
      }  /* end of if ptr */
   }  /* end of cfp */
   /*   Set PSSM type:  1 is Patmat (FR)
                        2 is Gribskov (GR)
                        3 is Altschul pseudo counts (FR & AL)
                        4 is Claverie pseudo counts (FR & CL)     
                        5 is Dirichlet pseudo counts (FR & DI) 
                        6 is Gibbs pseudo counts (FR) 
			7 is Gribskov with qij (GQ)
			8 is Steve's (ST)
   */
   /*    Can only have one type of total pseudo counts */
   if (RTot > 0 && BTot > 0)  BTot = -1;
   type = 0;
   /* If only have FR; PSSM type = 1 */
   if (Ffr != NULL && Fdi == NULL && Fal == NULL && Fcl == NULL && 
       Fgr == NULL && Fgq == NULL)
       type = 1;
   /*  Steve's method is type 8 */
   if (Ffr != NULL && Steve[0] != NULL && nsteve >= 1)
   {
      type = 8;
      if (Fdi != NULL) fclose(Fdi);
      if (Fcl != NULL) fclose(Fcl);
      if (Fal != NULL) fclose(Fal);
      if (Fgr != NULL) fclose(Fgr);
   }
   /* If have GR, ignore DI and FR and CL; PSSM type = 2 */
   if (Fgr != NULL)
   {
      type = 2;
      if (Fdi != NULL) fclose(Fdi);
      if (Fcl != NULL) fclose(Fcl);
      if (Fal != NULL) fclose(Fal);
      if (Ffr != NULL) fclose(Ffr);
   }
   /* If have GQ,  PSSM type = 7 */
   if (Fgq != NULL)
   {
      type = 7;
      if (Fdi != NULL) fclose(Fdi);
      if (Fcl != NULL) fclose(Fcl);
      if (Fal != NULL) fclose(Fal);
      if (Ffr != NULL) fclose(Ffr);
   }
   /* If have AL, ignore DI and FR and CL; PSSM type = 3 */
   if (Fal != NULL && Ffr != NULL)
   {
      type = 3;
      if (Fdi != NULL) fclose(Fdi);
      if (Fcl != NULL) fclose(Fcl);
      if (Fgr != NULL) fclose(Fgr);
   }
   /* If have CL, ignore the rest */
   if (Fcl != NULL && Ffr != NULL)
   {
      type = 4;
      if (Fal != NULL) fclose(Fal);
      if (Fdi != NULL) fclose(Fdi);
      if (Fgr != NULL) fclose(Fgr);
   }
   /* If have DI, ignore the rest */
   if (Fdi != NULL && Ffr != NULL)
   {
      type = 5;
      if (Fal != NULL) fclose(Fal);
      if (Fcl != NULL) fclose(Fcl);
      if (Fgr != NULL) fclose(Fgr);
   }
   /*  If have FR and GI, type = 6 */
   if (type == 1 && gibbs) type = 6;

   if (type == 0)
      printf("\nNo valid PSSM type specified\n");
   /* Must always have BL and EX */
   if (Fbl == NULL)
   {
      printf("\nMissing BL (input block) file\n");
      type = 0;
   }
   if (Fex == NULL)
   {
      printf("\nMissing EX (output PSSM) file\n");
      type = 0;
   }

   return(type);
}  /* end of read_cf */
/*======================================================================
=======================================================================*/
FILE *steves_qij(col)
struct working *col;
{
   FILE *fst;
   int i;
   char fname[FNAMELEN];
   double ratio;

   ratio = ratio_counts(col);
   fst = NULL;
   fname[0] = '\0';
   i = 0;
   while (!strlen(fname) && Steve[i] != NULL && i < MAXMAT)
   {
      if (ratio >= Steve[i]->nmin &&
          ratio < Steve[i]->nmax)
             strcpy(fname, Steve[i]->qijname);
      i++;
   }
   if ( (fst=fopen(fname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", fname);
      exit(-1);
   }

   return(fst);
}  /* end of steves_qij */
/*======================================================================
   Dirichlet input file order (0-19) is  ARNDCQEGHILKMFPSTWYV
   Blimps order (0-24) is               -ARNDCQEGHILKMFPSTWYVBZX*
   Store Dirichlet alphas in positions 1-20 to match blimps
Different arg than version in convert.c
=======================================================================*/
struct dirichlet *load_diri2(fin)
FILE *fin;
{
   int aa, numc, type;
   char line[MAXLINE], *ptr;
   struct dirichlet *diric;

   diric = (struct dirichlet *) malloc(sizeof(struct dirichlet));
   if (diric == NULL)
   {
      printf("\nOUT OF MEMORY\n");
      exit(-1);
   }
   numc = 0;
   while (numc < MAXCOMP && !feof(fin) && fgets(line, MAXLINE, fin) != NULL)
   {
      type = 0;
      if (strstr(line, "Mixture=") != NULL) type = 1;
      if (strstr(line, "Alpha=") != NULL)  type = 2;
      if (type > 0)
      {
         ptr = strtok(line, "="); ptr = strtok(NULL, "\t\n\r ");
         switch (type)
         {
	    case 1:
               diric->q[numc] = atof(ptr);
               break;
            case 2:
               diric->altot[numc] = atof(ptr);
               aa = 1;
               while (aa < AAS && ptr != NULL)
               {
                  ptr = strtok(NULL, "\t\n\r ");
                  diric->alpha[numc][aa++] = atof(ptr);
               }
               numc++;
               break;
            default:
               break;
         }
      }
   }  /* end of while */
   diric->ncomp = numc;

   fclose(fin);
   return(diric);
}   /* end of load_diri2 */
/*===================================================================
    Returns log of gamma using Lanczos' approximation.
    Taken from "Numerical Recipes in C".
    NOTE:  Alternative to Sun's lgamma() function

    gamma(x) = integral(0,infinity) y^(x-1) * e^(-y) dy
      gamma(0.5) = sqrt(pi)
      gamma(1) = gamma(2) = 1
      gamma(x) = (x-1) * gamma(x-1), x > 2
      If x is an integer, gamma(x) = (x-1)!
      gamma(1-x) = (pi * x)/{gamma(1+x) * sine(pi * x)}
===================================================================*/
double nrgamma(x)
double x;
{
   double xx, dtemp, dtemp2, lg, g;
   int j;

   if (x <= 0.0) lg = 0.0;
   else if (x < 1.0)   		/*  use the reflection formula */
   {
     dtemp = PI * (1.0 - x);
     dtemp2 = sin(dtemp);
     lg = log(dtemp) - nrgamma(2.0 - x) - log(dtemp2);
   }
   else
   {

      xx = x - 1.0;
      dtemp = xx + 5.5;
      dtemp -= (xx + 0.5) * log(dtemp);
      dtemp2 = 1.0;
      for (j=0; j <= 5; j++)
      {
          xx += 1.0;
          dtemp2 += Cof[j] / xx;
      }
      lg = -dtemp + log(LCof * dtemp2);
      if (lg <= 50) g = exp(lg);		/* overflows quickly */
      else g = 1e50;
   }

   return(lg);
}  /* end of nrgamma */
/*======================================================================*/
Matrix *make_patmat(block, freqs, obs_freqs)
Block *block;
double *freqs;
Matrix *obs_freqs;
{
   double dtemp, sum, temp[AASALL];
   int pos, aa;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *bruno;

   col = make_col();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;

   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);

      sum = 0.0;
      for (aa=1; aa < AAS; aa++)
      {
         if (obs_freqs != NULL)
         {
	    dtemp = 100. * col->cnt[aa] / col->totcnt;
	    obs_freqs->weights[aa][pos] = round(dtemp);
         }
          if (freqs[aa] > 0.0)
             temp[aa] = col->cnt[aa] / freqs[aa];
          else temp[aa] = 0.0;
          sum += temp[aa];
      }
      for (aa=1; aa < AAS; aa++)
      {
         dtemp = 99.0 * temp[aa] / sum;
         matrix->weights[aa][pos] = round(dtemp);
      }
      compute_BZX(freqs, matrix, pos);
   }  /*  end of for pos */

   free(col);
   if (bruno != NULL) free(bruno);
   return(matrix);

}  /* end of make_patmat */
/*==========================================================================
     Uses Gribskov's method 
     Assumes a non-negative substition matrix (min. value = 0)
     Sets 20 aas plus B and Z from the matrix; X, etc to zero = min. value
     Index for B is 21, for Z is 22
===========================================================================*/
Matrix *make_gribs(block, subst, obs_freqs)
Block *block;
double subst[AASALL][AASALL];
Matrix *obs_freqs;
{
   double dtemp, sum, temp[AASALL];
   int pos, aa, aa1;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *bruno;

   col = make_col();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;

   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);

      sum = 0.0;
      for (aa=0; aa <= 22; aa++)
      {
         if (obs_freqs != NULL)
         {
	    dtemp = 100. * col->cnt[aa] / col->totcnt;
	    obs_freqs->weights[aa][pos] = round(dtemp);
         }
         temp[aa] = 0.0;
         for (aa1=1; aa1 <= 22 ; aa1++)
         {
            temp[aa] += col->cnt[aa1] * subst[aa][aa1];
         }
         temp[aa] /= col->totcnt;
         sum += temp[aa];
      }
      for (aa=1; aa <= 22; aa++)
      {
         dtemp = temp[aa];
         matrix->weights[aa][pos] = round(dtemp);
      }
      /*  Set X, * and - to zero */
      matrix->weights[0][pos] = matrix->weights[23][pos] = 0;
      matrix->weights[24][pos] = matrix->weights[25][pos] = 0;
   }  /*  end of for pos */

   free(col);
   if (bruno != NULL) free(bruno);
   /*  scale final matrix to lie between 0 and 99 */
   positive_matrix(block, matrix);
   return(matrix);
}   /*  end of make_gribs */
/*==========================================================================
     Uses Gribskov's method with log(qij/pipj) instead of sij
     NOTE: no BZX values
===========================================================================*/
Matrix *make_gribq(block, qij, obs_freqs)
Block *block;
struct float_qij *qij;
Matrix *obs_freqs;
{
   double dtemp, sum, temp[AASALL];
   int pos, aa, aa1, minval;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *bruno;

   col = make_col();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;

   minval = 99999;			/* min. val in matrix  */
   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);

      sum = 0.0;
      for (aa=1; aa <= 20; aa++)
      {
         if (obs_freqs != NULL)
         {
	    dtemp = 100. * col->cnt[aa] / col->totcnt;
	    obs_freqs->weights[aa][pos] = round(dtemp);
         }
         temp[aa] = 0.0;
         for (aa1=1; aa1 <= 20 ; aa1++)
         {
            dtemp = qij->value[aa][aa1] / (qij->marg[aa] * qij->marg[aa1]);
            dtemp = log(dtemp) / log(2.0);	/* sij scaled in bits */
            temp[aa] += col->cnt[aa1] * dtemp;
         }
         temp[aa] /= col->totcnt;
         sum += temp[aa];
      }
      for (aa=1; aa <= 20; aa++)
      {
         dtemp = 100.0 * temp[aa];	/* beef up weights for scaling */
         matrix->weights[aa][pos] = round(dtemp);  /* weights are ints */
	 if (matrix->weights[aa][pos] < minval)
		minval = matrix->weights[aa][pos];
      }
   }  /*  end of for pos */

   /*  Set B, Z, X, * and - to min. value */
   for (pos = 0; pos < block->width; pos++)
   {
      matrix->weights[0][pos] = matrix->weights[23][pos] = minval;
      matrix->weights[24][pos] = matrix->weights[25][pos] = minval;
      matrix->weights[21][pos] = matrix->weights[22][pos] = minval;
   }

   free(col);
   if (bruno != NULL) free(bruno);
   /*  scale final matrix to lie between 0 and 99 */
   positive_matrix(block, matrix);
   return(matrix);
}   /*  end of make_gribq */
/*==========================================================================
     Uses Altschul's method of getting pseudo-counts with a qij matrix,
===========================================================================*/
Matrix *make_alts(block, freqs, qij, obs_freqs)
Block *block;
double *freqs;
struct float_qij *qij;
Matrix *obs_freqs;
{
   double dtemp, epsilon, maxsubst, minfreq;
   int pos, aa, row;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *pssm, *bruno;

   col = make_col();
   pssm = make_pssm();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;

   /*--------------  Do one position at a time -------------------*/
   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);
/*      epsilon = sqrt(col->totcnt); 
      epsilon = 1.0 / col->totcnt;
      epsilon += compute_entropy(col); 
*/
      /*    epsilon = total number of pseudo counts in the column   */
      if (RTot >= 0.0) epsilon = (double) RTot * count_residues(col);
      else if (BTot >= 0.0) epsilon = BTot;
      else epsilon = sqrt(col->totcnt);

      /*---------- get the pseudo counts -------------------------------*/
      pseudo_alts(col, qij, epsilon);

      /*---------   Fill in the matrix entries --------------------*/
      fillin(pos, freqs, col, pssm, obs_freqs);

   }  /*  end of for pos */
   /*------ Now make the final scores; make log scores non-neg    */
   /*       by subtracting the min. value for all positions ----- */
   final(block, freqs, pssm, matrix);

   free(col);
   free(pssm);
   if (bruno != NULL) free(bruno);
   return(matrix);
}  /* end of make_alts */
/*==========================================================================
     Uses Steve's modification of
         Altschul's method of getting pseudo-counts with a qij matrix,
         different matrix for each column.
===========================================================================*/
Matrix *make_steves(block, freqs, obs_freqs)
Block *block;
double *freqs;
Matrix *obs_freqs;
{
   double dtemp, epsilon, maxsubst, minfreq;
   int pos, aa, row;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *pssm, *bruno;
   struct float_qij *qij;
   FILE *fin;

   col = make_col();
   pssm = make_pssm();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;
   qij = NULL;
   fin = NULL;

   /*--------------  Do one position at a time -------------------*/
   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);
      if (RTot >= 0.0) epsilon = (double) RTot * count_residues(col);
      else if (BTot >= 0.0) epsilon = BTot;
      else epsilon = sqrt(col->totcnt);
      if (qij != NULL) free(qij);
      fin = steves_qij(col);
      qij = load_qij(fin);
      fclose(fin);

      /*---------- get the pseudo counts -------------------------------*/
      pseudo_alts(col, qij, epsilon);

      /*---------   Fill in the matrix entries --------------------*/
      fillin(pos, freqs, col, pssm, obs_freqs);

   }  /*  end of for pos */
   /*------ Now make the final scores; make log scores non-neg    */
   /*       by subtracting the min. value for all positions ----- */
   final(block, freqs, pssm, matrix);

   free(col);
   free(pssm);
   if (bruno != NULL) free(bruno);
   return(matrix);
}  /* end of make_steves */
/*==========================================================================
     Uses Claverie's method of getting pseudo-counts with a subst. matrix,
     not Gribskov's method
===========================================================================*/
Matrix *make_clav(block, freqs, subst, obs_freqs)
Block *block;
double *freqs;
double subst[AASALL][AASALL];
Matrix *obs_freqs;
{
   double dtemp, epsilon, maxsubst, minfreq;
   int pos, aa, row;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *pssm, *bruno;

   col = make_col();
   pssm = make_pssm();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;

   /*-----------------  Get the scaling value ------------------*/
   maxsubst = -999.9; minfreq = 999.9;
   for (row = 1; row < AAS; row++)
   {
      if (freqs[row] < minfreq && freqs[row] > 0.0)
           minfreq = freqs[row];
      for (aa = row; aa < AAS; aa++)
         if (subst[row][aa] > maxsubst) maxsubst = subst[row][aa];
   }

   /*--------------  Do one position at a time -------------------*/
   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);
      epsilon = (minfreq * sqrt(col->totcnt)) / maxsubst;

      /*---------- get the pseudo counts -------------------------------*/
      pseudo_clav(col, subst, epsilon);

      /*---------   Fill in the matrix entries --------------------*/
      fillin(pos, freqs, col, pssm, obs_freqs);

   }  /*  end of for pos */
   /*------ Now make the final scores; make log scores non-neg    */
   /*       by subtracting the min. value for all positions ----- */
   final(block, freqs, pssm, matrix);

   free(col);
   free(pssm);
   if (bruno != NULL) free(bruno);
   return(matrix);
} /* end of make_clav */
/*==========================================================================
     Uses simple background frequencies to make pseudo counts,
     b[aa] = sqrt(#seqs) * freq[aa]
     After Chip Lawrence's Gibbs sampling paper
===========================================================================*/
Matrix *make_gibbs(block, freqs, obs_freqs)
Block *block;
double *freqs;
Matrix *obs_freqs;
{
   double dtemp, epsilon, maxsubst, minfreq;
   int pos, aa, row;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *pssm, *bruno;

   col = make_col();
   pssm = make_pssm();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;

   /*--------------  Do one position at a time -------------------*/
   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);
/*
      epsilon = 1.0 / (double) block->num_sequences;
      epsilon += compute_entropy(col);
      epsilon = (double) RTot * count_residues(col);
*/
      if (RTot >= 0.0) epsilon = (double) RTot * count_residues(col);
      else if (BTot >= 0.0) epsilon = BTot;
      else epsilon = sqrt( (double) block->num_sequences); 

      /*---------- get the pseudo counts -------------------------------*/
      pseudo_gibbs(col, freqs, epsilon);

      /*---------   Fill in the matrix entries --------------------*/
      fillin(pos, freqs, col, pssm, obs_freqs);

   }  /*  end of for pos */
   /*------ Now make the final scores; make log scores non-neg    */
   /*       by subtracting the min. value for all positions ----- */
   final(block, freqs, pssm, matrix);

   free(col);
   free(pssm);
   if (bruno != NULL) free(bruno);
   return(matrix);
} /* end of make_gibbs */
/*======================================================================*/
Matrix *make_diri(block, freqs, diric, obs_freqs)
Block *block;
double *freqs;
struct dirichlet *diric;
Matrix *obs_freqs;
{
   double dtemp;
   int pos, aa;
   Matrix *matrix;
   struct working *col;
   struct work_pssm *pssm, *bruno;

   col = make_col();
   pssm = make_pssm();
   matrix = make_matrix(block);
   if (BrunoCounts || HybridCounts) bruno = bruno_rind(block);
   else bruno = NULL;

   for (pos = 0; pos < block->width; pos++)
   {
      /*-------- count the number of each aa in this position ------------*/
      if (BrunoCounts) counts_bruno(bruno, col, pos);
      else if (HybridCounts) counts_hybrid(bruno, block, col, pos);
           else if (ClumpCounts) counts_clumps(block, col, pos);
                else counts(block, col, pos);

      /*--------  get the Dirichlet mixture pseudo-counts ---------------*/
      pseudo_diric(col, diric);

/*    printf("\npos=%d\n", pos);
      for (aa = 1; aa < AAS; aa++)
         printf("%c: actual=%f diric=%f diric/Z=%f\n",
              aa_btoa[aa], col->cnt[aa], col->cnt[aa] + col->reg[aa],
              (col->cnt[aa] + col->reg[aa])/(col->totcnt + col->totreg) );
*/
  
      /*---------   Fill in the matrix entries --------------------*/
      fillin(pos, freqs, col, pssm, obs_freqs);
       
   }  /*  end of for pos */
   /*------ Now make the final scores; make log scores non-neg    */
   /*       by subtracting the min. value for all positions ----- */
   final(block, freqs, pssm, matrix);

   free(col);
   free(pssm);
   if (bruno != NULL) free(bruno);
   return(matrix);

}  /* end of make_diri */
/*===============================================================
      Returns log(e^x + e^y)
================================================================*/
double addlogs(lx, ly)
double lx, ly;
{
   if (lx > ly)  return(lx + log(1.0 + exp(ly - lx)));
   else          return(ly + log(1.0 + exp(lx - ly)));
}  /*  end of addlogs */


/*=================================================================
 * load_frequencies
 *   reads in the frequencies if there is a frequency file.
 *   Parameters: none
 *   Return codes: TRUE if there was a frequency file and the data was 
 *                 sucessfully read in, FALSE if not.
 *   Error codes: none
 =================================================================*/

int load_frequencies(ffp, frequency)
FILE *ffp;
double frequency[AASALL];
{
  int i;
  int seq_type;
  double J_weight, O_weight, U_weight;


#define NAR '|'   /* a char that get converted to AAID_NAR for the codes so */
		  /* that when reading in the frequencies entries for J, O, */
		  /* an U do not overwrite the entry for X.  Also if the */
		  /* idea of have non-code alpha characters being treated as */
		  /* X ever changes, there shouldn't be a change needed */
		  /* (assuming that J, O, U are weighted the same). */

  /* old style format */
  frequency[aa_atob['-']] = read_freq(ffp);
  frequency[aa_atob['A']] = read_freq(ffp);
  frequency[aa_atob['B']] = read_freq(ffp);
  frequency[aa_atob['C']] = read_freq(ffp);
  frequency[aa_atob['D']] = read_freq(ffp);
  frequency[aa_atob['E']] = read_freq(ffp);
  frequency[aa_atob['F']] = read_freq(ffp);
  frequency[aa_atob['G']] = read_freq(ffp);
  frequency[aa_atob['H']] = read_freq(ffp);
  frequency[aa_atob['I']] = read_freq(ffp);

  J_weight = read_freq(ffp);
  frequency[aa_atob[NAR]] = J_weight; /* 'J' */

  frequency[aa_atob['K']] = read_freq(ffp);
  frequency[aa_atob['L']] = read_freq(ffp);
  frequency[aa_atob['M']] = read_freq(ffp);
  frequency[aa_atob['N']] = read_freq(ffp);

  O_weight = read_freq(ffp);
  frequency[aa_atob[NAR]] = O_weight; /* 'O' */

  frequency[aa_atob['P']] = read_freq(ffp);
  frequency[aa_atob['Q']] = read_freq(ffp);
  frequency[aa_atob['R']] = read_freq(ffp);
  frequency[aa_atob['S']] = read_freq(ffp);
  frequency[aa_atob['T']] = read_freq(ffp);

  U_weight = read_freq(ffp);
  frequency[aa_atob[NAR]] = U_weight; /* 'U' */

  frequency[aa_atob['V']] = read_freq(ffp);
  frequency[aa_atob['W']] = read_freq(ffp);
  frequency[aa_atob['X']] = read_freq(ffp);
  frequency[aa_atob['Y']] = read_freq(ffp);
  frequency[aa_atob['Z']] = read_freq(ffp);
  frequency[aa_atob['*']] = read_freq(ffp);

#undef NAR


  /* check the frequency array for zero values */
  for (i=0; i= 0 && col < AASALL)
	    {
	       alpha[row] = col;
	       row++;
	    }
	    else if (isalpha(line[i])) row++; /* skip over other alpha */
	 }
      }
/*-------Get the data values now ------------*/
      for (row=0; row 1)
	 {
	    if (alpha[nrows] >= 0 && alpha[nrows] < AASALL)
	    {
	       row = alpha[nrows]; ncols = 0;
	       ptr = strtok(line, " ,\t\n");
	       while (ptr != NULL)
	       {
		  if (strspn(ptr, "+-0123456789") == strlen(ptr))
		  {
		     col = alpha[ncols];
		     if (col >= 0 && col < AASALL)
			subst[row][col] = (double) atoi(ptr);
		     ncols++;
		  }
		  ptr = strtok(NULL, " ,\t\n");
	       }
	    }
	    nrows++;
	 }
      }

/*-------If some entries are still missing, assume symmetry ---------*/
      for (row=0; rownum_sequences; seq++)
      sum += block->sequences[seq].weight;
   factor = block->num_sequences / sum;
   for (seq = 0; seq < block->num_sequences; seq++)
      block->sequences[seq].weight *= factor;
}  /*  end of normalize */
/*===================================================================*/
Matrix *make_matrix(block)
Block *block;
{
   Matrix *matrix;
   char ctemp[MAXLINE], *ptr;

   /*---------  Create the matrix --------------------------*/
   matrix = new_matrix(block->width);
   matrix->block = block;
   strcpy(ctemp, block->id);
   strncpy(strstr(ctemp, "BLOCK"), "MATRIX\0", 7);
   strcpy(matrix->id, ctemp);
   strcpy(matrix->ac, block->ac);
   strcpy(matrix->de, block->de);
   strcpy(matrix->ma, block->bl);
   strcpy(matrix->number, block->number);
   strcpy(matrix->motif, block->motif);
   matrix->width = matrix->max_length = block->width;
   matrix->num_sequences = block->num_sequences;
   matrix->percentile = block->percentile;
   matrix->strength = block->strength;
   matrix->patterns = NULL;
   matrix->undefined_ptr = NULL;
   /*  Add seqs= to MA line if not there */
   if (strstr(matrix->ma, "seqs=") == NULL)
   {
	strcpy(ctemp, matrix->ma);
	ptr = strtok(ctemp, "\n\r");
	sprintf(matrix->ma, "%s seqs=%d",
		ptr, matrix->num_sequences);
   }

   return(matrix);
}  /* end of make_matrix */
/*======================================================================*/
void counts(block, col, pos)
Block *block;
struct working *col;
int pos;
{
   int seq, aa;

      col->totcnt = col->totraw = col->totreg = 0.0;
      for (aa = 0; aa < AASALL; aa++) 
      { col->cnt[aa] = col->raw[aa] = col->reg[aa] = 0.0; }

      /*  Only count the real 20 aas, combine B(21) with D & Z(22) with E  */
      for (seq = 0; seq < block->num_sequences; seq++)
      {
         aa = block->residues[seq][pos];
         if (aa == 21) aa = 4;			/* combine B with D */
	 if (aa == 22) aa = 7;			/* combine Z with E */
         if (aa >= 1 && aa < AAS)
         {
            col->cnt[aa] += block->sequences[seq].weight;
            col->totcnt += block->sequences[seq].weight;
	    col->raw[aa] += 1.0;
            col->totraw += 1.0;
         }
         else printf("Uncounted character for %s: %d\n",
              block->number, block->residues[seq][pos]);
      }
}  /* end of counts */
/*======================================================================
    Get col->totcnt from Bruno but col->cnt[aa] from sequence weights
    Each column has a different col->totcnt
======================================================================*/
void counts_hybrid(bruno, block, col, pos)
struct work_pssm *bruno;
Block *block;
struct working *col;
int pos;
{
   int aa;
   double totbruno, factor;

   counts_bruno(bruno, col, pos);
   totbruno = col->totcnt;
   counts(block, col, pos);
   /*   Re-normalize sequence-weighted counts to add to Bruno total */
   factor = totbruno / col->totcnt;
   for (aa = 0; aa < AASALL; aa++) col->cnt[aa] *= factor;
   col->totcnt = totbruno;
}  /* end of counts_hybrid */
/*======================================================================
    Get col->totcnt from # clumps but col->cnt[aa] from sequence weights
    Each column has the same col->totcnt = ClumpsTot
======================================================================*/
void counts_clumps(block, col, pos)
Block *block;
struct working *col;
int pos;
{
   int aa;
   double factor;

   counts(block, col, pos);
   /*   Re-normalize sequence-weighted counts to add to clumps total */
   factor = ClumpTot / col->totcnt;
   for (aa = 0; aa < AASALL; aa++) col->cnt[aa] *= factor;
   col->totcnt = ClumpTot;
}  /* end of counts_clumps */
/*=====================================================================*/
double compute_entropy(col)
struct working *col;
{
   int aa;
   double entropy, dtemp;

   entropy = 0.0;
   for (aa=1; aa < AAS ; aa++)
   {
      dtemp = col->cnt[aa] / col->totcnt;
      if (dtemp > 0.0000) entropy -= dtemp * log(dtemp);
   }
   entropy /= Log2;		/* convert it to bits */
   return(entropy);
}   /* end of compute_entropy */
/*=====================================================================*/
int count_residues(col)
struct working *col;
{
   int aa, nr;

   nr = 0;
   for (aa = 1; aa < AAS; aa++)
      if (col->cnt[aa] > 0.0) nr++;

   return(nr);
}  /*  end of count_residues */
/*=======================================================================
    Count all pairs of amino acids in a column. Return the ratio of
    diagonal counts (identities) to off-diagonal counts.
    Working from the sequence-weighted aa counts in the column,
    not the actual block column.
    The total number of pairwise counts is tot*(tot-1)/2
========================================================================*/
double ratio_counts(col)
struct working *col;
{
   int aa;
   double ndiag, total, ratio;

   total = col->totcnt * (col->totcnt - 1.0) / 2.0;
   ndiag = 0.0;
   for (aa = 1; aa < AAS; aa++)
      if (col->cnt[aa] > 1.0)
         ndiag += col->cnt[aa] * (col->cnt[aa] - 1.0) / 2.0;

   if (ndiag < total) ratio = ndiag/(total - ndiag);
   else               ratio = 10.0;			/* infinity */
   return(ratio);
}  /*  end of ratio_counts */
/*=====================================================================*/
void pseudo_diric(col, diric)
struct working *col;
struct dirichlet *diric;
{
   int j, aa;
   double denom, dtemp;

      /*-----------   compute equation (3), Prob(n|j) ------------  */
      for (j = 0; j < diric->ncomp; j++)
      {
         col->probn[j] = lgamma(col->totcnt + 1.0) + lgamma(diric->altot[j]);
         col->probn[j] -= lgamma(col->totcnt + diric->altot[j]);
         /*   Note range on aa varies; Diric values only for 1-20 */
         for (aa = 1; aa < AAS; aa++)
         {
         /*  ni = cnt[i] */
            if (col->cnt[aa] >= 0.0)
            {
               dtemp = lgamma(col->cnt[aa] + diric->alpha[j][aa]);
               dtemp -= lgamma(col->cnt[aa] + 1.0);
               dtemp -= lgamma(diric->alpha[j][aa]);
               col->probn[j] += dtemp;
            }
         }
      }

      /*------ compute sum qk * p(n|k) using logs & exponents ----------*/
      denom = log(diric->q[0]) + col->probn[0];
      for (j = 1; j < diric->ncomp; j++)
      {
         dtemp = log(diric->q[j]) + col->probn[j];
         denom = addlogs(denom, dtemp);
      }

      /*   compute equation (3), Prob(j|n)  */
      for (j = 0; j < diric->ncomp; j++)
      {
         col->probj[j] = log(diric->q[j]) + col->probn[j] - denom;
/*       printf("j=%d probn[j]=%f probj[j]=%f\n",
             j, exp(col->probn[j]), exp(col->probj[j]));
*/
      }

      /* ----- compute equation (4), ni + bi, bi = Prob(j|n) * alpha[j][i]  */
      for (aa = 1; aa < AAS; aa++)
      {
         for (j = 0; j < diric->ncomp; j++)
            col->reg[aa] += (exp(col->probj[j]) * diric->alpha[j][aa]);
         col->totreg += col->reg[aa];
      }

}  /* end of pseudo_diric */
/*=====================================================================*/
void pseudo_alts(col, qij, epsilon)
struct working *col;
struct float_qij *qij;
double epsilon;
{
   int aa, row;

   /*---------- get the pseudo counts -------------------------------*/
   for (aa=1; aa < AAS; aa++)
   {
      col->reg[aa] = 0.0;
      for (row = 1; row < AAS; row++)
      {
        col->reg[aa] += (col->cnt[row] * qij->value[aa][row] / qij->marg[row]);
/*
        col->reg[aa] += (col->raw[row] * qij->value[aa][row] / qij->marg[row]);
*/
      }
      col->reg[aa] *= epsilon;
/*    col->reg[aa] /= col->totraw;
*/
      col->reg[aa] /= col->totcnt;
      col->totreg += col->reg[aa];
   }
}  /* end of pseudo_alts */
/*=====================================================================*/
void pseudo_clav(col, subst, epsilon)
struct working *col;
double subst[AASALL][AASALL];
double epsilon;
{
   int aa, row;

      /*---------- get the pseudo counts -------------------------------*/
      for (aa=1; aa < AAS; aa++)
      {
         col->reg[aa] = 0.0;
         for (row = 1; row < AAS; row++)
         {
            col->reg[aa] += col->cnt[row] * subst[aa][row];
         }
         col->reg[aa] *= epsilon;
         col->reg[aa] /= col->totcnt;
         col->totreg += col->reg[aa];
      }
}  /* end of pseudo_clav */
/*=====================================================================*/
void pseudo_gibbs(col, freqs, epsilon)
struct working *col;
double *freqs;
double epsilon;
{
   int aa;

   /*---------- get the pseudo counts -------------------------------*/
   col->totreg = 0.0;
   for (aa=1; aa < AAS; aa++)
   {
      col->reg[aa] = epsilon * freqs[aa];
      col->totreg += col->reg[aa];
   }
}  /* end of pseudo_gibbs */
/*=====================================================================*/
void fillin(pos, freqs, col, pssm, obs_freqs)
int pos;
double *freqs;
struct working *col;
struct work_pssm *pssm;
Matrix *obs_freqs;
{
      int aa;
      double dtemp;

      pssm->sum[pos] = 0.0; 
      for (aa=1; aa < AAS; aa++)
      {
         if (NoCounts)
         {
            pssm->value[pos][aa] = col->reg[aa];
            pssm->value[pos][aa] /= col->totreg;
         }
         else
         {
            pssm->value[pos][aa] = col->cnt[aa] + col->reg[aa];
            pssm->value[pos][aa] /= (col->totcnt + col->totreg);
         }
	 if (obs_freqs != NULL)
         {
             dtemp = 100. * pssm->value[pos][aa];
	     obs_freqs->weights[aa][pos] = round(dtemp);
         }
         if (freqs[aa] > 0.0)
             pssm->value[pos][aa] /= freqs[aa];

         if (LogScores && pssm->value[pos][aa] > 0.0)
             pssm->value[pos][aa] = log(pssm->value[pos][aa]);

         pssm->sum[pos] += pssm->value[pos][aa];
      }
}  /* end of fillin */
/*=========================================================================
      Adds negative minval to give all positive matrix,
      then multiplies by 99/maxval to give scores ranging from 0 to99 
===========================================================================*/
void final(block, freqs, pssm, matrix)
Block *block;
double *freqs;
struct work_pssm *pssm;
Matrix *matrix;
{
   int pos, aa;
   double factor, maxval, minval, dtemp;

   minval = 9999.9;
   maxval = -9999.9;
   for (pos = 0; pos < block->width; pos++)
      for (aa=1; aa < AAS; aa++)
      {
         if (pssm->value[pos][aa] < minval) minval = pssm->value[pos][aa];
         if (pssm->value[pos][aa] > maxval) maxval = pssm->value[pos][aa];
      }

   if (minval < 0.0) factor = 99.0 / (maxval - minval);
   else              factor = 99.0 / maxval;
   if (factor < 1.0) factor = 1.0;
   for (pos = 0; pos < block->width; pos++)
   {
      for (aa=1; aa < AAS; aa++)
      {
         if (FloatPt)		/* Just copy pssm to matrix */
         {
            matrix->weights[aa][pos] = pssm->value[pos][aa];
         }
         else			/* Rescale it */
         {
            if (LogScores) 
            {
               if (minval < 0.0)
                  dtemp = factor * (pssm->value[pos][aa] - minval);
               else dtemp = factor * pssm->value[pos][aa];
            }
            else 
            { 
              dtemp = 99.0 * pssm->value[pos][aa] / pssm->sum[pos];
            }
            matrix->weights[aa][pos] = round(dtemp);
         }	/* end of if not floating point */
      }   /* end of aa */
      compute_BZX(freqs, matrix, pos);
   }  /*  end of for pos */
}  /* end of final */
/*=====================================================================*/
void compute_BZX(frequency, matrix, col)
double *frequency;
Matrix *matrix;
int col;
{
  int res;
  double part_D;		/* the partition of D for B. */
				/* = freq[D] / ( freq[D] + freq[N] ) */
  double part_N;		/* the partition of N for B. */
				/* = freq[N] / ( freq[D] + freq[N] ) */
  double part_E;		/* the partition of E for Z. */
				/* = freq[E] / ( freq[E] + freq[Q] ) */
  double part_Q;		/* the partition of Q for Z. */
				/* = freq[Q] / ( freq[E] + freq[Q] ) */
  /*
   * find the partitions of D, N, E, and Q for B and Z
   */
  part_D = frequency[aa_atob['D']] / 
    ( frequency[aa_atob['D']] + frequency[aa_atob['N']] );
  part_N = frequency[aa_atob['N']] / 
    ( frequency[aa_atob['D']] + frequency[aa_atob['N']] );
  part_E = frequency[aa_atob['E']] / 
    ( frequency[aa_atob['E']] + frequency[aa_atob['Q']] );
  part_Q = frequency[aa_atob['Q']] / 
    ( frequency[aa_atob['E']] + frequency[aa_atob['Q']] );

    /* fill in the matrix for B, Z, X, gap, stop and non */
    matrix->weights[aa_atob['B']][col] = 
      (int) ((part_D * matrix->weights[aa_atob['D']][col] +
	      part_N * matrix->weights[aa_atob['N']][col]) + 0.5);
				/* rounding to ints by adding 0.5 */
    matrix->weights[aa_atob['Z']][col] =
      (int) ((part_E * matrix->weights[aa_atob['E']][col] +
	      part_Q * matrix->weights[aa_atob['Q']][col]) + 0.5);
				/* rounding to ints by adding 0.5 */
    matrix->weights[aa_atob['X']][col] = 
      (int) (frequency[aa_atob['X']] + 0.5);
				/* rounding to ints by adding 0.5 */
    matrix->weights[aa_atob['-']][col] = 
      (int) (frequency[aa_atob['-']] + 0.5);
				/* rounding to ints by adding 0.5 */
    matrix->weights[aa_atob['*']][col] = 
      (int) (frequency[aa_atob['*']] + 0.5);
				/* rounding to ints by adding 0.5 */
}  /* end of compute_BZX */

/*=====================================================================*/
struct work_pssm *make_pssm()
{
   struct work_pssm *pssm;
   int pos, aa;

   pssm = (struct work_pssm *) malloc(sizeof(struct work_pssm));
   if (pssm == NULL)
   {
      printf("make_pssm: OUT OF MEMORY\n");
      exit(-1);
   }
   for (pos = 0; pos < MAXWIDTH; pos++)
   {
      pssm->sum[pos] = 0.0;
      for (aa=0; aa < AASALL; aa++)
         pssm->value[pos][aa] = 0.0;
   }
   return(pssm);

}  /* end of make_pssm */
/*==================================================================*/
struct working *make_col()
{
   struct working *col;
   int aa;

   col = (struct working *) malloc(sizeof(struct working));
   if (col == NULL)
   {
      printf("make_col:  OUT OF MEMORY\n");
      exit(-1);
   }

   col->totcnt = col->totreg = 0.0;
   for (aa=0; aa < AASALL; aa++)
   {
      col->cnt[aa] = col->reg[aa] = 0.0;
   }

   return(col);
}  /* end of make_col */

/*======================================================================*/
struct float_qij *load_qij(fin)
FILE *fin;
{
   char line[MAXLINE], *ptr;
   double total;
   int alpha[AAS], nrows, ncols, row, col, i;
   struct float_qij *new;

   new = (struct float_qij *) malloc(sizeof(struct float_qij));
   if (new == NULL)
   { 
      printf("\nfloat_qij: OUT OF MEMORY\n");  exit(-1);
   }

   /*----------Read file until first non-blank line --------------*/
   /* Skip comments at beginning of file - 1st char = #, > or ;   */
   line[0] = '\0';
   while (((int) strlen(line) < 1 || line[0]=='#' ||
                                     line[0]=='>' || line[0]==';')
          && fgets(line, sizeof(line), fin) != NULL)
	    ;
/*------See if the first line has characters on it ------------*/
   for (col=0; col < AAS; col++) alpha[col] = -1;
   if (strstr(line, "A") != NULL)	/* This line has characters */
   {
      row = 0;	/* # of alphabetic characters on the line */
      for (i=0; i < (int) strlen(line); i++)
      {
	 col = -1;
         col = aa_atob[line[i]];
	 if (col >= 0 && col < AAS)
	 {
	    alpha[row] = col;
	    row++;
	 }
	 else if (isalpha(line[i])) row++;
      }
   }
/*-------Get the data values now ------------*/
   for (row=0; rowvalue[row][col] = -1.0;		/* Null value */
   nrows = 0;
   line[0] = '\0';
   while (fgets(line, sizeof(line), fin) != NULL)
   {
      if ((int) strlen(line) > 1 && nrows < AAS)
      {
	 if (alpha[nrows] >= 0 && alpha[nrows] < AAS)
	 {
	    row = alpha[nrows]; ncols = 0;
	    ptr = strtok(line, " ,\n");
	    while (ptr != NULL)
	    {
	       if (strspn(ptr, ".+-0123456789") == strlen(ptr))
	       {
		  col = alpha[ncols];
		  if (col >= 0 && col < AAS)
		     new->value[row][col] = (double) atof(ptr);
		  ncols++;
	       }
	       ptr = strtok(NULL, " ,\n");
	    }
	 }
	 nrows++;
      }
   }

   /*-------If some entries are still missing, assume symmetry ---------*/
   for (row=0; rowvalue[row][col] < 0.0)
            new->value[row][col] = new->value[col][row];

   /*-------compute the marginal probabilities ---------*/
   total = 0.0;
   for (row=1; rowmarg[row] = 0.0;
     for (col=1; colmarg[row] += new->value[row][col];
     total += new->marg[row];
   }

   return(new);
}  /* end of load_qij */

/*=======================================================================
    Bill Bruno's character counts:
	creates file "data" with sequences
	executes program "rind" & waits for it to finish
	reads output file "counts" to get counts
     Computes counts for all positions at once
========================================================================*/
struct work_pssm *bruno_rind(block)
Block *block;
{
   struct work_pssm *bruno;
   FILE *fp;
   int seq, pos, aa, baa;
   char line[1000], *ptr;
   double dtemp;

   bruno = make_pssm();
   /*------Turn the block into file "data" for rind --------------*/
   if ( (fp = fopen("data", "w")) == NULL)
   {
       printf("\nbruno_rind(): Cannot open file data\n");
       return(bruno);
   }
   for (seq=0; seq < block->num_sequences; seq++)
   {
      fprintf(fp, "%10s ", block->sequences[seq].name);
      for (pos=0; pos < block->width; pos++)
         fprintf(fp, "%c", aa_btoa[ block->residues[seq][pos] ]);
      fprintf(fp, "\n");
   }
   fclose(fp);
   /*------Execute rind ------------------------------------------*/
   printf("\nExecuting rind ....\n");
   sprintf(line, "rind");
   if (system(line) != 0)
   {
       printf("\nbruno_rind(): Execution of rind failed\n");
       exit(-1);
/*       return(bruno);  */
   }
   /*------Get the counts from "counts"-------------------------*/
   if ( (fp = fopen("counts", "r")) == NULL)
   {
       printf("\nbruno_rind(): Cannot open file counts\n");
       return(bruno);
   }
   pos = baa = -1;
   while (pos < block->width && 
          !feof(fp) && fgets(line, 1000, fp) != NULL)
   {
      if (strstr(line, "position") != NULL)
      {
         pos++; baa = 0;
         bruno->sum[pos] = 0.0;
      }
      else if (pos >= 0 && baa == 0)
      {
         ptr = strtok(line, " \t");
         while (baa < 25 && ptr != NULL)
         {
            dtemp = atof(ptr);
            bruno->value[pos][ Bruno_Order[baa] ] = dtemp;
            bruno->sum[pos] += dtemp;
            baa++;
            ptr = strtok(NULL, "-");
	    ptr = strtok(NULL, " \t");
	    ptr = strtok(NULL, " \t");
         }
      }
   }
   fclose(fp);
   /*--------------------------------------------------------------*/
   return(bruno);
}  /* end of bruno_rind()  */
/*=======================================================================
        Looks up Bruno counts
========================================================================*/
void counts_bruno (bruno, col, pos)
struct work_pssm *bruno;
struct working *col;
int pos;
{ 
   int aa;

   for (aa = 0; aa < AASALL; aa++) 
   { col->cnt[aa] = col->raw[aa] = col->reg[aa] = 0.0; }
   for (aa=1; aa < AAS; aa++)
      col->cnt[aa] = bruno->value[pos][aa];
   col->totcnt = bruno->sum[pos];

} /* end of counts_bruno */

/*======================================================================*/
/*    Cluster sequences in a block based on the number of               */
/*    identities within the block. Sets Block.cluster & Block.ncluster  */
/*      1. Compute number of identities for each possible pair of seqs. */
/*         Results stored in lower half of matrix (pairs).              */
/*      2. Use clustering threshold % of # of AAs in trimmed block.     */
/*      3. Cluster recursively by traversing cols, rows of matrix.      */
/*UNIX NOTE:  Program aborts when running under UNIX at free(pairs),
   so use the fixed size declaration pairs & remove the malloc() &
   free() calls when compiling for UNIX                                 */
/*======================================================================*/
int clump_seqs(block)
Block *block;
{
   int clus, npair, threshold, s1, s2, l1, l2, px, i, i1, i2;
   int minclus, oldclus;
   struct pair *pairs;
   struct clump_work *clumps;
/*UNIX   struct pair pairs[MAXNSEQ*(MAXNSEQ-1)/2];  */

   npair = block->num_sequences * (block->num_sequences - 1) / 2;
   pairs = (struct pair *) malloc (npair * sizeof(struct pair));
   clumps = (struct clump_work *) malloc (sizeof(struct clump_work));
   if (pairs == NULL || clumps == NULL)
   {
      printf("\nclump_seqs: Unable to allocate pair structure!\n");
      exit(-1);
   }
   threshold = (int) (ClumpCounts * (block->width))/100;

/*    Compute scores for all possible pairs of sequences            */
   for (s1=0; s1num_sequences - 1; s1++) /* col = 0, n-2     */
   {
      l1 = 0;
      for (s2=s1+1; s2num_sequences; s2++)	/* row = col+1, n-1 */
      {
	 l2 = 0;
	 px = INDEX(block->num_sequences, s1, s2);
	 pairs[px].score = 0;
	 pairs[px].cluster = -1;
	 for (i=0; i<=block->width; i++)
	 {
	    i1 = l1+i;  i2 = l2+i;
	    if (i1 >= 0 && i1 < block->width &&
		i2 >= 0 && i2 < block->width &&
                block->residues[s1][i1] == block->residues[s2][i2])
		   pairs[px].score += 1;
	 }
      }  /* end of s2 */
   }  /* end of s1 */

/*-------Cluster if score exceeds threshold by scanning cols (s1) */
   for (s1=0; s1num_sequences; s1++)
   {
      clumps->cluster[s1] = -1;	/* clear out old values */
      clumps->ncluster[s1] = 1;
      clumps->nclus[s1] = 0;
   }
   clus = 0;        				/* cluster number */
   for (s1=0; s1num_sequences - 1; s1++) 	/* col = 0, n-2     */
      for (s2=s1+1; s2num_sequences; s2++)	/* row = col+1, n-1 */
      {
	 px = INDEX(block->num_sequences, s1, s2);
	 if (pairs[px].score >= threshold)	/*  cluster this pair */
	 {
	    if (clumps->cluster[s1] < 0)          /* s1 not yet clustered */
	    {
	       if (clumps->cluster[s2] < 0)       /* new cluster */
	       {
		  clumps->cluster[s1] = clus++;
		  clumps->cluster[s2] = clumps->cluster[s1];
	       }
	       else  				/* use s2's cluster  */
		  clumps->cluster[s1] =  clumps->cluster[s2];
	    }
	    /*  use s1's cluster if it has one and s2 doesn't */
	    else if (clumps->cluster[s1] >= 0 && clumps->cluster[s2] < 0)
	       clumps->cluster[s2] = clumps->cluster[s1];
	    /* merge the two clusters into the lower number */
	    else if (clumps->cluster[s1] >= 0 && clumps->cluster[s2] >= 0)
	    {
	       minclus = clumps->cluster[s1]; oldclus = clumps->cluster[s2];
	       if (clumps->cluster[s2] < clumps->cluster[s1])
	       {
		  minclus = clumps->cluster[s2]; oldclus = clumps->cluster[s1];
	       }
	       for (i1=0; i1num_sequences; i1++)
		 if (clumps->cluster[i1] == oldclus)
		     clumps->cluster[i1] = minclus;
	    }
	 }  /* end of if pairs */
      }  /* end of s2 */

   /*---  Set ncluster, get rid of negative cluster numbers --*/
   for (s1=0; s1num_sequences; s1++)
      if (clumps->ncluster[s1] >= 0)  clumps->nclus[clumps->cluster[s1]]++;
   for (s1=0; s1num_sequences; s1++)
   {
      if (clumps->cluster[s1] < 0)
      {
	  clumps->cluster[s1] = clus++;
	  clumps->ncluster[s1] = 1;
      }
      else
	  clumps->ncluster[s1] = clumps->nclus[clumps->cluster[s1]];
   }
   free(pairs);
   return(clus);
}  /*  end of clump_seqs */
/*=========================================================================
    Scales positive matrix to lie between 0 and 99
===========================================================================*/
void positive_matrix(block, matrix)
Block *block;
Matrix *matrix;
{
   int pos, aa;
   double factor, maxval, minval, dtemp;

   minval = 9999.9;
   maxval = -9999.9;
   for (pos = 0; pos < block->width; pos++)
      for (aa=0; aa < AASALL; aa++)
      {
         if (matrix->weights[aa][pos] < minval)
             minval = matrix->weights[aa][pos];
         if (matrix->weights[aa][pos] > maxval)
             maxval = matrix->weights[aa][pos];
      }

   if (minval < 0.0) factor = 99.0 / (maxval - minval);
   else              factor = 99.0 / maxval;
/*   if (factor < 1.0) factor = 1.0;     ????why????? */
   for (pos = 0; pos < block->width; pos++)
   {
      for (aa=0; aa < AASALL; aa++)
      {
            if (minval < 0.0)
               dtemp = factor * (matrix->weights[aa][pos] - minval);
            else dtemp = factor * matrix->weights[aa][pos];
            matrix->weights[aa][pos] = round(dtemp);
      }
   }  /*  end of for pos */
}  /* end of positive_matrix */
/*=====================================================================*/
/*    Find patterns & add them to output file containing the matrix    */
/*    There is at most one pattern per matrix position, and it will    */
/*    have only one non-x position in it. Patterns may be made more    */
/*    general later on                                                 */

void add_patterns(matrix, Fpa)
Matrix *matrix;
FILE *Fpa;
{
   int pos, aa, npos, naa, i;
   int aas[AASALL];
   char pattern[MAXLINE], ctemp[5], *ptr;

   /*    Change MATRIX to PATMAT on id line    */
   strcpy(pattern, matrix->id);
   ptr = strtok(pattern, ";");
   if (ptr != NULL) strcat(pattern, "; PATMAT");
   fprintf(Fpa, "ID   %s\n", pattern);
   fprintf(Fpa, "AC   %s\n", matrix->ac);
   fprintf(Fpa, "DE   %s\n", matrix->de);
   fprintf(Fpa, "PA   %s\n", matrix->ma);
   for (pos = 0; pos < matrix->width; pos++)
   {
      npos = naa = 0;
      pattern[0] = '\0';
      for (aa=1; aa <= 20; aa++)
      {
         if (matrix->weights[aa][pos] >= PatternCutoff)
         {
            aas[naa] = aa;
            naa++;
         }
      }
      if (naa == 1)
      {
         for (i=0; i < pos; i++) strcat(pattern, "x");
         ctemp[0] = aa_btoa[ aas[0] ]; ctemp[1] = '\0';
         strcat(pattern, ctemp);   /* this is i = pos */
         for (i=pos+1; i < matrix->width; i++) strcat(pattern, "x");
         npos++;
      }
      else if (naa > 1)
           {
              for (i=0; i < pos; i++) strcat(pattern, "x");
              strcat(pattern, "[");
              ctemp[1] = '\0';
              for (i=0; i < naa; i++)
              {
                 ctemp[0] = aa_btoa[ aas[i] ];
                 strcat(pattern, ctemp);
              }
              strcat(pattern, "]");
              for (i=pos; i < matrix->width; i++) strcat(pattern, "x");
              npos++;
           }
      if (npos > 0) fprintf(Fpa, "%s\n", pattern);
   }
   fprintf(Fpa, "//\n");
}  /* end of add_patterns */
++)
         new->marg[row] += new->value[row][col];
     total += new->marg[row];
   }

   return(new);
}  /* end of load_qij */

/*=======================================================================
    Bill Bruno's character counts:
	creates file "data" with sequences
	executes program "rind" & wablimps-3.9/blimps/pattern.c000064400001460000012000000341350774312250100162640ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* pattern.c: */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

/*	system headers not in global.h   */
#include 
/*	blimps library headers  */
#include 
#include 
#include 	/* includes sequences.h, output.h */
#include 	/* includes pattern.h */
#include 
#include 


/*
 * Exported variables and data structures
 */

Boolean UsePatterns = FALSE;

/*
 * Local variables and data structures
 */

SkipList Patterns;
Boolean ListInitialized = FALSE;

#define PATTERN_ARRAY_START 30
#define PATTERN_ARRAY_INC 20

/*
 * Function definitions
 */

static Boolean headers_match();
static Boolean search_for_pattern();
static Pattern *scan_pattern();
static void find_residues();
static PatternResidue *parse_residue();
static void print_patterns();
static void print_pattern();
static void print_residue();
static int print_residue_for_list();



/*
 * scan_patterns
 *
 * scans in the pattern entries from the pattern file for the given
 * matrix and puts them in the matrix.
 * 
 */

void 
scan_patterns(matrix)
     Matrix *matrix;
{
  int max_patterns_for_array = 0;
  int num_patterns_seen = 0;
  Boolean cont;
  Pattern **patterns;
  Pattern **tmp_ptr;
  SkipList residue_list;

  char *pat;

  FILE *pat_file;

  if (! UsePatterns) {
    matrix->patterns = NULL;
    return;
  }

  /* is the pattern already here? */
  if (matrix->patterns != NULL) {
    /* if so, then do nothing */
    return;
  }
  else {
    /* otherwise, we need to read in the patterns */

    /* allocate space for the array of pointers to patterns */
    CheckMem(
	     patterns = (Pattern **) malloc(sizeof(Pattern *) * PATTERN_ARRAY_START)
	     );
    
    max_patterns_for_array = PATTERN_ARRAY_START;
    num_patterns_seen = 0;

    /* prepare the residue list for storing residues. */
    /* this is done outside of the call to scan_pattern() so as to cut */
    /* down on initialization/cleanup time */
    /* Note that Patterns is global to save some startup/cleanup time */
    if (! ListInitialized) {
      Patterns = NewSL(residue_compare_function, NULL, ALLOW_DUPLICATES);
      ListInitialized = TRUE;
    }
    residue_list = Patterns;

/*printf("Searching for: %s\n", matrix->number);*/

    /* find the pattern entry that matches the PSSM */
    if (! headers_match(matrix)) {
/*printf("Pattern not found\n");*/
      rewind_file(PATTERN_FILES);

      if (! search_for_pattern(matrix)) {
	sprintf(ErrorBuffer,
		"Unable to find pattern for PSSM %s\n", matrix->number);
	ErrorReport(WARNING_ERR_LVL);

	matrix->patterns = NULL;
	return;
      }
    }
    
    /* file should be positioned somewhere in the pattern header */
    cont = FALSE;
    pat_file = get_file(PATTERN_FILES);
    /* there should be something there regardless */
    /* probably should mention bad file format */
    assert(pat_file != NULL);

    /* scan until after the PA line */
    while (fgets(Buffer, LARGE_BUFF_LENGTH, pat_file) &&
	   !((Buffer[0] == 'P') && (Buffer[1] == 'A')));

    /* read in each pattern line until "//" is seen */

    cont = TRUE;    do {
      /* read in a line */
      fgets(Buffer, LARGE_BUFF_LENGTH, pat_file);

      /* if it is "//" then we are done */
      if ((Buffer[0] == '/') && (Buffer[1] == '/')) {
	cont = FALSE;
      }
      else {
	/* shift to the beginning of the pattern */
	pat = get_token(Buffer);

	/* put a null at the end of the pattern */
	remove_trailing_whitespace(pat);
	
	/* increase the size if need be */
	/* (adding one early to allow room for the NULL ptr */
	if (num_patterns_seen >= (max_patterns_for_array-1)) {
	  max_patterns_for_array += PATTERN_ARRAY_INC;
	  CheckMem(
		   tmp_ptr = (Pattern **) realloc(patterns,
						  max_patterns_for_array *
						  sizeof(Pattern *))
		   );
	  patterns = tmp_ptr;
	}

	/* make null for safety */
	patterns[num_patterns_seen] = NULL;
	patterns[num_patterns_seen+1] = NULL;

	/* scan in this pattern and place it in the array */
	patterns[num_patterns_seen] = scan_pattern(pat, residue_list);

	/* only move ahead if something was scanned */
	if (patterns[num_patterns_seen] != NULL) {
	  num_patterns_seen++;
	} 
      }
    } while (cont);

    /* make the last position NULL */
    patterns[num_patterns_seen] = NULL;

    /* the patterns have been read in and we can update the matrix */
    matrix->patterns = patterns;
    
/*print_patterns(matrix->patterns);*/

    assert(NumInSL(residue_list) == 0);

  }
}

Boolean
pattern_matches(seq, compare_start, pattern)
     Sequence *seq;
     int compare_start;
     Pattern *pattern;
{
  Residue *sequence;
  int seq_length;
  PatternResidue *p;
  Boolean ok;
  int x, num, offset;

  sequence = seq->sequence;
  seq_length = seq->length;


  /* optimize for the common case of one residue */
  if (pattern->num_residues == 1) {
    /* get first residue */
    p = pattern->pat;
    
    /* check the residue(s) */
    
    offset = p->offset;
    
    /* only check if it is ok if it is within the sequence */
    if (((compare_start+offset) < seq_length) &&
	((compare_start+offset) >= 0)) {
      
      num = p->num_residues;
      
      /* optimize for the common case by only checking the one */
      if (num == 1) {
	/* this saves an assignment and an additional compare and a
	   loop back*/
	if (aa_btoa[sequence[compare_start+offset]] ==
	    toupper(p->residues[0])) {
	  /* can return true here since there is only one residue */
	  return TRUE;
	}
      }
      else {
	for (x=0; !ok && xresidues[x])) {
	    /* can return true here since there is only one residue */
	    return TRUE;
	  }
	}
      }
      
      /* if we have reached this point nothing matched */
      return FALSE;
    }
  }
  /* otherwise do the general case */
  else {

    /* get first residue */
    p = pattern->pat;
    
    /* while the residue is there (the pointer != NULL) */
    while (p != NULL) {
      /* check the residue(s) */
      
      offset = p->offset;
      
      /* only check if it is ok if it is within the sequence */
      if (((compare_start+offset) < seq_length) &&
	  ((compare_start+offset) >= 0)) {
	ok = FALSE;
	
	num = p->num_residues;
	
	/* optimize for the common case by only checking the one */
	if (num == 1) {
	  /* this saves an assignment and an additional compare and a
	     loop back*/
	  if (aa_btoa[sequence[compare_start+offset]] ==
	      toupper(p->residues[0])) {
	    ok = TRUE;
	  }
	}
	else {
	  for (x=0; !ok && xresidues[x])) {
	      ok = TRUE;
	    }
	  }
	}
	
	/* if it/they didn't match, return FALSE */
	if (! ok) {
	  return FALSE;
	}
      }
      
      /* get the next residue */
      p = p->next;
    }
  }
  return TRUE;
}


/*************************************************************************
 *************************************************************************
 *
 *             Local Functions
 *
 *************************************************************************
 *************************************************************************
 */



/*
 * residue_compare_function
 *
 * compare two residue structures.  This is for the skiplist ordering.
 * The shorter residues are placed first, then they are sorted by
 * alphabetical order.
 *
 */
  
int
residue_compare_function(res1, res2)
     PatternResidue *res1;
     PatternResidue *res2;
{
  if (res1->num_residues != res2->num_residues) {
    return res1->num_residues - res2->num_residues;
  }
  else {
    return strcmp(res1->residues, res2->residues);
  }
  assert(0);
}


/* 
 * headers_match
 *
 * scan the pattern file from the current point and if the matrix and
 * header match (have the same base name) return true.
 *
 */

static Boolean 
headers_match(matrix)
     Matrix *matrix;
{
  char *tmp;
  FILE *pat_file;


  /* foreach of the pattern files */
  while ((pat_file = get_file(PATTERN_FILES)) != NULL) {
    while (fgets(Buffer, LARGE_BUFF_LENGTH, pat_file) && !feof(pat_file)) {
      /* if we are past the header, stop and return FALSE */
      if ((Buffer[0] == '/') && (Buffer[1] == '/')) {
	return FALSE;
      }
      /* otherwise, if it is the AC line, check */
      else if ((Buffer[0] == 'A') && (Buffer[1] == 'C')) {
	/* get the number of the pattern.  Be sure to truncate the ';' */
	tmp = get_token(Buffer);
	tmp = get_token(NULL);
	if (tmp[strlen(tmp)-1] == ';') {
	  tmp[strlen(tmp)-1] = '\0';
	}
	
	/* must skip over the BL/MA stuff (so add two) */
	return (strcmp(tmp+2, (matrix->number)+2) == 0);
      }  
      /* otherwise, skip it and go to the next line */
    }
  }
}

/*
 * search_for_pattern
 *
 * scan from the current file position in the pattern file searching
 * for the pattern.  If none found, return FALSE, otherwise return
 * TRUE.
 *
 */

static Boolean
search_for_pattern(matrix)
     Matrix *matrix;
{
  FILE *pat_file;
  char *tmp;

  /* foreach of the pattern files */
  while ((pat_file = get_file(PATTERN_FILES)) != NULL) {
    while (fgets(Buffer, LARGE_BUFF_LENGTH, pat_file) && !feof(pat_file)) {
      if ((Buffer[0] == 'A') && (Buffer[1] == 'C')) {
	/* get the number of the pattern.  Be sure to truncate the ';' */
	tmp = get_token(Buffer);
	tmp = get_token(NULL);
	if (tmp[strlen(tmp)-1] == ';') {
	  tmp[strlen(tmp)-1] = '\0';
	}
	
	if ((strcmp(tmp+2, (matrix->number)+2) == 0)) {
	  return TRUE;
	}
      }
    }
  }
  
  /* reached the end of the file, so return FALSE */
  return FALSE;
}





/*
 * scan_pattern
 *
 * scan the current pattern (the string is only stuff in the pattern)
 * and return a pointer to the pattern data structure
 *
 * NULL is returned if there are no residues for the pattern
 * 
 */

static Pattern *
scan_pattern(pat, residue_list)
     char *pat;
     SkipList residue_list; /* declared externally for reuse to save time */
				/* it should start and end empty */
{
  Pattern *pattern;
  PatternResidue *p, *s;
  int start;

  assert(NumInSL(residue_list) == 0);

  CheckMem(
	   pattern = (Pattern *) malloc(sizeof(Pattern))
	   );

  /* get all the residues in the pattern and place them in the ordered list */
  find_residues(pat, residue_list);
  /* the list is now full of residues */

  /* prints the contents of the ordered residues list */
  /* DoForSL(residue_list, print_residue_for_list, NULL); */

  if (NumInSL(residue_list) == 0) {
    free(pattern);
    return NULL;
  }

  pattern->num_residues = NumInSL(residue_list);

  p = Nth(residue_list, 0);
  DeleteSL(residue_list, p);

  start = p->offset;
  p->offset = 0;
  pattern->pat = p;
  pattern->beg_offset = start;

  while (NumInSL(residue_list) != 0) {
    s = Nth(residue_list, 0);
    DeleteSL(residue_list, s);
    s->offset = s->offset - start;
    p->next = s;
    p = s;
  }

  p->next = NULL; /* just being safe */

  assert(NumInSL(residue_list) == 0);

  return pattern;
}



static void
find_residues(pat, residue_list)
     char *pat;
     SkipList residue_list;	/* to fill with the residues */
{
  int offset = 0;
  PatternResidue *patres;

  while (pat[0] != '\0') {
    if ((pat[0] != 'x') && (pat[0] != 'X')) {
      patres = parse_residue(offset, &pat);
      InsertSL(residue_list, patres);
    }
    offset++;
    pat++;
  }
}


/*
 *
 * parse_residue
 *
 * creates a pattern residue to be added to the pattern.  The residue
 * at the current possition is the one used.  THIS DOES NOT CHECK THAT
 * THE RESIDUE IS A VALID RESIDUE (eg 'X').
 *
 */

static PatternResidue *
parse_residue(offset, pat)
     int offset;
     char **pat;		/* this is so that the possition in the */
				/* pattern string is updated */
{
  PatternResidue *pr;
  int num = 0;
  char *tmp;

  if (**pat != '[') {		/* it is only one residue */

    /* declare space for the pattern residue and the character string */
    CheckMem(
	     pr = (PatternResidue *) malloc(sizeof(PatternResidue))
	     );
    CheckMem(
	     pr->residues = (char *) malloc(sizeof(char)*2)
	     );

    /* initialize the structure */
    pr->offset = offset;
    pr->num_residues = 1;
    pr->next = NULL;
    
    /* set the residues string */
    pr->residues[0] = **pat;
    pr->residues[1] = '\0';
    
    /* don't move the move the pattern pointer/marker ahead since it
       is done once in the calling function. */

    return pr;
  }
  else {			/* it is more than one residue */
    num = 0;
    tmp = *pat;
    tmp++;			/* move over the '[' */
    while (*tmp != ']') {
      num++;
      tmp++;
    }
    *tmp = '\0';		/* make place a null to end the residues */
    
    /* declare space for the pattern residue and the character string */
    CheckMem(
	     pr = (PatternResidue *) malloc(sizeof(PatternResidue))
	     );
    CheckMem(
	     pr->residues = (char *) malloc(sizeof(char)*(num+1))
	     );
    
    /* initialize the structure */
    pr->offset = offset;
    pr->num_residues = num;
    pr->next = NULL;

    /* set the residues string */
    strcpy(pr->residues, (*pat)+1);
    pr->residues[num] = '\0';

    /* move the pattern pointer/marker ahead, all but one.  It is
       moved ahead one position automatically */
    *pat = *pat + 1 + num;

    return pr;
  }

  assert(0);			/* shouldn't get here */

}


static void
print_patterns(patterns)
     Pattern **patterns;
{
  int x;
  for (x = 0; patterns[x] != NULL; x++) {
    printf("%d: ", x);
    print_pattern(patterns[x]);
  }
}
static void
print_pattern(pattern)
     Pattern *pattern;
{
  if (pattern == NULL) {
    printf("(null)\n");
  }

  printf("%d: ", pattern->beg_offset);
  print_residue(pattern->pat);
}

void
static print_residue(pat)
     PatternResidue *pat;
{
  if (pat == NULL) {
    printf(";\n");
    return;
  }
  printf("(%d, [%s]) ", pat->offset, pat->residues);
  print_residue(pat->next);
}

int
static print_residue_for_list(pat, arg)
     PatternResidue *pat;
     void *arg;
{
  print_residue(pat);
  return SL_CONTINUE;
}

/* Change log information follows. */
/* $Log: pattern.c,v $
 * Revision 2.2010  1995/07/28  23:47:14  billa
 * Added new convert method and pattern matching and minor updates merged.
 *
 */

this pattern and place it in the array */
	patterns[num_patterns_seen] = scan_pattern(pat, residue_list);

	/* only move ahead if something was scanned */
	if (patterns[num_patterns_seen] != NULL) {
	  num_patterns_seen++;
	} 
      }
    } while (cont);

    /* make the last position NULL */
    patterns[num_patterns_seen] = NULL;

    /* the patterns have been read in and we can update the matrix */
    matrix->pablimps-3.9/blimps/prints2blocks.c000064400001460000012000000611220774312250100174020ustar00jorjastaff00000400000027/* COPYRIGHT 1995-2001 Fred Hutchinson Cancer Research Center */
/* This program will convert a Prints protein motifs database to a 
   blocks database. By Shmuel Pietrokovski */

/* Feb 8 96' ver 5 (previous version 4)
   If verbose flag is on, program outputs to stderr the lines it reads
   until it reaches the first line of a prints entry ("gc; ..."). This 
   is implemented in order to catch errors in the number of prints in an 
   entry (line "gn; ..). If the number is smaller than the actual number the
   program would not read the last prints. If the verbose flag is on these
   prints will be shown, if there are no such errors only the entry-separating
   lines (if any) will be shown.

 Feb 8 96' ver 4 (previous version 3)
   Changed in main the loop calling transform_a_prints_entry. The program 
   now doesn't exit when error is encountered but reports it and goes on to
   the next entry. Depending on the error, some motifs from the erroneus entry
   might be transformed. The data for these in the .info file might not be
   accurate.

 Aug 21 95' ver 3 (previous version 2)
   PRINTS version 9 introduced an accession field (gx) the accession is 7
   characters long, begins with "PR" and is followed by 5 digits. This is
   used as the blocks accession (previously the block accession was assigned
   according to the order of the entry int database 
*/

#define EXTERN


#include 

#define OK    0
#define ERROR 1
#define MAXNAME 80
#define MAXLINELEN 5000

/* variables set by the configuration file in blimps program */

int BlockToMatrixConversionMethod=2 ; /* default method is two */


int    entries=0, motifs=0 ;
Boolean verbose=FALSE ;
char   transform_a_prints_entry() ; 

/*
 * main
 */

int main(argc, argv)
     int argc;
     char *argv[];
{

   FILE   *inpf, *outf[2] ;
   char   inpfname[MAXNAME], outfname[2][MAXNAME] ;

/* ---------------1st arg = Prints database file name ------------------------*/
   if (argc > 1)
      strcpy(inpfname, argv[1]);
   else
      {
      printf(
       "\nEnter name of input file (Prints protein motifs database): ");
      gets(inpfname);
      }

   if ( (inpf=fopen(inpfname, "r")) == NULL)
      {
      printf("\nCannot open input file %s\n", inpfname);
      exit(-1);
      }

/* ---------------2nd arg = verbose flag state, unprompted ------------------*/
   if (argc > 2) verbose = atoi(argv[2]);

/* open output files */

   sprintf(outfname[0], "%s.dat", inpfname) ;

   if ( (outf[0]=fopen(outfname[0], "w")) == NULL)
      {
      printf("\nCannot open output file %s\n", outfname[0]);
      exit(-1);
      }

   sprintf(outfname[1], "%s.info", inpfname) ;

   if ( (outf[1]=fopen(outfname[1], "w")) == NULL)
      {
      printf("\nCannot open output file %s\n", outfname[1]);
      exit(-1);
      }

   fprintf(outf[1],
      "Block family PRINTS entry name    # of   Cross references to -\n") ;
   fprintf(outf[1],
      "                                  blocks PROSITE    BLOCKS     PRINTS\n"
          ) ;
   fprintf(outf[1],
      "------------ -------------------- ------ ---------- ---------- ----------\n") ;


                                             /* go through all entries in db */
/* note that each entry usually has a number of motifs each of which is 
   transformated into a block. The transformation is done in the procedure.
   A Prints entry, termed finger print, is analogous to a block family and each
   finger print motif is analogous to a block.                               */

                             /* read a Prints entry and write out its blocks */
  while (! feof(inpf))
      if (transform_a_prints_entry(inpf,outf[0],outf[1]) == OK) entries++ ;

  fclose(inpf) ; 
  fclose(outf[0]) ; 
  fclose(outf[1]) ; 

  printf("\n%d entries with %d motifs read from Prints database %s\n", 
         entries, motifs, inpfname) ;
  printf("and written as blocks in file %s.\n", outfname[0]) ;
  printf("Information about the processed entries written in file %s.\n", 
         outfname[1]) ;

  exit(0) ;

}  /* end of main */



/****************************************************************************
 *
 * Read a PRINTS entry from the input file, for each motif put all relevant 
 * data in a block structure and write it out to the output file. 
 * While doing that the program also writes to another file some general 
 * information about each translated entry - its name, the block family name 
 * assigned to it, how many motifs (blocks) did it comprise of, and cross
 * references (if any) to BLOCKS and PROSITE entries. 
 * 
 ****************************************************************************/

char transform_a_prints_entry(dbin,dbout,outf2)

#define BLOCK_SEQUENCE_INCREASE_SIZE 50   /* default number of sequences to */
                                  /* allocate since the number of sequences */
                                  /* in the entries motifs is not specified */
                                  /* when starting to read them.            */


FILE   *dbin, *dbout, *outf2 ;

{
   Block    *block ;
   char     line[MAXLINELEN], word[MAXLINELEN], entry_name[MAXLINELEN] ;
   char     fam_acc[8] ;
   char     PS_crssref[11] = "-", BL_crssref[11] = "-" ;
   char     PR_crssref[MAXLINELEN] = "" ;
   char     *ptr ;
   int      i1, i2, num_blocks, num_seqs, rc, max_pos, min_pos, temp ;
   Boolean  SIMPLE_entry ;
   Sequence *sequence_pointer ;
   Residue  *residue_pointer ;


             /* read until a prints entry first line - begins with a "gc; " */
/* only the first two chars compared here and elsewhere in the program because
  a few typos (colon ":" instead of semi colon ";") were found in PRINTS7.0 */ 

   while((fgets(line, MAXLINELEN, dbin)) != NULL && 
         strncmp(line, "gc;", 2) != 0) 
   {
      if (verbose) fprintf(stderr, "%s", line) ;
      /*   Check for extra motifs from previous entry;
	   the gn; COMPOUND() line may not
	   match the actual number of motifs in the entry   */
      if (strncmp(line, "fc;", 2) == 0)
      {
          printf("Extra motif: %s\n", line);
      }
   }

                           /* check if required line or end of file reached */
   if (strncmp(line, "gc;", 2) != 0) return(-1) ;

                              /* get the entry's name, 2nd word in gc line */
   ptr = get_token(line) ;

   if ((ptr = get_token(NULL)) == NULL) 
      {
      printf("Error ! Problem in format of Prints entry gc line,\n") ;
      printf("can't find the general code\n") ;
      return(-2) ;
      }

   strcpy(entry_name,ptr) ;

               /* read until a prints accession line - begins with a "gx; " */
   while((fgets(line, MAXLINELEN, dbin)) != NULL && 
         strncmp(line, "gx;", 2) != 0) ;

                           /* check if required line or end of file reached */
   if (strncmp(line, "gx;", 2) != 0)
      {
      printf(
           "Error ! Accession line (gx; ...) not found in Prints entry %s.\n",
             entry_name) ; 
      return(-3) ;
      }

                           /* get the entry's accession, 2nd word in gc line */
   ptr = get_token(line) ;

   if ((ptr = get_token(NULL)) == NULL) 
      {
      printf("Error ! Problem in format of Prints entry %s gx line.\n",
             entry_name) ;
      printf("Can't find the accession code.\n") ;
      return(-2) ;
      }

            /* check that the accession code in no longer than 7 characters */ 
   if ((int) strlen(ptr) > 7)
      {
/*
      printf(
      "Error ! Accession code of Prints entry %s (\"%s\") is too long (>7).\n",
             entry_name) ;
      return(-2) ;
*/
      ptr[7] = '\0';
      }
   else if ((int) strlen(ptr) < 7)    /* add "_"s until code is 7 chars long*/
      {
      printf("Note - the accesion code of Prints %s (\"%s\")\n",
             entry_name, ptr) ;
      printf("is shorter than 7 characters.\n") ;

      for (i1=(int) strlen(ptr); i1<=7; i1++) ptr[i1] = '_' ;
      ptr[i1] = '\0' ;
      }

   strcpy(fam_acc,ptr) ;

              /* read until a prints entry type line - begins with a "gn; " */
   while((fgets(line, MAXLINELEN, dbin)) != NULL && 
         strncmp(line, "gn;", 2) != 0) ;

                           /* check if required line or end of file reached */
   if (strncmp(line, "gn;", 2) != 0)
      {
      printf("Error ! Type line (gn; ...) not found in Prints entry %s.\n",
             entry_name) ; 
      return(-3) ;
      }

   if (strstr(line,"SIMPLE") != NULL)           /* a simple entry - 1 block */
      {
      num_blocks = 1 ;
      SIMPLE_entry = TRUE ;
      }
   else if (strstr(line,"COMPOUND") != NULL)/* a compound entry - blocks > 1*/
      {
                                        /* get the entry's number of motifs */
      if ((ptr = strstr(line, ")")) == NULL) 
         {
         printf(
           "Error ! Problem in format of gn line in Prints entry %s -\n",
                entry_name) ; 
         printf("%s", line) ;
         printf("can't find closing )\n") ;
         return(-3) ;
         }

      *ptr = '\0' ;
      if ((ptr = strstr(line,"(")) == NULL) 
         {
         printf("Error ! Problem in format of gn line, can't find (\n") ;
         printf("in Prints entry %s.\n", entry_name) ; 
         return(-3) ;
         }

      num_blocks = atoi(ptr + 1) ;  /* convert number of motifs to a number */

      SIMPLE_entry = FALSE ;
      }
   else
      {
      printf("Error ! Type line (gn; ...) is neither SIMPLE or COMPOUND\n") ;
      printf("in Prints entry %s.\n", entry_name) ; 
      return(-3) ;
      }

                                               /* allocate space for blocks */
   CheckMem(block = (Block *) calloc(num_blocks, sizeof(Block))) ;

  /* save blocks general code and accessions, give the values common to all */

   for(i1=0; i1 < num_blocks; i1++)
      {
      if (num_blocks > 1)
                   /* 65+i1 translates 0 into ascii value of A, 1 to B etc. */
         sprintf(block[i1].number, "%s%c", fam_acc, 65+i1) ;
      else      /* No letter suffix for accessions of single block families */
         sprintf(block[i1].number, "%s", fam_acc) ;
      sprintf(block[i1].ac, "%s;", block[i1].number) ;
      sprintf(block[i1].id, "%s; BLOCK", entry_name) ;

      block[i1].num_clusters = block[i1].max_clusters = 1 ; 
      block[i1].motif[0] = '\0';
      block[i1].percentile = 0 ;
      block[i1].strength = 0 ;
      }

       /* read until a prints descriptive title line - begins with a "gt; " */
   while((fgets(line, MAXLINELEN, dbin)) != NULL && 
         strncmp(line, "gt;", 2) != 0) ;

                           /* check if required line or end of file reached */
   if (strncmp(line, "gt;", 2) != 0)
      {
      printf("Error ! title line (gt; ...) not found in Prints entry %s.\n",
             entry_name) ; 
      return(-4) ;
      }

   if ((ptr=strchr(line,'\n')) != NULL) *ptr = '\0' ;     /* get rid of EOL */

   ptr = line + 4 ;       /* get description - begining in 5th char of line */

                                                 /* save blocks description */
   for(i1=0; i1 < num_blocks; i1++) 
      strncpy(block[i1].de, ptr, SMALL_BUFF_LENGTH) ;
                           /* in case word is longer than SMALL_BUFF_LENGTH 
                                      and thus the last char copied isnt \0 */ 
   block[i1].de[SMALL_BUFF_LENGTH-1] = '\0' ;

            /* read until a prints final motifs line - begins with a "fm; " */
   while((fgets(line, MAXLINELEN, dbin)) != NULL && 
         strncmp(line, "fm;", 2) != 0) 
      if (strncmp(line, "gp;", 2) == 0) /* search for cross reference lines */
      {
         if (strstr(line, "PROSITE") != NULL) /* cross reference to PROSITE */ 
	    {
              /* get the cross referenced entry's name, 3rd word in gp line */
            ptr = get_token(line) ;
            ptr = get_token(NULL) ;
            if ((ptr = get_token(NULL)) != NULL) strncpy(PS_crssref,ptr,11) ;
	    }
         else
         if (strstr(line, "BLOCKS") != NULL)   /* cross reference to BLOCKS */ 
	    {
              /* get the cross referenced entry's name, 3rd word in gp line */
            ptr = get_token(line) ;
            ptr = get_token(NULL) ;
            if ((ptr = get_token(NULL)) != NULL) strncpy(BL_crssref,ptr,11) ;
	    }
         else
         if (strstr(line, "PRINTS") != NULL)   /* cross reference to PRINTS */ 
	    {
/* get the cross referenced entries name, begining with 3rd word in gp line */
            ptr = get_token(line) ;
            ptr = get_token(NULL) ;
            while ((ptr = get_token(NULL)) != NULL)
	       {
              /* strip possible separator (";", "," etc.) from end of word */
               if (!(isalnum(ptr[(int) strlen(ptr) - 1]))) 
                  ptr[(int) strlen(ptr) - 1] = '\0' ;
               strcat(PR_crssref, ptr) ;
               strcat(PR_crssref, " ") ;
	       }
	    }
      }

                           /* check if required line or end of file reached */
   if (strncmp(line, "fm;", 2) != 0)
      {
      printf(
        "Error ! Final motifs line (fm; ...) not found in Prints entry %s.\n",
             entry_name) ; 
      return(-5) ;
      }

                                             /* write out entry information */
   fprintf(outf2, "%-12s %-20s %5d  %-10s %-10s %s\n", 
          fam_acc, entry_name, num_blocks, PS_crssref, BL_crssref, 
          PR_crssref) ;

   for(i1=0; i1 < num_blocks; i1++)                       /* for each motif */
      {

      min_pos = 10000 ;
      max_pos = 0 ;

              /* read until a final motif code line - begins with a "fc; " */
      while((fgets(line, MAXLINELEN, dbin)) != NULL && 
            strncmp(line, "fc;", 2) != 0) ;

                           /* check if required line or end of file reached */
      if (strncmp(line, "fc;", 2) != 0)
         {
         printf("Error ! final motif code line (fc; ...) not found in\n") ;
         printf("motif %d of Prints entry %s.\n", i1+1, entry_name) ; 
         return(-6) ;
         }

                               /* check that the motif belongs to the entry 
                                   (entry name is in the motif's code line) */
      if (strstr(line, entry_name) == NULL)
         {
         printf("Error ! Problem in motif %d of Prints entry %s.\n", 
                i1+1, entry_name) ; 
         printf(
     "  The motif's code line (fc; ...) does not contain the entry name = %s\n",
		entry_name) ;
         printf("%s", line) ;
         return(-6) ;
         }

             /* read until a final motif length line - begins with a "fl; " */
      while((fgets(line, MAXLINELEN, dbin)) != NULL && 
            strncmp(line, "fl;", 2) != 0) ;

                           /* check if required line or end of file reached */
      if (strncmp(line, "fl;", 2) != 0)
         {
         printf("Error ! final motif length line (fl; ...) not found in\n") ;
         printf("motif %d of Prints entry %s.\n", i1+1, entry_name) ; 
         return(-6) ;
         }

                             /* get the motif's length, 2nd word in fl line */
      ptr = get_token(line) ;

      if ((ptr = get_token(NULL)) == NULL || 
          (block[i1].width = atoi(ptr)) <= 0) 
         {
         printf(
       "Error ! Problem in format of final motif length line (fl; ...) in\n") ;
         printf("motif %d of Prints entry %s.\n", i1+1, entry_name) ; 
         return(-6) ;
         }

                        /* following part adapted from 
                            blimps procedure read_block_body by Bill Alford */

                                 /* since number of sequences not known yet */
      block[i1].max_sequences = BLOCK_SEQUENCE_INCREASE_SIZE ;
 
        /* allocate space for all the Sequences of the block sequence array */
      CheckMem(
            sequence_pointer = 
            (Sequence *) calloc(block[i1].max_sequences, sizeof(Sequence))) ;

                                    /* initialize the block sequences array */
      block[i1].sequences = sequence_pointer;

                                         /* allocate space for the clusters */
      CheckMem(block[i1].clusters = (Cluster *) 
                            calloc(block[i1].max_clusters, sizeof(Cluster))) ;

                                         /* allocate space for all residues */
      CheckMem(
            residue_pointer = (Residue *)  
            calloc(block[i1].width * block[i1].max_sequences,
                                                         sizeof(Residue))) ;

                                       /* initialize the residues 2-d array */
      CheckMem(
            block[i1].residues = (Residue **) calloc(block[i1].max_sequences,
                                                       sizeof(Residue *))) ;

	                                /* initialize sequences and residues */
      for(i2=0; i2 block[i1].sequences[num_seqs].length) 
               {
              /* BIG Error, an undocumented return value from read_sequence */
               printf(
              "read_a_prodom_entry(): Error reading sequence %s in block %s,",
 	             block[i1].sequences[num_seqs].name,block[i1].number) ;

               printf("Undocumented return value, %d, from read_sequence().\n",
                      rc) ;
               } /* else, ret_value == seq.length, OK */

                 /* sequences have no weights give all equal weights of 100 */
            block[i1].sequences[num_seqs].weight =  100.0 ;

       /* continue reading the rest of the sequence line - sequence name, 
          start position and distance from previous motif or sequence start */

                                               /* read next word - seq name */
            if ((ptr = get_token(NULL)) == NULL)
               {
               printf("Error ! Problem in format of sequence line %d in\n", 
                      num_seqs+1) ;
               printf("motif %d of Prints entry %s.\n", i1+1, entry_name) ; 
               printf("Sequence name not found in line.\n") ; 
               return(-7) ;
               }
 
            strncpy(block[i1].sequences[num_seqs].name, ptr, 
                    SMALL_BUFF_LENGTH) ;

                           /* in case word is longer than SMALL_BUFF_LENGTH 
                                      and thus the last char copied isnt \0 */ 
            block[i1].sequences[num_seqs].name[SMALL_BUFF_LENGTH-1] = '\0' ; 

                                         /* read next word - start position */
            if ((ptr = get_token(NULL)) == NULL ||
                (block[i1].sequences[num_seqs].position = atoi(ptr)) <= 0) 
               {
               printf("Error ! Problem in format of sequence line %d (%s) in\n", 
                      num_seqs+1, block[i1].sequences[num_seqs].name) ;
               printf("motif %d of Prints entry %s.\n", i1+1, entry_name) ; 
               printf("Error reading sequence start position.\n") ; 
               return(-7) ;
               }

            if (SIMPLE_entry)
               temp = block[i1].sequences[num_seqs].position ; 
     /* SIMPLE entries don't have the distance field in their single motif */
            else                              /* read next word - distance */
	       {
               if ((ptr = get_token(NULL)) == NULL) 
                  {
                  printf("Error ! Problem in format of sequence line %d (%s) in\n", 
                         num_seqs+1, block[i1].sequences[num_seqs].name) ;
                  printf("motif %d of Prints entry %s.\n", i1+1, entry_name) ; 
                  printf("Error reading sequence distance from last motif.\n") ; 
                  return(-7) ;
                  }

               temp = atoi(ptr) ; /* (no simple test for the distance value 
                                because in PRINTS it can also be negative) */
	       }

                          /* find min and max start positions of sequences */
            if (temp > max_pos) max_pos = temp ;
            if (temp < min_pos) min_pos = temp ;

            num_seqs++ ;
            }
                           /* check if required line or end of file reached */
      if (strncmp(line, "bb;", 2) != 0)
         {
         printf("Error ! End of file reached while reading") ;
         printf("motif %d of Prints entry %s.\n", i1+1, entry_name) ; 
         return(-8) ;
         }

      block[i1].num_sequences = block[i1].max_sequences = num_seqs ;

          /* assign the sequences to the cluster (space has been allocated) */

      block[i1].clusters[0].num_sequences = block[i1].num_sequences ;

      block[i1].clusters[0].sequences = &(block[i1].sequences[0]) ;



/* add min and max distance from previous block (sequence start) to AC line */
      sprintf(word, " distance from previous block=(%d,%d)", 
              min_pos, max_pos);
      strcat(block[i1].ac, word) ;

      sprintf(block[i1].bl, "adapted from PRINTS entry; width=%d; seqs=%d;",
              block[i1].width, block[i1].num_sequences) ;

/*output_block(block[i1], stdout) ;*/ 
      output_block(block[i1], dbout) ;        /* write block to output file */

      motifs++ ;                       /* update number of blocks processed */

                            /* free memory allocated to the block structure */
      free(block[i1].residues);
      free(block[i1].clusters);
      free(block[i1].sequences[0].sequence);
      free(block[i1].sequences);
      }  /* end for i1 = num_blocks */

                    /* free memory allocated to the arrays block structures */
   free(block);

   return(OK) ;
} /* end of transform_a_prints_entry */

d of Prints entry %s.\n", i1+1, entry_name) ; 
         return(-6) ;
         }

                             /* get the motif's length, 2nd word in fl line */
      ptr = get_token(line) ;

      if ((ptr = get_token(NULL)) == NULL || 
          (block[i1].width = atoi(ptr)) <= 0) 
         {
         printf(
       "Error ! Problem in format of final motif length line (fl; ...) in\n") ;
         printf("motif %d of Prints enblimps-3.9/blimps/protomat.c000064400001460000012000000472600774312250100164570ustar00jorjastaff00000400000027/*=======================================================================
(C) Copyright 1999, Fred Hutchinson Cancer Research Center
     protomat.c
     motmisc.c    Miscellaneous PROTOMAT routines.
	minus those routines duplicated in blimps
-------------------------------------------------------------------------
   2/11/99  J. Henikoff
   6/25/00  Updates to get_ids() and check_entry() for multi-part seq ids
=========================================================================*/
#include 
#include 
#include 
/*	blimps library header, has stdio, etc.  */
#include 

/*---- Global scoring matrix , order is :
		  A R N D C Q E G H I L K M F P S T W Y V X   -----------*/

/* BLOSUM60 matrix with each cell offset by 8 to make all scores
   non-negative */
int bl60_highpass = 8;
char bl60_matrix[21][21]={
12, 7, 7, 6, 7, 7, 7, 8, 7, 7, 7, 7, 7, 6, 8, 9, 8, 5, 6, 8, 8, /*A*/
 7,13, 8, 7, 5, 9, 8, 6, 8, 5, 6,10, 7, 6, 6, 7, 7, 6, 6, 6, 8, /*R*/
 7, 8,14, 9, 6, 8, 8, 8, 8, 5, 5, 8, 6, 5, 6, 9, 8, 6, 6, 5, 8, /*N*/
 6, 7, 9,14, 4, 8, 9, 7, 7, 5, 5, 7, 5, 5, 6, 8, 7, 4, 6, 5, 8, /*D*/
 7, 5, 6, 4,17, 6, 5, 6, 5, 7, 7, 5, 6, 6, 6, 7, 7, 5, 5, 7, 8, /*C*/
 7, 9, 8, 8, 6,13,10, 6, 9, 6, 6, 9, 8, 5, 7, 8, 7, 6, 6, 6, 8, /*Q*/
 7, 8, 8, 9, 5,10,13, 6, 8, 5, 6, 9, 6, 5, 7, 8, 7, 6, 6, 6, 8,
 8, 6, 8, 7, 6, 6, 6,14, 6, 5, 5, 7, 5, 5, 6, 8, 7, 6, 5, 5, 8,
 7, 8, 8, 7, 5, 9, 8, 6,15, 5, 5, 7, 6, 7, 6, 7, 6, 6, 9, 5, 8,
 7, 5, 5, 5, 7, 6, 5, 5, 5,12,10, 6, 9, 8, 5, 6, 7, 6, 7,11, 8,
 7, 6, 5, 5, 7, 6, 6, 5, 5,10,12, 6,10, 8, 6, 6, 7, 6, 7, 9, 8,
 7,10, 8, 7, 5, 9, 9, 7, 7, 6, 6,12, 7, 5, 7, 8, 7, 5, 6, 6, 8,
 7, 7, 6, 5, 6, 8, 6, 5, 6, 9,10, 7,14, 8, 6, 6, 7, 6, 7, 9, 8,
 6, 6, 5, 5, 6, 5, 5, 5, 7, 8, 8, 5, 8,14, 5, 6, 6, 9,11, 7, 8,
 8, 6, 6, 6, 6, 7, 7, 6, 6, 5, 6, 7, 6, 5,15, 7, 7, 5, 6, 6, 8,
 9, 7, 9, 8, 7, 8, 8, 8, 7, 6, 6, 8, 6, 6, 7,12, 9, 6, 6, 6, 8,
 8, 7, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 9,12, 6, 6, 8, 8,
 5, 6, 6, 4, 5, 6, 6, 6, 6, 6, 6, 5, 6, 9, 5, 6, 6,18,10, 6, 8,
 6, 6, 6, 6, 5, 6, 6, 5, 9, 7, 7, 6, 7,11, 6, 6, 6,10,15, 7, 8,
 8, 6, 5, 5, 7, 6, 6, 5, 5,11, 9, 6, 9, 7, 6, 6, 8, 6, 7,12, 8,
 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 0  /* X */
};

/* BLOSUM62 matrix with each cell offset by 4 to make all scores
   non-negative */
int bl62_highpass = 4;
/* A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  X  */
char bl62_matrix[21][21]={
   8, 3, 2, 2, 4, 3, 3, 4, 2, 3, 3, 3, 3, 2, 3, 5, 4, 1, 2, 4, 0, 
   3, 9, 4, 2, 1, 5, 4, 2, 4, 1, 2, 6, 3, 1, 2, 3, 3, 1, 2, 1, 0, 
   2, 4,10, 5, 1, 4, 4, 4, 5, 1, 1, 4, 2, 1, 2, 5, 4, 0, 2, 1, 0, 
   2, 2, 5,10, 1, 4, 6, 3, 3, 1, 0, 3, 1, 1, 3, 4, 3, 0, 1, 1, 0, 
   4, 1, 1, 1,13, 1, 0, 1, 1, 3, 3, 1, 3, 2, 1, 3, 3, 2, 2, 3, 0, 
   3, 5, 4, 4, 1, 9, 6, 2, 4, 1, 2, 5, 4, 1, 3, 4, 3, 2, 3, 2, 0, 
   3, 4, 4, 6, 0, 6, 9, 2, 4, 1, 1, 5, 2, 1, 3, 4, 3, 1, 2, 2, 0, 
   4, 2, 4, 3, 1, 2, 2,10, 2, 0, 0, 2, 1, 1, 2, 4, 2, 2, 1, 1, 0, 
   2, 4, 5, 3, 1, 4, 4, 2,12, 1, 1, 3, 2, 3, 2, 3, 2, 2, 6, 1, 0, 
   3, 1, 1, 1, 3, 1, 1, 0, 1, 8, 6, 1, 5, 4, 1, 2, 3, 1, 3, 7, 0, 
   3, 2, 1, 0, 3, 2, 1, 0, 1, 6, 8, 2, 6, 4, 1, 2, 3, 2, 3, 5, 0, 
   3, 6, 4, 3, 1, 5, 5, 2, 3, 1, 2, 9, 3, 1, 3, 4, 3, 1, 2, 2, 0, 
   3, 3, 2, 1, 3, 4, 2, 1, 2, 5, 6, 3, 9, 4, 2, 3, 3, 3, 3, 5, 0, 
   2, 1, 1, 1, 2, 1, 1, 1, 3, 4, 4, 1, 4,10, 0, 2, 2, 5, 7, 3, 0, 
   3, 2, 2, 3, 1, 3, 3, 2, 2, 1, 1, 3, 2, 0,11, 3, 3, 0, 1, 2, 0, 
   5, 3, 5, 4, 3, 4, 4, 4, 3, 2, 2, 4, 3, 2, 3, 8, 5, 1, 2, 2, 0, 
   4, 3, 4, 3, 3, 3, 3, 2, 2, 3, 3, 3, 3, 2, 3, 5, 9, 2, 2, 4, 0, 
   1, 1, 0, 0, 2, 2, 1, 2, 2, 1, 2, 1, 3, 5, 0, 1, 2,15, 6, 1, 0, 
   2, 2, 2, 1, 2, 3, 2, 1, 6, 3, 3, 2, 3, 7, 1, 2, 2, 6,11, 3, 0, 
   4, 1, 1, 1, 3, 2, 2, 1, 1, 7, 5, 2, 5, 3, 2, 2, 4, 1, 3, 8, 0, 
   0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0  
};
/*=======================================================================*/
/* Number to amino acid                  */
char *num_to_aachar(num)
int num;
{
  switch (num) {
    case 0: return("A");
    case 1: return("R");
    case 2: return("N");
    case 3: return("D");
    case 4: return("C");
    case 5: return("Q");
    case 6: return("E");
    case 7: return("G");
    case 8: return("H");
    case 9: return("I");
    case 10: return("L");
    case 11: return("K");
    case 12: return("M");
    case 13: return("F");
    case 14: return("P");
    case 15: return("S");
    case 16: return("T");
    case 17: return("W");
    case 18: return("Y");
    case 19: return("V");
    case 20: return("X");
    case -1: return(".");
    default: return("*");		/* Should never happen */
    }
}
/*======================================================================*/
/* Amino acid to number                  */
/*  B is changed to D, Z is changed to E, O and J are changed to X  */
int aachar_to_num(ch)
char ch;
{
  if (ch >= 97 && ch <= 122) ch = ch - 32;	/* Make letters upper case */
  switch (ch) {
    case 'A': return(0);
    case 'R': return(1);
    case 'N': return(2);
    case 'D': return(3);
    case 'B': return(3);
    case 'C': return(4);
    case 'Q': return(5);
    case 'E': return(6);
    case 'Z': return(6);
    case 'G': return(7);
    case 'H': return(8);
    case 'I': return(9);
    case 'L': return(10);
    case 'K': return(11);
    case 'M': return(12);
    case 'F': return(13);
    case 'P': return(14);
    case 'S': return(15);
    case 'T': return(16);
    case 'W': return(17);
    case 'Y': return(18);
    case 'V': return(19);
    case 'J': return(20);
    case 'O': return(20);
    case 'X': return(20);
    case '.': return(-1);
    default: return(-1);
    }
}
/*=====================================================================*/
/* Use internal numerical representation to print amino acid: */
void pr_num_to_aa(num)
char num;
{
  switch (num) {
    case 0: printf("A"); break;
    case 1: printf("R"); break;
    case 2: printf("N"); break;
    case 3: printf("D"); break;
    case 4: printf("C"); break;
    case 5: printf("Q"); break;
    case 6: printf("E"); break;
    case 7: printf("G"); break;
    case 8: printf("H"); break;
    case 9: printf("I"); break;
    case 10: printf("L"); break;
    case 11: printf("K"); break;
    case 12: printf("M"); break;
    case 13: printf("F"); break;
    case 14: printf("P"); break;
    case 15: printf("S"); break;
    case 16: printf("T"); break;
    case 17: printf("W"); break;
    case 18: printf("Y"); break;
    case 19: printf("V"); break;
    case 20: printf("."); break;
    case -1: printf("."); break;
    default: printf("*");		/* Should never happen */
    }
}
/*======================================================================*/
void pr_num_to_aa_space(c)
char c;
{
	pr_num_to_aa(c);
	printf(" ");
}
/*=======================================================================
      getscore reads a file containing a scoring matrix and
      loads it into Score[MATSIZE][MATSIZE].  Assumes alphabet for file is
      listed on first non-blank line.
=========================================================================*/
void getscore(matrix)
struct score *matrix;
{
   char filename[FNAMELEN], line[MAXLINE], chigh[6], *ptr;
   FILE *fin, *fstp;
   int alpha[MATSIZE+10], nrows, ncols, row, col, i;

   if ((fstp = fopen("protomat.stp", "rt")) == NULL)
   {
      fin = NULL;
      strcpy(filename, "def");
   }
   else
   {
      line[0] = filename[0] = '\0';
      while(fgets(line, sizeof(line), fstp) != NULL)
      {
	  if (strncmp(line, "SCORE", 5) == 0)
	  {
	     ptr = strtok(line, " ,\t\n");
	     if (ptr != NULL)
	     {
		ptr = strtok(NULL, " ,\t\n");
		if (ptr != NULL) strcpy(filename, ptr);
	     }
	     if ((fin = fopen(filename, "rt")) == NULL)
	     {
	printf("Could not open %s, using default BLOSUM scoring matrix\n",
			    filename);
		strcpy(filename, "def");
	     }
	  }
	  else if (strncmp(line, "HIGH", 4) == 0)
	  {
	     ptr = strtok(line, " ,\t\n");
	     if (ptr != NULL)
	     {
		ptr = strtok(NULL, " ,\t\n");
		if (ptr != NULL) strcpy(chigh, ptr);
		matrix->highpass = atoi(chigh);
	     }
	  }
      }
      fclose(fstp);
   }

/*----------Read file until first non-blank line --------------*/
   if (fin != NULL)
   {
      printf("\nUsing scoring matrix from %s\n", filename);
      line[0] = '\0';
      while (strlen(line) < 1 && fgets(line, sizeof(line), fin) != NULL)
	    ;
/*------See if the first line has characters on it ------------*/
      for (col=0; col < 30; col++) alpha[col] = -1;
      if (strstr(line, "A") != NULL)	/* This line has characters */
      {
	 row = 0;	/* # of alphabetic characters on the line */
	 for (i=0; i= 0)
	    {
	       alpha[row] = col;
	       row++;
	    }
	    else if (isalpha(line[i])) row++; /* skip over other alpha */
	 }
      }
/*-------Get the data values now ------------*/
      for (row=0; rowscores[row][col] = -99;		/* Null value */
      nrows = 0;
      line[0] = '\0';
      while (fgets(line, sizeof(line), fin) != NULL)
      {
	 if (strlen(line) > 1)
	 {
	    if (alpha[nrows] >= 0 && alpha[nrows] < MATSIZE)
	    {
	       row = alpha[nrows]; ncols = 0;
	       ptr = strtok(line, " ,\t\n");
	       while (ptr != NULL)
	       {
		  if (strspn(ptr, "+-0123456789") == strlen(ptr))
		  {
		     col = alpha[ncols];
		     if (col >= 0 && col < MATSIZE)
			matrix->scores[row][col] = atoi(ptr);
		     ncols++;
		  }
		  ptr = strtok(NULL, " ,\t\n");
	       }
	    }
	    nrows++;
	 }
      }

/*-------If some entries are still missing, assume symmetry ---------*/
      for (row=0; rowscores[row][col] == -99)
		  matrix->scores[row][col] = matrix->scores[col][row];
/*	   printf("%2d ", matrix->scores[row][col]); */
	}
/*	printf("\n"); */
      }
      fclose(fin);
   }
   else    /*   no input file  */
   {
      printf("\nUsing BLOSUM62 scoring matrix.\n");
      matrix->highpass = bl62_highpass;
      for (row=0; rowscores[row][col] = bl62_matrix[row][col];
/*	    printf("%2d ", matrix->scores[row][col]);*/
	 }
/*	 printf("\n");*/
      }
   }
   matrix->highpass *= 100;
/*   printf("HighPass = %d", matrix->highpass);*/
}   /* end of getscore() */
/*====================================================================*/
/*  This is Kernighan & Ritchie's ASCII to integer conversion (p. 58) */
/*====================================================================*/
int kr_atoi(s)
char s[];
{
   int i, n, sign;

   for (i=0; s[i]==' ' || s[i]=='\n' || s[i]=='\t'; i++)
		;
   sign = 1;
   if (s[i] == '+' || s[i] == '-')
      sign = (s[i++]=='+') ? 1 : -1;
   for (n=0; s[i] >= '0' && s[i] <= '9'; i++)
      n = 10 * n + s[i] - '0';
   return(sign * n);
}  /* end of kr_atoi */
/*=====================================================================*/
/*  This is Kernighan & Ritchie's integer to ASCII conversion (p. 60) */
/*====================================================================*/
void kr_itoa(n, s)
int n;
char s[];
{
   int c, i, j, sign;

   sign = n;
   if (sign < 0) n = -n;
   i = 0;
   do {
      s[i++] = n % 10 + '0';
   }  while ( (n /= 10) > 0);
   if (sign < 0) s[i++] = '-';
   s[i] = '\0';
   for (i=0, j=strlen(s)-1; idir_len=new->file_len=new->name_len=0;
   i = strlen(filename);
   /*-------  Read the file name backwards ---------------*/
   while (i>=0 && (!ext_len || !new->dir_len))
   {
      /*---  Last period in string => file extension ----*/
      if (filename[i] == '.') ext_len = strlen(filename)-i;
      /*--- Last slash in string => directory -----------*/
      if (filename[i] == '/' && new->dir_len == 0) new->dir_len = i+1;
      /*--- Last colon and no slash after it => DOS directory -----*/
/*      if (filename[i] == ':' && new->dir_len == 0) new->dir_len = i+1; */
      i--;
   }
   new->file_len = strlen(filename)-new->dir_len;
   new->name_len = new->file_len - ext_len;

   return(new);
}
/*========================================================================
  dir_dos(): DOS code to get name of directory from line and
       create it if necessary
===========================================================================*/
/*char *dir_dos(line)
char *line;
{
   char tname[FNAMELEN], mem[MAXLINE], pros[FNAMELEN], *ptr;
   char filename[FNAMELEN];
   int test;
   FILE *ftmp;

   pros[0] = '\0';
   if (line[0] != '>' &&
	  (strstr(line, "\\") != NULL || strstr(line, ":") != NULL) )
   {
         ptr = strtok(line, "\n\r");
         strcpy(pros, ptr);
	 if (pros[strlen(pros)-1] != '\\') strcat(pros, "\\");
   }
*/
/*-------------------Create the directory ---------------------------------*/
/*
   if (strlen(pros))
   {
      tmpnam(tname);
      strcpy(filename, pros);
      strcat(filename, tname);
      if ( (ftmp=fopen(filename, "w"))== NULL)
      {
	 strcpy(tname, pros);     
	 tname[strlen(pros)-1] = '\0';
	 sprintf(mem, "md %s", tname);
	 test = system(mem);
	 if (test == 0) printf("\nCreated directory %s", tname);
	 else
	 {
	    printf("\nUnable to create directory %s", tname);
	    printf("\nProtein files will be placed in current directory");
	    pros[0] = '\0';
	 }
      }
      else
      {
	 fclose(ftmp);
	 unlink(filename);
      }
   }
   return(pros);
} 
*/
/*=======================================================================
  dir_unix(): UNIX code to get name of directory from line and
	      create it if necessary
==========================================================================*/
char *dir_unix(line)
char *line;
{
   char tname[FNAMELEN], mem[MAXLINE], pros[FNAMELEN], *ptr;
   int test;
   DIR *dp;

   pros[0] = '\0';
   if (line[0] != '>' && (strstr(line, "/") != NULL) )
   {
         ptr = strtok(line, "\n\r");
         strcpy(pros, ptr);
	 if (pros[strlen(pros)-1] != '/') strcat(pros, "/");
   }
/*-----------------Create the directory ---------------------------------*/
   if (strlen(pros))
   {
      strcpy(tname, pros);
      tname[strlen(pros)-1] = '\0';
      sprintf(mem, "mkdir %s", tname);
      if ((dp=opendir(tname))==NULL)
      {
         test=system(mem);
         if (test == 0) printf("\nCreated directory %s\n", tname);
         else
         {
            printf("\nUnable to create directory %s", tname);
            printf("\nProtein files will be placed in current directory\n");
            pros[0] = '\0';
         }
      }
   }
   return(pros);
}    /* end of dir_unix */
/*======================================================================
     Create & intialize a db_id structure
========================================================================*/
struct db_id *makedbid()
{
   struct db_id *new;

   new = (struct db_id *) malloc (sizeof(struct db_id));
   new->entry[0] = new->full_entry[0] = '\0';
   new->ps[0] = '\0';
   new->info[0] = '\0';
   new->len = 0;
   new->rank = new->score = 0;
   new->lst = NO;
   new->found = NO;
   new->block = NO;
   new->frag = NO;
   new->search = NO;
   new->pvalue = (double) 0.0;
   new->next = NULL;
   new->prior = NULL;
   return(new);
}  /*  end of makedbid */

/*======================================================================
     get_ids() reads a .lis or .lst file & inserts the sequences
       found in it into a list sorted by sequence name.
========================================================================*/
int get_ids(flis, ids)
FILE *flis;
struct db_id *ids;
{
   char line[MAXLINE], ctemp[20], *ptr;
   struct db_id *id, *last, *new;
   int len, nids, i, bar;

   nids = 0;
   while(!feof(flis) && fgets(line, MAXLINE, flis) != NULL)
   {		/* skip over title or directory lines */
      if (strlen(line) && 
          line[0] != '>' && strstr(line, "/") == NULL &&
	  strstr(line,"\\") == NULL && strstr(line, ":") == NULL)
      {
	 nids += 1;
	 new = makedbid();
/*-----  Copy up to the first space or carriage return ------------*/
	 len = strcspn(line, " \t\r\n");
	 if (len > 2*SNAMELEN) len = 2*SNAMELEN;
	 strncpy(new->full_entry, line, len);  new->full_entry[len] = '\0';
	 if (len > SNAMELEN) len = SNAMELEN;
	 strncpy(new->entry, line, len);  new->entry[len] = '\0';
	 /* Only want max of two parts in id->entry   */
         bar=NO; i=0;
	 for (i=0; ientry[i] == '|')
		{
		   if (!bar) { bar=YES;   }
		   else { new->entry[i] = '\0'; i = len;  }
		}
         }
	 last = ids;  id = ids->next;
/*-------- Get any other information on the .lis file line --------*/
	 if (strstr(line, "FRAGMENT") != NULL) new->frag = YES;
	 if (strstr(line, "BLOCK") != NULL) new->block = YES;
	 if (strstr(line, "LST") != NULL) new->lst = YES;
	 ptr = strstr(line, "PS=");
	 if (ptr != NULL)
         {
	    strncpy(new->ps, ptr+3, 1); new->ps[1] = '\0';
            if (strcmp(new->ps, "P") == 0) new->frag = YES;
         }
	 ptr = strstr(line, "LENGTH=");
	 if (ptr != NULL)
	 {
	    len = strcspn(ptr+7, " \t\r\n");
	    if (len > 0)
	    {
	       strncpy(ctemp, ptr+7, len); ctemp[len] = '\0';
	       new->len = atoi(ctemp);
	    }
	 }
/*------  Insert id into a sorted list ----------------------------*/
	 while (id != NULL && id->entry != NULL &&
	     strcmp(id->entry, new->entry) < 0)
	 {
	    last = id;
	    id = id->next;
	 }
	 new->prior = last;
	 new->next = id;
	 last->next = new;
	 if (id != NULL) id->prior = new;
	 new = NULL;
      }
   }
   return(nids);
}  /*  end of get_ids */
/*====================================================================
    See if a an entry name is in a list of entries
======================================================================*/
struct db_id *check_entry(ids, entry)
struct db_id *ids;
char *entry;
{
   struct db_id *id;
   int i, tot, bar, len;
   char *ptr, idtemp[SNAMELEN*6 + 6], dbtemp[SNAMELEN*6 + 6];
   char ctemp[SNAMELEN*6 + 6];
   char idlist[10][SNAMELEN*6 + 6];

   id = ids->next;
   while (id != NULL)
   {
      if (id->found == NO)
      {
         if (strcmp(id->entry, "-") == 0)  /* just take the first sequence */
         {
             return(id);
         }
         else
         {
            /*	Store the id names because can't use strtok
		for two things simultaneously    */
            strcpy(idtemp, id->entry);
            tot = 0;
            ptr = strtok(idtemp, "| \0\r\n\t");
            while(ptr != NULL)
            {
	      if (tot < 10) strcpy(idlist[tot++], ptr);
              ptr = strtok(NULL, "| \0\r\n\t");
            }
	    len = strlen(entry);
	    if (len > SNAMELEN*6) len = SNAMELEN*6;
            strncpy(dbtemp, entry, len); dbtemp[len] = '\0';
            ptr = strtok(dbtemp, "| \0\r\n\t");
            while(ptr != NULL)
            {
               for (i=0; i< tot; i++)
               {
	         if (strcmp(ptr, idlist[i]) == 0) 
                 {
                   strncpy(ctemp, entry, len); ctemp[len] = '\0'; 
	           /* Only want max of two parts in id->entry   */
                   bar=NO; i=0;
	           for (i=0; ifull_entry, ctemp);
                    return(id);
                 }
               }
               ptr = strtok(NULL, "| \0\r\n\t");
            }
         }
      }
      id = id->next;
   }
   return(NULL);
}  /* end of check_entry */
cores[row][col]); */
	}
/*	printf("\n"); */
      }
      fclose(fin);
   }
   else    /*   no input file  */
   {
      printf("\nUsing BLOSUM62 scoring matrix.\n");
      matrix->highpass = bl62_highpass;
      for (row=0; rowscores[row][col] = bl62_matrix[rblimps-3.9/blimps/pssmBL.c000064400001460000012000000063650774312250100160130ustar00jorjastaff00000400000027/*   pssmBL.c   Read blocks db & pssmdist.dat file, insert
                99.5%= and strength= on BL line
		pssmBL   
--------------------------------------------------------------------
 4/ 8/95 J. Henikoff 
 4/12/95 Open blocks.out for append instead of write.
10/ 6/99 Changes for Blimps 3.3
====================================================================*/

#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#include 

void get_info();

/*=======================================================================*/
int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *bfp, *ofp, *pfp;
  Block *block;
  char bdbname[MAXNAME], conname[MAXNAME], pssmname[MAXNAME];

/* ------------1st arg = pssmdist.dat file------------------------------*/
   if (argc > 1)
      strcpy(pssmname, argv[1]);
   else
   {
      printf("\nEnter name of pssmdist.dat file: ");
      gets(pssmname);
   }
   if ( (pfp=fopen(pssmname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", pssmname);
      exit(-1);
   }
/* ------------2st arg = blocks database -------------------------------*/
   if (argc > 2)
      strcpy(bdbname, argv[2]);
   else
   {
      printf("\nEnter name of blocks database: ");
      gets(bdbname);
   }
   if ( (bfp=fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbname);
      exit(-1);
   }
/* ------------3nd arg = new blocks database ---------------------*/
   if (argc > 3)
      strcpy(conname, argv[3]);
   else
   {
      printf("\nEnter name of new blocks database: ");
      gets(conname);
   }
   if ( (ofp=fopen(conname, "a")) == NULL)
   {
      printf("\nCannot open file %s\n", conname);
      exit(-1);
   }

/*-----------------------------------------------------------------*/

  while ((block = read_a_block(bfp)) != NULL)
  {
     get_info(pfp, block);
     output_block(block, ofp);
     free_block(block);
  }
   
  fclose(bfp); fclose(ofp); fclose(pfp);
  exit(0);

}  /* end of main */
/*=======================================================================
	Get 99.5% & strength from pssmdist.dat file & replace any
	values already in block
========================================================================*/
void get_info(pfp, block)
FILE *pfp;
Block *block;
{
   char line[MAXNAME], *ptr;

   if (fgets(line, MAXNAME, pfp) != NULL)
   {
      ptr = strtok(line, " \t\r\n");		/* AC */
      if (ptr != NULL && strcmp(ptr, block->number) == 0)
      {
         ptr = strtok(NULL, " \t\r\n");		/* 99.5% score */
         if (ptr != NULL)
         {
            block->percentile = atoi(ptr);
            ptr = strtok(NULL, " \t\r\n");	/* Median TP score */
            if (ptr != NULL)
            {
               ptr = strtok(NULL, " \t\r\n");	/* Strength */
               if (ptr != NULL) block->strength = atoi(ptr);
	       if (block->strength < 0) block->strength = 0;  /*pssmdist bug?*/
            }
         }
      }
      /*   Now rewrite the BL line  */
      strcpy(line, block->bl);
      ptr = strtok(line, "; \t\r\n");		/* motif or other info */
      sprintf(block->bl, "%s; width=%d; seqs=%d; 99.5%%=%d; strength=%d;",
	ptr, block->width, block->num_sequences, 
	block->percentile, block->strength);
   }
   
}  /* end of get_info */
----------1st arg = pssmdist.dat file------------------------------*/
   if (argc > 1)
      strcpy(pssmname, argv[1]);
   else
   {
      printf("\nEnter name of pssmdist.dat file: ");
      gets(pssmname);
   }
   if ( (pfp=fopen(pssmname, "r")) == NULL)
   {
     blimps-3.9/blimps/pssmdist.c000064400001460000012000000607251001174303500164520ustar00jorjastaff00000400000027/*>>>>>  pssmdist IPR001624.mats IPR001624.obsf default.amino.frq 80000 29085965*/
/* COPYRIGHT 2003 Fred Hutchinson Cancer Research Center */
/*>>>>> Problem: for TPs, if the observed frequencies in a column don't
	add up to EXACTLY 100, the total probability in compute() won't
	be 1.0 and there will be problems, eg PR00184G
	Should 1) Modify papssm so that they add to 100 after rounding,
	       2) Modify pssmdist to renormalize them to 100
*/
/*     pssmdist.c:  compute distribution of PSSM scores
	pssmdist    SWISS SWISSAA  
	matrix file:	precomputed integer PSSM from blpssm (EX)
	obs freq file:  observed frequency file from blpssm (OU)
		        The 20 main aa frequencies should add to exactly 1.000.
	frequency file: blimps format aa frequency file (20 main aa
			frequencies must add to exactly 1.0000)
	SWISS:		Number of sequences in typical database search
			EG  28164
	SWISSAA:	Number of amino acids in   "
			EG  9545427
        outname:	default is pssmdist
	cum:		word "cum" to write pssmdist.cum file
	Writes outname.dat & outname.cum files
---------------------------------------------------------------------------
 10/19/94 J. Henikoff 
 10/20/94 Changed to only count the 20 basic AAs plus gap for off ends,
	  but are counting alignments with gaps in other positions too!
          Added histogram
 10/21/94 Only count gaps off ends.
 10/25/94 Added some expected counts for a wide block vs swiss29
 10/26/94 Print the top scores out
	  Why don't the probs add to 1.0? They add to the 10 .frq values.
 10/31/94 Reads a .lis file to get the # of TPs, writes value of
          [0.005 x( SWISS - #TPs) + #TPs]th score to pssmdist.dat
	  Counts fragments as if they were TPs.
 11/1/94  Write [0.005 x SWISS] score; ignore #TPs.
 11/14/94 Compute weights for probabilities, including for ends.
 11/30/94 Input SWISS and SWISSAA
 12/ 7/94 Read observed frequencies & calculate TP distribution.
  4/ 6/95 Write tpmed and strength to pssmdist.dat file
  4/ 8/95 Count #TP scores above TN995 & write to pssmdist.dat file
  4/25/96 Renormalize observed frequencies in a column to add to 100,
	  fix_freqs(). Requires blimps-3.0.1 with MatType = double
	  instead of int to work properly.
 11/25/97 Increased MAXCOL from 60 to 200 for Peer Bork's groups
  1/16/99 Added pssmdist.cum output file = cumulative probs
  1/27/99 Make pssmdist.cum optional. Report 80%tile as well as 99.5%
  4/ 5/00 Write block width to pssmdist.dat
  8/27/03 Make fix_freqs() double instead of integer; mats and obsf input
	matrices can be integer or floating point
 11/11/03 Renamed load_frequencies() to load_freqs(), conflicts with
		frequency.c:load_frequencies() - should use that one!
 11/12/03 Renamed read_freq() to read_a_freq() - identical to
		frequency.c:read_freq() but that is defined static
  2/ 9/04 Increased MAXSCORE and quit if it is not big enough.
  2/ 9/04 Optionally use named file for pssmdist.dat
====================================================================*/

#define EXTERN
#define MAXNAME 80	/* Maximum file name length */
#define MAXSCORE 15000  /* Maximum score value = block width x max col */
#define HISTO 20	/* size of a score histogram bucket */
#define TOPN 300	/* report the top scores */
#define SWISS 28164	/* number of sequences in a search */
#define SWISSAA 9545427  /* number of AAs in all sequences searched */
#define TPS 100		/* number of TPs in a search */
#define AASALL 26
#define MAXCOL 200	/* Maximum block width */
#define MAXPROB 0.0005	/* Maximum cumulative prob. to write to pssmdist.cum */
/* 0- 1A 2R 3N 4D 5C 6Q 7E 8G 9H 10I 11L 12K 13M 14F 15P 16S 17T 18W 19Y
   20V 21B 22Z 23X 24* 25J,O,U  */

#include 

/*
 * Local variables and data structures
 */

struct score_struct {
	double ways, prob;
} Scores[2][MAXSCORE];

int compute();
int load_freqs();
double read_a_freq();
void fix_freqs();
int count_tps();

double Search, SearchAA;	/* search size */
int TN995, TN800, TPmed;
double TPabove;
/*=======================================================================*/
/*
 * main
 *   controls flow of program
 *   Parameters: argc, argv
 *   Error codes:
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *mfp, *ffp, *fdt, *fcum, *ofp;
  Matrix *matrix, *obs_freqs;
  char mname[MAXNAME], fname[MAXNAME], oname[MAXNAME], *ptr, ctemp[MAXNAME];
  char outname[MAXNAME];
  double freqs[AASALL];
  int strength;

/* ------------1st arg = matrix database -------------------------------*/
   if (argc > 1)
      strcpy(mname, argv[1]);
   else
   {
      printf("\nEnter name of matrix database: ");
      gets(mname);
   }
   if ( (mfp=fopen(mname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", mname);
      exit(-1);
   }
/* ------------2rd arg = observed freqs db -------------------------------*/
   if (argc > 2)
      strcpy(oname, argv[2]);
   else
   {
      printf("\nEnter name of observed frequencies database: ");
      gets(oname);
   }
   if ( (ofp=fopen(oname, "r")) == NULL)
   {
      printf("\nCannot open file %s, TP distribution not computed.\n", oname);
   }
/* ------------3rd arg = frequency file -------------------------------*/
   if (argc > 3)
      strcpy(fname, argv[3]);
   else
   {
      printf("\nEnter name of frequency file: ");
      gets(fname);
   }
   if ( (ffp=fopen(fname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", fname);
      exit(-1);
   }
   load_freqs(ffp, freqs);
   fclose(ffp);
/* ------------4th arg = #sequences in a search--------------------*/
   Search = SWISS;
   if (argc > 4)
      strcpy(ctemp, argv[4]);
   else
   {
      printf("\nEnter number of sequences in a typical search [%.0f]: ",
		 Search);
      gets(ctemp);
   }
   if (strlen(ctemp)) Search = atof(ctemp);
/* ------------5th arg = #aas in a search--------------------*/
   SearchAA = SWISSAA;
   if (argc > 5)
      strcpy(ctemp, argv[5]);
   else
   {
      printf("\nEnter number of amino acids in a typical database [%.0f]: ",
		SearchAA);
      gets(ctemp);
   }
   if (strlen(ctemp)) SearchAA = atof(ctemp);
   printf ("Assuming %.0f sequences, %.0f amino acids in a search\n",
		Search, SearchAA);
   printf("and 100 true positive alignments\n");
/* ------------6th arg = name of output file-------------------*/
   strcpy(outname, "pssmdist");
   if (argc > 6) strcpy(outname, argv[6]);
   sprintf(ctemp, "%s.dat", outname);
   if ( (fdt=fopen(ctemp, "a")) == NULL)
   {
      printf("\nCannot open file ctemp\n");
      fdt = NULL;
   }
/* ------------7th arg = cum---------------------------------*/
   fcum = NULL;
   if (argc > 7) strcpy(ctemp, argv[7]);
   if (ctemp[0] == 'c' || ctemp[0] == 'C')
   {
      sprintf(ctemp, "%s.cum", outname);
      if ( (fcum=fopen(ctemp, "a")) == NULL)
      {
         printf("\nCannot open file ctemp\n");
      }
   }

/*-----------------------------------------------------------------*/
  while ((matrix = read_a_matrix(mfp)) != NULL)
  {
	printf("\n======>%s\n", matrix->ac);
	if (ofp != NULL)
        { obs_freqs = read_a_matrix(ofp); fix_freqs(obs_freqs);  }
	else             obs_freqs = NULL;
        if (fcum != NULL) fprintf(fcum, ">%s\n", matrix->number);
	TN995 = compute(matrix, 0, freqs, obs_freqs, fcum);
	if (obs_freqs != NULL && strcmp(matrix->ma, obs_freqs->ma) == 0)
	    TPmed = compute(matrix, 1, freqs, obs_freqs, NULL);
        else TPmed = 0;
        if (fdt != NULL)
        {
	  ptr = strtok(matrix->ac, " ;");
	  if (TN995 > 0)
		 strength = (int) (1000.0 * (float) TPmed / (float) TN995);
/*
          fprintf(fdt, "%s %d %d %d %d %d\n",
                  ptr, TN995, TPmed, strength, TN800, matrix->width);
*/

          fprintf(fdt, "%s %d %d  %d %.4lf %d %d\n",
                  ptr, TN995, TPmed, strength, TPabove, TN800, matrix->width);

        }
        free_matrix(matrix);
	if (obs_freqs != NULL) free_matrix(obs_freqs);
  }
   
  fclose(mfp); fclose(ofp); fclose(fdt); 
  if (fcum != NULL) fclose(fcum);
  exit(0);

}  /* end of main */
/*=======================================================================
    ftype == 0 => use freqs (TN distribution)
    ftype == 1 => use obs_freqs (TP distribution)
>>>>maxcol, etc. are truncated to integers from matrix, s.b. rounded
========================================================================*/
int compute(matrix, ftype, freqs, obs_freqs, fcum)
Matrix *matrix, *obs_freqs;
int ftype;
double *freqs;
FILE *fcum;
{
  struct score_struct *last, *this, histo[MAXSCORE/HISTO], ends[MAXSCORE];
  struct score_struct middle[MAXSCORE];
  int col, aa, minvalue, maxvalue, minscore, maxscore, mincol, maxcol;
  int x, xreport, score, minfirst, minlast, pflag, itemp;
  double cum, aligns, report, report80, ftemp, dtemp, probwt[MAXCOL];
  double cumprob[MAXSCORE];

  /*   compute which score to report */
  if (ftype == 1) report = (double) 0.5 * TPS;		/* median TP */
  else            report = (double) 0.005 * Search;	/* 99.5% TN  */
  report80 = 0.020 * Search;				/* 90.0% TN */
  minscore = maxscore = 0;
  maxvalue = -1;		/* assumes no negative scores */
  minvalue = 9999;
  probwt[0] = 20.0;
  for (col = 0; col < matrix->width; col++)
  {
     /*  Intialize probability weights with powers of 20 */
     if (col > 0) probwt[col] = probwt[col - 1] * 20.0;
     mincol = 9999; maxcol = -1;
/*   for (aa = 0; aa < AASALL; aa++) */
     for (aa = 1; aa <= 20; aa++)
     {
        itemp = round(matrix->weights[aa][col]);
        if (itemp > maxvalue) maxvalue = itemp;
	if (itemp < minvalue) minvalue = itemp;
        if (itemp > maxcol) maxcol = itemp;
	if (itemp < mincol) mincol = itemp;
     }
     maxscore += maxcol;
     minscore += mincol;
     if (col == 0) minfirst = mincol;
     if (col == (matrix->width - 1) ) minlast = mincol;
   }
   /*    Probability weights: weights applied to probs depending
         on how many columns of the block are aligned, the
         full alignment width gets about 19/21 = .905, alignments
         off either end of the sequence get the remainder */
   dtemp = probwt[matrix->width - 1] * 21.0 - 40.0;
   cum = 0.0;
   for (col = 0; col < matrix->width; col++)
   {
      probwt[col] = probwt[col] * 19.0 / dtemp;
      cum += probwt[col];
      if (col < matrix->width - 1) cum += probwt[col];
   }
   /* ---- Min. score could be just first or last column ----*/
   if (ftype == 1) printf("\nTrue positive distribution\n");
   else            printf("\nRandom distribution\n");
   printf("minscore without ends=%d\n", minscore);
   if (minfirst < minscore) minscore = minfirst;
   if (minlast < minscore)  minscore = minlast;
   printf("minvalue=%d maxvalue=%d minscore=%d maxscore=%d\n",
	   minvalue, maxvalue, minscore, maxscore);
   /*-----------------------------------------------------------------*/
   if (maxscore > MAXSCORE) 
   { 
      maxscore = MAXSCORE - 1;
      fprintf(stderr, "maxscore is too big, increase MAXSCORE from %d\n",
              maxscore + 1);
      return(0);
   }
   last = Scores[0]; this = Scores[1];
   for (x = minvalue; x <= maxscore; x++)
   {  last[x].ways = last[x].prob = this[x].ways = this[x].prob = 0.0; 
      ends[x].ways = ends[x].prob = middle[x].ways = middle[x].prob = 0.0; }

   /*---------Initialize from first column -------------------------------*/
   /*   use obs_freqs->weights[aa][col] instead of freqs[aa] for TP probs */
   col = 0;
/* for (aa=0; aa < AASALL; aa++) */
   for (aa=1; aa <= 20; aa++)
   {
      x = round(matrix->weights[aa][col]);
      last[x].ways += 1.0;
      if (ftype == 1) ftemp = obs_freqs->weights[aa][col] / 100.;
      else            ftemp = freqs[aa];
      last[x].prob += ftemp;   
   }

   /*---- Now enumerate all possible scores, expanding one column
          at a time ----------*/
   for (col=1; col < matrix->width; col++)
   {
      /*--------- Save the alignments hanging off the left end ------*/
      /*    There are currently col+1 columns of the block aligned  */
      for (x=minvalue; x <= maxscore; x++)
      {
            ends[x].ways += last[x].ways;
            ends[x].prob += last[x].prob * probwt[col - 1];
      }
/*    for (aa=0; aa < AASALL; aa++) */
      for (aa=1; aa <= 20; aa++)
      {
         for (x=minvalue; x <= maxscore; x++)
         {
            if (last[x].ways > 0)
            {
               score = x + round(matrix->weights[aa][col]);
               this[score].ways += last[x].ways;
               if (ftype == 1) ftemp = obs_freqs->weights[aa][col] / 100.;
               else            ftemp = freqs[aa];
               this[score].prob += last[x].prob * ftemp;
            }
         } /* end of score x */
      }  /* end of aa */
      /*---------   Switch the arrays ------------------------------*/
      if (this == Scores[1])
      {  last = Scores[1]; this = Scores[0]; }
      else
      {  last = Scores[0]; this = Scores[1]; }
      for (x = minvalue; x <= maxscore; x++)
      {  this[x].ways = this[x].prob = 0.0;  }
   }  /* end of col */

   /*-------- last now has the final counts of all combinations
      of column scores for full blocks, and ends has the counts
      for alignments off the left end. Still have to get counts
      for alignments off the right end and need two arrays to do
      it. So have to keep last results in another array--------*/
   for (x=minvalue; x <= maxscore; x++)
   {
	middle[x].ways = last[x].ways;
	middle[x].prob = last[x].prob * probwt[matrix->width - 1];
	last[x].ways = last[x].prob = 0.0;
   }

   /*-------- Get the alignments hanging off the right end -------*/
   /*    Initialize with last column   */
   col = matrix->width - 1;
   for (aa=1; aa <= 20; aa++)
   {
      x = round(matrix->weights[aa][col]);
      last[x].ways += 1.0;
      if (ftype == 1) ftemp = obs_freqs->weights[aa][col] / 100.;
      else            ftemp = freqs[aa];
      last[x].prob += ftemp;   
   }
   for (col = matrix->width - 2; col >= 1; col--)
   {
      /*--------- Save the gapped alignments off the right end ------*/
      /*  There are currently length-col columns of the block aligned */
      for (x=minvalue; x <= maxscore; x++)
      {
            ends[x].ways += last[x].ways;
            ends[x].prob += last[x].prob * probwt[matrix->width - col - 2];
      }
      for (aa=1; aa <= 20; aa++)
      {
         for (x=minvalue; x <= maxscore; x++)
         {
            if (last[x].ways > 0)
            {
               score = x + round(matrix->weights[aa][col]);
               this[score].ways += last[x].ways;
               if (ftype == 1) ftemp = obs_freqs->weights[aa][col] / 100.;
               else            ftemp = freqs[aa];
               this[score].prob += last[x].prob * ftemp;
            }
         } /* end of score x */
      }  /* end of aa */
      /*---------   Switch the arrays ------------------------------*/
      if (this == Scores[1])
      {  last = Scores[1]; this = Scores[0]; }
      else
      {  last = Scores[0]; this = Scores[1]; }
      for (x = minvalue; x <= maxscore; x++)
      {  this[x].ways = this[x].prob = 0.0;  }
   }  /* end of column */
   /*--------- Save the gapped alignments off the right end ------*/
   /*  Need to get the length - 1 counts from the right   */
   for (x=minvalue; x <= maxscore; x++)
   {
         ends[x].ways += last[x].ways;
         ends[x].prob += last[x].prob * probwt[matrix->width - 2];
   } 

   /*--------cumprob[x] has sum from x to maxscore of prob[x]; this
	is the prob(score >= x) -------------------------------------*/
   cum = 0.0;
   for (x = maxscore; x >= minvalue; x--)
   {
      if (middle[x].ways > 0.0 || ends[x].ways > 0.0)
      {
         cum += (middle[x].prob + ends[x].prob);
      }
      cumprob[x] = cum;
      if (fcum != NULL && cum < MAXPROB)
      { fprintf(fcum, "%d %6.2g\n", x, cum); }
   }

   /*------- Make a histogram now for display ----*/
   cum = dtemp = 0.0;
   for (col=0; col < MAXSCORE/HISTO; col++)
   { histo[col].ways = histo[col].prob = 0.0; }
   for (x = minvalue; x <= maxscore; x++)
   {
      if (middle[x].ways > 0.0 || ends[x].ways > 0.0)
      {
/*       printf("%4d %8.4f %11.8f\n", x, log10(middle[x].ways),
                middle[x].prob ); */
         histo[ (int) x/HISTO ].ways += middle[x].ways;
         histo[ (int) x/HISTO ].prob += middle[x].prob;
         histo[ (int) x/HISTO ].ways += ends[x].ways;
         histo[ (int) x/HISTO ].prob += ends[x].prob; 
         cum += middle[x].prob; dtemp += ends[x].prob;
      }
/*    else
         printf("%4d   none\n", x); */
   }
   printf("Sum of probabilities = %8.4f\n", cum + dtemp);

   /*   number of alignments done in a hypothetical search   */
   /*   Always assume one alignment per TP sequence          */
   if (ftype == 1) aligns = TPS;
   else aligns = (double) SearchAA + Search * (matrix->width - 1); 
/* else aligns = 10000000; */

   /*   Print the histogram  */
   if (ftype == 1) pflag = 0; else pflag = 1;   /* don't print 0 TP buckets */
   printf("Score range  log(Possible ways)  Probability  Expected scores\n");
   for (x = (int) minvalue/HISTO; x <= (int) maxscore/HISTO; x++)
   {
      if (ftype == 1 && histo[x].ways > 0.0) pflag = 1;
      if (pflag)
      {
         if (histo[x].ways > 0.0)
            printf("%4d %4d  %8.4f      %11.8f      %8.2f\n",
                 x*HISTO, x*HISTO+HISTO-1, log10(histo[x].ways),
                histo[x].prob, histo[x].prob * aligns );
         else
            printf("%4d %4d       0.0000       0.000000\n", 
		x*HISTO, x*HISTO+HISTO-1);
      }
   }

   /* Count the TP scores above 99.5% of TN scores, x is the score */
   if (ftype == 1 && TN995 > 0)
   {
      x = maxscore; TPabove = 0.0;
      while (x > TN995)
      {
         if (middle[x].prob > 0.0 || ends[x].prob > 0.0)
         {
            TPabove += (middle[x].prob + ends[x].prob) * aligns;
         }
         x--;
      }
   }

   /* Print the top scores, x is the score, cum is the
	cumulative number of expected scores,
	report is the cutoff number of scores */
   x = maxscore; cum = 0.0;
   printf("\nCumScrs  Score   ExpectedScrs\n");
   while (cum < report && x >= 0)
   {
       if (middle[x].prob > 0.0 || ends[x].prob > 0.0)
       {
          if (cum > 100.0)
             printf("%8.4f %4d %8.4f\n", 
		cum, x, (middle[x].prob + ends[x].prob) * aligns);
          cum += (middle[x].prob + ends[x].prob) * aligns;
       }
       x--;
   }
   xreport = x;

   if (ftype == 1)
   { 
	printf("Median TP score = %d, TPabove = %lf\n", xreport, TPabove); 
   }
   else
   { 
      while (cum < report80 && x >= 0)
      {
          if (middle[x].prob > 0.0 || ends[x].prob > 0.0)
          {
             if (cum > 100.0)
                printf("%8.4f %4d %8.4f\n", 
	   	cum, x, (middle[x].prob + ends[x].prob) * aligns);
             cum += (middle[x].prob + ends[x].prob) * aligns;
          }
          x--;
      }
	TN800 = x;
	printf("99.5 TN score = %d, 80.0 = %d\n", xreport, TN800); 
   }

   return(xreport);		/* TN995 if ftype == 0 */
}  /* end of compute */
/*=================================================================
 * load_freqs
 *   reads in the frequencies if there is a frequency file.
 *   Parameters: none
 *   Return codes: TRUE if there was a frequency file and the data was 
 *                 sucessfully read in, FALSE if not.
 *   Error codes: none
 =================================================================*/

int load_freqs(ffp, frequency)
FILE *ffp;
double frequency[AASALL];
{
  int i;
  int seq_type;
  double J_weight, O_weight, U_weight;


#define NAR '|'   /* a char that get converted to AAID_NAR for the codes so */
		  /* that when reading in the frequencies entries for J, O, */
		  /* an U do not overwrite the entry for X.  Also if the */
		  /* idea of have non-code alpha characters being treated as */
		  /* X ever changes, there shouldn't be a change needed */
		  /* (assuming that J, O, U are weighted the same). */

  /* old style format */
  frequency[aa_atob['-']] = read_a_freq(ffp);
  frequency[aa_atob['A']] = read_a_freq(ffp);
  frequency[aa_atob['B']] = read_a_freq(ffp);
  frequency[aa_atob['C']] = read_a_freq(ffp);
  frequency[aa_atob['D']] = read_a_freq(ffp);
  frequency[aa_atob['E']] = read_a_freq(ffp);
  frequency[aa_atob['F']] = read_a_freq(ffp);
  frequency[aa_atob['G']] = read_a_freq(ffp);
  frequency[aa_atob['H']] = read_a_freq(ffp);
  frequency[aa_atob['I']] = read_a_freq(ffp);

  J_weight = read_a_freq(ffp);
  frequency[aa_atob[NAR]] = J_weight; /* 'J' */

  frequency[aa_atob['K']] = read_a_freq(ffp);
  frequency[aa_atob['L']] = read_a_freq(ffp);
  frequency[aa_atob['M']] = read_a_freq(ffp);
  frequency[aa_atob['N']] = read_a_freq(ffp);

  O_weight = read_a_freq(ffp);
  frequency[aa_atob[NAR]] = O_weight; /* 'O' */

  frequency[aa_atob['P']] = read_a_freq(ffp);
  frequency[aa_atob['Q']] = read_a_freq(ffp);
  frequency[aa_atob['R']] = read_a_freq(ffp);
  frequency[aa_atob['S']] = read_a_freq(ffp);
  frequency[aa_atob['T']] = read_a_freq(ffp);

  U_weight = read_a_freq(ffp);
  frequency[aa_atob[NAR]] = U_weight; /* 'U' */

  frequency[aa_atob['V']] = read_a_freq(ffp);
  frequency[aa_atob['W']] = read_a_freq(ffp);
  frequency[aa_atob['X']] = read_a_freq(ffp);
  frequency[aa_atob['Y']] = read_a_freq(ffp);
  frequency[aa_atob['Z']] = read_a_freq(ffp);
  frequency[aa_atob['*']] = read_a_freq(ffp);

#undef NAR


  /* check the frequency array for zero values */
  for (i=0; iwidth; col++)
   {
      tot = 0;
      for (aa = 1; aa <= 20; aa++) tot += obs_freqs->weights[aa][col];
      for (aa = 1; aa <= 20; aa++)
      {
         if (obs_freqs->weights[aa][col] > 0.0)
         {
            obs_freqs->weights[aa][col] *= 100.0;
            obs_freqs->weights[aa][col] /= tot;
         }
      }
   }
   
}  /* end of fix_freqs  */
/*===================================================================
     count the number of sequence names in a .lis file
=====================================================================*/
int count_tps(flis)
FILE *flis;
{
   int nids;
   char line[MAXLINE];

   nids = 0;

   while(!feof(flis) && fgets(line, MAXLINE, flis) != NULL &&
	 strlen(line) > 2)
   {		/* skip over title or directory lines */
      if (line[0] != '>' && strstr(line, "/") == NULL &&
	  strstr(line,"\\") == NULL && strstr(line, ":") == NULL)
      {
	 nids++;
      }
   }
    return (nids);
}  /* end of count_tps */
arrays ------------------------------*/
   blimps-3.9/blimps/Makefile.Linux000064400001460000012000003027351042724345400172110ustar00jorjastaff00000400000027# Makefile: makefile for BLIMPS blocks searcher
# Written by: Bill Alford
# (C) Copyright 1993-9, Fred Hutchinson Cancer Research Center 
# Use, modification or distribution of these programs is subject to 
# the terms of the non-commercial licensing agreement in license.h. 

# Instructions for use:
# 1. Change DEFINES, SYSTEM, OPTIMIZ, RANLIB, CC for your system
# 2. make depend
# 3. make install (updates ../bin and ../lib)


# System defines.  The main reason for this is that on the Sun there is a 
# function malloc_debug() wich will raise a signal if there are problems
# with memory.  The problem is that there is no function like that on other
# machines, at least that I've seen.  Defines are set up so that the
# malloc_debug call is only in the Sun code.

# Generic -- Should work on most systems not listed below.
#DEFINES = -DNO_STRDUP
#SYSTEM  = generic 
#OPTIMIZ =
#RANLIB = ../bin/ranlib

# SunOS
#DEFINES = 
#SYSTEM  = sun4.1.3
#OPTIMIZ = -O
#RANLIB = /bin/ranlib
## For debugging.
# DEFINES = -DMALLOC_DEBUG
# OTHER_OBJS = /usr/lib/debug/malloc.o 

# Sun Solaris
#DEFINES = 
#SYSTEM = solaris
#	Some programs don't give the same results when compiled with -fast,
#	e.g. codehop.c; offending options -fsimple=2
#OPTIMIZ = -fast
#OPTIMIZ = -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=2 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit 
#OPTIMIZ = -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit
#OPTIMIZ = -g
#	RANLIB is obsolete under Solaris 2.5; just put something here
#	so the Makefile continues to work.

# Linux
DEFINES = 
SYSTEM  = 
OPTIMIZ = -Wall -O2
RANLIB = ls

MAKE = make
DEPEND = makedepend

#	ar -t libpssm.a for table of contents
AR = ar
RM = rm -f
MV = mv -f 
CP = cp


# C compiler
CC = /usr/bin/gcc
#CC = /opt/SUNWspro/bin/cc

# Optimization level (or debugging)
#OPTIMIZ = -g
#OPTIMIZ = -g -O $(WARNS) $(XWARN)
#OPTIMIZ = -p
WARNS = -W \
	-Wreturn-type \
	-Wswitch \
	-Wcomment \
	-Wtrigraphs \
	-Wformat \
	-Wparentheses 

# like -Wall but without 
#   -Wimplicit  -- gets all the printf's etc..
#   -Wunused    -- gets all the rcsid and 3 funcs. I know about
#   -Wchar-subscripts -- gets all ??_atob arrays (ascii to binary residue)
#   -Wuninitialized -- Caught 4 places which are tricky cases but are OK.

WARNS2 = -Wall
XWARN = -Wshadow \
	-Wcast-qual \
	-Wcast-align \
	-Wpointer-arith \
	-Waggregate-return \
	-Wredundant-decls \
	-Wnested-externs \
	-Winline

#    -Wtraditional -- gets printf, fprintf, etc.
#    -Wid-clash-16 -- causes lots of warnings.
#    -Wwrite-strings -- causes a LOT of warnings, think all are needed.
#    -Wconversion  -- causes a lot of warnings, but they look like they 
#                       should be OK.
#    -Wstrict-prototypes -Wmissing-prototypes -- too many to count...

XXWARN = -Werror

INCLUDE_DIR = ../include
INCLUDES = -I$(INCLUDE_DIR)


# C Flags to compiler
#CFLAGS = `getconf LFS_CFLAGS` $(OPTIMIZ) $(DEFINES) $(INCLUDES)
CFLAGS = $(OPTIMIZ) $(DEFINES) $(INCLUDES)


# Linker Flags
LDFLAGS = $(CFLAGS)
LDLIBS = -lblimps -ly -lm
LDOPTIONS = $(LDFLAGS) $(LDDIR)
# cc ld options


#LIBRARY_DIR = ../lib
LIBRARY_DIR = ./
LDDIR = -L$(LIBRARY_DIR)


# source files
SRCS =  blimps-mem.c \
	blimps.c \
	blweight.c \
	blalign.c \
	bldist.c \
	blk2pssm.c \
	rank_matrix.c \
	retblock.c \
	codehop.c \
        htmlize-codehop.c \
        oligo_melt.c \
	mablock.c \
	cobbler.c \
	addseqs.c \
	fastaseqs.c \
	LAMA.c \
	find_biassed_blocks.c \
	makeblockmap.c \
	prints2blocks.c \
	lisblk.c \
	coduse.c \
	narrow.c \
	blk2slx.c \
	blkprob.c \
	blocks.c \
	config.c \
	convert.c \
	errors.c \
	files.c \
	frequency.c \
	gcode.c \
	lists.c \
	matrix.c \
	memory.c \
	pattern.c \
	scores.c \
	scoring.c \
	sequences.c \
	sl.c \
	strutil.c \
	version.c \
	options.c \
	protomat.c  \
	interpro.c \
	pssmdist.c \
	pssmBL.c \
	papssm.c \
	matrix_logob.c \
	makelogob.c \
	blocks_search.c \
	LAMA_search.c \
	block_vis.c \
	format_block.c \
	biassed_blocks_finder.c \
	htmlize-LAMA.c \
	show_aligned_blocks.c \
	blk2mot.c 

HDRS =  blimps.h \
	blweight.h \
	blimps-mem.h \
	config.h \
	lists.h \
	scores.h \
	scoring.h \
	protomat.h \
	p2c.h


# need the OBJS for blimps dependencies on the .o files.  I don't know a 
# way around this.

OTHER_OBJS_DEBUG =	/usr/lib/debug/malloc.o \
		/usr/lib/debug/mallocmap.o

LIBOBJS = pattern.o \
	files.o \
	frequency.o \
	convert.o \
	blocks.o \
	errors.o \
	gcode.o \
	matrix.o \
	memory.o \
	sequences.o \
	strutil.o \
	sl.o \
	version.o \
	options.o \
	blimps-mem.o \
	config.o \
	lists.o \
	scores.o \
	scoring.o \
	p2clib.o \
	util.o \
        protomat.o


# need malloc.o for malloc_debug() which will have free() raise SIGABRT
# if it is unable to free the space.

LIBRARIES = libblimps.a


########################################################################
########################################################################
#
# main dependencies
#
########################################################################
########################################################################

install: clean all move-lib move-bin

all: lib blimps blweight blalign bldist blk2pssm rank_matrix retblock codehop htmlize-codehop oligo_melt mablock cobbler addseqs fastaseqs LAMA find_biassed_blocks makeblockmap prints2blocks lisblk coduse narrow blk2slx blkprob interpro pssmdist pssmBL papssm matrix_logob makelogob blocks_search LAMA_search block_vis format_block biassed_blocks_finder htmlize-LAMA show_aligned_blocks makelis blk2mot 

blimps: $(LIBRARIES) blimps.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blimps.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

makelis: $(LIBRARIES)  makelis.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  makelis.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blweight: $(LIBRARIES) blweight.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blweight.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blalign: $(LIBRARIES) blalign.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blalign.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

bldist: $(LIBRARIES) bldist.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  bldist.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 
blk2pssm: $(LIBRARIES) blk2pssm.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blk2pssm.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

rank_matrix: $(LIBRARIES) rank_matrix.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  rank_matrix.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

retblock: $(LIBRARIES) retblock.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  retblock.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

codehop: $(LIBRARIES) codehop.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  codehop.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

htmlize-codehop: $(LIBRARIES) htmlize-codehop.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  htmlize-codehop.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

oligo_melt: $(LIBRARIES) oligo_melt.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  oligo_melt.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

mablock: $(LIBRARIES) mablock.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  mablock.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

cobbler: $(LIBRARIES) cobbler.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  cobbler.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

addseqs: $(LIBRARIES) addseqs.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  addseqs.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

fastaseqs: $(LIBRARIES) fastaseqs.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  fastaseqs.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

LAMA: $(LIBRARIES) LAMA.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  LAMA.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

find_biassed_blocks: $(LIBRARIES) find_biassed_blocks.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  find_biassed_blocks.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

makeblockmap: $(LIBRARIES) makeblockmap.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  makeblockmap.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

prints2blocks: $(LIBRARIES) prints2blocks.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  prints2blocks.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

lisblk: $(LIBRARIES) lisblk.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  lisblk.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

coduse: $(LIBRARIES) coduse.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  coduse.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

narrow: $(LIBRARIES) narrow.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  narrow.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blk2slx: $(LIBRARIES) blk2slx.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blk2slx.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blkprob: $(LIBRARIES) blkprob.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blkprob.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

interpro: $(LIBRARIES) interpro.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  interpro.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

pssmdist: $(LIBRARIES) pssmdist.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  pssmdist.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

pssmBL: $(LIBRARIES) pssmBL.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  pssmBL.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

papssm: $(LIBRARIES) papssm.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  papssm.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

matrix_logob: $(LIBRARIES) matrix_logob.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  matrix_logob.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

makelogob: $(LIBRARIES) makelogob.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  makelogob.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blocks_search: $(LIBRARIES) blocks_search.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  blocks_search.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

LAMA_search: $(LIBRARIES) LAMA_search.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  LAMA_search.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

block_vis: $(LIBRARIES) block_vis.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  block_vis.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

format_block: $(LIBRARIES) format_block.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  format_block.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

biassed_blocks_finder: $(LIBRARIES) biassed_blocks_finder.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  biassed_blocks_finder.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

htmlize-LAMA: $(LIBRARIES) htmlize-LAMA.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  htmlize-LAMA.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

show_aligned_blocks: $(LIBRARIES) show_aligned_blocks.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  show_aligned_blocks.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blk2mot: $(LIBRARIES) blk2mot.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  blk2mot.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 


$(LIBOBJS):


########################################################################
########################################################################
#
# include dependencies
#
########################################################################
########################################################################

# none




########################################################################
########################################################################
#
# library dependencies
#
########################################################################
########################################################################

lib: ranlib $(LIBRARIES)

ranlib:
	$(GET_FILES)

#	( cd $(LIBRARY_DIR) ; $(MAKE) $(MFLAGS) )

#
# The libraries.
#

libblimps.a: $(LIBOBJS)
	$(AR) cr $@ $(LIBOBJS) ; $(RANLIB) $@

########################################################################
########################################################################
#
# Local building (for us)
#
########################################################################
########################################################################

#  os = OS_machinename_version
local: clean clean-include clean-lib 
	echo " " ; \
	echo "Making directories..." ; \
	echo " " ; \
	os="`uname -sr | tr ' ' '_'`" ; \
	osdir="../$$os" ; \
	rm -rf $$osdir ; \
	mkdir $$osdir $$osdir/bin $$osdir/include $$osdir/lib ; \
	echo " " ; \
	echo "Running 'make depend' and 'make all'..." ; \
	echo " " ; \
	make depend ; make all	; \
	echo " " ; \
	echo "Copying libraries..." ; \
	echo " " ; \
	cp ../lib/*.a $$osdir/lib ; \
	echo " " ; \
	echo "Copying header files..." ; \
	echo " " ; \
	cp ../include/*.h $$osdir/include ; \
	echo " " ; \
	echo "Copying binary..." ; \
	echo " " ; \
	cp blimps $$osdir/bin





########################################################################
########################################################################
#
# Maintenance dependencies
#
########################################################################
########################################################################


tags: 
	etags ./*.[ch] $(INCLUDE_DIR)/*.[ch]


depend: 
	 $(DEPEND) -- $(CFLAGS) -- -s "# DO NOT DELETE" -- $(SRCS)


clean::
	$(RM) blimps blweight blalign bldist blk2pssm rank_matrix retblock codehop htmlize-codehop oligo_melt mablock makeblockmap prints2blocks lisblk coduse narrow blkprob blk2slx LAMA find_biassed_blocks fastaseqs addseqs cobbler interpro pssmdist pssmBL papssm matrix_logob makelogob blocks_search LAMA_search block_vis format_block biassed_blocks_finder htmlize-LAMA show_aligned_blocks makelis blk2mot 
	$(RM) *.a *.o *~ 
	@echo " "

move-lib:
	$(MV) lib*.a ../lib

move-bin:
	$(MV) blimps ../bin
	$(MV) blweight ../bin
	$(MV) blalign ../bin
	$(MV) bldist ../bin
	$(MV) blk2pssm ../bin
	$(MV) rank_matrix ../bin
	$(MV) retblock ../bin
	$(MV) codehop ../bin
	$(MV) htmlize-codehop ../bin
	$(MV) oligo_melt ../bin
	$(MV) mablock ../bin
	$(MV) makeblockmap ../bin
	$(MV) prints2blocks ../bin
	$(MV) lisblk ../bin
	$(MV) coduse ../bin
	$(MV) narrow ../bin
	$(MV) blkprob ../bin
	$(MV) blk2slx ../bin
	$(MV) LAMA ../bin
	$(MV) find_biassed_blocks ../bin
	$(MV) fastaseqs ../bin
	$(MV) addseqs ../bin
	$(MV) cobbler ../bin
	$(MV) interpro ../bin
	$(MV) pssmdist ../bin
	$(MV) pssmBL ../bin
	$(MV) papssm ../bin
	$(MV) matrix_logob ../bin
	$(MV) makelogob ../bin
	$(MV) blocks_search ../bin
	$(MV) LAMA_search ../bin
	$(MV) block_vis ../bin
	$(MV) format_block ../bin
	$(MV) biassed_blocks_finder ../bin
	$(MV) htmlize-LAMA ../bin
	$(MV) show_aligned_blocks ../bin
	$(MV) makelis ../bin
	$(MV) blk2mot ../bin


##########
##########
#
# Distribution dependencies
#
##########
##########

SOURCEDIR  = /lab/billa/blimps/dev
BUILDDIR   = /lab/billa/blimps/build-local
DISTRIBDIR = /lab/billa/blimps/distrib
VERSIONDISTRIB = $(DISTRIBDIR).$(VERSION)
BLIMPSDIR  = $(DISTRIBDIR)/blimps
FTPDIR     = /lab/ftp/blimps

TXTVER = `echo  $(VERSION) | \
	 awk -F. '{printf("%d.%d%c", $$1, $$2 / 1000 , \
	 ( $$2 % 1000 ) / 100 + 65)}'`

#
# REMEMBER: each line executes in the directory make started in
#

local-binary: clean-local-binary
	@if [ "$(VERSION)" = "" ] ; then \
		echo "No version specified, bailing out." ; \
		echo "use as: make [ target ... ] VERSION=1.1001" ; \
		echo "    ex: make distrib VERSION=1.1001" ; \
		bail-out-here ; \
	fi
	
	@echo Building local binary for distribution . . .
	@echo " "
	
	@echo Making local build directory . . .
	@mkdir -p $(BUILDDIR)
	
	@echo Making blimps, lib, and include subdirectories . . .
	@mkdir -p $(BUILDDIR)/blimps
	@mkdir -p $(BUILDDIR)/lib
	@mkdir -p $(BUILDDIR)/include
	
	@echo Copying Makefiles over . . .
	@echo REMOVING RCS SUBDIR DEPENDENCY BY THE GREP > /dev/null
	@cat $(SOURCEDIR)/blimps/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BUILDDIR)/blimps/Makefile
	@cat $(SOURCEDIR)/lib/Makefile | grep -v 'RCS/\$$\$$\@,v' >    $(BUILDDIR)/lib/Makefile
	@cat $(SOURCEDIR)/include/Makefile | grep -v 'RCS/\$$\$$\@,v' >$(BUILDDIR)/include/Makefile
	
	@ln -s $(SOURCEDIR)/blimps/RCS  $(BUILDDIR)/blimps/RCS
	@ln -s $(SOURCEDIR)/lib/RCS     $(BUILDDIR)/lib/RCS
	@ln -s $(SOURCEDIR)/include/RCS $(BUILDDIR)/include/RCS
	
	@echo Making local version dependencies . . .
	cd $(BUILDDIR)/blimps ; make VERSION="$(VERSION)" clean ; make VERSION="$(VERSION)" depend 
	
	@echo Removing RCS files to test distrib compilation
	@rm -f $(BUILDDIR)/blimps/RCS
	@rm -f $(BUILDDIR)/lib/RCS
	@rm -f $(BUILDDIR)/include/RCS
	
	@echo Making local version . . .
	cd $(BUILDDIR)/blimps ; make VERSION="$(VERSION)" blimps
	
	@echo Moving local binary into distribution directory . . .
	@mv $(BUILDDIR)/blimps/blimps $(SOURCEDIR)/bin/blimps.$(SYSTEM)
	@echo " "

clean-local-binary:
	@echo Cleaning local build directory \($(BUILDDIR)\) . . .
	rm -rf $(BUILDDIR)
	@echo " "


distrib: local-binary clean-distrib
	@if [ "$(VERSION)" = "" ] ; then \
		echo "No version specified, bailing out." ; \
		echo "use as: make [ target ... ] VERSION=1.1001" ; \
		echo "    ex: make distrib VERSION=1.1001" ; \
		bail-out-here ; \
	fi
	
	@echo Making distribution . . .
	@echo " "
	
	@echo Making distribution directories . . .
	@mkdir -p $(DISTRIBDIR)
	@mkdir -p $(BLIMPSDIR) \
		  $(BLIMPSDIR)/docs \
		  $(BLIMPSDIR)/blimps \
		  $(BLIMPSDIR)/lib \
		  $(BLIMPSDIR)/include \
		  $(BLIMPSDIR)/bin
	@ln -s $(SOURCEDIR)/blimps/RCS  $(BLIMPSDIR)/blimps/RCS
	@ln -s $(SOURCEDIR)/lib/RCS     $(BLIMPSDIR)/lib/RCS
	@ln -s $(SOURCEDIR)/include/RCS $(BLIMPSDIR)/include/RCS
	@ln -s $(SOURCEDIR)/docs/RCS    $(BLIMPSDIR)/docs/RCS
	
	@echo Copying Makefiles over . . .
	@cat $(SOURCEDIR)/blimps/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BLIMPSDIR)/blimps/Makefile
	@cat $(SOURCEDIR)/lib/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BLIMPSDIR)/lib/Makefile
	@cat $(SOURCEDIR)/include/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BLIMPSDIR)/include/Makefile
	
	@echo Making depend on the Makefiles to checkout the files
	cd $(BLIMPSDIR)/blimps ; make VERSION="$(VERSION)" depend
	@rm -f $(BLIMPSDIR)/blimps/RCS
	@rm -f $(BLIMPSDIR)/lib/RCS
	@rm -f $(BLIMPSDIR)/include/RCS
	
	@echo Copying distribution documents of version $(VERSION) into docs directory . . .
	@cd $(BLIMPSDIR)/docs ; co -q -r$(VERSION) RCS/*
	@rm -f $(BLIMPSDIR)/docs/RCS
	@cd $(BLIMPSDIR)/docs ; cp README INSTALL ..
	
	@echo Copying pre-compiled binaries into bin directory . . .
	@cp $(SOURCEDIR)/bin/* $(BLIMPSDIR)/bin/
	
	@echo Moving blimps to blimps.$(TXTVER)
	@mv $(BLIMPSDIR) $(DISTRIBDIR)/blimps.$(TXTVER)
	@echo " "
	
	@echo Making tar file . . .
	@cd $(DISTRIBDIR) ; tar cf blimps.$(TXTVER).tar blimps.$(TXTVER)
	
	@echo Compressing tar file . . .
	@cd $(DISTRIBDIR) ; compress blimps.$(TXTVER).tar
	@echo " "
	
	@echo Moving distrib dir to distrib.$(VERSION)
	@mv $(DISTRIBDIR) $(VERSIONDISTRIB)

clean-distrib:
	@echo  Cleaning distribution directories:
	@echo "     $(DISTRIBDIR)"
	@echo "     $(VERSIONDISTRIB)"
	@echo " . . . "
	rm -rf $(DISTRIBDIR) $(VERSIONDISTRIB)
	@echo " "

$(VERSIONDISTRIB):	distrib

ftp:	$(VERSIONDISTRIB)
	@echo Moving files to the ftp directory . . .
	@echo " "
	
	@echo Copying tar file to the ftp directory . . .
	@cp $(VERSIONDISTRIB)/blimps.$(TXTVER).tar.Z $(FTPDIR)
	@echo " "
	
	@echo Copying README and INSTALL files to the ftp directory . . .
	@rm -f $(FTPDIR)/README $(FTPDIR)/INSTALL 
	@cp $(VERSIONDISTRIB)/blimps.$(TXTVER)/docs/README \
	  $(VERSIONDISTRIB)/blimps.$(TXTVER)/docs/INSTALL $(FTPDIR)
	@echo " "



###########################################################################

 
###########################################################################
# dependencies generated by makedepend
 
# DO NOT DELETE

blimps-mem.o: ../include/global.h /usr/include/stdlib.h
blimps-mem.o: /usr/include/features.h /usr/include/sys/cdefs.h
blimps-mem.o: /usr/include/gnu/stubs.h
blimps-mem.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
blimps-mem.o: /usr/include/stdio.h /usr/include/bits/types.h
blimps-mem.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
blimps-mem.o: /usr/include/libio.h /usr/include/_G_config.h
blimps-mem.o: /usr/include/wchar.h /usr/include/bits/wchar.h
blimps-mem.o: /usr/include/gconv.h
blimps-mem.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
blimps-mem.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
blimps-mem.o: /usr/include/string.h /usr/include/ctype.h
blimps-mem.o: /usr/include/endian.h /usr/include/bits/endian.h
blimps-mem.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
blimps-mem.o: ../include/errors.h ../include/memory.h blimps-mem.h blimps.h
blimps-mem.o: lists.h ../include/skiplist.h
blimps.o: /usr/include/math.h /usr/include/features.h
blimps.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
blimps.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
blimps.o: /usr/include/bits/mathcalls.h /usr/include/signal.h
blimps.o: /usr/include/bits/sigset.h /usr/include/bits/types.h
blimps.o: /usr/include/bits/wordsize.h
blimps.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
blimps.o: /usr/include/bits/typesizes.h /usr/include/bits/signum.h
blimps.o: ../include/global.h /usr/include/stdlib.h /usr/include/stdio.h
blimps.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
blimps.o: /usr/include/bits/wchar.h /usr/include/gconv.h
blimps.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
blimps.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
blimps.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
blimps.o: /usr/include/bits/endian.h /usr/include/malloc.h
blimps.o: ../include/license.h ../include/strutil.h ../include/errors.h
blimps.o: ../include/memory.h ../include/version.h ../include/residues.h
blimps.o: ../include/blastapp.h /usr/include/limits.h
blimps.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
blimps.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blimps.o: ../include/gcode.h ../include/files.h ../include/blocks.h
blimps.o: ../include/output.h ../include/sequences.h ../include/matrix.h
blimps.o: ../include/pattern.h ../include/convert.h ../include/frequency.h
blimps.o: ../include/options.h blimps.h blimps-mem.h config.h scores.h
blimps.o: scoring.h lists.h ../include/skiplist.h
blweight.o: ../include/blocksprogs.h /usr/include/stdlib.h
blweight.o: /usr/include/features.h /usr/include/sys/cdefs.h
blweight.o: /usr/include/gnu/stubs.h
blweight.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
blweight.o: /usr/include/stdio.h /usr/include/bits/types.h
blweight.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
blweight.o: /usr/include/libio.h /usr/include/_G_config.h
blweight.o: /usr/include/wchar.h /usr/include/bits/wchar.h
blweight.o: /usr/include/gconv.h
blweight.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
blweight.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
blweight.o: /usr/include/string.h /usr/include/math.h
blweight.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
blweight.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
blweight.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
blweight.o: /usr/include/ctype.h /usr/include/endian.h
blweight.o: /usr/include/bits/endian.h ../include/global.h
blweight.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
blweight.o: ../include/errors.h ../include/memory.h ../include/residues.h
blweight.o: ../include/blastapp.h /usr/include/limits.h
blweight.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
blweight.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blweight.o: ../include/gcode.h ../include/blocks.h ../include/output.h
blweight.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blweight.o: ../include/convert.h ../include/frequency.h ../include/files.h
blweight.o: ../include/protomat.h /usr/include/sys/time.h /usr/include/time.h
blweight.o: /usr/include/bits/time.h /usr/include/sys/select.h
blweight.o: /usr/include/bits/select.h /usr/include/bits/sigset.h
blalign.o: ../include/blocksprogs.h /usr/include/stdlib.h
blalign.o: /usr/include/features.h /usr/include/sys/cdefs.h
blalign.o: /usr/include/gnu/stubs.h
blalign.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
blalign.o: /usr/include/stdio.h /usr/include/bits/types.h
blalign.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
blalign.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
blalign.o: /usr/include/bits/wchar.h /usr/include/gconv.h
blalign.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
blalign.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
blalign.o: /usr/include/string.h /usr/include/math.h
blalign.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
blalign.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
blalign.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
blalign.o: /usr/include/ctype.h /usr/include/endian.h
blalign.o: /usr/include/bits/endian.h ../include/global.h
blalign.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
blalign.o: ../include/errors.h ../include/memory.h ../include/residues.h
blalign.o: ../include/blastapp.h /usr/include/limits.h
blalign.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
blalign.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blalign.o: ../include/gcode.h ../include/blocks.h ../include/output.h
blalign.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blalign.o: ../include/convert.h ../include/frequency.h ../include/files.h
blalign.o: ../include/protomat.h
bldist.o: ../include/blocksprogs.h /usr/include/stdlib.h
bldist.o: /usr/include/features.h /usr/include/sys/cdefs.h
bldist.o: /usr/include/gnu/stubs.h
bldist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
bldist.o: /usr/include/stdio.h /usr/include/bits/types.h
bldist.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
bldist.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
bldist.o: /usr/include/bits/wchar.h /usr/include/gconv.h
bldist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
bldist.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
bldist.o: /usr/include/string.h /usr/include/math.h
bldist.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
bldist.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
bldist.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
bldist.o: /usr/include/ctype.h /usr/include/endian.h
bldist.o: /usr/include/bits/endian.h ../include/global.h
bldist.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
bldist.o: ../include/errors.h ../include/memory.h ../include/residues.h
bldist.o: ../include/blastapp.h /usr/include/limits.h
bldist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
bldist.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
bldist.o: ../include/gcode.h ../include/blocks.h ../include/output.h
bldist.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
bldist.o: ../include/convert.h ../include/frequency.h ../include/files.h
bldist.o: ../include/protomat.h
blk2pssm.o: ../include/blocksprogs.h /usr/include/stdlib.h
blk2pssm.o: /usr/include/features.h /usr/include/sys/cdefs.h
blk2pssm.o: /usr/include/gnu/stubs.h
blk2pssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
blk2pssm.o: /usr/include/stdio.h /usr/include/bits/types.h
blk2pssm.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
blk2pssm.o: /usr/include/libio.h /usr/include/_G_config.h
blk2pssm.o: /usr/include/wchar.h /usr/include/bits/wchar.h
blk2pssm.o: /usr/include/gconv.h
blk2pssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
blk2pssm.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
blk2pssm.o: /usr/include/string.h /usr/include/math.h
blk2pssm.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
blk2pssm.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
blk2pssm.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
blk2pssm.o: /usr/include/ctype.h /usr/include/endian.h
blk2pssm.o: /usr/include/bits/endian.h ../include/global.h
blk2pssm.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
blk2pssm.o: ../include/errors.h ../include/memory.h ../include/residues.h
blk2pssm.o: ../include/blastapp.h /usr/include/limits.h
blk2pssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
blk2pssm.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blk2pssm.o: ../include/gcode.h ../include/blocks.h ../include/output.h
blk2pssm.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blk2pssm.o: ../include/convert.h ../include/frequency.h ../include/files.h
blk2pssm.o: ../include/protomat.h
rank_matrix.o: ../include/blocksprogs.h /usr/include/stdlib.h
rank_matrix.o: /usr/include/features.h /usr/include/sys/cdefs.h
rank_matrix.o: /usr/include/gnu/stubs.h
rank_matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
rank_matrix.o: /usr/include/stdio.h /usr/include/bits/types.h
rank_matrix.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
rank_matrix.o: /usr/include/libio.h /usr/include/_G_config.h
rank_matrix.o: /usr/include/wchar.h /usr/include/bits/wchar.h
rank_matrix.o: /usr/include/gconv.h
rank_matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
rank_matrix.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
rank_matrix.o: /usr/include/string.h /usr/include/math.h
rank_matrix.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
rank_matrix.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
rank_matrix.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
rank_matrix.o: /usr/include/ctype.h /usr/include/endian.h
rank_matrix.o: /usr/include/bits/endian.h ../include/global.h
rank_matrix.o: /usr/include/malloc.h ../include/license.h
rank_matrix.o: ../include/strutil.h ../include/errors.h ../include/memory.h
rank_matrix.o: ../include/residues.h ../include/blastapp.h
rank_matrix.o: /usr/include/limits.h
rank_matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
rank_matrix.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
rank_matrix.o: ../include/gcode.h ../include/blocks.h ../include/output.h
rank_matrix.o: ../include/sequences.h ../include/matrix.h
rank_matrix.o: ../include/pattern.h ../include/convert.h
rank_matrix.o: ../include/frequency.h ../include/files.h
rank_matrix.o: ../include/protomat.h
retblock.o: ../include/blocksprogs.h /usr/include/stdlib.h
retblock.o: /usr/include/features.h /usr/include/sys/cdefs.h
retblock.o: /usr/include/gnu/stubs.h
retblock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
retblock.o: /usr/include/stdio.h /usr/include/bits/types.h
retblock.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
retblock.o: /usr/include/libio.h /usr/include/_G_config.h
retblock.o: /usr/include/wchar.h /usr/include/bits/wchar.h
retblock.o: /usr/include/gconv.h
retblock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
retblock.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
retblock.o: /usr/include/string.h /usr/include/math.h
retblock.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
retblock.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
retblock.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
retblock.o: /usr/include/ctype.h /usr/include/endian.h
retblock.o: /usr/include/bits/endian.h ../include/global.h
retblock.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
retblock.o: ../include/errors.h ../include/memory.h ../include/residues.h
retblock.o: ../include/blastapp.h /usr/include/limits.h
retblock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
retblock.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
retblock.o: ../include/gcode.h ../include/blocks.h ../include/output.h
retblock.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
retblock.o: ../include/convert.h ../include/frequency.h ../include/files.h
retblock.o: ../include/protomat.h
codehop.o: ../include/blocksprogs.h /usr/include/stdlib.h
codehop.o: /usr/include/features.h /usr/include/sys/cdefs.h
codehop.o: /usr/include/gnu/stubs.h
codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
codehop.o: /usr/include/stdio.h /usr/include/bits/types.h
codehop.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
codehop.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
codehop.o: /usr/include/bits/wchar.h /usr/include/gconv.h
codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
codehop.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
codehop.o: /usr/include/string.h /usr/include/math.h
codehop.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
codehop.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
codehop.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
codehop.o: /usr/include/ctype.h /usr/include/endian.h
codehop.o: /usr/include/bits/endian.h ../include/global.h
codehop.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
codehop.o: ../include/errors.h ../include/memory.h ../include/residues.h
codehop.o: ../include/blastapp.h /usr/include/limits.h
codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
codehop.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
codehop.o: ../include/gcode.h ../include/blocks.h ../include/output.h
codehop.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
codehop.o: ../include/convert.h ../include/frequency.h ../include/files.h
codehop.o: ../include/protomat.h codehop.h /usr/include/sys/time.h
codehop.o: /usr/include/time.h /usr/include/bits/time.h
codehop.o: /usr/include/sys/select.h /usr/include/bits/select.h
codehop.o: /usr/include/bits/sigset.h
htmlize-codehop.o: /usr/include/stdio.h /usr/include/features.h
htmlize-codehop.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
htmlize-codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
htmlize-codehop.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
htmlize-codehop.o: /usr/include/bits/typesizes.h /usr/include/libio.h
htmlize-codehop.o: /usr/include/_G_config.h /usr/include/wchar.h
htmlize-codehop.o: /usr/include/bits/wchar.h /usr/include/gconv.h
htmlize-codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
htmlize-codehop.o: /usr/include/bits/stdio_lim.h
htmlize-codehop.o: /usr/include/bits/sys_errlist.h /usr/include/string.h
htmlize-codehop.o: /usr/include/stdlib.h
oligo_melt.o: ../include/blocksprogs.h /usr/include/stdlib.h
oligo_melt.o: /usr/include/features.h /usr/include/sys/cdefs.h
oligo_melt.o: /usr/include/gnu/stubs.h
oligo_melt.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
oligo_melt.o: /usr/include/stdio.h /usr/include/bits/types.h
oligo_melt.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
oligo_melt.o: /usr/include/libio.h /usr/include/_G_config.h
oligo_melt.o: /usr/include/wchar.h /usr/include/bits/wchar.h
oligo_melt.o: /usr/include/gconv.h
oligo_melt.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
oligo_melt.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
oligo_melt.o: /usr/include/string.h /usr/include/math.h
oligo_melt.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
oligo_melt.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
oligo_melt.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
oligo_melt.o: /usr/include/ctype.h /usr/include/endian.h
oligo_melt.o: /usr/include/bits/endian.h ../include/global.h
oligo_melt.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
oligo_melt.o: ../include/errors.h ../include/memory.h ../include/residues.h
oligo_melt.o: ../include/blastapp.h /usr/include/limits.h
oligo_melt.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
oligo_melt.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
oligo_melt.o: ../include/gcode.h ../include/blocks.h ../include/output.h
oligo_melt.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
oligo_melt.o: ../include/convert.h ../include/frequency.h ../include/files.h
oligo_melt.o: ../include/protomat.h
mablock.o: ../include/blocksprogs.h /usr/include/stdlib.h
mablock.o: /usr/include/features.h /usr/include/sys/cdefs.h
mablock.o: /usr/include/gnu/stubs.h
mablock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
mablock.o: /usr/include/stdio.h /usr/include/bits/types.h
mablock.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
mablock.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
mablock.o: /usr/include/bits/wchar.h /usr/include/gconv.h
mablock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
mablock.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
mablock.o: /usr/include/string.h /usr/include/math.h
mablock.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
mablock.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
mablock.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
mablock.o: /usr/include/ctype.h /usr/include/endian.h
mablock.o: /usr/include/bits/endian.h ../include/global.h
mablock.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
mablock.o: ../include/errors.h ../include/memory.h ../include/residues.h
mablock.o: ../include/blastapp.h /usr/include/limits.h
mablock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
mablock.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
mablock.o: ../include/gcode.h ../include/blocks.h ../include/output.h
mablock.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
mablock.o: ../include/convert.h ../include/frequency.h ../include/files.h
mablock.o: ../include/protomat.h
cobbler.o: ../include/blocksprogs.h /usr/include/stdlib.h
cobbler.o: /usr/include/features.h /usr/include/sys/cdefs.h
cobbler.o: /usr/include/gnu/stubs.h
cobbler.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
cobbler.o: /usr/include/stdio.h /usr/include/bits/types.h
cobbler.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
cobbler.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
cobbler.o: /usr/include/bits/wchar.h /usr/include/gconv.h
cobbler.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
cobbler.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
cobbler.o: /usr/include/string.h /usr/include/math.h
cobbler.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
cobbler.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
cobbler.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
cobbler.o: /usr/include/ctype.h /usr/include/endian.h
cobbler.o: /usr/include/bits/endian.h ../include/global.h
cobbler.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
cobbler.o: ../include/errors.h ../include/memory.h ../include/residues.h
cobbler.o: ../include/blastapp.h /usr/include/limits.h
cobbler.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
cobbler.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
cobbler.o: ../include/gcode.h ../include/blocks.h ../include/output.h
cobbler.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
cobbler.o: ../include/convert.h ../include/frequency.h ../include/files.h
cobbler.o: ../include/protomat.h /usr/include/sys/time.h /usr/include/time.h
cobbler.o: /usr/include/bits/time.h /usr/include/sys/select.h
cobbler.o: /usr/include/bits/select.h /usr/include/bits/sigset.h
addseqs.o: ../include/blocksprogs.h /usr/include/stdlib.h
addseqs.o: /usr/include/features.h /usr/include/sys/cdefs.h
addseqs.o: /usr/include/gnu/stubs.h
addseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
addseqs.o: /usr/include/stdio.h /usr/include/bits/types.h
addseqs.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
addseqs.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
addseqs.o: /usr/include/bits/wchar.h /usr/include/gconv.h
addseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
addseqs.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
addseqs.o: /usr/include/string.h /usr/include/math.h
addseqs.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
addseqs.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
addseqs.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
addseqs.o: /usr/include/ctype.h /usr/include/endian.h
addseqs.o: /usr/include/bits/endian.h ../include/global.h
addseqs.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
addseqs.o: ../include/errors.h ../include/memory.h ../include/residues.h
addseqs.o: ../include/blastapp.h /usr/include/limits.h
addseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
addseqs.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
addseqs.o: ../include/gcode.h ../include/blocks.h ../include/output.h
addseqs.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
addseqs.o: ../include/convert.h ../include/frequency.h ../include/files.h
addseqs.o: ../include/protomat.h
fastaseqs.o: ../include/blocksprogs.h /usr/include/stdlib.h
fastaseqs.o: /usr/include/features.h /usr/include/sys/cdefs.h
fastaseqs.o: /usr/include/gnu/stubs.h
fastaseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
fastaseqs.o: /usr/include/stdio.h /usr/include/bits/types.h
fastaseqs.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
fastaseqs.o: /usr/include/libio.h /usr/include/_G_config.h
fastaseqs.o: /usr/include/wchar.h /usr/include/bits/wchar.h
fastaseqs.o: /usr/include/gconv.h
fastaseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
fastaseqs.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
fastaseqs.o: /usr/include/string.h /usr/include/math.h
fastaseqs.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
fastaseqs.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
fastaseqs.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
fastaseqs.o: /usr/include/ctype.h /usr/include/endian.h
fastaseqs.o: /usr/include/bits/endian.h ../include/global.h
fastaseqs.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
fastaseqs.o: ../include/errors.h ../include/memory.h ../include/residues.h
fastaseqs.o: ../include/blastapp.h /usr/include/limits.h
fastaseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
fastaseqs.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
fastaseqs.o: ../include/gcode.h ../include/blocks.h ../include/output.h
fastaseqs.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
fastaseqs.o: ../include/convert.h ../include/frequency.h ../include/files.h
fastaseqs.o: ../include/protomat.h
LAMA.o: ../include/blocksprogs.h /usr/include/stdlib.h
LAMA.o: /usr/include/features.h /usr/include/sys/cdefs.h
LAMA.o: /usr/include/gnu/stubs.h
LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
LAMA.o: /usr/include/stdio.h /usr/include/bits/types.h
LAMA.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
LAMA.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
LAMA.o: /usr/include/bits/wchar.h /usr/include/gconv.h
LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
LAMA.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
LAMA.o: /usr/include/string.h /usr/include/math.h
LAMA.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
LAMA.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
LAMA.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
LAMA.o: /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h
LAMA.o: ../include/global.h /usr/include/malloc.h ../include/license.h
LAMA.o: ../include/strutil.h ../include/errors.h ../include/memory.h
LAMA.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
LAMA.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
LAMA.o: ../include/gcode.h ../include/blocks.h ../include/output.h
LAMA.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
LAMA.o: ../include/convert.h ../include/frequency.h ../include/files.h
LAMA.o: ../include/protomat.h LAMA.h
find_biassed_blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h
find_biassed_blocks.o: /usr/include/features.h /usr/include/sys/cdefs.h
find_biassed_blocks.o: /usr/include/gnu/stubs.h
find_biassed_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
find_biassed_blocks.o: /usr/include/stdio.h /usr/include/bits/types.h
find_biassed_blocks.o: /usr/include/bits/wordsize.h
find_biassed_blocks.o: /usr/include/bits/typesizes.h /usr/include/libio.h
find_biassed_blocks.o: /usr/include/_G_config.h /usr/include/wchar.h
find_biassed_blocks.o: /usr/include/bits/wchar.h /usr/include/gconv.h
find_biassed_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
find_biassed_blocks.o: /usr/include/bits/stdio_lim.h
find_biassed_blocks.o: /usr/include/bits/sys_errlist.h /usr/include/string.h
find_biassed_blocks.o: /usr/include/math.h /usr/include/bits/huge_val.h
find_biassed_blocks.o: /usr/include/bits/mathdef.h
find_biassed_blocks.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
find_biassed_blocks.o: /usr/include/bits/posix_opt.h
find_biassed_blocks.o: /usr/include/bits/confname.h /usr/include/ctype.h
find_biassed_blocks.o: /usr/include/endian.h /usr/include/bits/endian.h
find_biassed_blocks.o: ../include/global.h /usr/include/malloc.h
find_biassed_blocks.o: ../include/license.h ../include/strutil.h
find_biassed_blocks.o: ../include/errors.h ../include/memory.h
find_biassed_blocks.o: ../include/residues.h ../include/blastapp.h
find_biassed_blocks.o: /usr/include/limits.h
find_biassed_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
find_biassed_blocks.o: ../include/alphabet.h ../include/aabet.h
find_biassed_blocks.o: ../include/ntbet.h ../include/gcode.h
find_biassed_blocks.o: ../include/blocks.h ../include/output.h
find_biassed_blocks.o: ../include/sequences.h ../include/matrix.h
find_biassed_blocks.o: ../include/pattern.h ../include/convert.h
find_biassed_blocks.o: ../include/frequency.h ../include/files.h
find_biassed_blocks.o: ../include/protomat.h blkvblk.h
makeblockmap.o: ../include/blocksprogs.h /usr/include/stdlib.h
makeblockmap.o: /usr/include/features.h /usr/include/sys/cdefs.h
makeblockmap.o: /usr/include/gnu/stubs.h
makeblockmap.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
makeblockmap.o: /usr/include/stdio.h /usr/include/bits/types.h
makeblockmap.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
makeblockmap.o: /usr/include/libio.h /usr/include/_G_config.h
makeblockmap.o: /usr/include/wchar.h /usr/include/bits/wchar.h
makeblockmap.o: /usr/include/gconv.h
makeblockmap.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
makeblockmap.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
makeblockmap.o: /usr/include/string.h /usr/include/math.h
makeblockmap.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
makeblockmap.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
makeblockmap.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
makeblockmap.o: /usr/include/ctype.h /usr/include/endian.h
makeblockmap.o: /usr/include/bits/endian.h ../include/global.h
makeblockmap.o: /usr/include/malloc.h ../include/license.h
makeblockmap.o: ../include/strutil.h ../include/errors.h ../include/memory.h
makeblockmap.o: ../include/residues.h ../include/blastapp.h
makeblockmap.o: /usr/include/limits.h
makeblockmap.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
makeblockmap.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
makeblockmap.o: ../include/gcode.h ../include/blocks.h ../include/output.h
makeblockmap.o: ../include/sequences.h ../include/matrix.h
makeblockmap.o: ../include/pattern.h ../include/convert.h
makeblockmap.o: ../include/frequency.h ../include/files.h
makeblockmap.o: ../include/protomat.h blockmap.h
prints2blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h
prints2blocks.o: /usr/include/features.h /usr/include/sys/cdefs.h
prints2blocks.o: /usr/include/gnu/stubs.h
prints2blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
prints2blocks.o: /usr/include/stdio.h /usr/include/bits/types.h
prints2blocks.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
prints2blocks.o: /usr/include/libio.h /usr/include/_G_config.h
prints2blocks.o: /usr/include/wchar.h /usr/include/bits/wchar.h
prints2blocks.o: /usr/include/gconv.h
prints2blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
prints2blocks.o: /usr/include/bits/stdio_lim.h
prints2blocks.o: /usr/include/bits/sys_errlist.h /usr/include/string.h
prints2blocks.o: /usr/include/math.h /usr/include/bits/huge_val.h
prints2blocks.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h
prints2blocks.o: /usr/include/unistd.h /usr/include/bits/posix_opt.h
prints2blocks.o: /usr/include/bits/confname.h /usr/include/ctype.h
prints2blocks.o: /usr/include/endian.h /usr/include/bits/endian.h
prints2blocks.o: ../include/global.h /usr/include/malloc.h
prints2blocks.o: ../include/license.h ../include/strutil.h
prints2blocks.o: ../include/errors.h ../include/memory.h
prints2blocks.o: ../include/residues.h ../include/blastapp.h
prints2blocks.o: /usr/include/limits.h
prints2blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
prints2blocks.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
prints2blocks.o: ../include/gcode.h ../include/blocks.h ../include/output.h
prints2blocks.o: ../include/sequences.h ../include/matrix.h
prints2blocks.o: ../include/pattern.h ../include/convert.h
prints2blocks.o: ../include/frequency.h ../include/files.h
prints2blocks.o: ../include/protomat.h
lisblk.o: ../include/blocksprogs.h /usr/include/stdlib.h
lisblk.o: /usr/include/features.h /usr/include/sys/cdefs.h
lisblk.o: /usr/include/gnu/stubs.h
lisblk.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
lisblk.o: /usr/include/stdio.h /usr/include/bits/types.h
lisblk.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
lisblk.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
lisblk.o: /usr/include/bits/wchar.h /usr/include/gconv.h
lisblk.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
lisblk.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
lisblk.o: /usr/include/string.h /usr/include/math.h
lisblk.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
lisblk.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
lisblk.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
lisblk.o: /usr/include/ctype.h /usr/include/endian.h
lisblk.o: /usr/include/bits/endian.h ../include/global.h
lisblk.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
lisblk.o: ../include/errors.h ../include/memory.h ../include/residues.h
lisblk.o: ../include/blastapp.h /usr/include/limits.h
lisblk.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
lisblk.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
lisblk.o: ../include/gcode.h ../include/blocks.h ../include/output.h
lisblk.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
lisblk.o: ../include/convert.h ../include/frequency.h ../include/files.h
lisblk.o: ../include/protomat.h
coduse.o: ../include/blocksprogs.h /usr/include/stdlib.h
coduse.o: /usr/include/features.h /usr/include/sys/cdefs.h
coduse.o: /usr/include/gnu/stubs.h
coduse.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
coduse.o: /usr/include/stdio.h /usr/include/bits/types.h
coduse.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
coduse.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
coduse.o: /usr/include/bits/wchar.h /usr/include/gconv.h
coduse.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
coduse.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
coduse.o: /usr/include/string.h /usr/include/math.h
coduse.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
coduse.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
coduse.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
coduse.o: /usr/include/ctype.h /usr/include/endian.h
coduse.o: /usr/include/bits/endian.h ../include/global.h
coduse.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
coduse.o: ../include/errors.h ../include/memory.h ../include/residues.h
coduse.o: ../include/blastapp.h /usr/include/limits.h
coduse.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
coduse.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
coduse.o: ../include/gcode.h ../include/blocks.h ../include/output.h
coduse.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
coduse.o: ../include/convert.h ../include/frequency.h ../include/files.h
coduse.o: ../include/protomat.h
narrow.o: ../include/blocksprogs.h /usr/include/stdlib.h
narrow.o: /usr/include/features.h /usr/include/sys/cdefs.h
narrow.o: /usr/include/gnu/stubs.h
narrow.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
narrow.o: /usr/include/stdio.h /usr/include/bits/types.h
narrow.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
narrow.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
narrow.o: /usr/include/bits/wchar.h /usr/include/gconv.h
narrow.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
narrow.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
narrow.o: /usr/include/string.h /usr/include/math.h
narrow.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
narrow.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
narrow.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
narrow.o: /usr/include/ctype.h /usr/include/endian.h
narrow.o: /usr/include/bits/endian.h ../include/global.h
narrow.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
narrow.o: ../include/errors.h ../include/memory.h ../include/residues.h
narrow.o: ../include/blastapp.h /usr/include/limits.h
narrow.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
narrow.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
narrow.o: ../include/gcode.h ../include/blocks.h ../include/output.h
narrow.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
narrow.o: ../include/convert.h ../include/frequency.h ../include/files.h
narrow.o: ../include/protomat.h
blk2slx.o: ../include/blocksprogs.h /usr/include/stdlib.h
blk2slx.o: /usr/include/features.h /usr/include/sys/cdefs.h
blk2slx.o: /usr/include/gnu/stubs.h
blk2slx.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
blk2slx.o: /usr/include/stdio.h /usr/include/bits/types.h
blk2slx.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
blk2slx.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
blk2slx.o: /usr/include/bits/wchar.h /usr/include/gconv.h
blk2slx.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
blk2slx.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
blk2slx.o: /usr/include/string.h /usr/include/math.h
blk2slx.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
blk2slx.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
blk2slx.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
blk2slx.o: /usr/include/ctype.h /usr/include/endian.h
blk2slx.o: /usr/include/bits/endian.h ../include/global.h
blk2slx.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
blk2slx.o: ../include/errors.h ../include/memory.h ../include/residues.h
blk2slx.o: ../include/blastapp.h /usr/include/limits.h
blk2slx.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
blk2slx.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blk2slx.o: ../include/gcode.h ../include/blocks.h ../include/output.h
blk2slx.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blk2slx.o: ../include/convert.h ../include/frequency.h ../include/files.h
blk2slx.o: ../include/protomat.h
blkprob.o: ../include/blocksprogs.h /usr/include/stdlib.h
blkprob.o: /usr/include/features.h /usr/include/sys/cdefs.h
blkprob.o: /usr/include/gnu/stubs.h
blkprob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
blkprob.o: /usr/include/stdio.h /usr/include/bits/types.h
blkprob.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
blkprob.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
blkprob.o: /usr/include/bits/wchar.h /usr/include/gconv.h
blkprob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
blkprob.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
blkprob.o: /usr/include/string.h /usr/include/math.h
blkprob.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
blkprob.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
blkprob.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
blkprob.o: /usr/include/ctype.h /usr/include/endian.h
blkprob.o: /usr/include/bits/endian.h ../include/global.h
blkprob.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
blkprob.o: ../include/errors.h ../include/memory.h ../include/residues.h
blkprob.o: ../include/blastapp.h /usr/include/limits.h
blkprob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
blkprob.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blkprob.o: ../include/gcode.h ../include/blocks.h ../include/output.h
blkprob.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blkprob.o: ../include/convert.h ../include/frequency.h ../include/files.h
blkprob.o: ../include/protomat.h
blocks.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
blocks.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
blocks.o: /usr/include/stdio.h /usr/include/bits/types.h
blocks.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
blocks.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
blocks.o: /usr/include/bits/wchar.h /usr/include/gconv.h
blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
blocks.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
blocks.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
blocks.o: /usr/include/bits/endian.h /usr/include/malloc.h
blocks.o: ../include/license.h ../include/strutil.h ../include/errors.h
blocks.o: ../include/memory.h ../include/blocks.h ../include/output.h
blocks.o: ../include/sequences.h ../include/residues.h ../include/blastapp.h
blocks.o: /usr/include/limits.h
blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
blocks.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blocks.o: ../include/gcode.h
config.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
config.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
config.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
config.o: /usr/include/stdio.h /usr/include/bits/types.h
config.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
config.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
config.o: /usr/include/bits/wchar.h /usr/include/gconv.h
config.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
config.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
config.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
config.o: /usr/include/bits/endian.h /usr/include/malloc.h
config.o: ../include/license.h ../include/strutil.h ../include/errors.h
config.o: ../include/memory.h ../include/files.h ../include/sequences.h
config.o: ../include/pattern.h ../include/options.h config.h blimps.h
config.o: scoring.h lists.h ../include/skiplist.h
convert.o: /usr/include/assert.h /usr/include/features.h
convert.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
convert.o: /usr/include/math.h /usr/include/bits/huge_val.h
convert.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h
convert.o: ../include/global.h /usr/include/stdlib.h
convert.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
convert.o: /usr/include/stdio.h /usr/include/bits/types.h
convert.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
convert.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
convert.o: /usr/include/bits/wchar.h /usr/include/gconv.h
convert.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
convert.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
convert.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
convert.o: /usr/include/bits/endian.h /usr/include/malloc.h
convert.o: ../include/license.h ../include/strutil.h ../include/errors.h
convert.o: ../include/memory.h ../include/options.h ../include/blocks.h
convert.o: ../include/output.h ../include/sequences.h ../include/matrix.h
convert.o: ../include/pattern.h ../include/residues.h ../include/blastapp.h
convert.o: /usr/include/limits.h
convert.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
convert.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
convert.o: ../include/gcode.h ../include/frequency.h ../include/protomat.h
convert.o: ../include/convert.h blimps.h
errors.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
errors.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
errors.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
errors.o: /usr/include/stdio.h /usr/include/bits/types.h
errors.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
errors.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
errors.o: /usr/include/bits/wchar.h /usr/include/gconv.h
errors.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
errors.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
errors.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
errors.o: /usr/include/bits/endian.h /usr/include/malloc.h
errors.o: ../include/license.h ../include/strutil.h ../include/errors.h
errors.o: ../include/memory.h
files.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
files.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
files.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
files.o: /usr/include/stdio.h /usr/include/bits/types.h
files.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
files.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
files.o: /usr/include/bits/wchar.h /usr/include/gconv.h
files.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
files.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
files.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
files.o: /usr/include/bits/endian.h /usr/include/malloc.h
files.o: ../include/license.h ../include/strutil.h ../include/errors.h
files.o: ../include/memory.h ../include/files.h ../include/sequences.h
frequency.o: ../include/global.h /usr/include/stdlib.h
frequency.o: /usr/include/features.h /usr/include/sys/cdefs.h
frequency.o: /usr/include/gnu/stubs.h
frequency.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
frequency.o: /usr/include/stdio.h /usr/include/bits/types.h
frequency.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
frequency.o: /usr/include/libio.h /usr/include/_G_config.h
frequency.o: /usr/include/wchar.h /usr/include/bits/wchar.h
frequency.o: /usr/include/gconv.h
frequency.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
frequency.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
frequency.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
frequency.o: /usr/include/bits/endian.h /usr/include/malloc.h
frequency.o: ../include/license.h ../include/strutil.h ../include/errors.h
frequency.o: ../include/memory.h ../include/blocks.h ../include/output.h
frequency.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
frequency.o: ../include/frequency.h ../include/convert.h ../include/files.h
frequency.o: ../include/residues.h ../include/blastapp.h
frequency.o: /usr/include/limits.h
frequency.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
frequency.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
frequency.o: ../include/gcode.h
gcode.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
gcode.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
gcode.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
gcode.o: /usr/include/stdio.h /usr/include/bits/types.h
gcode.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
gcode.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
gcode.o: /usr/include/bits/wchar.h /usr/include/gconv.h
gcode.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
gcode.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
gcode.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
gcode.o: /usr/include/bits/endian.h /usr/include/malloc.h
gcode.o: ../include/license.h ../include/strutil.h ../include/errors.h
gcode.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
gcode.o: /usr/include/limits.h
gcode.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
gcode.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
gcode.o: ../include/gcode.h ../include/sequences.h
lists.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
lists.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
lists.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
lists.o: /usr/include/stdio.h /usr/include/bits/types.h
lists.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
lists.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
lists.o: /usr/include/bits/wchar.h /usr/include/gconv.h
lists.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
lists.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
lists.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
lists.o: /usr/include/bits/endian.h /usr/include/malloc.h
lists.o: ../include/license.h ../include/strutil.h ../include/errors.h
lists.o: ../include/memory.h ../include/blocks.h ../include/output.h
lists.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
lists.o: lists.h ../include/skiplist.h blimps.h scores.h
matrix.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
matrix.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
matrix.o: /usr/include/stdio.h /usr/include/bits/types.h
matrix.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
matrix.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
matrix.o: /usr/include/bits/wchar.h /usr/include/gconv.h
matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
matrix.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
matrix.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
matrix.o: /usr/include/bits/endian.h /usr/include/malloc.h
matrix.o: ../include/license.h ../include/strutil.h ../include/errors.h
matrix.o: ../include/memory.h ../include/blocks.h ../include/output.h
matrix.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
matrix.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
matrix.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
matrix.o: ../include/gcode.h
memory.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
memory.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
memory.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
memory.o: /usr/include/stdio.h /usr/include/bits/types.h
memory.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
memory.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
memory.o: /usr/include/bits/wchar.h /usr/include/gconv.h
memory.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
memory.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
memory.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
memory.o: /usr/include/bits/endian.h /usr/include/malloc.h
memory.o: ../include/license.h ../include/strutil.h ../include/errors.h
memory.o: ../include/memory.h
pattern.o: /usr/include/assert.h /usr/include/features.h
pattern.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
pattern.o: ../include/global.h /usr/include/stdlib.h
pattern.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
pattern.o: /usr/include/stdio.h /usr/include/bits/types.h
pattern.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
pattern.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
pattern.o: /usr/include/bits/wchar.h /usr/include/gconv.h
pattern.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
pattern.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
pattern.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
pattern.o: /usr/include/bits/endian.h /usr/include/malloc.h
pattern.o: ../include/license.h ../include/strutil.h ../include/errors.h
pattern.o: ../include/memory.h ../include/files.h ../include/blocks.h
pattern.o: ../include/output.h ../include/sequences.h ../include/matrix.h
pattern.o: ../include/pattern.h ../include/residues.h ../include/blastapp.h
pattern.o: /usr/include/limits.h
pattern.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
pattern.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
pattern.o: ../include/gcode.h ../include/skiplist.h
scores.o: /usr/include/math.h /usr/include/features.h
scores.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
scores.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
scores.o: /usr/include/bits/mathcalls.h ../include/global.h
scores.o: /usr/include/stdlib.h
scores.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
scores.o: /usr/include/stdio.h /usr/include/bits/types.h
scores.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
scores.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
scores.o: /usr/include/bits/wchar.h /usr/include/gconv.h
scores.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
scores.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
scores.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
scores.o: /usr/include/bits/endian.h /usr/include/malloc.h
scores.o: ../include/license.h ../include/strutil.h ../include/errors.h
scores.o: ../include/memory.h ../include/blocks.h ../include/output.h
scores.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
scores.o: scores.h blimps.h scoring.h lists.h ../include/skiplist.h
scoring.o: /usr/include/math.h /usr/include/features.h
scoring.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
scoring.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
scoring.o: /usr/include/bits/mathcalls.h ../include/global.h
scoring.o: /usr/include/stdlib.h
scoring.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
scoring.o: /usr/include/stdio.h /usr/include/bits/types.h
scoring.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
scoring.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
scoring.o: /usr/include/bits/wchar.h /usr/include/gconv.h
scoring.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
scoring.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
scoring.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
scoring.o: /usr/include/bits/endian.h /usr/include/malloc.h
scoring.o: ../include/license.h ../include/strutil.h ../include/errors.h
scoring.o: ../include/memory.h ../include/blocks.h ../include/output.h
scoring.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
scoring.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
scoring.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
scoring.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
scoring.o: ../include/gcode.h scoring.h blimps.h scores.h lists.h
scoring.o: ../include/skiplist.h
sequences.o: ../include/global.h /usr/include/stdlib.h
sequences.o: /usr/include/features.h /usr/include/sys/cdefs.h
sequences.o: /usr/include/gnu/stubs.h
sequences.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
sequences.o: /usr/include/stdio.h /usr/include/bits/types.h
sequences.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
sequences.o: /usr/include/libio.h /usr/include/_G_config.h
sequences.o: /usr/include/wchar.h /usr/include/bits/wchar.h
sequences.o: /usr/include/gconv.h
sequences.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
sequences.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
sequences.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
sequences.o: /usr/include/bits/endian.h /usr/include/malloc.h
sequences.o: ../include/license.h ../include/strutil.h ../include/errors.h
sequences.o: ../include/memory.h ../include/sequences.h ../include/residues.h
sequences.o: ../include/blastapp.h /usr/include/limits.h
sequences.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
sequences.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
sequences.o: ../include/gcode.h
sl.o: /usr/include/assert.h /usr/include/features.h /usr/include/sys/cdefs.h
sl.o: /usr/include/gnu/stubs.h /usr/include/time.h /usr/include/bits/types.h
sl.o: /usr/include/bits/wordsize.h
sl.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
sl.o: /usr/include/bits/typesizes.h ../include/global.h /usr/include/stdlib.h
sl.o: /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h
sl.o: /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h
sl.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
sl.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
sl.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
sl.o: /usr/include/bits/endian.h /usr/include/malloc.h ../include/license.h
sl.o: ../include/strutil.h ../include/errors.h ../include/memory.h
sl.o: ../include/skiplist.h
strutil.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
strutil.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
strutil.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
strutil.o: /usr/include/stdio.h /usr/include/bits/types.h
strutil.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
strutil.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
strutil.o: /usr/include/bits/wchar.h /usr/include/gconv.h
strutil.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
strutil.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
strutil.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
strutil.o: /usr/include/bits/endian.h /usr/include/malloc.h
strutil.o: ../include/license.h ../include/strutil.h ../include/errors.h
strutil.o: ../include/memory.h
version.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
version.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
version.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
version.o: /usr/include/stdio.h /usr/include/bits/types.h
version.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
version.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
version.o: /usr/include/bits/wchar.h /usr/include/gconv.h
version.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
version.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
version.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
version.o: /usr/include/bits/endian.h /usr/include/malloc.h
version.o: ../include/license.h ../include/strutil.h ../include/errors.h
version.o: ../include/memory.h ../include/version.h
options.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
options.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
options.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
options.o: /usr/include/stdio.h /usr/include/bits/types.h
options.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
options.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
options.o: /usr/include/bits/wchar.h /usr/include/gconv.h
options.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
options.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
options.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
options.o: /usr/include/bits/endian.h /usr/include/malloc.h
options.o: ../include/license.h ../include/strutil.h ../include/errors.h
options.o: ../include/memory.h ../include/options.h
protomat.o: /usr/include/sys/types.h /usr/include/features.h
protomat.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
protomat.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
protomat.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
protomat.o: /usr/include/bits/typesizes.h /usr/include/time.h
protomat.o: /usr/include/dirent.h /usr/include/bits/dirent.h
protomat.o: /usr/include/ctype.h /usr/include/endian.h
protomat.o: /usr/include/bits/endian.h ../include/protomat.h
protomat.o: /usr/include/stdlib.h /usr/include/stdio.h /usr/include/libio.h
protomat.o: /usr/include/_G_config.h /usr/include/wchar.h
protomat.o: /usr/include/bits/wchar.h /usr/include/gconv.h
protomat.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
protomat.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
protomat.o: /usr/include/string.h
interpro.o: ../include/blocksprogs.h /usr/include/stdlib.h
interpro.o: /usr/include/features.h /usr/include/sys/cdefs.h
interpro.o: /usr/include/gnu/stubs.h
interpro.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
interpro.o: /usr/include/stdio.h /usr/include/bits/types.h
interpro.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
interpro.o: /usr/include/libio.h /usr/include/_G_config.h
interpro.o: /usr/include/wchar.h /usr/include/bits/wchar.h
interpro.o: /usr/include/gconv.h
interpro.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
interpro.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
interpro.o: /usr/include/string.h /usr/include/math.h
interpro.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
interpro.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
interpro.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
interpro.o: /usr/include/ctype.h /usr/include/endian.h
interpro.o: /usr/include/bits/endian.h ../include/global.h
interpro.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
interpro.o: ../include/errors.h ../include/memory.h ../include/residues.h
interpro.o: ../include/blastapp.h /usr/include/limits.h
interpro.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
interpro.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
interpro.o: ../include/gcode.h ../include/blocks.h ../include/output.h
interpro.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
interpro.o: ../include/convert.h ../include/frequency.h ../include/files.h
interpro.o: ../include/protomat.h
pssmdist.o: ../include/blocksprogs.h /usr/include/stdlib.h
pssmdist.o: /usr/include/features.h /usr/include/sys/cdefs.h
pssmdist.o: /usr/include/gnu/stubs.h
pssmdist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
pssmdist.o: /usr/include/stdio.h /usr/include/bits/types.h
pssmdist.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
pssmdist.o: /usr/include/libio.h /usr/include/_G_config.h
pssmdist.o: /usr/include/wchar.h /usr/include/bits/wchar.h
pssmdist.o: /usr/include/gconv.h
pssmdist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
pssmdist.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
pssmdist.o: /usr/include/string.h /usr/include/math.h
pssmdist.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
pssmdist.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
pssmdist.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
pssmdist.o: /usr/include/ctype.h /usr/include/endian.h
pssmdist.o: /usr/include/bits/endian.h ../include/global.h
pssmdist.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
pssmdist.o: ../include/errors.h ../include/memory.h ../include/residues.h
pssmdist.o: ../include/blastapp.h /usr/include/limits.h
pssmdist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
pssmdist.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
pssmdist.o: ../include/gcode.h ../include/blocks.h ../include/output.h
pssmdist.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
pssmdist.o: ../include/convert.h ../include/frequency.h ../include/files.h
pssmdist.o: ../include/protomat.h
pssmBL.o: ../include/blocksprogs.h /usr/include/stdlib.h
pssmBL.o: /usr/include/features.h /usr/include/sys/cdefs.h
pssmBL.o: /usr/include/gnu/stubs.h
pssmBL.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
pssmBL.o: /usr/include/stdio.h /usr/include/bits/types.h
pssmBL.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
pssmBL.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
pssmBL.o: /usr/include/bits/wchar.h /usr/include/gconv.h
pssmBL.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
pssmBL.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
pssmBL.o: /usr/include/string.h /usr/include/math.h
pssmBL.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
pssmBL.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
pssmBL.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
pssmBL.o: /usr/include/ctype.h /usr/include/endian.h
pssmBL.o: /usr/include/bits/endian.h ../include/global.h
pssmBL.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
pssmBL.o: ../include/errors.h ../include/memory.h ../include/residues.h
pssmBL.o: ../include/blastapp.h /usr/include/limits.h
pssmBL.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
pssmBL.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
pssmBL.o: ../include/gcode.h ../include/blocks.h ../include/output.h
pssmBL.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
pssmBL.o: ../include/convert.h ../include/frequency.h ../include/files.h
pssmBL.o: ../include/protomat.h
papssm.o: ../include/blocksprogs.h /usr/include/stdlib.h
papssm.o: /usr/include/features.h /usr/include/sys/cdefs.h
papssm.o: /usr/include/gnu/stubs.h
papssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
papssm.o: /usr/include/stdio.h /usr/include/bits/types.h
papssm.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
papssm.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
papssm.o: /usr/include/bits/wchar.h /usr/include/gconv.h
papssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
papssm.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
papssm.o: /usr/include/string.h /usr/include/math.h
papssm.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
papssm.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
papssm.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
papssm.o: /usr/include/ctype.h /usr/include/endian.h
papssm.o: /usr/include/bits/endian.h ../include/global.h
papssm.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
papssm.o: ../include/errors.h ../include/memory.h ../include/residues.h
papssm.o: ../include/blastapp.h /usr/include/limits.h
papssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
papssm.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
papssm.o: ../include/gcode.h ../include/blocks.h ../include/output.h
papssm.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
papssm.o: ../include/convert.h ../include/frequency.h ../include/files.h
papssm.o: ../include/protomat.h blimps.h
matrix_logob.o: /usr/include/sys/types.h /usr/include/features.h
matrix_logob.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
matrix_logob.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
matrix_logob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
matrix_logob.o: /usr/include/bits/typesizes.h /usr/include/time.h
matrix_logob.o: /usr/include/sys/stat.h /usr/include/bits/stat.h
matrix_logob.o: ../include/blocksprogs.h /usr/include/stdlib.h
matrix_logob.o: /usr/include/stdio.h /usr/include/libio.h
matrix_logob.o: /usr/include/_G_config.h /usr/include/wchar.h
matrix_logob.o: /usr/include/bits/wchar.h /usr/include/gconv.h
matrix_logob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
matrix_logob.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
matrix_logob.o: /usr/include/string.h /usr/include/math.h
matrix_logob.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
matrix_logob.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
matrix_logob.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
matrix_logob.o: /usr/include/ctype.h /usr/include/endian.h
matrix_logob.o: /usr/include/bits/endian.h ../include/global.h
matrix_logob.o: /usr/include/malloc.h ../include/license.h
matrix_logob.o: ../include/strutil.h ../include/errors.h ../include/memory.h
matrix_logob.o: ../include/residues.h ../include/blastapp.h
matrix_logob.o: /usr/include/limits.h
matrix_logob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
matrix_logob.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
matrix_logob.o: ../include/gcode.h ../include/blocks.h ../include/output.h
matrix_logob.o: ../include/sequences.h ../include/matrix.h
matrix_logob.o: ../include/pattern.h ../include/convert.h
matrix_logob.o: ../include/frequency.h ../include/files.h
matrix_logob.o: ../include/protomat.h
makelogob.o: p2c.h /usr/include/stdio.h /usr/include/features.h
makelogob.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
makelogob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
makelogob.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
makelogob.o: /usr/include/bits/typesizes.h /usr/include/libio.h
makelogob.o: /usr/include/_G_config.h /usr/include/wchar.h
makelogob.o: /usr/include/bits/wchar.h /usr/include/gconv.h
makelogob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
makelogob.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
makelogob.o: /usr/include/stdlib.h /usr/include/string.h /usr/include/ctype.h
makelogob.o: /usr/include/endian.h /usr/include/bits/endian.h
makelogob.o: /usr/include/math.h /usr/include/bits/huge_val.h
makelogob.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h
makelogob.o: /usr/include/setjmp.h /usr/include/bits/setjmp.h
makelogob.o: /usr/include/bits/sigset.h /usr/include/assert.h
blocks_search.o: /usr/include/stdio.h /usr/include/features.h
blocks_search.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
blocks_search.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
blocks_search.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
blocks_search.o: /usr/include/bits/typesizes.h /usr/include/libio.h
blocks_search.o: /usr/include/_G_config.h /usr/include/wchar.h
blocks_search.o: /usr/include/bits/wchar.h /usr/include/gconv.h
blocks_search.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
blocks_search.o: /usr/include/bits/stdio_lim.h
blocks_search.o: /usr/include/bits/sys_errlist.h /usr/include/stdlib.h
blocks_search.o: ../include/global.h /usr/include/string.h
blocks_search.o: /usr/include/ctype.h /usr/include/endian.h
blocks_search.o: /usr/include/bits/endian.h /usr/include/malloc.h
blocks_search.o: ../include/license.h ../include/strutil.h
blocks_search.o: ../include/errors.h ../include/memory.h
blocks_search.o: /usr/include/unistd.h /usr/include/bits/posix_opt.h
blocks_search.o: /usr/include/bits/confname.h
LAMA_search.o: ../include/blocksprogs.h /usr/include/stdlib.h
LAMA_search.o: /usr/include/features.h /usr/include/sys/cdefs.h
LAMA_search.o: /usr/include/gnu/stubs.h
LAMA_search.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
LAMA_search.o: /usr/include/stdio.h /usr/include/bits/types.h
LAMA_search.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
LAMA_search.o: /usr/include/libio.h /usr/include/_G_config.h
LAMA_search.o: /usr/include/wchar.h /usr/include/bits/wchar.h
LAMA_search.o: /usr/include/gconv.h
LAMA_search.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
LAMA_search.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
LAMA_search.o: /usr/include/string.h /usr/include/math.h
LAMA_search.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
LAMA_search.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
LAMA_search.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
LAMA_search.o: /usr/include/ctype.h /usr/include/endian.h
LAMA_search.o: /usr/include/bits/endian.h ../include/global.h
LAMA_search.o: /usr/include/malloc.h ../include/license.h
LAMA_search.o: ../include/strutil.h ../include/errors.h ../include/memory.h
LAMA_search.o: ../include/residues.h ../include/blastapp.h
LAMA_search.o: /usr/include/limits.h
LAMA_search.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
LAMA_search.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
LAMA_search.o: ../include/gcode.h ../include/blocks.h ../include/output.h
LAMA_search.o: ../include/sequences.h ../include/matrix.h
LAMA_search.o: ../include/pattern.h ../include/convert.h
LAMA_search.o: ../include/frequency.h ../include/files.h
LAMA_search.o: ../include/protomat.h
block_vis.o: ../include/blocksprogs.h /usr/include/stdlib.h
block_vis.o: /usr/include/features.h /usr/include/sys/cdefs.h
block_vis.o: /usr/include/gnu/stubs.h
block_vis.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
block_vis.o: /usr/include/stdio.h /usr/include/bits/types.h
block_vis.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
block_vis.o: /usr/include/libio.h /usr/include/_G_config.h
block_vis.o: /usr/include/wchar.h /usr/include/bits/wchar.h
block_vis.o: /usr/include/gconv.h
block_vis.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
block_vis.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
block_vis.o: /usr/include/string.h /usr/include/math.h
block_vis.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
block_vis.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
block_vis.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
block_vis.o: /usr/include/ctype.h /usr/include/endian.h
block_vis.o: /usr/include/bits/endian.h ../include/global.h
block_vis.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
block_vis.o: ../include/errors.h ../include/memory.h ../include/residues.h
block_vis.o: ../include/blastapp.h /usr/include/limits.h
block_vis.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
block_vis.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
block_vis.o: ../include/gcode.h ../include/blocks.h ../include/output.h
block_vis.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
block_vis.o: ../include/convert.h ../include/frequency.h ../include/files.h
block_vis.o: ../include/protomat.h blockmap.h
format_block.o: ../include/blocksprogs.h /usr/include/stdlib.h
format_block.o: /usr/include/features.h /usr/include/sys/cdefs.h
format_block.o: /usr/include/gnu/stubs.h
format_block.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
format_block.o: /usr/include/stdio.h /usr/include/bits/types.h
format_block.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
format_block.o: /usr/include/libio.h /usr/include/_G_config.h
format_block.o: /usr/include/wchar.h /usr/include/bits/wchar.h
format_block.o: /usr/include/gconv.h
format_block.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
format_block.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
format_block.o: /usr/include/string.h /usr/include/math.h
format_block.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
format_block.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
format_block.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
format_block.o: /usr/include/ctype.h /usr/include/endian.h
format_block.o: /usr/include/bits/endian.h ../include/global.h
format_block.o: /usr/include/malloc.h ../include/license.h
format_block.o: ../include/strutil.h ../include/errors.h ../include/memory.h
format_block.o: ../include/residues.h ../include/blastapp.h
format_block.o: /usr/include/limits.h
format_block.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
format_block.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
format_block.o: ../include/gcode.h ../include/blocks.h ../include/output.h
format_block.o: ../include/sequences.h ../include/matrix.h
format_block.o: ../include/pattern.h ../include/convert.h
format_block.o: ../include/frequency.h ../include/files.h
format_block.o: ../include/protomat.h
biassed_blocks_finder.o: ../include/blocksprogs.h /usr/include/stdlib.h
biassed_blocks_finder.o: /usr/include/features.h /usr/include/sys/cdefs.h
biassed_blocks_finder.o: /usr/include/gnu/stubs.h
biassed_blocks_finder.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
biassed_blocks_finder.o: /usr/include/stdio.h /usr/include/bits/types.h
biassed_blocks_finder.o: /usr/include/bits/wordsize.h
biassed_blocks_finder.o: /usr/include/bits/typesizes.h /usr/include/libio.h
biassed_blocks_finder.o: /usr/include/_G_config.h /usr/include/wchar.h
biassed_blocks_finder.o: /usr/include/bits/wchar.h /usr/include/gconv.h
biassed_blocks_finder.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
biassed_blocks_finder.o: /usr/include/bits/stdio_lim.h
biassed_blocks_finder.o: /usr/include/bits/sys_errlist.h
biassed_blocks_finder.o: /usr/include/string.h /usr/include/math.h
biassed_blocks_finder.o: /usr/include/bits/huge_val.h
biassed_blocks_finder.o: /usr/include/bits/mathdef.h
biassed_blocks_finder.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
biassed_blocks_finder.o: /usr/include/bits/posix_opt.h
biassed_blocks_finder.o: /usr/include/bits/confname.h /usr/include/ctype.h
biassed_blocks_finder.o: /usr/include/endian.h /usr/include/bits/endian.h
biassed_blocks_finder.o: ../include/global.h /usr/include/malloc.h
biassed_blocks_finder.o: ../include/license.h ../include/strutil.h
biassed_blocks_finder.o: ../include/errors.h ../include/memory.h
biassed_blocks_finder.o: ../include/residues.h ../include/blastapp.h
biassed_blocks_finder.o: /usr/include/limits.h
biassed_blocks_finder.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
biassed_blocks_finder.o: ../include/alphabet.h ../include/aabet.h
biassed_blocks_finder.o: ../include/ntbet.h ../include/gcode.h
biassed_blocks_finder.o: ../include/blocks.h ../include/output.h
biassed_blocks_finder.o: ../include/sequences.h ../include/matrix.h
biassed_blocks_finder.o: ../include/pattern.h ../include/convert.h
biassed_blocks_finder.o: ../include/frequency.h ../include/files.h
biassed_blocks_finder.o: ../include/protomat.h
htmlize-LAMA.o: /usr/include/stdlib.h /usr/include/features.h
htmlize-LAMA.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
htmlize-LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
htmlize-LAMA.o: /usr/include/stdio.h /usr/include/bits/types.h
htmlize-LAMA.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
htmlize-LAMA.o: /usr/include/libio.h /usr/include/_G_config.h
htmlize-LAMA.o: /usr/include/wchar.h /usr/include/bits/wchar.h
htmlize-LAMA.o: /usr/include/gconv.h
htmlize-LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
htmlize-LAMA.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
show_aligned_blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h
show_aligned_blocks.o: /usr/include/features.h /usr/include/sys/cdefs.h
show_aligned_blocks.o: /usr/include/gnu/stubs.h
show_aligned_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
show_aligned_blocks.o: /usr/include/stdio.h /usr/include/bits/types.h
show_aligned_blocks.o: /usr/include/bits/wordsize.h
show_aligned_blocks.o: /usr/include/bits/typesizes.h /usr/include/libio.h
show_aligned_blocks.o: /usr/include/_G_config.h /usr/include/wchar.h
show_aligned_blocks.o: /usr/include/bits/wchar.h /usr/include/gconv.h
show_aligned_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
show_aligned_blocks.o: /usr/include/bits/stdio_lim.h
show_aligned_blocks.o: /usr/include/bits/sys_errlist.h /usr/include/string.h
show_aligned_blocks.o: /usr/include/math.h /usr/include/bits/huge_val.h
show_aligned_blocks.o: /usr/include/bits/mathdef.h
show_aligned_blocks.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
show_aligned_blocks.o: /usr/include/bits/posix_opt.h
show_aligned_blocks.o: /usr/include/bits/confname.h /usr/include/ctype.h
show_aligned_blocks.o: /usr/include/endian.h /usr/include/bits/endian.h
show_aligned_blocks.o: ../include/global.h /usr/include/malloc.h
show_aligned_blocks.o: ../include/license.h ../include/strutil.h
show_aligned_blocks.o: ../include/errors.h ../include/memory.h
show_aligned_blocks.o: ../include/residues.h ../include/blastapp.h
show_aligned_blocks.o: /usr/include/limits.h
show_aligned_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
show_aligned_blocks.o: ../include/alphabet.h ../include/aabet.h
show_aligned_blocks.o: ../include/ntbet.h ../include/gcode.h
show_aligned_blocks.o: ../include/blocks.h ../include/output.h
show_aligned_blocks.o: ../include/sequences.h ../include/matrix.h
show_aligned_blocks.o: ../include/pattern.h ../include/convert.h
show_aligned_blocks.o: ../include/frequency.h ../include/files.h
show_aligned_blocks.o: ../include/protomat.h
blk2mot.o: ../include/blocksprogs.h /usr/include/stdlib.h
blk2mot.o: /usr/include/features.h /usr/include/sys/cdefs.h
blk2mot.o: /usr/include/gnu/stubs.h
blk2mot.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
blk2mot.o: /usr/include/stdio.h /usr/include/bits/types.h
blk2mot.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
blk2mot.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
blk2mot.o: /usr/include/bits/wchar.h /usr/include/gconv.h
blk2mot.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
blk2mot.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
blk2mot.o: /usr/include/string.h /usr/include/math.h
blk2mot.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
blk2mot.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
blk2mot.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
blk2mot.o: /usr/include/ctype.h /usr/include/endian.h
blk2mot.o: /usr/include/bits/endian.h ../include/global.h
blk2mot.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
blk2mot.o: ../include/errors.h ../include/memory.h ../include/residues.h
blk2mot.o: ../include/blastapp.h /usr/include/limits.h
blk2mot.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
blk2mot.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blk2mot.o: ../include/gcode.h ../include/blocks.h ../include/output.h
blk2mot.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blk2mot.o: ../include/convert.h ../include/frequency.h ../include/files.h
blk2mot.o: ../include/protomat.h
earch.o: /usr/include/limits.h
LAMAblimps-3.9/blimps/rank_matrix.c000064400001460000012000000115401042724133200171160ustar00jorjastaff00000400000027/* COPYRIGHT 2001 Fred Hutchinson Cancer Research Center
    rank_matrix.c  Construct aa rank matrix from an aa matrix
	rank_matrix matrix
--------------------------------------------------------------------
12/30/00 J. Henikoff from Pauline Ng's code
====================================================================*/

#define RANK_C_
#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#include 

struct rank_cell {
        int aa;
        double value;
};
void construct_rank_matrix();
void copy_values_to_ranklist ();
void sort_ranks();
void assign_ranks();
double frequency[MATRIX_AA_WIDTH];    /* for frequency.c */

/*=======================================================================*/

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *fmat;
  char matname[MAXNAME];
  struct float_qij *mat;
  int aa1, aa2, rank_matrix[AAS][AAS];
  struct rank_cell aalist[AAS];

/* ------------1st arg = aa score matrix -------------------------------*/
   if (argc > 1)
      strcpy(matname, argv[1]);
   else
   {
      printf("\nEnter name of scoring matrix: ");
      gets(matname);
   }
   if ( (fmat=fopen(matname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", matname);
      exit(-1);
   }
   mat = load_qij(fmat);
   fclose(fmat);


/*-------This uses $BLIMPD_DIR/docs/default.sij--------------------
   construct_rank_matrix(rank_matrix);
*/

   for (aa1 = 0; aa1 < AAS; aa1++) 
   {
       copy_values_to_ranklist (aalist, aa1, mat);
       sort_ranks (aalist);
       assign_ranks (rank_matrix, aalist, aa1);
   }
  
/*----------------------------------------------------------------------*/
  /*  rank_matrix[aa1][aa2] has ranks for aa1 sorted in the row */
  printf("# Rank matrix constructed from scoring matrix %s\n", matname);
  printf("# Each aa row contains the rank of the score for the all aas\n");
  printf("  ");
  for (aa1=1; aa1< AAS; aa1++) printf(" %c ", aa_btoa[aa1]);
  printf("\n");
  for (aa1=1; aa1< AAS; aa1++)
  {
     printf("%c ", aa_btoa[aa1]);
     for (aa2=1; aa2< AAS; aa2++)
     {
        printf("%2d ", rank_matrix[aa1][aa2]);
     }
     printf("\n");
  }

  free(mat);
  fclose(fmat);
  exit(0);

}  /* end of main */
/*======================================================================*/
void construct_rank_matrix (rank_matrix)
int rank_matrix[AAS][AAS];
{
        struct rank_cell aalist[AAS];
        int original_aa;
	struct float_qij* rank_Qij;
	FILE* sijfp;
        char *blimps_dir, sijname[SMALL_BUFF_LENGTH];

   blimps_dir = getenv("BLIMPS_DIR");
   if (blimps_dir != NULL)
   {
      sprintf(sijname, "%s/docs/default.sij", blimps_dir);
/*>>>>> Need to check that sijname actually exists
        for WWW servers would be better to check in current
        directory first  <<<<<<*/
   }
   else
   {
      sprintf(sijname, "default.sij");
   }

	if ( (sijfp = fopen (sijname, "r")) == NULL) 
        {
            sprintf (ErrorBuffer, "construct_rank_matrix(): Cannot open %s\n",
		sijname);
            ErrorReport(FATAL_ERR_LVL);
	}
        else
	{      rank_Qij = load_qij(sijfp); fclose(sijfp);   }

        for (original_aa = 0; original_aa < AAS; original_aa++) {
                copy_values_to_ranklist (aalist, original_aa, rank_Qij);
                sort_ranks (aalist);
                assign_ranks (rank_matrix, aalist, original_aa);
        }
	free (rank_Qij);
} /* end of construct_rank_matrix */

/*======================================================================*/
void copy_values_to_ranklist (aalist, original_aa, rankQij) 
struct rank_cell aalist[AAS];
int original_aa;
struct float_qij *rankQij;
{

        int aa;

        for (aa = 0; aa < AAS; aa++) {
                aalist[aa].aa = aa;
                aalist[aa].value = rankQij->value[original_aa][aa];
        }
} /* end of copy_values_to_ranklist */

/*======================================================================*/
void sort_ranks (aalist)
struct rank_cell aalist[AAS];
{
        int i, j;
        struct rank_cell tmp;

        /* don't include aalist[0] in the sort, it's for gaps JGH */
        for (i = 2; i < AAS; i++) {
                tmp.aa = aalist[i].aa;
                tmp.value = aalist[i].value;
                for (j = i; j > 1 && aalist[j-1].value < tmp.value; j--) {
                        aalist[j].value = aalist[j-1].value;
                        aalist[j].aa = aalist[j-1].aa;
                }
                aalist[j].value = tmp.value;
                aalist[j].aa = tmp.aa;
        }
} /* end of sort_ranks */

/*======================================================================*/
void assign_ranks (rank_matrix, aalist, original_aa)
int rank_matrix[AAS][AAS];
struct rank_cell aalist[AAS];
int original_aa;
{
        int rank, aa;

        for (rank = 0; rank < AAS; rank++) {
                aa = aalist[rank].aa;
                rank_matrix[original_aa][aa] = rank; 
        }
} /* end of assign_ranks */

blimps-3.9/blimps/readchk.c000064400001460000012000000033650774312250100162110ustar00jorjastaff00000400000027/*    Read a PSI-BLAST checkpoint file into a blimps matrix structure */
#define EXTERN
#include 

int main(argc, argv)
int argc;
char *argv[];
{
   FILE *chk;
   char chkname[80] ;
   Matrix *pssm;
   Sequence *seq;
   int pos, aa;
   long length;
   double dtemp;

   /*------------1st arg = PSI-BLAST checkpoint file--------------------*/
   if (argc > 1)
      strcpy(chkname, argv[1]);
   else
   {
      printf("\nEnter name of configuration file: ");
      gets(chkname);
   }
   if ( (chk=fopen(chkname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", chkname);
      exit(-1);
   }

   /* this is the length of the query seq = width of the pssm */
   fread(&length, sizeof(long), 1, chk);
   if (length > 0)
   { 
       pssm = new_matrix( (int) length);
       strcpy(pssm->id, "PSI-BLAST");
       strcpy(pssm->ac, "PSI-BLAST");
       strcpy(pssm->de, chkname);
       seq = (Sequence *) malloc(sizeof(Sequence));
       seq->max_length = seq->length = length;
       strcpy(seq->name, "PSI-BLAST");
       strcpy(seq->info, chkname);
       seq->position = 0;
       seq->weight = 100;
       seq->sequence = (Residue *) calloc(length, sizeof(Residue));
   }
   else
   { 
       printf("\nProblem reading %s\n", chkname);
       exit(-1);
   }
   /*  this is the query sequence */
   fread(seq->sequence, sizeof(char), length, chk);
   seq->sequence[length] = '\0';

   /* these are the target frequencies - are they sequence-weighted?
	have pseudo counts been added?   */
   for (pos=0; pos < length; pos++)
   {
      for (aa=1; aa < 21; aa++)
      {
         fread(&dtemp, sizeof(double), 1, chk);
         pssm->weights[aa][pos] = dtemp;
      }
   }

   output_matrix_st(pssm, stdout, FLOAT_OUTPUT);

   exit(0);
}  /* end of main */
blimps-3.9/blimps/readmast.c000064400001460000012000000075270774312250100164140ustar00jorjastaff00000400000027/*  Copyright 2000 Fred Hutchinson Cancer Research Center
    Read a MAST log-odds file into a blimps matrix structure
	readmast  

	Mast log-odds file is assumed to look like this:
ALPHABET= ARND...
log-odds matrix: alength=  w= 
nw*na numbers
----------------------------------------------------------------------*/
#define EXTERN
#include 

int main(argc, argv)
int argc;
char *argv[];
{
   FILE *chk;
   char chkname[80], line[MAXLINE], *ptr, *ptr1;
   Matrix *pssm;
   int pos, aa, alpha[MATRIX_AA_WIDTH], width, alength, itemp, okay, type;
   double dtemp, dmin;

   /*------------1st arg = MAST log-odds file--------------------*/
   if (argc > 1)
      strcpy(chkname, argv[1]);
   else
   {
      printf("\nEnter name of configuration file: ");
      gets(chkname);
   }
   if ( (chk=fopen(chkname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", chkname);
      exit(-1);
   }

   type = 1;	/* 0=> as-is, 1=>integer */
   for (aa=0; aa < MATRIX_AA_WIDTH; aa++) alpha[aa] = -1;
   alength = width = pos = 0;
   dmin = 9999999.99;
   pssm = NULL;
   okay = NO;

   while ( !feof(chk) && fgets(line, MAXLINE, chk) != NULL )
   {
      if (pssm != NULL) okay = YES;	/* have alphabet & width */

      if (strncmp(line, "ALPHABET", 7) == 0)
      {
	ptr = strtok(line, " ");
        if (ptr != NULL)
        {
		ptr = strtok(NULL, " \r\t\n");
		if (ptr != NULL) alength = (long) strlen(ptr);
		else alength = 0;
        }
        if (alength == 0)
        {
		printf("\nProblem finding ALPHABET in %s\n", chkname);
		exit(-1);
        }
	for (itemp=0; itemp= 0 && aa < MATRIX_AA_WIDTH) alpha[itemp] = aa;
	}
      }   /* end of ALPHABET */

      /* alength= %d w= %d  */
      if (strncmp(line, "log-odds", 8) == 0)
      {
	ptr1 = strstr(line, "alength=");
        if (ptr1 != NULL)
        {
		sscanf(ptr1, "alength= %d w=%d", &itemp, &width);
		if (itemp != alength)
		{
		   printf("\nALPHABET length (%d) not alength (%d)\n", 
				alength, itemp);
		   exit(-1);
		}
        }
        if (width == 0)
        {
		printf("\nProblem finding width in %s\n", chkname);
		exit(-1);
        }
	else
	{
		pssm = new_matrix( (int) width);
		pssm->width = width;
		strcpy(pssm->id, "MAST");
		strcpy(pssm->ac, "MAST");
		strcpy(pssm->de, chkname);
		sprintf(pssm->ma, "width=%d;", width);
	}
      }  /* end of log-odds */

      if (okay)
      { 
	 ptr = strtok(line, " \t\r\n");
         for (aa=0; aa < alength; aa++)
         {
		if (ptr != NULL)
		{
			dtemp = atof(ptr);
			pssm->weights[ alpha[aa] ][pos] = dtemp;
			if (dtemp < dmin) dmin = dtemp;
			ptr = strtok(NULL, " \t\r\n");
		}
		else
		{
			printf("\nProblem finding value for pos=%d aa=%c\n",
				pos, aa_btoa[aa]);
		}
         }
	 pos++;
      }
   }   /* end of while */

   if (type)	/* positive integers */
   {
      /*  Normalize weights to add to 100 in each position */
      for (pos=0; posweights[ aa_atob['B'] ][pos] = dmin;
         pssm->weights[ aa_atob['Z'] ][pos] = dmin;
         pssm->weights[ aa_atob['X'] ][pos] = dmin;
         pssm->weights[ aa_atob['*'] ][pos] = dmin;
         pssm->weights[ aa_atob['-'] ][pos] = dmin;
         if (dmin < 0)   /* make all weights positive */
         {
            dtemp = 0.0 - dmin;
            for (aa=0; aaweights[aa][pos] = pssm->weights[aa][pos] + dtemp; }
         }
	 dtemp = 0.0;
         for (aa=0; aaweights[aa][pos]; }
         for (aa=0; aaweights[aa][pos] = 100.0 * pssm->weights[aa][pos] / dtemp; }
      }
      output_matrix_st(pssm, stdout, FLOAT_OUTPUT);
   }
   else  /* output it as-is */
   {
      output_matrix_st(pssm, stdout, FLOAT_OUTPUT);
   }

   exit(0);
}  /* end of main */
blimps-3.9/blimps/retblock.c000064400001460000012000000073470774312250100164210ustar00jorjastaff00000400000027/*  COPYRIGHT 1997-1999 Fred Hutchinson Cancer Research Center
    retblock.c  Extract some or all blocks from a blocks database to
		  separate out files or to stdout
           retblock   [-n] [-f]
	   Creates files named AC.blk
--------------------------------------------------------------------
 1/10/97 J. Henikoff (from extblock.c & blexplode.c)
 4/14/97 Added floating point output options.
 7/31/97 Compares shorter of input AC and block AC.
 1/23/99 exit(-2) if requested block wasn't found
 6/14/99 Adjustments for longer sequence names
====================================================================*/

#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#include 

/*=======================================================================*/
/*
 * main
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
   FILE *bfp, *ofp;
   Block *block;
   char bdbname[MAXNAME], outname[MAXNAME], acname[MAXNAME];
   int outfloat, outflag, allflag, aclen, okay, nout;

   if (argc < 2)
   {
      printf("RETBLOCK: Copyright 1997 Fred Hutchinson Cancer Research ");
      printf("Center\n");
      printf("Extract blocks from a Blocks Database\n");
      printf("USAGE:  retblock   [[-n] -f]\n");
      printf("           = file of blocks\n");
      printf("           => extract AC or all blocks\n");
      printf("          -n       => output to stdout, otherwise each block\n");
      printf("                      will be written to AC?.blk\n");
      printf("		-f	=> floating point output\n");
   }

   allflag = outflag = FALSE;
/* ------------1st arg = blocks database -------------------------------*/
   if (argc > 1)
      strcpy(bdbname, argv[1]);
   else
   {
      printf("\nEnter name of blocks database: ");
      gets(bdbname);
   }
   if ( (bfp=fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbname);
      exit(-1);
   }

/* ------------2nd arg = AC --------------------------------------------*/
   allflag = FALSE;
   if (argc > 2)
      strcpy(acname, argv[2]);
   else
   {
      strcpy(acname, "all");
      printf("\nEnter AC of blocks to extract, or all [%s]: ", acname);
      gets(acname);
   }
   if (strcasecmp(acname, "all") == 0) allflag = TRUE;

   /* ------------3rd & 4th optional arg = stdout flag/floating point-------*/
   outflag = FALSE;
   outfloat = FALSE;
   if (argc > 3 && strcasecmp(argv[3], "-n") == 0) outflag = TRUE;
   if (argc > 3 && strcasecmp(argv[3], "-f") == 0) outfloat = TRUE;
   if (argc > 4 && strcasecmp(argv[4], "-n") == 0) outflag = TRUE;
   if (argc > 4 && strcasecmp(argv[4], "-f") == 0) outfloat = TRUE;

   /*-----------------------------------------------------------------*/

   nout = 0;
   while ((block = read_a_block(bfp)) != NULL)
   {
     okay = FALSE;
     aclen = strlen(acname);
     /* If they type BL00031A, but there's only a single block, BL00031,
        then be sure to return that */
     if (strlen(block->number) < aclen) aclen = strlen(block->number);
     if (allflag || strncasecmp(acname, block->number, aclen) == 0)
        okay = TRUE;
     if (okay)
     { 
        if (!outflag)
        {
           strcpy(outname, block->number);
           strcat(outname, ".blk");
           if ( (ofp=fopen(outname, "w")) == NULL)
           {
               printf("\nCannot open file %s\n", outname);
               exit(-1);
           }
        }
        else ofp = stdout;
        if (outfloat) output_block_s(block, ofp, FLOAT_OUTPUT);
        else          output_block_s(block, ofp, INT_OUTPUT);
        if (!outflag) fclose(ofp);
        nout++;
      }
      free_block(block);
   }
   
   fclose(bfp);
   if (nout > 0) exit(0);
   else          exit(-2);

}  /* end of main */
=====================================================================*/
/*
 * main
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
   FILE *bfp, *ofp;
   Block *block;
   char bdbname[MAXNAME], outname[MAXNAME], acname[MAXNAME];
   int outfloat, outflag, allflag, aclblimps-3.9/blimps/scores.c000064400001460000012000000313420774312250100161020ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* scores.c: score structure manipulation and scoring routines */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

/*	system headers not in global.h */
#include 
/*	blimps library headers */
#include 
#include 	/* includes sequences.h, output.h */
#include 	/* includes pattern.h */
/*	headers in current directory */
#include "scores.h"
#include "blimps.h"
#include "scoring.h"
#include "lists.h"


/*
 * Exported variables and data structures
 */

/*
 * Local variables and data structures
 */
static int output_formatted_score();
static void print_score();
static void print_score_summary();
static void score_and_enter_switch();
static void select_with_pattern();



/*
 * Function definitions
 */



/* 
 * score_and_enter
 *   Calls the appropriate function for scoring.  If it is to select patterns
 *   the function select_with_pattern() is called, otherwise it calls the 
 *   appropriate scoring method in score_and_enter_switch().
 *   Note: the sequence must be an AA_SEQ.
 *   Parameters:
 *     Sequence *seq: the sequence to score
 *     Matrix *matrix: the matrix used for scoring
 *     int frame: the frame we are looking at (0 = aa seq.,
 *                1, 2, 3, -1, -2, -3 = na seqs.)
 *     Boolean repeats: enter repeats into the score_list?
 *     int search_type: the type of search we are doing.  If it is a 
 *                      SEARCH_TYPE_MATRIX search (block vs sequences), 
 *                      do NOT divide by the block percentile.  If it is a 
 *                      SEARCH_TYPE_BLOCK search (sequence vs blocks), DO 
 *                      divide by the block percentile. 
 *   Return Codes: TRUE if the sequence is an AA_SEQ, FALSE otherwise.  The
 *                 score is inserted into the scores list.
 *   Error Codes: returns FALSE if the sequence was not an AA_SEQ and does not 
 *                score the sequence.
 */

int score_and_enter(seq, matrix, frame, repeats, search_type)
     Sequence *seq;
     Matrix *matrix;
     int frame;
     Boolean repeats;
     int search_type;
{
  /* check for the correct sequence type */
  if (seq->type != AA_SEQ) {
    sprintf(ErrorBuffer, 
	    "score_and_enter(): Tried to score a sequence that is not an");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "                   amino acid sequence.  Not scoring the");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "                   sequence %s\n", seq->name);
    ErrorReport(PROGRAM_ERR_LVL);
    return FALSE;
  }

  if (UsePatterns) {
    /* select the patterns to score and score them */
    select_with_pattern(seq, matrix, frame, repeats, search_type);
  }
  else {
    /* we are scorint the whole sequence */
    score_and_enter_switch(seq, matrix, frame, repeats, search_type, FALSE);
  }

  return TRUE;
  
}


/*
 * score_and_enter_switch
 *   computes the score of the sequence against the matrix.  If repeats is
 *   TRUE, all of the pairwise scores are entered into the score_list, 
 *   otherwise only the best score is entered.
 *   The scoring algorithm is selected by setting SequenceMatrixScoringMethod
 *   appropriately.  
 *   Note: the sequence must be an AA_SEQ.
 *   Parameters:
 *     Sequence *seq: the sequence to score
 *     Matrix *matrix: the matrix used for scoring
 *     int frame: the frame we are looking at (0 = aa seq.,
 *                1, 2, 3, -1, -2, -3 = na seqs.)
 *     Boolean repeats: enter repeats into the score_list?
 *     int search_type: the type of search we are doing.  If it is a 
 *                      SEARCH_TYPE_MATRIX search (block vs sequences), 
 *                      do NOT divide by the block percentile.  If it is a 
 *                      SEARCH_TYPE_BLOCK search (sequence vs blocks), DO 
 *                      divide by the block percentile. 
 *   Return Codes: none
 *   Error Codes: none
 */

static void
score_and_enter_switch(seq, matrix, frame, repeats, search_type, 
		       pattern_search)
     Sequence *seq;
     Matrix *matrix;
     int frame;
     Boolean repeats;
     int search_type;
     Boolean pattern_search;
{
  switch (SequenceMatrixScoringMethod) {
  case 0:
  default:

    if (SequenceMatrixScoringMethod != 0) {
      sprintf(ErrorBuffer, 
	      "Invalid matrix-sequence scoring method specified, %d.",
	      SequenceMatrixScoringMethod);
      ErrorReport(WARNING_ERR_LVL);
      sprintf(ErrorBuffer,
	      "Setting the method to the default value and using the");
      ErrorReport(WARNING_ERR_LVL);
      sprintf(ErrorBuffer,
	      "default scoring method.\n");
      ErrorReport(WARNING_ERR_LVL);
      SequenceMatrixScoringMethod = 0;
    }

    default_scoring_method(seq, matrix, frame, repeats, search_type, 
			   pattern_search);

    break;

  } /* end switch of SequenceMatrixScoringMethod */
}



static void
select_with_pattern(seq, matrix, frame, repeats, search_type)
     Sequence *seq;
     Matrix *matrix;
     int frame;
     Boolean repeats;
     int search_type;
{
  int x, y;
  int seq_length = seq->length;
  int mat_length = matrix->width -1;
  int seq_pos_scored_length = (mat_length*2) + seq_length;
  Boolean seq_pos_scored[1000];

  Pattern **patterns;
  int seq_compare_start;	/* the place to start, in the seq_pos_scored */
				/* reference frame */

/*printf("mat_length: %d \tseq_length: %d\n", mat_length, seq_length);*/

  /* build the patterns for the matrix if not done so already */
  scan_patterns(matrix);

  if ((matrix->patterns == NULL) ||
      (matrix->patterns[0] == NULL)) {
    sprintf(ErrorBuffer,
	    "No pattern for matrix %s, Scoring the entire matrix\n",
	    matrix->number);
    ErrorReport(WARNING_ERR_LVL);

    score_and_enter_switch(seq, matrix, frame, repeats, search_type, FALSE);
    return;
  }

  for (x=0; x<(mat_length+seq_length); x++) {
    /* Fill the array with falses */
    seq_pos_scored[x] = FALSE;
  }

  patterns = matrix->patterns;

  for (x=0; xbeg_offset;

      /* check that it is within range of the array */
      if ((seq_compare_start >= 0) &&
	  (seq_compare_start < seq_pos_scored_length)) {
	/* check that it hasn't been scored */
	if (seq_pos_scored[seq_compare_start] == FALSE) {
	  /* check if this is scorable */ 
	  if (pattern_matches(seq, x-mat_length, patterns[y])) {
	    
	    /* shift it back to the sequences' reference point */
	    seq->undefined = seq_compare_start - mat_length;
	    /*printf("Possition is: %d  \tScore pos is: %d\n", x-mat_length,seq->undefined);*/
	    seq_pos_scored[seq_compare_start] = TRUE;
	    score_and_enter_switch(seq, matrix, frame, repeats, 
				   search_type, TRUE);
	  }
	}
      }
    }
  }
}


/*
 * score_comparison
 *   Compares two score records.   It compares by the value in the score
 *   field.  
 *   Parameters:
 *     ScoreListEntry a, b: the entries to compare
 *   Return codes:  a return value > 0 if a > b, a return value = 0 if a == b,
 *                  and a return value < 0 if a < b
 *   Error codes: none
 */

int score_comparison(a, b)
     Score *a, *b;
{
  return (a->score - b->score);	
}

/*
 * neg_score_comparison
 *   Returns the negative of score_comparison.  Effectively the opposite
 *   logic of score_comparison. 
 *   Parameters:
 *     ScoreListEntry a, b: the entries to compare
 *   Return codes:  a return value < 0 if a < b, a return value = 0 if a == b,
 *                  and a return value > 0 if a > b
 *   Error codes: none
 */
int neg_score_comparison(a, b)
     Score *a, *b;
{
  return (- (score_comparison(a, b))); /* reversed because we want the */
				       /* highest score first */
}

/* 
 * free_score
 *   Deletes the score list entry and the sub elements.
 *   Parameters: 
 *     Score *score: the score to free
 *   Return code: none
 *   Error code: none
 */

void free_score(score) 
     Score *score;
{
  free(score);
}

/*
 * Score printing.
 */

/* 
 * output_scores
 *   Prints out the score list in the final format.
 *   Parameters:
 *     int num_to_report: the number of scores to report, if <1 reports all.
 *     FILE *ofp:         the file to output scores to
 *   Error codes: none
 */

void output_scores(num_to_report, ofp)
     int num_to_report;
     FILE *ofp;
{
  /* make the PrintScores list */
  DoForSL(Scores, enter_score_into_print_scores, NULL);
  
  DoForSL(PrintScores, output_formatted_score, ofp);
                              /* pass the print function and the output file */
}


/* 
 * output_formatted_score
 *   Prints a score and related data to the specified file.  This function
 *   controls what the final output for the scores will look like.
 *   Parameters:
 *     Score *score:  the score to print
 *     FILE *ofp: the output file pointer.  May be stdout.
 *   Return code: SL_CONTINUE, always.  So that when going through the list
 *                it will always behave the same.  See the function 
 *                description of DoForSL in the skiplist functions.doc and 
 *                the defines in skiplist.h.
 *   Error codes: none
 */

static int output_formatted_score(score, ofp)
     Score *score;
     FILE *ofp;
{
  if (SearchType == SEARCH_TYPE_BLOCK) { /* seq vs blocks */
    fprintf(ofp, 
	    "%-11.11s %-50.50s      %4d   %4d %2d %6d %s\n",
	    score->matrix_number, /* accession number */
	    score->matrix_desc,	/* description, de or info field trimed */
	    score->strength,	/* strength */
	    score->score,	/* score */
	    score->frame,	/* reading frame */
	    score->position,	/* position in the sequence */
	    score->consensus);	/* the consensus string */

  }
  else if (SearchType == SEARCH_TYPE_MATRIX) { /* block vs sequences */
    fprintf(ofp, 
	    "%-20.20s %-62.62s %4d %2d %5d %6d %s\n",
	    score->sequence_number, /* accession number */
	    score->sequence_desc, /* description, de or info field trimed */
	    score->score,	/* score */
	    score->frame,	/* reading frame */
	    score->position,	/* position in the sequence */
	    score->seq_length,  /* length of the sequence */
	    score->consensus);		/* the consensus string */
    
  }
  else if (SearchType == SEARCH_TYPE_UNKNOWN) {	/* blocks vs sequences */
    fprintf(ofp, 
	    "%-8s vs %-7s   %-20s... & %-20s... %4d %4d %2d %6d %6d %s\n",
	    score->matrix_number, /* accession number */
	    score->sequence_number, /* accession number */
	    score->matrix_desc,	/* description, de or info field trimed */
	    score->sequence_desc, /* description, de or info field trimed */
	    score->strength,	/* strength */
	    score->score,	/* score */
	    score->frame,	/* reading frame */
	    score->position,	/* position in the sequence */
	    score->seq_length,  /* length of the sequence */
	    score->consensus);		/* the consensus string */

  }
  else {
    fprintf(ofp, 
	    "%-8s %4u %-45s      %4d   %4d %2d %6d %s\n",
	    "--------",		/* accession number */
	    0,			/* record number, I don't use */
	    "---------------------------------------------", 
				/* description, de or info field trimed */
	    score->strength,	/* strength */
	    score->score,	/* score */
	    score->frame,	/* reading frame */
	    score->position,	/* position in the sequence */
	    score->consensus);	/* the consensus string */
    
  }

  return SL_CONTINUE;
}


/*
 * print_score
 *   Prints a Score data structure.  Primarily for debugging purposes.
 *   Parameters: 
 *     Score *score:  the score to print
 *   Error Codes: none
 */

static void print_score(score)
     Score *score;
{
  printf("--- score ---\n");

  printf("\tScore: %d\n", score->score);
  
  printf("\tPosition: %d\n", score->position);

  printf("\tFrame: %d\n", score->frame);

  printf("\tMat Num: %s\n", score->matrix_number);

  printf("\tSeq Num: %s\n", score->sequence_number);

  printf("\tMat Desc: %s\n", score->matrix_desc);

  printf("\tSeq Desc: %s\n", score->sequence_desc);

  printf("\tConsensus: %s\n", score->consensus);

  printf("--- ----- ---\n");
}


/*
 * print_score_summary
 *   Prints a Score data structure in a compact format.  Primarily for 
 *   debugging purposes.
 *   Parameters: 
 *     Score *score:  the score to print
 *   Error Codes: none
 */

static void print_score_summary(score)
     Score *score;
{
  printf("S:% 6d\tP:% 6d\tF:% 6d\n", score->score, score->position, score->frame);

}




/* Change log information follows. */
/* 
 Changes since 3.3.1:
 10/ 2/99  Added more includes for standard C libraries.
 Changes since 3.2.5:
 4/29/99 output_formatted_score() Don't print the 0 before description.

 Changes since 3.2.3:
 5/13/98 Print 1st 20 instead of 1st 11 chars of sequence names.
 *
 *
 */

s;
     int search_type;
     Boolean pattern_search;
{
  switch (SequenceMatrixScoringMethod) {
  case 0:
  default:

    if (SequenceMatrixScoringMethod != 0) {
      sprintf(ErrorBuffer, 
	      "Invalid matrix-sequence scoring method specified, %d.",
	      SequenceMatrixScoringMetblimps-3.9/blimps/scoring.c000064400001460000012000000407440774312250100162560ustar00jorjastaff00000400000027/* (C) Copyright 1993-9, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* scoring.c: functions for different methods of scoring a sequence against */
/*            a matrix */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

/*	system headers not in global.h  */
#include 
/*	blimps library headers */
#include 
#include 	/* includes sequences.h, output.h */
#include 	/* includes pattern.h */
#include 
/*	headers in current directory */
#include "scoring.h"
#include "blimps.h"
#include "scores.h"
#include "lists.h"
/* #include 	*/	/* for DoHistogram */



/*
 * Exported variables and data structures
 */

double Alignments_Done = 0.0;
double Scores_Done = 0.0;
int histogram[NUM_HIST_COLS];  /* according to ansii C these initialize as 0 */
Boolean DoHistogram = FALSE;

/*
 * Local variables and data structures
 */

static void enter_score();
static Score *make_score();


/*
 * Function definitions
 */

/*************************************************************************
 *************************************************************************
 *                                                                       *
 *                    I M P O R T A N T   N O T E ! ! !                  *
 *                                                                       *
 *      All scoring methods need to check if UsePatterns is set.         *
 *      If it is set, the scoring method must only score the first       *
 *      full alignment.  eg pos. 1- pos. 1, 2-2, 3-3, etc...             *
 *                                                                       *
 *************************************************************************
 *************************************************************************
 */
/*
compile block ! ! ! @ # $ % ^ &* * ( ) _ + @^ *#&^$ 
stuck...
Need to decide if the repeats is needed for the scoring of patterns
  If not, continue with the current stuff, otherwise, back to the chalkboard

Note, currently planning on using the optional integer field in the sequence
structure to carry the information on where the pattern matching is to start.
There will also be another parameter to tell if there is pattern matching
involved (note, this invalidates the above comment note).
*/
/* most recent approach is to tell the scoring method if it is a */
/* patterns search.  If it is then we treat it as a score all repeats. */
/* The method to try for not scoring repeats is this.  Make the */
/* scoring return info about the score if it was a patterns search. */
/* This way, since the patterns score is only a single score, the */
/* calling function can keep track of the scores and enter only the */
/* best one into the scores list.  Not that it will need to keep track */
/* of the other information needed also. */


/*
 * default_scoring_method
 *   The default scoring method.  Basically a score is the sum of the scores 
 *   in the matrix at each position-amino acid pair for one alignment.
 *   Parameters:
 *     Sequence *seq: the sequence to score
 *     Matrix *matrix: the matrix used for scoring
 *     int frame: the frame we are looking at (0 = aa seq.,
 *                1, 2, 3, -1, -2, -3 = na seqs.)
 *     Boolean repeats: enter repeats into the score_list?
 *     int search_type: the type of search we are doing.  If it is a 
 *                      SEARCH_TYPE_MATRIX search (block vs sequences), 
 *                      do NOT divide by the block percentile.  If it is a 
 *                      SEARCH_TYPE_BLOCK search (sequence vs blocks), DO 
 *                      divide by the block percentile. 
 *     Boolean pattern_search: whether or not to use the pattern search stuff
 *   Error codes: none
 */

void default_scoring_method(seq, matrix, frame, repeats, search_type,
			    pattern_search) 
     Sequence *seq;
     Matrix *matrix;
     int frame;
     Boolean repeats;
     int search_type;
     Boolean pattern_search;
{
  int aa, mat_pos, seq_pos;
  int matrix_length, seq_length;
  int scan_pos;
  double max_aa_score, max_score;
  double seq_score, max_seq_score;
  int best_position;
  Boolean seen_pattern;

  /* get the lengths, gets rid of the indirrection */
  matrix_length = matrix->width;
  seq_length    = seq->length;
  
  /* Make sure these lengths are > 0 */
  if (matrix_length <= 0) {
    sprintf(ErrorBuffer,
	    "default_scoring_method(): matrix %s has length <= 0",
		matrix->number);
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "default_scoring_method(): Not scoring the sequence.\n");
    ErrorReport(PROGRAM_ERR_LVL);
    return;
  }
  if (seq_length <= 0) {
    sprintf(ErrorBuffer,
      "default_scoring_method(): sequence %s has length (amino acids) <= 0",
		seq->name);
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "default_scoring_method(): Not scoring the sequence.\n");
    ErrorReport(PROGRAM_ERR_LVL);
    return;
  }

  /* compute the maximum possible score for this matrix */
  /* this is used in standardizing the scores in a BLOCK search with a  */
  /* block without a percentile ranking (only calulate max_score if this */
  /* is the case) */
  max_score = 0.0;
  if ((search_type == SEARCH_TYPE_BLOCK) &&
      (matrix->percentile <= 0)) {
    for (mat_pos=0; mat_pos < matrix_length; mat_pos++) {
      max_aa_score = 0.0;
      for (aa=0; aa < MATRIX_AA_WIDTH; aa++) {
	if (matrix->weights[aa][mat_pos] > max_aa_score) {
	  max_aa_score = matrix->weights[aa][mat_pos];
	}
      }
      max_score = max_score + max_aa_score;
    }
  }

  

  /* 
   * score the matrix vs the sequence for each pairwise line up 
   */
  max_seq_score = 0.0;
  
  /* for every alignment of the matrix and sequence score the alignment. */
  /* there are (seq_length + matrix_length  - 1) different alignments. */
  /* Note: seq_pos is the relative position of the 1st matrix column to the */
  /*       1st sequence column */
  /* Note: the indexing is shifted to make the calculation of scan_pos */
  /*       (see below) easier/faster */
  seen_pattern = FALSE;
  for (seq_pos= -matrix_length+1; seq_pos < seq_length; seq_pos++) 
  {
    if (pattern_search) {
      /* This is a pattern!  Only score the first full alignment. */
      if (seen_pattern) {
	break; /* break out of the for loop.  I know it is a hack, but this *
		* does the least damage to the other logic. */
      }
      else {
	seen_pattern = TRUE; /* stop after this one time through the loop */
	seq_pos = seq->undefined;
      }
    }
    

    /* 
     * score this alignment
     */
    seq_score = 0.0;

    /* for each position in the matrix add the weight to the total score */
    /* Note: mat_pos is the current column of the matrix */
    for (mat_pos=0; mat_pos < matrix_length; mat_pos++) 
    {
      /* make sure the sequence and the matrix overlap at this point */
      /* Note: scan_pos is where the current matrix column is in the */
      /*       sequence */
      scan_pos = seq_pos + mat_pos;
      if ((scan_pos >= 0) && (scan_pos < seq_length)) { /* if in the seq */
	seq_score += matrix->weights[seq->sequence[scan_pos]][mat_pos];
      }
      else {		/* not in the sequence, score as gap */
	seq_score += matrix->weights[aa_atob['-']][mat_pos]; 
      }
      
    } /* end of for mat_pos: score this alignment */
    Alignments_Done += 1.0;
    
    /*
     * adjust the score if it is a SEARCH_TYPE_BLOCK search 
     */
    if (search_type == SEARCH_TYPE_BLOCK) {
      if (matrix->percentile > 0) {
	seq_score = (int) ((seq_score/matrix->percentile ) 
			   * 1000 );
      }
      else {
	seq_score = (int) (((seq_score/max_score) 
			    * log10((double) matrix->width))
			   * 1000 );
      }
    } /* end adjust score */

    if (seq_score > max_seq_score) {
	max_seq_score = seq_score;
	best_position = seq_pos;
    }

    /*   Save all scores for repeats */   
    if (repeats && (!SavedScoresFlag || seq_score >= MIN_SAVE_SCORE) )
    {
         enter_score((int)seq_score, seq_pos, frame, matrix, seq);
    }
  } /* end of for seq_pos */ 
    
  /*
   * if repeats were not allowed then save the best score seen
   */
 if (!repeats && (!SavedScoresFlag || seq_score >= MIN_SAVE_SCORE) )
 {
    enter_score((int)max_seq_score, best_position, frame, matrix, seq);
 }
  
}  /*  end of default_scoring_method */


/*
 * enter_score
 *   takes the data for a score entry and enters it into the list if it is
 *   ok to enter it. Note that not entering the score if it will be deleted 
 *   anyway saves time with the allocating and deallocating of score records.
 *   Parameters:
 *     int score:          the score
 *     int position:       the position
 *     int frame:          the frame we are looking at 
 *                             (0 = aa seq., 1, 2, 3, -1, -2, -3 na seqs.)
 *     Matrix *matrix:     the matrix
 *     Sequence *sequence: the sequence
 *   Error codes: none
 */

static void enter_score(score, position, frame, 
			matrix, sequence)
     int score;
     int position;
     int frame;
     Matrix *matrix;
     Sequence *sequence;
{  
  int result;

  /* increase the number of scores done */
  Scores_Done += 1.0;

  /* enter into the histogram array if keeping track */
  if (DoHistogram) {
    histogram[min((max(0, (int)score/HIST_BOX_SIZE)), (NUM_HIST_COLS-1))]++;
  }

  /* if score is worth entering into the list, enter it */
  /*   if the number of scores in the list is not yet to the max, we */
  /*   still need to enter the score, no matter what */
  if (!(score < MinScoreOfList) || 
      ((NumberToReport >= 0) && 
       (NumInSL(Scores) < NumberToReport))) {
    /* save score into score_list */
    result = 
      insert_in_score_list(make_score(score, position, frame, 
				      matrix, sequence));
    if (result == FALSE) {
      sprintf(ErrorBuffer, 
	      "enter_score(): Error placing matrix score into list\n");
      ErrorReport(PROGRAM_ERR_LVL);
    }
  }
}



/*
 * make_score
 *   allocates space for the structure that contains the score, sequence
 *   position matrix, and sequence information to be added to the Scores list.
 *   Parameters:
 *     int score:          the score
 *     int position:       the position
 *     int frame:          the frame we are looking at 
 *                             (0 = aa seq., 1, 2, 3, -1, -2, -3 na seqs.)
 *     Matrix *matrix:     the matrix
 *     Sequence *sequence: the sequence
 *   Return codes: returns a ScoreListEntry to be used later.
 *   Error codes:
 */

static Score *make_score(score, position, frame, matrix, sequence)
     int score;
     int position;
     int frame;
     Matrix *matrix;
     Sequence *sequence;
{  
  int block_length;		/* the length of the block */
  int seq_length;		/* the length of the sequence */
  int block_pos;		/* the position in the block */
  int scan_pos;			/* where we are related to block[0] */
  int seq_loop;			/* looping index through all the sequences */
				/* in the block*/
  char *consensus;
  Residue block_res, seq_res;	/* temporary places for the residues that */
				/* are being compared */
  Block *block;

  Score *new_score;

  CheckMem(
	   new_score = (Score *) malloc(sizeof(struct score_struct))
	   );

  new_score->score = score;
  new_score->strength = matrix->strength;
  new_score->position = position;
  new_score->seq_length = sequence->length;
  new_score->frame = frame;
  strncpy(new_score->sequence_number, sequence->name, NUMBER_WIDTH);
  strncpy(new_score->sequence_desc, sequence->info, DESC_WIDTH);
  if (matrix->block != NULL) {
    /* there is a block to use */
    strncpy(new_score->matrix_number, matrix->block->number, NUMBER_WIDTH);
    strncpy(new_score->matrix_desc, matrix->block->de, DESC_WIDTH);
  }
  else {			
    /* no block to use */
    strncpy(new_score->matrix_number, matrix->number, NUMBER_WIDTH);
    strncpy(new_score->matrix_desc, matrix->de, DESC_WIDTH);
  }

  /* if there is a block to look at and use to make the consensus sequence */
  /* then make the consensus sequence */
  /* otherwise, just use the sequence segment as the consensus    JGH*/
  consensus = new_score->consensus;
  seq_length = sequence->length;
  
  if (matrix->block != NULL) {
    block = matrix->block;

    block_length = block->width;
    
    /* for each position in the block figure out what case to use in the */
    /* consensus sequence to be printed out */
    /* Note: block_pos is the current column of the block */
    for (block_pos=0; block_pos < min(block_length, DESC_WIDTH); block_pos++) {

      /* make sure the sequence and the block overlap at this point */
      /* Note: scan_pos is where the current block column is in the */
      /*       sequence */
      scan_pos = position + block_pos;
      if (scan_pos < 0) {	/* before the sequence */
	consensus[block_pos] = ' ';
      }
      else if ((scan_pos >= 0) && (scan_pos < seq_length)) { /* in the seq */
	/*
	 * check for a consensus 
	 */
	consensus[block_pos] = tolower(aa_btoa[sequence->sequence[scan_pos]]);
	/* for every sequence in the block, check the residue.  if there */
	/* is one that is the same as the sequence, then change the case */
	seq_res = sequence->sequence[scan_pos];
	for (seq_loop=0; seq_loop< block->num_sequences; seq_loop++) {
	  block_res = block->sequences[seq_loop].sequence[block_pos];
	  if (seq_res == block_res) {
	    consensus[block_pos] = toupper(aa_btoa[seq_res]);
	    break;
	  }
	  /* if it is an ambiguity code, change the case */
	  else if (((seq_res == aa_atob['B']) &&
		    ((block_res == aa_atob['D']) || 
		     (block_res == aa_atob['N']))) ||
		   ((seq_res == aa_atob['Z']) &&
		    ((block_res == aa_atob['E']) || 
		     (block_res == aa_atob['Q']))) ||
		   ((block_res == aa_atob['B']) &&
		    ((seq_res == aa_atob['D']) || 
		     (seq_res == aa_atob['N']))) ||
		   ((block_res == aa_atob['Z']) &&
		    ((seq_res == aa_atob['E']) || 
		     (seq_res == aa_atob['Q'])))) {
	    consensus[block_pos] = toupper(aa_btoa[seq_res]);
	    break;
	  }
	}
	/* make sure that all X's are lower case */
	if (seq_res == aa_atob['X']) {
	  consensus[block_pos] = tolower(aa_btoa[seq_res]);
	}
      }
      else {			/* after the sequence */
	break;			/* don't need to keep going */
      }
    }
    consensus[block_pos] = '\0';
  }
  else { /* no block to make a consensus sequence from */
 
    block_length = matrix->width;
     
    /* for each position in the block figure out what case to use in the */
    /* consensus sequence to be printed out */
    /* Note: block_pos is the current column of the block */
    for (block_pos=0; block_pos < min(block_length, DESC_WIDTH); block_pos++) {
 
      /* make sure the sequence and the block overlap at this point */
      /* Note: scan_pos is where the current block column is in the */
      /*       sequence */
      scan_pos = position + block_pos;
      if (scan_pos < 0) {	/* before the sequence */
 	consensus[block_pos] = ' ';
      }
      else if ((scan_pos >= 0) && (scan_pos < seq_length)) { /* in the seq */
 	/*
 	 * copy the sequence as the "consensus"
 	 */
 	consensus[block_pos] = tolower(aa_btoa[sequence->sequence[scan_pos]]);
 	/* for every sequence in the block, check the residue.  if there */
 	/* is one that is the same as the sequence, then change the case */
      }
      else {			/* after the sequence */
 	break;			/* don't need to keep going */
      }
    }
    consensus[block_pos] = '\0';
  }

  return new_score;
}




/* 
 * print_histogram
 *   ouputs the histogram array from scoring.[ch] to the output stream ofp.
 *   Parameters:
 *     FILE *ofp: the output file pointer
 *   Return codes: none
 *   Error codes: none
 */

void print_histogram(ofp)
     FILE *ofp;
{
  int i, maxi;

  /*  Find highest non-empty cell   JGH */
  maxi = NUM_HIST_COLS - 1;
  while (histogram[maxi] == 0) {
    maxi--;
  }

  fprintf(ofp, "Histogram:\n");
/*  fprintf(ofp, "         < %-5d : %d\n", HIST_BOX_SIZE, histogram[0]);*/

  for (i=0; i<=maxi; i++) {
    fprintf(ofp, "   %5d - %-5d : %d\n", i*HIST_BOX_SIZE, 
	    (i+1)*HIST_BOX_SIZE-1,
	    histogram[i]);
  }

  fprintf(ofp, "   %5d -       : %d\n", 
	  (i)*HIST_BOX_SIZE, 
	  0);
  fprintf(ofp, "\n");
}





/* Change log information follows. */
/*
  Changes since version 3.3.1:
  10/ 2/99 Added includes for more standard C libraries.
  Changes since version 3.2.5:
  5/25/99 Scores_Done & Alignments_Done changed to double.
  2/3/99  default_scoring_method():
          If SavedScoresFlag, don't save scores < MIN_SAVE_SCORE
  Changes since version 3.1:
  1/16/97  Clarified error message. JGH
  Changes since version 3.0.0:
  3/25/96  Print out sequence name if error reading db.  JGH
*/
op after this one time throublimps-3.9/blimps/sequences.c000064400001460000012000001155761041505332000166030ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* sequences.c: sequence manipulation functions */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

/*	system headers not in global.h  */
/*	blimps library headers */
#include 
#include 
#include 

/*
 * Exported variables and data structures
 */


struct db_info DbInfo[MAXDB] = 
{ 
  { 
    "GenBank",			/* type */
    "LOCUS",			/* start */
    "DEFINITION",		/* desc */
    "ORIGIN",			/* seq */
    "//",			/* end */
    12,				/* title_offset */
    10 },			/* seq_offset */
  {   /* pir has numbers in the first line following the sequence signif. */
    "PIR",			/* type */
    "ENTRY",			/* start */
    "TITLE",			/* desc */
    "SEQUENCE",			/* seq */
    "///",			/* end */
    16,				/* title_offset */
    8 },			/* seq_offset */
  {   /* EMBL and SwissProt have the same id's */
    "EMBL/SwissProt",		/* type */
    "ID   ",			/* start */
    "DE   ",			/* desc */
    "SQ",			/* seq */
    "//",			/* end */
    5,				/* title_offset */
    5 },			/* seq_offset */
  {   /* GCG has non-sequence info in the first three lines following the */
      /* sequence signifier */
      /* NOTE: these delimiters are used to help control the flow of */
      /*       the sequence algorithms.  If they are changed be very */
      /*       careful to make sure the changes work. */
    "GCG",			/* type */
    "",				/* start */
    "",				/* desc */
    "",				/* seq */
    "",				/* end */
    0,				/* title_offset */
    10 },			/* seq_offset */
  {   /* GCG has non-sequence info in the first three lines following the */
      /* sequence signifier */
    "GCG-GenBank",		/* type */
    "LOCUS",			/* start */
    "DEFINITION",		/* desc */
    "ORIGIN",			/* seq */
    "LOCUS",			/* end */
    12,				/* title_offset */
    10 },			/* seq_offset */
  {   /* GCG has non-sequence info in the first three lines following the */
      /* sequence signifier */
      /* This is not what the GCG PIR entries look like.  They have another */
      /* format that would be very difficult to parse with the current */
      /* algorithm.  As it is a GCG PIR sequence will be recognized as plain */
      /* GCG. */
    "GCG-PIR",			/* type */
    "ENTRY",			/* start */
    "TITLE",			/* desc */
    "SEQUENCE",			/* seq */
    "ENTRY",			/* end */
    16,				/* title_offset */
    10 },			/* seq_offset */
  {   /* GCG has non-sequence info in the first three lines following the */
      /* sequence signifier */
      /* EMBL and SwissProt have the same id's */
    "GCG-EMBL",			/* type */
    "ID",			/* start */
    "DE",			/* desc */
    "SQ",			/* seq */
    "ID",			/* end */
    5,				/* title_offset */
    10 },			/* seq_offset */
  {  
    "Fasta",			/* type */
    ">",			/* start */
    ">",			/* desc */
    "",				/* seq */
    ">",			/* end */
    1,				/* title_offset */
    0 },			/* seq_offset */
  {  
    "Universa",			/* type */
    ">",			/* start */
    ">",			/* desc */
    "",				/* seq */
    "*",			/* end */
    1,				/* title_offset */
    0 },			/* seq_offset */
  {  
    "Flat-file, no title",	/* type */
    "",				/* start */
    "",				/* desc */
    "",				/* seq */
    "",				/* end */
    0,				/* title_offset */
    0 }/*,*/			/* seq_offset */
/*  {   Uncomment the lines in function type_dbs */
/*    "VMS",			*//* type */
/*    ">",			*//* start */	   /* first line */
/*    "",		        *//* desc */	   /* second line */
/*    "",			*//* seq */	   /* third line */
/*    "*",			*//* end */
/*    4,			*//* title_offset */ /* first line only */
/*    0 },			*//* seq_offset */
};




/*
 * Local variables and data structures
 */

#define SEQUENCE_RESIDUE_INITIAL_SIZE 1000 
#define SEQUENCE_RESIDUE_INCREASE_SIZE 1000  /* default number of residues to */
				   /* allocate if the number of residues */
				   /* in the sequence is not specified */


/*
 * Function definitions
 */



#ifndef NO_SEQUENCE_READING

/* 
 * Sequence file related functions
 *
 *   Sequence *read_a_sequence()
 *   int sequence_type(str)
 *   int read_sequence(seq, seq_type, start_pos, str)
 *   void free_sequence(seq)
 *   void process_sequence_db_line(seq, buff)
 *   void resize_sequence(seq)
 *
 */

static int read_sequence_header();
static void process_sequence_db_line();
void resize_sequence();


/*
 * read_a_sequence
 *   reads a sequence from the data base and returns a pointer to the new
 *   Sequence data structure
 *   Parameters:
 *     FILE *sfp: the sequence file pointer 
 *     int db:    the database type of the file
 *     int type:  the type of sequences in the file 
 *   Error codes: Returns NULL if there was no sequence to read.
 */

Sequence *read_a_sequence(sfp, db, type)
     FILE *sfp;			/* the sequence file pointer */
     int db;			/* the database type of the file*/
     int type;			/* the type of sequences in the file */
{
  Sequence *new_sequence;

  char *ptr;

  /*>>>BIG PROBLEM here if sfp is rewound between calls to read_a_sequence()
	because lbuff[] isn't cleared!!! <<<*/
  static char lbuff[LARGE_BUFF_LENGTH];	/* local Buffer to save the info */
					/* from the last line of the */
					/* previous sequence.  FASTA and GCG */
					/* formats have no special separator */
					/* between sequences other than the */
					/* beginning key */

/*  sfp = get_file(SEQUENCE_FILES);*/

  if (sfp == NULL) {
    /* no more data to read into sequences */
    new_sequence = NULL;
    return new_sequence;
  }

  /* get the database type.  Note: shouldn't directly access SequenceFiles */
/*  db = get_sequence_db_db_type(); */

  /* allocate space for the new Sequence */
  CheckMem(
	   new_sequence = (Sequence *) malloc(sizeof(Sequence))
	   );


  /*
   * Read the header
   */
  
/*>>> reset static lbuff[] first time sfp is read, otherwise has contents
      from the last time read_a_sequence() was called and sfp may have been
      rewound in the interim, or may even be a different file, but if
      it's initialized here only reads every other fasta record.
      The only time lbuff[] is initialized is when read_sequence_header()
	hits eof, so calling programs must read to end of file before
	rewinding!
  lbuff[0] = '\0';
<<<*/
  if (read_sequence_header(sfp, db, new_sequence, lbuff) == FALSE) {
    free(new_sequence);
    return NULL;
  }

  
  /* 
   * Read the sequence 
   */
  
  /* set the position to zero since this _is_ the sequence */
  /* and not a subsequence like in a block */
  new_sequence->position = 0;

  /* set the max_length to an initial value and allocate space */
  new_sequence->max_length = SEQUENCE_RESIDUE_INITIAL_SIZE;
  CheckMem(
	  new_sequence->sequence = (Residue *) calloc(new_sequence->max_length,
					      sizeof(Residue))
	   );

  /* set the length to zero, will increase as we read in the residues */
  new_sequence->length = 0;
  new_sequence->undefined = 0;
  new_sequence->undefined_dbl = 0.0;
  new_sequence->undefined_ptr = NULL;
  
  /* set the type of the sequence */
  new_sequence->type = type;  /* get_sequence_db_seq_type(); */
  
  do {
    /* If there is is a blank line or the line is shorter than the */
    /* sequence offset skip it so that the data from the previous line */
    /* is not read again.  This can happen by indexing over the end of */
    /* line ('\0') character. */
    if (!blank_line(lbuff) && ((int)strlen(lbuff) > DbInfo[db].seq_offset)) {
      process_sequence_db_line(new_sequence, &(lbuff[DbInfo[db].seq_offset]));
    }
  } while (!feof(sfp) && 
	   fgets(lbuff, LARGE_BUFF_LENGTH, sfp) != NULL &&
	   ((strncmp(lbuff, DbInfo[db].end, strlen(DbInfo[db].end)) != 0) ||
	    (db == FLAT) ||
	    ((db == GCG) && 
	     !(((ptr = strstr(lbuff, "Length:")) != NULL) &&
	       /*((ptr = strstr(ptr, "Type:")) != NULL) &&*/
	       ((ptr = strstr(ptr, "Check:")) != NULL) &&
	       ((ptr = strstr(ptr, "..")) != NULL)))));
  
  /* return the new sequence */
  return new_sequence;
  
} /* end read_a_sequence */



/*
 * read_sequence_header
 *   Reads the header information for the sequence.
 *   Parameters:
 *     FILE *sfp:    the sequence file pointer. 
 *     int db:       the database type
 *     Sequence *new_sequence: the sequence to put the data in.
 *     char lbuff[]: the saved Buffer for the last line read.
 *   Error Codes: FALSE if the sequence could not be read, TRUE otherwise
>>>>If fasta title line is > LARGE_BUFF_LENGTH treats excess as sequence!<<<
 */

static int read_sequence_header(sfp, db, new_sequence, lbuff)
     FILE *sfp;			/* the sequence file pointer */
     int db;			/* the database type */
     Sequence *new_sequence;
     char lbuff[LARGE_BUFF_LENGTH];
{
  char *ptr;
  char title[LARGE_BUFF_LENGTH], temp[LARGE_BUFF_LENGTH];

  static Boolean first_time = TRUE;

  strcpy(new_sequence->name, "Unknown");
  strcpy(new_sequence->info, "Unknown");

  if (db != FLAT) {	/* if this is the flat file, there is no title */

    temp[0] = '\0';
    title[0] = '\0';
    
    /* move to the start of the sequence */
    /* NOTE: the order of the while loop is important.  In FASTA and GCG */
    /*       format the last line read when reading the previous sequence */
    /*       will have the title information of this sequence.  In order */
    /*       not to overwrite the information, it is necessary to fail */
    /*       before getting the next line. */
    if (first_time) {
      fgets(lbuff, LARGE_BUFF_LENGTH, sfp);
      lbuff = eat_whitespace(lbuff);
      first_time = FALSE;
    }
    while (strncmp(lbuff, DbInfo[db].start, strlen(DbInfo[db].start)) != 0 &&
	   fgets(lbuff, LARGE_BUFF_LENGTH, sfp) != NULL );
    
    /* if we reached the end of the file, then throw away the sequence */
    if (feof(sfp)) {
      return FALSE;		/* it did not read a sequence */
    }
    

    /* ------Working on the DbInfo[db].start line now, get ->name and also
             ->info if DbInfo[db].desc == .start             --------------*/
    /* if this is a simple GCG format, move to the info part.  the way */
    /* the simple GCG dbs entry is set up, it will work with this algorithm. */
    if (db == GCG) 
    {
      while(!(((ptr = strstr(lbuff, "Length:")) != NULL) &&
	      /*((ptr = strstr(ptr, "Type:")) != NULL) &&*/
	      ((ptr = strstr(ptr, "Check:")) != NULL) &&
	      ((ptr = strstr(ptr, "..")) != NULL)) &&
	    (fgets(lbuff, LARGE_BUFF_LENGTH, sfp) != NULL));
      /* if we reached the end of the file, then throw away the sequence */
      if (feof(sfp)) {
	return FALSE;		/* it did not read a sequence */
      }
    } /* end of GCG format */

    /* get the name of the sequence. */
    strcpy(temp, lbuff);
    ptr = get_token(&temp[DbInfo[db].title_offset]);
    if (ptr == NULL) { strcpy(new_sequence->name, "UNKNOWN"); }
    else   
    { 
       if (strlen(ptr) > SMALL_BUFF_LENGTH)
       {  ptr[SMALL_BUFF_LENGTH] = '\0'; }
       strcpy(new_sequence->name, ptr); 
    }
    temp[0] = '\0';
    
    /* check to see if the start and desc lines are the same, eg for 
       fasta and universa formats. If so, use the rest of this line
       for ->info */
    if (strcmp(DbInfo[db].start, DbInfo[db].desc) == 0) 
    {
     strcpy(temp, &lbuff[DbInfo[db].title_offset + strlen(new_sequence->name)]);
      remove_trailing_whitespace(temp);         /* get rid of CRLF */
      sprintf(title, "%s ", temp);
    }
    
    /*-----------------Done with DbInfo[db].start now ------------*/
    /* read up to the sequence and if see desc. information, save */
    /* NOTE: most of this is from universa.c */
    while(fgets(lbuff, LARGE_BUFF_LENGTH, sfp) != NULL &&
	  strncmp(lbuff, DbInfo[db].seq, strlen(DbInfo[db].seq)) != 0) 
    {
      if (strncmp(lbuff, DbInfo[db].desc, strlen(DbInfo[db].desc)) == 0 &&
	  ((int)(strlen(title) + strlen(lbuff) +1) < LARGE_BUFF_LENGTH) ) 
      {
	if (title[0] != '\0') {
	  strncpy(temp, title, LARGE_BUFF_LENGTH); 
	  strncat(temp, " ", LARGE_BUFF_LENGTH-strlen(temp));
	}
	strncat(temp, &lbuff[DbInfo[db].title_offset],
		LARGE_BUFF_LENGTH-strlen(temp));
	remove_trailing_whitespace(temp);         /* get rid of CRLF */
	strncpy(title, temp, LARGE_BUFF_LENGTH);
      }
    }   /*  end of DbInfo[db].desc */
    
    /* save the info that has been collected */
    strncpy(new_sequence->info, title, SMALL_BUFF_LENGTH); 
    
    /*-----------------Done with DbInfo[db].desc now ------------*/
    /* if this type of database does not start right off with the sequence */
    /* data (like most databases), read the next line to be on top of the */
    /* sequence data. */
/*>>>> for fasta & universa, if lbuff doesn't have end-of-line, 
then read more until first eol, seq starts after first eol. Sometimes
the title line is longer than LARGE_BUFF_LENGTH <<*/
    if (strcmp(DbInfo[db].seq, "") != 0 && !feof(sfp)) 
    {
      /* read in the next line, get to the sequence */
      fgets(lbuff, LARGE_BUFF_LENGTH, sfp);
    }
    
    /* if PIR, skip the top row of numbers */
    if (db == PIR && !feof(sfp)) 
    {  
      fgets(lbuff, LARGE_BUFF_LENGTH, sfp);
    }    
    /* if one of the GCG types (but not the simple GCG), */
    /* skip the top three rows */
    if (((db == GCG_GB) || (db == GCG_PIR) || ( db == GCG_EMBL)) &&
	!feof(sfp)) 
    { 
      fgets(lbuff, LARGE_BUFF_LENGTH, sfp);
      fgets(lbuff, LARGE_BUFF_LENGTH, sfp);
      fgets(lbuff, LARGE_BUFF_LENGTH, sfp);
    }    
    
  }  /* end of if the format is not FLAT (got the title and description */
  
  /* if we reached the end of the file, then throw away the sequence */
  if (feof(sfp)) {
    return FALSE;		/* it did not read a sequence */
  }

  return TRUE;			/* read in the header of the sequence  */
}  /*  end of read_sequence_header  */





/*
 * process_sequence_db_line
 *   Passed one line of the sequence portion of the database.  Reads the
 *   characters and converts them to the apropriate internal representation.
 *   Removes the excess spaces in the middle and ends.
 *   NOTE: this function adds the residues onto the end of the sequence 
 *         passed to it.
 *   Parameters:
 *     Sequence *seq: the sequence to put the residues into.
 *     char *buff:    the string with the characters to residues to
 *                      add to the sequence
 *   Error codes: none
 */

static void process_sequence_db_line(seq, buff)
     Sequence *seq;
     char *buff;
{
  int start_pos;
  int estimated_length;
  int saved_length;
  int num_entered;

  estimated_length = strlen(buff);
  saved_length = seq->length;

  /* if there are more residues than there is space for, resize. */
  /* Note: The buff may have characters that are not residues, this is */
  /*       ok, there will just be a little extra space */
  while ((saved_length + estimated_length) > seq->max_length) {
    resize_sequence(seq);
  }
  
  /* temporarily increase the room to put the sequence into */
  start_pos = seq->length;
  seq->length = seq->max_length;
  
  num_entered = read_sequence(seq, seq->type, start_pos, buff);

/*  if (num_entered < 0) {  shouldn't happen */
    /* Error, wasn't enough room for all the sequences */
    /* resize to get enough room for the extra residues } */
  
  seq->length = saved_length + num_entered;

}
#endif /* NO_SEQUENCE_READING */


/*
 * resize_sequence
 *   Adds more memory for the storage of the residues of a sequence.
 *   Parameter:
 *     Sequence *seq: the sequence to resize
 *   Error codes: none
 */

void resize_sequence(seq)
     Sequence *seq;
{
  Residue *tmp_ptr;		/* don't want to ruin pointer in case there */
				/* is a repeated realloc call */

  /* announce info */
  sprintf(ErrorBuffer,
	  "Ran out of room for sequence %s.  Allocating more space.\n",
	  seq->name);
  ErrorReport(INFO_ERR_LVL);

  seq->max_length += SEQUENCE_RESIDUE_INCREASE_SIZE;
  CheckMem(
	   tmp_ptr = (Residue *) realloc(seq->sequence,
					 seq->max_length *
					 sizeof(Residue))
	   );
  seq->sequence = tmp_ptr;
}



/*
 * sequence_type
 *   tries to guess the type of the sequence passed in the string.
 *   Note: if the sequence can not be matched to an NA_SEQ, it falls through
 *         to being a AA_SEQ.
 *   Parameters:
 *     char *str: the sequence string, no more than SMALL_BUFF_LENGTH long
 *   Return Codes: Returns either AA_SEQ or NA_SEQ depending on
 *                 if the sequence is an Amino Acid or Nucleic Acid.
 *   Error Codes: none
 */

int sequence_type(str)
     char *str;			/* no more than SMALL_BUFF_LENGTH long */
{
  int length;
  int num_na;
  char *str_pntr;
  char upper_str[SMALL_BUFF_LENGTH], *c_upper_str;
  char residue;

  /* Sets of residues:
   *
   *                               AA-amb = -ABCDEFGHI KLMN PQRST VWXYZ*   
   *                              !AA-amb =           J    O     U         
   *
   *                               NA-amb = -ABCD  GH  K MN   RST VW Y     
   *                              !NA-amb =      EF  IJ L  OPQ   U  X Z    
   *
   *    AA-amb intersect NA-amb           = -ABCD  GH  K MN   RST VW Y     
   * !(AA-amb intersect NA-amb) & !AA-amb  
   *                  = !NA-amb - !AA-amb =      EF  I  L   PQ      X Z    
   *                             the rest =           J    O     U         
   * 
   *                            AA-wo-amb = -A CDEFGHI KLMN PQRST VW Y *
   *                           !AA-wo-amb =   B       J    O     U  X Z
   *
   *                            NA-wo-amb = -A C   G      N     T      
   *                           !NA-wo-amb =   B DEF HIJKLM OPQRS UVWXYZ
   *
   */

  /* NOTE, U could be in a nucleotide sequence, if someone uses an RNA seq. */

  
  for (c_upper_str=upper_str; *str != '\0'; str++) {
    if (aa_atob[*str] <= AAID_MAX) { /* get rid of bad characters.  It is ok */
                                     /* to use aa_atob since all of the NT */
				     /* residue characters are included in */
				     /* that set. */
      *c_upper_str = toupper(*str);
      c_upper_str++;
    }
  }

  *c_upper_str = '\0';

  length = strlen(upper_str);

  /* checking first assuming using ambiguity codes */
  /* if see any in (!NA-amb - !AA-amb) this sequence is an AA_SEQ */
  for (str_pntr=upper_str; *str_pntr; str_pntr++) {
    residue = *str_pntr;
    if ((residue == 'E') ||
	(residue == 'F') ||
	(residue == 'I') ||
	(residue == 'L') ||
	(residue == 'P') ||	/* not using 'X', 'Z', or '*' since someone */
	(residue == 'Q')) {	/* might use in a NA_SEQ */
      return AA_SEQ;
    }
  }

  /* check frequency of 'A', 'C', 'G', 'T', 'U' & 'N'  if > 85% (NA_FREQ), */
  /* assume NA_SEQ */
  num_na = 0;
  for (str_pntr=upper_str; *str_pntr; str_pntr++) {
    residue = *str_pntr;
    if ((residue == 'A') ||
	(residue == 'C') ||
	(residue == 'G') ||
	(residue == 'T') ||
	(residue == 'U') ||
	(residue == 'N')) {
      num_na++;
    }
  }
  if ( (double)((double)num_na/(double)length) > NA_FREQ ) {
    return NA_SEQ;
  }
  else {
    return AA_SEQ;
  }

}


/*
 * read_sequence
 *   read_sequence reads from the string the sequence of the given type into
 *   the passed in Sequence data structure
 *   Parameters:
 *     Sequence *seq: the Sequence data structure to put the data in
 *     int seq_type:  the type of sequence (amino acid or nucleic acid)
 *     int start_pos: the position in the sequence to start entering the data
 *     char *str:     the string that has the sequence (NULL terminated)
 *   Note: The entire string up to the NULL character is considered the 
 *         sequence.
 *   Preconditions: seq.length must have a the value of the size allocated to 
 *                  the residues
 *   Postconditions: the residues from start_pos to either seq.length or
 *                   return value + start_pos in the seq.sequence have been
 *                   updated to the residues passed in by the string
 *                   seq.type is set to seq_type
 *   Return codes: returns the number of residues added to the sequence
 *   Error codes: returns the negative value of the number of residues left
 *                over after the sequence has been filled.  
 *   Note: A return value of zero is means that no residues were 
 *         added to the sequence.
 */

int read_sequence(seq, seq_type, start_pos, str)
     Sequence *seq;
     int seq_type;
     int start_pos;
     char *str;
{
  Residue *sequence;


/*   return 0; */


  int room_left;
  int num_seen;
  int num_left;

  int return_code;

  int stemp;
  char c;

  sequence = &(seq->sequence[start_pos]);
  room_left = seq->length - start_pos;

  num_seen = 0;

  if (str == NULL) { return num_seen; }

  c = *str;

  /*  NOTE:  the stemp business was added to side-step a problem
      with aa_atob[c] that I don't understand, crops up if there
      are numbers in the sequence; for instance, if c = '4' then
      stemp is a huge negative number ...
  */
  if (seq_type == AA_SEQ) {
    while ( (c != NULL) && (c != '\0') && (num_seen < room_left) ) {
      stemp = aa_atob[c];
      if (stemp < 0 || stemp > AAID_MAX) stemp = AAID_MAX + 1;
      if ( stemp <= AAID_MAX ) {
	*sequence = stemp;
	sequence++;
	num_seen++;
      }
      str++;
      c = *str;
    }
  }
  else if (seq_type == NA_SEQ) {
    while ( (c != '\0') && (num_seen < room_left) ) {
      if ( nt_atob[c] <= NUCID_MAX ) {
	*sequence = nt_atob[c];
	sequence++;
	num_seen++;
      }
      str++;
      c = *str;
    }
  }    
  else {
    sprintf(ErrorBuffer, 
	    "read_sequence(): Unknown sequence type,");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer, 
	    "                 asumming amino acid sequence\n");
    ErrorReport(PROGRAM_ERR_LVL);
    while ( (c != '\0') && (num_seen < room_left) ) {
      if ( aa_atob[c] <= AAID_MAX ) {
	*sequence = aa_atob[c];
	sequence++;
	num_seen++;
      }
      str++;
      c = *str;
    }
  }


  if (c != '\0') {		/* num_seen >= room_left */
    /* count the number that were left */
    num_left = 0;
    if (seq_type == NA_SEQ) {
      while (c != '\0') {
	if (nt_atob[c] <= NUCID_MAX ) {
	  num_left++;
	}
	str++;
	c = *str;
      }
    }
    else {			/* if not an NA_SEQ assuming an AA_SEQ */
      while (c != '\0') {
	if (aa_atob[c] <= AAID_MAX ) {
	  num_left++;
	}
	str++;
	c = *str;
      }
    }

    if (num_left == 0) {	/* read in all residues so just return */
      return_code = num_seen;	/* the number seen */
    }
    else {
      return_code = - num_left;
    }

  }
  else {		      /* c == '\0', reached the end of the residues */
    return_code = num_seen;
  }

  return return_code;

}


/* 
 * free_sequence
 *   Deletes the sequence and the sub elements.
 *   Parameters: 
 *     Sequence *sequence: the sequence to free
 *   Return code: none
 *   Error code: none
 */

void free_sequence(sequence) 
     Sequence *sequence;
{
  free(sequence->sequence);
  free(sequence);
}


/*
 * translate_sequence
 *   Given a frame (1, 2, 3, -1, -2, or -3), translates the DNA sequence 
 *   (NA_SEQ) into an amino acid sequence.
 *   Parameters:
 *     Sequence *seq: the DNA sequence
 *     int frame:     the frame to read
 *     unsigned char gcode[64]:    the genetic code (forward).  
 *                                   for frames 1, 2, 3
 *     unsigned char revgcode[64]: the genetic code (reverse complement)
 *                                   for frames -1, -2, -3
 *   Return code: a pointer to the new translated sequence
 *   Error codes: returns the original sequence if the sequence is not a
 *                NA_SEQ or the translation frame is incorrect.
 */

Sequence *translate_sequence(seq, frame, gcode, revgcode)
     Sequence *seq;
     int frame;
     unsigned char gcode[64];
     unsigned char revgcode[64];        /* genetic codes */
{
  Sequence *new_seq;
  Residue *res;
  Residue *new_res;

  int i, new_length;

  new_length = -1;

  /* make sure it is a NA_SEQ */
  if ( seq->type != NA_SEQ ) {
    sprintf(ErrorBuffer, 
	    "translate_sequence(): Not a nucleic acid sequence, not translating.");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer, 
	    "                      Returning the original sequence.\n");
    ErrorReport(PROGRAM_ERR_LVL);
    return seq;
  }

  /* make sure it is the right kind of frame */
  if ( (frame == 0) || (frame < -3) || (frame > 3) ) {
    sprintf(ErrorBuffer, 
	    "translate_sequence(): Unknown translation frame: %d.",
	    frame);
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer,
	    "                      Returning the original sequence.\n");
    ErrorReport(PROGRAM_ERR_LVL);
    return seq;
  }
  
  /* allocate space for new sequence */
  CheckMem(
	   new_seq = (Sequence *) malloc(sizeof(Sequence))
	   );

  /* allocate space for the new residues */
  CheckMem(
	   new_res = (Residue *) calloc((seq->length+2)/3,
					sizeof(Residue))
	   );
  new_seq->max_length = (seq->length+2)/3;

  /* translate the codons */
  res = seq->sequence;
  if (frame > 0) {		/* 1, 2, or 3 */
    frame--;
    for (i=frame, new_length=0; i<= seq->length - 3; i+=3, new_length++) {
      new_res[new_length] = (Residue) codon2aa(gcode,
				     res[i],
				     res[i+1],
				     res[i+2]);
    }
    /* do the last 1, or 2 residues */
    if ((seq->length - i) == 1) {
      new_res[new_length] = (Residue) codon2aa(gcode,
				     res[i],
				     nt_atob[UNKNOWN_NT_CHR],
				     nt_atob[UNKNOWN_NT_CHR]);
      new_length++;
    }
    else if ((seq->length - i) == 2) {
      new_res[new_length] = (Residue) codon2aa(gcode,
				     res[i],
				     res[i+1],
				     nt_atob[UNKNOWN_NT_CHR]);
      new_length++;
    }
  }

  else if (frame < 0) {
    frame = frame*-1;
    frame--;
    for (i=(seq->length-frame-1), new_length=0; i>=2; i-=3, new_length++) {
      new_res[new_length] = (Residue) codon2aa(revgcode,
				     res[i],
				     res[i-1],
				     res[i-2]);
    }
    /* do the last 1 or 2 residues */
    if (i == 0) {
      new_res[new_length] = (Residue) codon2aa(revgcode,
				     res[i],
				     nt_atob[UNKNOWN_NT_CHR],
				     nt_atob[UNKNOWN_NT_CHR]);
      new_length++;
    }
    else if (i == 1) {
      new_res[new_length] = (Residue) codon2aa(revgcode,
				     res[i],
				     res[i-1],
				     nt_atob[UNKNOWN_NT_CHR]);
      new_length++;
    }
  }      
  
  /* copy the sequence info into the new sequence */
  strncpy(new_seq->name, seq->name, SMALL_BUFF_LENGTH);
  strncpy(new_seq->info, seq->info, SMALL_BUFF_LENGTH);
  
  new_seq->position = seq->position;
  new_seq->length   = new_length;
  /* new_seq->max_length set when residues were allocated */

  new_seq->type = AA_SEQ;
  
  new_seq->sequence = new_res;

  return new_seq;

}


/*
 * sequence_comparison
 *   Compares two sequences.   It compares by the value in the name
 *   field if it exists.
 *   Parameters:
 *     SequenceListEntry a, b: the entries to compare
 *   Return codes:  a return value < 0 if a < b, a return value = 0 if a == b,
 *                  and a return value > 0 if a > b
 *   Error codes: none
 */

int sequence_comparison(a, b)
     Sequence *a, *b;
{
  char *sa, *sb;

  if (a->name != NULL) {    
    sa = a->name;
  }
  else {
    if (b->name != NULL) {  
      return -1;		/* NULL < something */
    }
    else {
      return 0;			/* NULL = NULL */
    }
  }
  
  if (b->name != NULL) {    
    sb = b->name;
  }
  else {
    return 1;			/* something > NULL */
  }

  return (int) (strcmp(sa, sb));
}





/* 
 * type_dbs
 *   Figures out the type of the database to be read.
 *   This is from motomisc.c used in the universa conversion program.
 *   Parameters:
 *     FILE *fin:            the database file
 *     struct db_info dbs[]: the information of the structure of the db's
 *   Return codes: the type of database the file is.
 *   Error code: the database number -1 is returned if the type of database
 *               cannot be figured out
 */
/* NOTE: DO NOT RETURN FLAT AS THE DATABASE, WANT TO NOTE THAT IT IS NOT */
/*       A GOOD FORMAT */

/* originally from motomisc.c.  used in universa.c */
/*======================================================================
      type_dbs() determines what type a database is from the allowable
      types
========================================================================*/
int type_dbs(fin, dbs)
FILE *fin;
struct db_info dbs[];
{
   int db, i;
   char line[LARGE_BUFF_LENGTH];
   char *ptr;

   db = -1;

   /* Figure out what type of input file it is */
   while (db < 0 && fgets(line, sizeof(line), fin) != NULL) {
     for (i=0; i= MAXDB) {
     db = -1;			/* can't tell what it is */
     sprintf(ErrorBuffer,
	     "Could not figure out database format.\n");
   }
   else {
     sprintf(ErrorBuffer,
	     "Decided on %s database format.\n", dbs[db].type);
   }
   ErrorReport(INFO_ERR_LVL);

   rewind (fin);

   return(db);
}  /* end of type_dbs */


/*
 * seq_type_dbs
 *   Finds the type or the database given.
 *   Parameters:
 *     FILE *fin:            the database file
 *     struct db_info dbs[]: the information of the structure of the db's
 *     int db:               the number of this database (indexes into dbs)
 *   Return codes: Returns the type of sequence of the first entry in the 
 *                 database.  This assumes that the entire database is of this
 *                 type.
 *   Error codes: none
 */

int seq_type_dbs(fin, dbs, db, seqtype) 
     FILE *fin;
     struct db_info dbs[];
     int db;
     int seqtype;
{
  char seq_check_buf[SMALL_BUFF_LENGTH];
  int check_length;
  char *ptr;

  /* skip the title to the sequence */
  if (db >= 0 && db != GCG) 
  {
    while(fgets(Buffer, LARGE_BUFF_LENGTH, fin) != NULL &&
	  strncmp(Buffer, dbs[db].seq, strlen(dbs[db].seq)) != 0);
  }
  else if (db != FLAT) { /* don't do anything if it is just sequence */
    while(fgets(Buffer, LARGE_BUFF_LENGTH, fin) != NULL &&
	  !(((ptr = strstr(Buffer, "Length:")) != NULL) &&
	    /*((ptr = strstr(ptr, "Type:")) != NULL) &&*/
	    ((ptr = strstr(ptr, "Check:")) != NULL) &&
	    ((ptr = strstr(ptr, "..")) != NULL)));
    fgets(Buffer, LARGE_BUFF_LENGTH, fin);
  }

  /* determine the sequence type */
  /* if PIR, skip the top row of numbers */
  if (db == PIR) { 
    fgets(Buffer, LARGE_BUFF_LENGTH, fin);
  }    
  /* if one of the GCG types, skip the top three rows */
  if ((db == GCG_GB) || (db == GCG_PIR) || ( db == GCG_EMBL)) { 
    fgets(Buffer, LARGE_BUFF_LENGTH, fin);
    fgets(Buffer, LARGE_BUFF_LENGTH, fin);
    fgets(Buffer, LARGE_BUFF_LENGTH, fin);
  }    

  check_length = 0;	   /* how much has been filled in the seq_check_buf */

  /* fill the seq_check_buf with sequence characters */
  /* db types with null end require special handling */
  if (db >= 0)
  {
     while(!feof(fin) && fgets(Buffer, LARGE_BUFF_LENGTH, fin) != NULL &&
	((strncmp(Buffer, dbs[db].end, strlen(dbs[db].end)) != 0) ||
         (db == FLAT) ||
	 ((db == GCG) && 
	  !(((ptr = strstr(Buffer, "Length:")) != NULL) &&
	    /*((ptr = strstr(ptr, "Type:")) != NULL) &&*/
	    ((ptr = strstr(ptr, "Check:")) != NULL) &&
	    ((ptr = strstr(ptr, "..")) != NULL))))        &&
	(check_length < SMALL_BUFF_LENGTH-1)) 
     {	/* -1 for the '\0' */
       strncpy(seq_check_buf + check_length, 
	    Buffer+dbs[db].seq_offset, 
	    SMALL_BUFF_LENGTH - check_length - 1);
       seq_check_buf[SMALL_BUFF_LENGTH-1] = '\0';
       check_length = strlen(seq_check_buf);
     }
  }
  
  rewind(fin);

  /*----  If the TY config file option was specified, use it ------*/
  if (seqtype == AA_SEQ || seqtype == NA_SEQ)
     return seqtype;
  else
     return sequence_type(seq_check_buf); /* get the sequence type */
  
} /* end of seq_type_dbs */



/*
 * Sequence printing.
 */

/*
 * print_sequence
 *   Prints a Sequence data structure.  Primarily for debugging purposes.
 *   Parameters: 
 *     Sequence *seq:  the sequence to print
 *   Error Codes: none
 */

void print_sequence(seq)
     Sequence *seq;
{
  int k;

  printf(">--- sequence ---\n");

  printf("%s\n", seq->info);
  printf(">%s \t", seq->name);
  printf("( %d:", seq->position);
  printf("%d, ",  seq->length);

  if (seq->type == AA_SEQ) {
    printf("AA) \t");
printf("\n");
    for(k=0; klength; k++) {
      printf("%c", aa_btoa[seq->sequence[k]]);
    }
  }
  else if (seq->type == NA_SEQ) {
    printf("NA) \t");
printf("\n");
    for(k=0; klength; k++) {
      printf("%c", nt_btoa[seq->sequence[k]]);
    }
  }    
  else {
    printf("??) \t");
printf("\n");
    for(k=0; klength; k++) {
      printf("%c", aa_btoa[seq->sequence[k]]);
    }
  }

  printf("\n");
  printf(">--- -------- ---\n");
}


/*
 * output_sequence
 *   Outputs a Sequence data structure to the given file.
 *   Parameters: 
 *     Sequence *seq:  the sequence to print
 *     FILE *osfp:     the output sequence file pointer
 *   Error Codes: none
 */

void output_sequence(seq, osfp)
     Sequence *seq;
     FILE *osfp;
{
  int k;


  fprintf(osfp, ">%s  %s\n", seq->name, seq->info);

  if (seq->type == AA_SEQ) {
    for(k=0; klength; k++) {
      fprintf(osfp, "%c", aa_btoa[seq->sequence[k]]);
      if ((k+1)%60 == 0) {
	fprintf(osfp, "\n");
      }
    }
  }
  else if (seq->type == NA_SEQ) {
    for(k=0; klength; k++) {
      fprintf(osfp, "%c", nt_btoa[seq->sequence[k]]);
      if ((k+1)%60 == 0) {
	fprintf(osfp, "\n");
      }
    }
  }    
  else {
    for(k=0; klength; k++) {
      if ((k+1)%60 == 0) {
	fprintf(osfp, "\n");
      }
      fprintf(osfp, "%c", aa_btoa[seq->sequence[k]]);
    }
  }

  fprintf(osfp, "\n");
}




/*
 * untranslate_sequence
 *   Translates an animo acid sequence into a  DNA sequence of degenerate
 *    codons
 *   Parameters:
 *     Sequence *seq: the amino acid sequence sequence
 *   Return code: a pointer to the new untranslated sequence
 *   Error codes: returns the original sequence if the sequence is not a
 *                AA_SEQ
 */

Sequence *untranslate_sequence(seq)
     Sequence *seq;
{
  Sequence *new_seq;
  Residue *res;
  Residue *new_res;
  int i;


  /* make sure it is a AA_SEQ */
  if ( seq->type != AA_SEQ ) {
    sprintf(ErrorBuffer, 
    "untranslate_sequence(): Not an amino acid sequence, not untranslating.");
    ErrorReport(PROGRAM_ERR_LVL);
    sprintf(ErrorBuffer, 
	    "                      Returning the original sequence.\n");
    ErrorReport(PROGRAM_ERR_LVL);
    return seq;
  }

  /* allocate space for new sequence */
  CheckMem(
	   new_seq = (Sequence *) malloc(sizeof(Sequence))
	   );

  /* allocate space for the new residues */
  CheckMem(
	   new_res = (Residue *) calloc((seq->length)*3, 
					sizeof(Residue))
	   );
  new_seq->length = new_seq->max_length = (seq->length) * 3;
  new_seq->type = NA_SEQ;
  new_seq->position = seq->position;
  strcpy(new_seq->name, seq->name);
  strcpy(new_seq->info, seq->info);

  /* untranslate the amino acids */
  res = seq->sequence;
  for (i=0; i < seq->length; i++)
  {
     aa2codon(res[i], &new_res[i*3], &new_res[i*3+1], &new_res[i*3+2]);
  }
  
  /* copy the sequence info into the new sequence */
  strncpy(new_seq->name, seq->name, SMALL_BUFF_LENGTH);
  strncpy(new_seq->info, seq->info, SMALL_BUFF_LENGTH);
  
  new_seq->sequence = new_res;

  return new_seq;

}




/* Change log information follows. */
/* 
  >Changes since version 3.6:
   4/15/04 Protect against aborts due to nulls strings
  >Changes since version 3.3.2:
  12/27/99 seq_types_db()  Check for db >= 0
  >Changes since version 3.2.5:
   5/22/99  Increased SEQUENCE_RESIDUE_INCREASE_SIZE from 500 to 1000.
	    Fixed unallocated memory problem in translate_sequence()
   4/22/99  Changed db->start for EMBL from "ID" to "ID   ", etc.
  >Changes since version 3.2.2:
  12/27/97  Increased SEQUENCE_RESIDUE_INCREASE_SIZE from 350 to 500.
            Added SEQUENCE_RESIDUE_INITIAL_SIZE = 1000.
  12/20/97  Don't duplicate ->name in ->info field.
  11/24/97  Made resize_sequence() external.
  10/25/97  read_sequence_header(): Use eat_whitespace() to get rid of
	    leading whitespace in sequence header (WWW problem).
  >Changes since version 3.2.1:
   7/12/97  Changed seq_type_dbs() to work correctly when dbs[db].end is null.
   7/ 7/97  Discarded old "universa" format where sequences have * at end
            because blimps required the * to be on a separate line. Now
	    this format is treated as fasta and any asterisk is scored as
	    as stop codon, which gets the minimum PSSM score for the 20
	    major AAs.
  >Changes since version 3.2:
   4/4/97   Initialized sequence->name & ->info in read_sequence_header().
  >Changes since version 3.1:
   1/20/97  Added untranslate_sequence().
  >Changes since version 3.0.0:
   4/24/96  Added seqtype to seq_type_dbs().
            Treat N as a valid DNA character in sequence_type().
   5/16/96  Problem with aa_atob[] in read_sequence() if sequence
	    has numbers in it ...
*/
ginning of the sequence */
     while (fgets(line, LARGE_BUFF_LENGTH, fin) &&
	    !((strncmp(line, dbs[GB].seq, strlen(dbs[GB].seblimps-3.9/blimps/show_aligned_blocks.c000064400001460000012000000117761054325701200206130ustar00jorjastaff00000400000027/*   COPYRIGHT 1999-2003 Fred Hutchinson Cancer Research Center
		show_aligned_blocks.c
      This program will print to the screen two specified blocks offset
      to show their alignment. Executed by LAMA_alignment.sh

6/20/99 Changed for longer sequence names (18 chars)
12/23/06 Changed for longer sequence names (20 chars)

====================================================================*/

#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#define YES 1
#define NO 0

#include 


/*
 * Local variables and data structures
 */

void   fprint_matrix() ;

/*=======================================================================*/
/*
 * main
 *   controls flow of program
 *   Parameters: argc, argv
 *   Error codes:
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE  *bfp1, *bfp2, *outf;
  Block *block1, *block2;
  char  bdbname1[MAXNAME], bdbname2[MAXNAME];
  char  blkname1[SMALL_BUFF_LENGTH], blkname2[SMALL_BUFF_LENGTH];
  char  offset[MAXNAME] ;
  int   start1, start2, alignment_length, i1, i2 ;

   if (argc != 8)
      {
      printf("%s  blocks_file  block1_accession  block1_alignment_start  blocks_file  block2_accession  block2_alignment_start  alignment_length\n", 
             argv[0]) ;
      exit(-1) ;
      }


/* ------------1st arg = blocks database -------------------------------*/
   strcpy(bdbname1, argv[1]);

   if ( (bfp1=fopen(bdbname1, "r")) == NULL)
      {
      fprintf(stderr,"\nCannot open file %s\n", bdbname1);
      exit(-2);
      }

/* ------------2nd arg = block1 accession -------------------------------*/
   strcpy(blkname1, argv[2]);

/* ------------4th arg = alignment start -------------------------------*/
   start1 = atoi(argv[3]) ;

   if (start1 < 1)
      {
      fprintf(stderr,"\nThird argument should be the start position of the aligned region in block 1\n");
      exit(-3);
      }

/* ------------4th arg = blocks database -------------------------------*/
   strcpy(bdbname2, argv[4]);

   if ( (bfp2=fopen(bdbname2, "r")) == NULL)
      {
      fprintf(stderr,"\nCannot open file %s\n", bdbname2);
      exit(-2);
      }

/* ------------5th arg = block2 accession -------------------------------*/
   strcpy(blkname2, argv[5]);


/* ------------6th arg = alignment start -------------------------------*/
   start2 = atoi(argv[6]) ;

   if (start2 < 1)
      {
      fprintf(stderr,"\nSixth argument should be the start position of the aligned region in block 2\n");
      exit(-3);
      }


/* ------------7th arg = alignment length -------------------------------*/
   alignment_length = atoi(argv[7]) ;

   if (alignment_length < 1)
      {
      fprintf(stderr,"\nSeventh argument should be the alignment length\n");
      exit(-3);
      }


/* output to screen */
   outf = stdout ;

/* get blocks */

   while ((block1 = read_a_block(bfp1)) != NULL && 
         (strcmp(block1->number,blkname1) != 0))  free_block(block1) ;

   if (block1 == NULL)
      {
      fprintf(stderr,"\nBlock %s not found in file %s\n", blkname1, bdbname1);
      exit(-4);
      }

   while ((block2 = read_a_block(bfp2)) != NULL && 
         (strcmp(block2->number,blkname2) != 0))  free_block(block2) ;

   if (block2 == NULL)
      {
      fprintf(stderr,"\nBlock %s not found in file %s\n", blkname2, bdbname2);
      exit(-4);
      }

/* consistency checks */

   if (start1 + alignment_length - 1 > block1->width ||
       start2 + alignment_length - 1 > block2->width ||
       start1 > block1->width ||
       start2 > block2->width)
      {
      fprintf(outf, "Something seems wrong in the alignment coordinates !!!\n\n") ;
      exit(-5) ;
      }

/* write block 1 */

   fprintf(outf, "%s\n", block1->number) ;
   for (i1=0; i1num_sequences; i1++) 
      {
      offset[0] = '\0' ;
      for (i2=0; i2 < (start2-start1); i2++) strcat(offset, " ") ;

      fprintf(outf, "%-20.20s (%5d) %s",
              block1->sequences[i1].name, block1->sequences[i1].position,
              offset) ;

      for (i2=0; i2sequences[i1].length; i2++) 
          {
	  fprintf(outf, "%c",
                  aa_btoa[block1->sequences[i1].sequence[i2]]);
	  }
      fprintf(outf, "\n") ;
      }

/* write alignment line */
   fprintf(outf, "\n                   aligned:") ;
   for(i1=0; i1number) ;
   for (i1=0; i1num_sequences; i1++) 
      {
      offset[0] = '\0' ;
      for (i2=0; i2 < (start1-start2); i2++) strcat(offset, " ") ;

      fprintf(outf, "%-20.20s (%5d) %s",
              block2->sequences[i1].name, block2->sequences[i1].position,
              offset) ;

      for (i2=0; i2sequences[i1].length; i2++) 
          {
	  fprintf(outf, "%c",
                  aa_btoa[block2->sequences[i1].sequence[i2]]);
	  }
      fprintf(outf, "\n") ;
      }

  free_block(block1) ;
  free_block(block2) ;

  fclose(bfp1);
  fclose(bfp2);

  exit(0);

}  /* end of main */

blimps-3.9/blimps/sl.c000064400001460000012000000374760774312250100152400ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* skiplist.c: This file contains a heavily hacked and generalized version */
/*             of the Example skiplist code distributed on mimsy.cs.umd.edu. */
/* Change log information is at the end of the file. */
/* most of this file is untouched from the distribution I started from, Bill */

/* This file contains a heavily hacked and generalized version of the
   Example skiplist code distributed on mimsy.cs.umd.edu.

 Here is a short excerpt from the original comment :

	 Example of Skip List source code for C :

	   Skip Lists are a probabilistic alternative to balanced trees,
	 as described in the June 1990 issue of CACM and were invented by
	 William Pugh in 1987.

 These are my additions :

     This file contains my (Dominic Giampaolo's) heavily hacked version
   of skip lists.  These work on any arbitrary data by using callback
   functions which you supply (at list creation time) to do the data
   comparisons.  You could instantly use this package to implement a
   symbol table for a compiler which would be blazingly fast and
   require zippo effort on your part.

     I've changed the function names (not to protect the innocent, but
   to make them easier to read :) and changed the data structures a bit.
   I've ansi'fied the code, added prototypes, and changed all those ugly
   do/while's to for loops.  I also removed the dependance on those silly
   NIL items at the end of the list (it just checks for regular NULL
   pointers instead).  Additionally, the code is more easily reentrant now,
   and doesn't depend on any global variables.  The code is quite a bit
   different looking than it originally was, but the underlying algorithims
   (of course) remain unchanged.

              -- THIS CODE IS UNDER THE GNU COPYLEFT --


      Dominic Giampaolo (nick@maxine.wpi.edu)
      Aug, 1991
*/
/*	system headers not in global.h*/
#include 
#include 
/*	blimps library headers */
#include 
#include 

/* define's */
#ifndef TRUE
#define TRUE  1
#endif
#ifndef FALSE
#define FALSE 0
#endif

#define MaxNumberOfLevels 16
#define MaxLevel (MaxNumberOfLevels-1)
/* #define NewNodeOfLevel(x) (SLNode)malloc(sizeof(struct SLNodeStruct)+(x)*sizeof(SLNode *)) */ /* commented out by Bill Alford */


/* private proto */
static int RandomLevelSL();

/* added by Bill Alford */
static void FreeSLNode(); /* node, level */
static SLNode NewNodeOfLevel(); /* level */


/* save structure */
#define SLNODES_TO_SAVE_PER_LEVEL_AT_START 10
int SLNodesToSave = SLNODES_TO_SAVE_PER_LEVEL_AT_START;

struct {
  int num_saved;
  int num_to_save;
  SLNode saved_nodes;
} SavedNodes[MaxNumberOfLevels];

int InitializedSaveList = FALSE;


/* functions added by Bill Alford */

static SLNode NewNodeOfLevel(level) 
     int level;
{
  register SLNode tmp;

  level--; /* change indexing to start at 0 */

  if (!SavedNodes[level].num_saved) {
    /* This prints out the level of the node being created. */
    /* It is useful for debugging. */
    /*
    fprintf(stderr, "making node level: %d\n", level);
    */
    CheckMem(
	     tmp = (SLNode) malloc(sizeof(struct SLNodeStruct) +
				   (level+1)*sizeof(SLNode *))
	     );
    return tmp;	       /* needed to use the tmp to work around the macro */
  }
  else {
    tmp = SavedNodes[level].saved_nodes;
    SavedNodes[level].saved_nodes = tmp->forward[0];
    SavedNodes[level].num_saved--;
    return tmp;
  }
}

static void FreeSLNode(node, level)
     SLNode node;
     int level;
{
  level--; /* change indexing to start at 0 */

  if (SavedNodes[level].num_saved >= SavedNodes[level].num_to_save) {
    free(node);
  }
  else {
    /* save the node */
    /* NOTE: This behaves like a stack.  It might be better to use another */
    /*       style of save list, maybe like FIFO.  This might help */
    /*       _slightly_ in the fragmentation problem. */
    node->forward[0] = SavedNodes[level].saved_nodes;
    SavedNodes[level].saved_nodes = node;
    SavedNodes[level].num_saved++;
  }
  /* This prints out the number of nodes in each list. */
  /* It is useful for debugging. */
  /*
  {
    int i;
    for (i=0; i SavedNodes[i].num_to_save) {
      tmp = SavedNodes[i].saved_nodes;
      SavedNodes[i].saved_nodes = tmp->forward[0];
      SavedNodes[i].num_saved--;
      free(tmp);
    }
  }
  return SavedNodes[0].num_to_save; /* the new save level */
}

/* end added by Bill Alford */

/* functions */
SkipList  NewSL(compare, freeitem, flags)
     int (*compare)();
     void (*freeitem)();
     int flags;
{
  SkipList l;
  int i;

  /* added by Bill Alford */ 
  /* initialize the saved nodes list */
  if (!InitializedSaveList) {
    for (i=0; ilevel = 1;
  l->header = NewNodeOfLevel(MaxNumberOfLevels);
  if (l->header == NULL)
    { free(l); return NULL; }

  for(i=0; i < MaxNumberOfLevels; i++)
    l->header->forward[i] = NULL;
  l->header->key = NULL;		 /* just to be sure */

  srand(time(NULL) | 0x01);   /* seed with an odd number */

  l->compare	 = compare;
  l->freeitem	 = freeitem;
  l->flags	 = flags;

  l->count = 0;

  return(l);
}


void FreeSL(l)
     SkipList l;
{
  register SLNode p,q;
  void (*freeitem)() = l->freeitem;

  if (l == NULL || l->header == NULL)
    return;

  p = l->header;	   /* free header node first, because it doesn't */
  q = p->forward[0];	   /* have a real key to it			 */
  free(p);
  p = q;

  while (p != NULL)
   {
     q = p->forward[0];
     if (freeitem)
       (*freeitem)(p->key);
     free(p);
     p = q;
   }

  free(l);
}




/*
 *   This RandomLevelSL function generates a very good representation of
 *   p=.25 (or p=.5, etc).  The number of nodes of each level works out
 *   to be very very close to what they should be.  I didn't check it
 *   statistically,  but on large data sets, I imagine it's +/- 5% of what
 *   it should be.  This P value is good for lists of up to 64K elements.
 *   
 *   For more info about the P value, see the papers by Mr. Pugh (available
 *   in postscript from mimsy.umd.edu).
 */
#define P_50   (RAND_MAX / 2)     /* p value of .50   */
#define P_25   (RAND_MAX / 4)     /* p value of .25   */
#define P_125  (RAND_MAX / 8)     /* p value of .125  */

static int RandomLevelSL(l)
     SkipList l;
{
  register int level = 0;

  while(rand() < P_25)
    {
      level++;
    }

  return (level > MaxLevel ? MaxLevel : level);
}


int InsertSL(l, key)
     SkipList l;
     void *key;
{
  register int i,k;
  SLNode update[MaxNumberOfLevels];
  register SLNode p,q;
  int (*compare)() = l->compare;

  p = l->header;
  
  for(k = l->level-1; k >= 0; k--)
   {
     while((q = p->forward[k]) && (*compare)(q->key, key) < 0)
	p = q;

     update[k] = p;
   }

  if ((l->flags & ALLOW_DUPLICATES) == FALSE) /* if no duplicates allowed */
   if (q && (*compare)(q->key, key) == 0)     /* item is a duplicate */
     {
       return DUPLICATE_ITEM;
     }


  k = RandomLevelSL(l);
  if (k >= l->level)
    {
      l->level++;
      k = l->level - 1;
      update[k] = l->header;
    }

  q = NewNodeOfLevel(k+1);

  if (q == NULL)
    return FALSE;

  l->count++;             /* update the number of nodes in the list */
  
  q->key = key;
  for(i=0; i < k; i++)
    q->forward[i] = NULL;

  for(; k >= 0; k--)
    {
      p = update[k];
      q->forward[k] = p->forward[k];
      p->forward[k] = q;
    }

  return TRUE;
}



int DeleteSL(l, key)
     SkipList l;
     void *key;
{
  register int k,m;
  SLNode update[MaxNumberOfLevels];
  register SLNode p,q;
  int  (*compare)()  = l->compare;
  void (*freeitem)() = l->freeitem;

  p = l->header;

  for(k=l->level-1; k >= 0; k--)
   {
     while((q = p->forward[k]) && (*compare)(q->key, key) < 0)
	p = q;

     update[k] = p;
   }
  q = p->forward[0];

  if (q && (*compare)(q->key, key) == 0)
    {
      m = l->level - 1;
      for(k=0; k <= m; k++)
	{
	  p = update[k];
	  if (p == NULL || p->forward[k] != q)
	    break;
	  p->forward[k] = q->forward[k];
	}

      l->count--;
      
      if (freeitem)
	(*freeitem)(q->key);
      
      /* added by Bill Alford */
      FreeSLNode(q, k);
      /* end added by Bill Alford */

      m = l->level - 1;
      while(l->header->forward[m] == NULL && m > 0)
	m--;

      l->level = m + 1;
      return TRUE;
    }
  else
    return FALSE;
}



void *SearchSL(l, key)
     SkipList l; 
     void *key;
{
  register int k;
  register SLNode p,q;
  int (*compare)() = l->compare;

  p = l->header;
  
  for(k=l->level-1; k >= 0; k--)
   {
     while((q = p->forward[k]) && (*compare)(q->key, key) < 0)
	p = q;
   }

  if (q == NULL || (*compare)(q->key, key) != 0)
    return NULL;

  return q->key;
}


void DoForSL(l, function, arg)
     SkipList l;
     int (*function)();
     void *arg;
{
  register SLNode p,q, fix;
  register int k, ret;
  SLNode save[MaxNumberOfLevels], who[MaxNumberOfLevels];
  void (*freeitem)() = l->freeitem;
  

  if (l == NULL || l->header == NULL || function == NULL)
    return;

  /* this is to make compilers happy.  Since the important values are copied */
  /* into the array below */
  for (k=0; k < MaxNumberOfLevels; k++)	{	/*JGH*/
    save[k] = who[k] = NULL; 
  }

  p = l->header;	   /* skip header node because it isn't a real node */

  /* Save the initial header info
   */
  for(k=0; k < l->level; k++)
   {
     save[k] = p->forward[k];
     who[k]  = p;
   }

  p = p->forward[0];      /* skip to the first data node */

  while (p != NULL)
   {
     q = p->forward[0];
     ret = (*function)(p->key, arg);

     if (ret & SL_DELETE)
      {
	k = 0;
	while(save[k] == p)
	 {
	   fix = who[k];
	   fix->forward[k] = p->forward[k];
	   save[k] = p->forward[k];
	   k++;
	 }

	l->count--;         /* decrement the count of items */
	
	if (freeitem)
	  (*freeitem)(p->key, arg);
	/* added by Bill Alford */
	FreeSLNode(p, k);
	/* end added by Bill Alford */
      }
     else
      {
	k = 0;
	while(save[k] == p)
	 {
	   save[k] = p->forward[k];
	   who[k]  = p;
	   k++;
	 }
      }
     
     if (ret & SL_QUIT)
       break;

     p = q;    /* advance to the next one */
   }
}


void DoForRangeSL(l, key, compare, func, arg)
     SkipList l;
     void *key;
     int (*compare)();
     int (*func)();
     void *arg;
{
  register int k;
  SLNode update[MaxNumberOfLevels];
  register SLNode p,q;
  void (*freeitem)() = l->freeitem;
  int  ret;

  p = l->header;

  for(k=l->level-1; k >= 0; k--)
   {
     while((q = p->forward[k]) && (*compare)(q->key, key) < 0)
	p = q;

     update[k] = p;
   }
  p = p->forward[0];

  if (p == NULL || (*compare)(p->key, key) != 0)   /* then nothing matched */
    return;

  do
   {
     q = p->forward[0];            /* save next pointer */
     ret = (*func)(p->key, arg);
     
     if (ret & SL_DELETE)
      {
	for(k=0; k < l->level && update[k] && update[k]->forward[k] == p; k++)
	  update[k]->forward[k] = p->forward[k];

	l->count--;         /* decrement the count of items */
	
	if (freeitem)
	  (*freeitem)(p->key, arg);
	/* added by Bill Alford */
	FreeSLNode(p, k);
	/* end added by Bill Alford */
      }
     
     if (ret & SL_QUIT)
       break;

     p = q;    /* advance to the next one */
   }
  while(p != NULL && (*compare)(p->key, key) == 0);

}


int NumInSL(l)
     SkipList l;
{
  return l->count;
}


/* 
 * Nth
 *
 * returns the Nth element in the list.  Counting starts at 0.
 *
 */

void *
Nth(l, n)
     SkipList l;
     int n;
{
  int x;
  SLNode p;

  /* range check */
  if ((NumInSL(l) < n) || (n < 0)) {
    return NULL;
  }
  
  p = l->header; /* skip header node because it isn't a real node */
  p = p->forward[0];      /* skip to the first data node */

  for (x=0; xforward[0];
  }
  
  assert(p->key != NULL);
  return p->key;
}


/* added by Bill Alford */
/* Change log information follows. */
/*
   06/23/94 Added Nth()   BJA
   10/4/94 Initialized pointers in DoForSLC()   jgh 
*/
/* $Log: sl.c,v $
 * Revision 2.2010  1995/07/28  23:47:14  billa
 * Added new convert method and pattern matching and minor updates merged.
 *
 * Revision 2.2000  1994/05/10  18:39:13  billa
 * System version 2.2 A [2.2000]
 * Goofed on dev. version.
 *
 * Revision 2.1100  1994/05/10  18:27:07  billa
 * System version 2.2 A [2.1100].
 * Created blimps library and fixed up minor bugs.  No major changes to the
 * program.
 *
 * Revision 2.1025  1994/05/10  00:51:47  billa
 * Added SCCS patterns to trick the what command into printing out the RCS
 * identifying patterns.
 *
 * Revision 2.1020  1994/04/27  21:59:11  billa
 * After library creation.  In testing phase.
 *
 * Revision 2.1015  1994/04/26  03:15:34  billa
 * Pre-library checkin.
 *
 * Revision 2.1010  1994/04/26  00:28:18  billa
 * Cleaned up warnings from gcc switches.
 *
 * Revision 2.1000  1994/03/09  22:23:59  billa
 * System version 2.1 A [2.1000]
 * Added reading and scoring of precomputed site specific scoring matricies.
 * Reconfigured files.[ch] into files.[ch] and config.[ch].
 *
 * Revision 2.0  1993/12/06  19:31:18  billa
 * System version 2.0 A [2.0000].
 * Changed source to remove some warnings.  Added sequence weights to the
 * blocks.  Added a conversion method to use the weights.  Made the method
 * the default.  Added some ifndef's in preparation of creating a library
 * of functions.  Added the ability to choose the genetic code to use for
 * translation.  Added the ability to read a flat file as a sequence if the
 * other types sequences fail to match.  Added some defines for strdup().
 *
 * Revision 1.1120  1993/12/02  03:44:22  billa
 * Development version 1.1120.  Right after copyright/license info added.
 *
 * Revision 1.1101  1993/12/02  03:37:12  billa
 * Added the copyright notice to the top of the file.
 *
 * Revision 1.1100  1993/09/09  17:23:19  billa
 * System version 1.1 B [1.1100].
 *
 * Revision 1.1000  1993/08/27  17:01:31  billa
 * System version 1.1 A, development version 1.1000.
 * Added the function reclaim_space() and the macro CheckMem(A) to handle
 * the situation when there is no more memory to allocate.
 *
 * Revision 1.0  1993/08/14  00:50:52  billa
 * System version 1.00
 *
 * Revision 0.110  1993/08/10  02:50:53  billa
 * System version update.  Added convert.[ch], scoring.[ch] and version.[ch].
 *
 * Revision 0.105  1993/08/04  19:53:40  billa
 * System version 0.105.  Post file structure reorganization.
 *
 * Revision 0.100  1993/08/03  00:48:46  billa
 * System version 0.100.  Pre file structure reorganization.
 *
 * Revision 0.52  1993/07/16  20:10:05  billa
 * Added a save list for deleted nodes so that the lists will not thrash
 * memory mallocing and freeing memory.
 *
 * Revision 0.51  1993/07/02  01:02:28  billa
 * un-ANSIfied the function argument decarations to be backward compatible.
 *
 * Revision 0.50  1993/07/02  00:36:31  billa
 * Entry into the system.  Addition of skiplists to the system.
 *
 */






izeof(struct _SkipList))
	   );
  if (l == NULL)
    return NULL;

  l->level = 1;
  l->header = NewNodeOfLevel(MaxNumberOfLevels);
  if (l->header == NULL)
    { free(l); return NULL; }

  for(blimps-3.9/blimps/sortblk.c000064400001460000012000000073740774312250100162740ustar00jorjastaff00000400000027#define SORTBLK_C_
#define EXTERN
#define YES 1
#define NO 0
#define MAXNAME 80      /* Maximum file name length */
#define MAXAA 26        /* Dimension of aa_ arrays */
#define MAXINT 32000
#define ROUND(x) ((x >= 0.0) ? (int) (x+0.5) : (int) (x-0.5))
#define ORD(x) ((int) x - 65)
#define INDEX(n, col, row) (col*n - (col*(col+3))/2 - 1 + row)

#include 
#include 

/*
 * Local variables and data structures
 */

Block *sort_it();
void sort_in();
int namecmp();

/*=======================================================================*/
/*
 * main
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *bfp, *ofp;
  Block *block, *sblock;
  int wtype, clus, stype;
  char bdbname[MAXNAME], conname[MAXNAME], ctemp[10];
  struct timeval tv;

  ErrorLevelReport = 5;                 /* don't want to see them */
  /* initialize random number generator */
  gettimeofday(&tv, NULL);
  srandom(tv.tv_sec^tv.tv_usec);

  if (argc < 2)
  {
     printf("BLWEIGHT: Copyright 1994-2000 by the Fred Hutchinson");
     printf(" Cancer Research Center, \n\tSeattle, WA, USA\n");
     printf("Add sequence weights to blocks.\n");
     printf("USAGE: blweight    \n");
     printf("\t=input file of blocks to weight\n");
     printf("\t=output file of weighted blocks\n");
     printf("\t=P (position-based) | V (Voronoi) | \n\t\t");
     printf("A (Vingron & Argos) | Cn (n percent clumping)\n");
     printf("\t=M (max=100) | N (sum=#seqs) | # (sum=#)\n");
  }
/* ------------1st arg = blocks database -------------------------------*/
   if (argc > 1)
      strcpy(bdbname, argv[1]);
   else
   {
      printf("\nEnter name of blocks database: ");
      gets(bdbname);
   }
   if ( (bfp=fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbname);
      exit(-1);
   }
/* ------------2nd arg = weighted blocks database ---------------------*/
   if (argc > 2)
      strcpy(conname, argv[2]);
   else
   {
      printf("\nEnter name of new sorted blocks database: ");
      gets(conname);
   }
   if ( (ofp=fopen(conname, "w")) == NULL)
   {
      printf("\nCannot open file %s\n", conname);
      exit(-1);
   }

   while ((block = read_a_block(bfp)) != NULL)
   {
/*
      sblock = sort_it(block);
      output_block(sblock,ofp);
*/
      sort_in(block);
      output_block(block,ofp);
   }
 
   fclose(bfp); fclose(ofp);
   exit(0);

}  /* end of main */

/*========================================================================*/
Block *sort_it(block)
Block *block;
{
   int iclus, npair, threshold, s1, s2, l1, l2, px, i, i1, i2, first;
   int width, nseq;
   Block *newblock;

   width = block->sequences[0].length;
   nseq = block->num_sequences;

   /*----------- Now rewrite the block ----------------------*/
   newblock = new_block(width, nseq);	/* allocates 1 Cluster */
   strcpy(newblock->id, block->id);
   strcpy(newblock->ac, block->ac);
   strcpy(newblock->number, block->number);
   strcpy(newblock->de, block->de);
   strcpy(newblock->bl, block->bl);
/*
   newblock->num_clusters = 0;
   newblock->max_clusters = iclus;
   newblock->clusters = (Cluster *) realloc(newblock->clusters, iclus*sizeof(Cluster));
*/

   for (s1=0; s1 < nseq; s1++)
   {
   }

   return(newblock);

}  /* end of sort_it */
/*========================================================================*/
void sort_in(block)
Block *block;
{
   qsort(block->sequences, block->num_sequences, sizeof(Sequence), namecmp);

   block->num_clusters = block->max_clusters = 1;
   block->clusters[0].num_sequences = block->num_sequences;

}  /* end of sort_in */
/*=======================================================================*/
int namecmp(s1, s2)
Sequence *s1, *s2;
{
   return(strcmp(s1->name, s2->name));
}
blimps-3.9/blimps/strutil.c000064400001460000012000000120210774312250100163030ustar00jorjastaff00000400000027/* (C) Copyright 1993-9, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* strutil.c: general string utilities */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */


/*	system headers not in global.h */
/*	blimps library headers not in global.h */
#include 

/*
 * Exported variables and data structures definitions
 */

char Buffer[LARGE_BUFF_LENGTH];

/*
 * Local variables and data structures
 */

/*
 * Function definitions
 */

/* 
 *  Boolean blank_line(s)
 *  char *eat_whitespace(s)
 *  void remove_trailing_whitespace(s)
 *  char *get_token(s)
 */

/* 
 * blank_line
 *  returns TRUE if the passed string is only whitespace
 *  Parameters:
 *    char* s: the string to check
 *  Return codes:
 *    TRUE if the line only has whitespace characters, FALSE otherwise.
 *  Error Codes:
 */

Boolean blank_line(s)
     char *s;
{
  char *tmp;
  int length;

  tmp = eat_whitespace(s);
  length = strlen(tmp);

  if (length == 0) {
    return TRUE;
  }
  else {
    return FALSE;
  }
}


/*
 * eat_whitespace
 *   Eats the whitespace at the beginning of the string s1 and returns a 
 *   pointer to the first non whitespace character.  The whitespace characters
 *   are: space, tab, and newline.
 *   Parameters:
 *     char *s : input string
 *   Return Value: the return value is the pointer to the first non-whitespace
 *                 character
 *   Error codes:
 */

char *eat_whitespace(s)
     char *s;
{
/*  
  int white_length; 
*/

  while ((*s == ' ') ||
	 (*s == '\t') ||
	 (*s == '\n') ||
	 (*s == '\r')) {
    s++;
  }
  
  return (s);

/*
  white_length = strspn(s, WHITE_SPACE_CHARS);
  
  return (s+white_length);
*/
}


/*
 * remove_trailing_whitespace
 *   Removes trailing whitespace by scanning back from the end of the string
 *   and replacing the leftmost trailing whitespace character with a NULL.
 *   Whitespace characters are: space, tab, newline and carriage return.
 *   NOTE: this is destructive
 *   Parameters:
 *     char *s : input string
 *   Return Value: returns its first argument
 *   Error codes:
 */

char *remove_trailing_whitespace(s)
     char *s;
{
  int length;

  length = strlen(s);

  /* if the string is empty, exit */
  if (length == 0) {
    return(NULL);
  }

  length--;				/* indexing starts at zero */

  while ((s[length] == ' ') ||
	 (s[length] == '\t') ||
	 (s[length] == '\n') ||
	 (s[length] == '\r')) {
    length--;
  }
  
  s[length+1] = '\0';

  return(s);
}

/*
 * get_token
 *   get_token returns a pointer to a token delimited by whitespace.  The
 *   first call with a string returns the first token.  Subsequent calls (with
 *   the string as NULL) returns pointers to the following tokens.  A NULL
 *   is placed following the token.
 *   Note: get_token must be called with a non-null string pointer the first
 *         time or the behavior is ambiguous.
 *   Whitespace is: space, tab, newline, carriage return
 *   Parameters: 
 *     char *s: the string of tokens
 *   Return Value: the pointer to the token, NULL when there are no more tokens
 *   Error codes:
 *   Notes: get_token() wraps strtok() because the separators will always be 
 *          whitespace and strtok() is cryptic and easy to forget. (for me).
 */

char *get_token(s)
     char *s;
{
#ifdef NO_STRTOK
  char c;
  char *return_string;
  static char *saved_string_pointer; /* pointer right after NULL char */



  if (s != NULL) {
    /* save the new string pointer */
    saved_string_pointer = s;
    remove_trailing_whitespace(saved_string_pointer);
  }

  /* if finished with this string last time, return NULL right away */
  if (saved_string_pointer == NULL) {
    return NULL;
  }

  /* eat up the beginning whitespace, if any */
  saved_string_pointer = eat_whitespace(saved_string_pointer);

  /* read ahead from saved pointer */
  return_string = saved_string_pointer;
  
  c = *saved_string_pointer;
  while ((c != ' ')  &&
    	 (c != '\t') &&
	 (c != '\n') &&
	 (c != '\r') &&
	 (c != '\0')) {
    saved_string_pointer++;
    c = *saved_string_pointer;
  }

  /* if saw '\0', finished the string */
  if (*saved_string_pointer == '\0') {
    saved_string_pointer = NULL;
    return return_string;
  }
  else {
    /* write in the null delimiting character */
    *saved_string_pointer = '\0';
    saved_string_pointer++;
    return return_string;
  }

#else
  return (char *)strtok(s, " \t\n\r\0");  
                                             /* typecast shouldn't be needed */
					     /* but compiler says it is a */
					     /* type mismatch of pointer and */
					     /* integer */
#endif /* NO_STRTOK */

}



/* Change log information follows. */
/* 
 * Revision 2.2002  1994/07/07  00:45:58  billa
 * Made remove_trailing_whitespace() return its argument.
 *
 * Revision 2.2001  1994/05/18  19:16:26  billa
 * Removed global.c and moved Buffer variable to strutil.[ch].
 *
 * Revision 2.1001  1994/04/21  01:03:18  billa
 * Creation.  Moved these from files.[ch].
 *
 */
blimps-3.9/blimps/translate.c000064400001460000012000000052620774312250100166030ustar00jorjastaff00000400000027/*    translate.c   Read a sequence, translate it, write it out
--------------------------------------------------------------------
11/30/94
====================================================================*/

#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#include "blocksprogs.h"

/*=======================================================================*/
/*
 * main
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *bfp, *ofp;
  Sequence *sequence, *trans;
  char sname[MAXNAME], outname[MAXNAME], ctemp[MAXNAME];
  unsigned char gcode[64], revgcode[64];
  int db_type, seq_type, frame, code;

/* ------------1st arg = sequence database -------------------------------*/
   if (argc > 1)
      strcpy(sname, argv[1]);
   else
   {
      printf("\nEnter name of sequence database: ");
      gets(sname);
   }
   if ( (bfp=fopen(sname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", sname);
      exit(-1);
   }
   db_type = type_dbs(bfp, DbInfo);
   seq_type = seq_type_dbs(bfp, DbInfo, db_type);;
   if (seq_type != NA_SEQ)
   {
      printf("\nNot a nucleotide sequence\n");
      exit(-1);
   }

/* ------------2nd arg = translated database ---------------------*/
   if (argc > 2)
      strcpy(outname, argv[2]);
   else
   {
      printf("\nEnter name of new translated sequence database: ");
      gets(outname);
   }
   if ( (ofp=fopen(outname, "w")) == NULL)
   {
      printf("\nCannot open file %s\n", outname);
      exit(-1);
   }
/*----------------3rd arg = translation frame ---------------------*/
   if (argc > 3) frame = atoi(argv[3]);
   else
   {
      printf("\nEnter translation frame: ");
      gets(ctemp);
      frame = atoi(ctemp);
   }
   if (frame == 0 || frame < -3 || frame > 3) frame = 1;

/*----------------4rd arg = genetic code ---------------------*/
   if (argc > 4) code = atoi(argv[4]);
   else
   {
      for (code = 0; code < NUMBER_OF_GENETIC_CODES; code++)
          printf("\n %d %s", code, gcodes[code].name);
      printf("\nEnter genetic code: ");
      gets(ctemp);
      code = atoi(ctemp);
   }
   if (code < 0 || code > 8) code = 0;
   init_gcode(&gcodes[code], gcode, revgcode);

/*-----------------------------------------------------------------*/

  while ((sequence = read_a_sequence(bfp, db_type, seq_type)) != NULL)
  {
     trans = translate_sequence(sequence, frame, gcode, revgcode);
     output_sequence(trans, ofp);
  }

/*-----------------------------------------------------------------*/

  while ((sequence = read_a_sequence(bfp)) != NULL)
  {
     trans = translate_sequence(sequence, frame, gcode, revgcode);
     output_sequence(trans, ofp);
  }
   
  fclose(bfp); fclose(ofp);
  exit(0);

}  /* end of main */
blimps-3.9/blimps/util.c000064400001460000012000000054631003527371600155710ustar00jorjastaff00000400000027#include 
#include 

#define LF 10
#define CR 13

void getword(char *word, char *line, char stop) {
    int x = 0,y;

    for(x=0;((line[x]) && (line[x] != stop));x++)
        word[x] = line[x];

    word[x] = '\0';
    if(line[x]) ++x;
    y=0;

    while(line[y++] = line[x++]);
}

char *makeword(char *line, char stop) {
    int x = 0,y;
    char *word = (char *) malloc(sizeof(char) * (strlen(line) + 1));

    for(x=0;((line[x]) && (line[x] != stop));x++)
        word[x] = line[x];

    word[x] = '\0';
    if(line[x]) ++x;
    y=0;

    while(line[y++] = line[x++]);
    return word;
}

char *fmakeword(FILE *f, char stop, int *cl) {
    int wsize;
    char *word;
    int ll;

    wsize = 102400;
    ll=0;
    word = (char *) malloc(sizeof(char) * (wsize + 1));

    while(1) {
        word[ll] = (char)fgetc(f);
        if(ll==wsize) {
            word[ll+1] = '\0';
            wsize+=102400;
            word = (char *)realloc(word,sizeof(char)*(wsize+1));
        }
        --(*cl);
        if((word[ll] == stop) || (feof(f)) || (!(*cl))) {
            if(word[ll] != stop) ll++;
            word[ll] = '\0';
            return word;
        }
        ++ll;
    }
}

char x2c(char *what) {
    register char digit;

    digit = (what[0] >= 'A' ? ((what[0] & 0xdf) - 'A')+10 : (what[0] - '0'));
    digit *= 16;
    digit += (what[1] >= 'A' ? ((what[1] & 0xdf) - 'A')+10 : (what[1] - '0'));
    return(digit);
}

void unescape_url(char *url) {
    register int x,y;

    for(x=0,y=0;url[y];++x,++y) {
        if((url[x] = url[y]) == '%') {
            url[x] = x2c(&url[y+1]);
            y+=2;
        }
    }
    url[x] = '\0';
}

void plustospace(char *str) {
    register int x;

    for(x=0;str[x];x++) if(str[x] == '+') str[x] = ' ';
}

int rind(char *s, char c) {
    register int x;
    for(x=strlen(s) - 1;x != -1; x--)
        if(s[x] == c) return x;
    return -1;
}

int getline(char *s, int n, FILE *f) {
    register int i=0;

    while(1) {
        s[i] = (char)fgetc(f);

        if(s[i] == CR)
            s[i] = fgetc(f);

        if((s[i] == 0x4) || (s[i] == LF) || (i == (n-1))) {
            s[i] = '\0';
            return (feof(f) ? 1 : 0);
        }
        ++i;
    }
}

void send_fd(FILE *f, FILE *fd)
{
    char c;

    while (1) {
        c = fgetc(f);
        if(feof(f))
            return;
        fputc(c,fd);
    }
}

int ind(char *s, char c) {
    register int x;

    for(x=0;s[x];x++)
        if(s[x] == c) return x;

    return -1;
}

void escape_shell_cmd(char *cmd) {
    register int x,y,l;

    l=strlen(cmd);
    for(x=0;cmd[x];x++) {
        if(ind("&;`'\"|*?~<>^()[]{}$\\",cmd[x]) != -1){
            for(y=l+1;y>x;y--)
                cmd[y] = cmd[y-1];
            l++; /* length has been increased */
            cmd[x] = '\\';
            x++; /* skip the character */
        }
    }
}

 *makeword(char *line, char stop) {
    int x = 0,y;
    char *word = (char *) malloc(sizeof(char) * (strlen(line) + 1));

    for(x=0;((line[x]) && (line[x] != stop));x++)
        word[x] = line[x];

    blimps-3.9/blimps/version.c000064400001460000012000000154230774312250100162730ustar00jorjastaff00000400000027/* (C) Copyright 1993-9, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* version.c: Keeps track of the system version level. */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

/*	system headers not in global.h  */
/*	blimps library headers; global.h must be first  */
#include 
#include 

/****
The note about versions is out of date.  

Versions are now as follows:
major_release.minor_release.updates

Major releases, minor releases, and updates are described as below.

*****/
/**************************************************************************
A NOTE ABOUT VERSIONS:

The way I am computing system versions is this: 
  Take the RCS version number of version.c (the development version)
  The whole number part of the system version is the same as the whole
    number part of the version.c version.
  The fractional part of the system version is the integer value of
    the fractional part of version.c modulus 1000.
  The letter part of the version is the 100's place of the fractional
    part (taken as an integer).  eg. A = 0, B = 1, C = 2, ...
  
  version.c version: a.xxxxyzz  --> system version: a.xxxx ('A' + y)

With this method of versions every system version update can be done
by checking out and checking in everything at that level.  This makes
the system version level consistient and allows 99 incremental
updates.  Also to retrieve an earlier system version, all that is
needed to be done is to check out all the files of that development
version.

A caveat: ALWAYS check in a new version of version.c everytime another
          system file is checked in (use ci -f).  And ALWAYS say what
	  files and their version number in the log of the version.c
	  checkin.  If this is always done, we should be able to get
	  to any of the incremental versions between the system
	  versions.

Another caveat: Only the first system version of the development
                version is released.  This way to get any particular
		version, all the files only have to be checked out at
		one development version level.  Also the minor changes
		in the incremental versions will not be in different
		copies of the same system version. eg.:
		  development    system
		  1.0          = 1.0 A
		  1.1-1.99     = incremental increase from 1.0 A to 1.0 B
		  1.100        = 1.0 B
		  1.101-1.199  = incremental increase from 1.0 B to 1.0 C
		  ...
		  1.1000       = 1.1 A
		  ...

The plan for the difference between versions:
  Major release:  
    A major release would be something like a reconstruction of the
    interface.  New file formats or configuration keys that are
    necessary in order to run.  Also changes to the program structure
    should be limited to a major release.  An example would be
    changing the way the frequency file is laid out.

    ex. system: 1.x c    --> 2.0 A
        dev.    1.xxxyzz --> 2.0

  Minor release:  
    A minor release would be something like an important enhancement
    to a file format or a configuration that could change the
    performance (but not the output) of the program, enhancements to
    the program that do not change the data, but make the program
    better.  An example would be memory management code or new
    names to the configuration file or reading of a matrix database/file.

    ex. system: 1.2 c    --> 1.3 A
        dev.    1.2yzz   --> 1.3000

  Updates:     
    An update would be something that would not get in the way of
    earlier file formats and that could be used by earlier versions of
    this minor release.  Nothing that changes the way the program is
    called.  Examples of updates would be new conversion and scoring
    routines added or a new configuration key that will change the way
    data is output (eg. outputs a matrix) or the ability to read a new
    sequence database format.  Note that reading a new block format
    would be a minor release because there is only one block database
    and it is key to the way the program behaves.  Also note that
    something like being able to read a new sequence database format
    is more suited to an update since there are many different formats
    and external to the program they can be converted to one that
    blimps can already read.  Updates are also for bug fixes.
   
    ex. system: 1.2 B    --> 1.2 C
        dev.    1.22yy   --> 1.2300

**************************************************************************/



/*
 * Local variables and data structures
 */

static char ProgramString[SMALL_BUFF_LENGTH];
static char VersionString[SMALL_BUFF_LENGTH];
static char VersionInfo[SMALL_BUFF_LENGTH];
static char DateString[SMALL_BUFF_LENGTH];
static char CopyrightString[SMALL_BUFF_LENGTH];

static char TitleString[SMALL_BUFF_LENGTH] = { '\0' }; 
				/* make sure it is initialized to null */

/*
 * Function definitions
 */

/*
 * version_strings
 *   Enters the strings to be used by the version output function 
 *   (print_version).
 *   Parameters:
 *     char *program_string:   the name of the program
 *     char *version_string:   the RCS revision number 
 *     char *version_info:     additional version info
 *     char *date_string:      the RCS date
 *     char *copyright_string: the copyright info
 *   Error codes: none
 */

void version_strings(program_string, version_string, version_info, 
		     date_string, copyright_string)
     char *program_string, *version_string, *version_info, 
       *date_string, *copyright_string;
{
  strncpy(ProgramString,   program_string,   SMALL_BUFF_LENGTH);
  strncpy(VersionString,   version_string,   SMALL_BUFF_LENGTH);
  strncpy(VersionInfo,     version_info,     SMALL_BUFF_LENGTH);
  strncpy(DateString,      date_string,      SMALL_BUFF_LENGTH);
  strncpy(CopyrightString, copyright_string, SMALL_BUFF_LENGTH);
}


/*
 * print_version
 *   Prints the version of the current release.  
 *   Parameters:
 *     FILE *fp: the file to print the verson info, typically stdout and the
 *               output file
 *   Error codes: none
 */

void print_version(fp)
     FILE *fp;
{

  if (TitleString[0] == '\0') {
    /* if the development version is different from the system version */
    /* then make the development_version string */
    /* if something in ones or tens place, this is a develoment version */
    if (VersionInfo[0] != '\0') {
      sprintf(TitleString, 
	      "%s   Version %s (%s)  %s%s\n", 
	      ProgramString, VersionString, VersionInfo, 
	      DateString, VERSION_FROM_MAKE);
    }
    else {
      sprintf(TitleString, 
	      "%s   Version %s  %s%s\n", 
	      ProgramString, VersionString, DateString, VERSION_FROM_MAKE);
    }
  }

  fprintf(fp, TitleString);
  fprintf(fp, CopyrightString);

}

/* Change log information follows. */
/* 
 *
 */
blimps-3.9/blimps/Makefile.OSX000064400001460000012000005213031042724464400165570ustar00jorjastaff00000400000027# Makefile: makefile for BLIMPS blocks searcher
# Written by: Bill Alford
# (C) Copyright 1993-2005, Fred Hutchinson Cancer Research Center 
# Use, modification or distribution of these programs is subject to 
# the terms of the non-commercial licensing agreement in license.h. 

# Instructions for use:
# 1. Change DEFINES, SYSTEM, OPTIMIZ, RANLIB, CC for your system
# 2. make depend
# 3. make install (updates ../bin and ../lib)


# System defines.  The main reason for this is that on the Sun there is a 
# function malloc_debug() wich will raise a signal if there are problems
# with memory.  The problem is that there is no function like that on other
# machines, at least that I've seen.  Defines are set up so that the
# malloc_debug call is only in the Sun code.

# Generic -- Should work on most systems not listed below.
#DEFINES = -DNO_STRDUP
#SYSTEM  = generic 
#OPTIMIZ =
#RANLIB = ../bin/ranlib

# SunOS
#DEFINES = 
#SYSTEM  = sun4.1.3
#OPTIMIZ = -O
#RANLIB = /bin/ranlib
## For debugging.
# DEFINES = -DMALLOC_DEBUG
# OTHER_OBJS = /usr/lib/debug/malloc.o 

# Sun Solaris
#DEFINES = 
#SYSTEM = solaris
#	Some programs don't give the same results when compiled with -fast,
#	e.g. codehop.c; offending options -fsimple=2
#OPTIMIZ = -fast
#OPTIMIZ = -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=2 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit 
#OPTIMIZ = -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit
#OPTIMIZ = -g
#	RANLIB is obsolete under Solaris 2.5; just put something here
#	so the Makefile continues to work.
#RANLIB = ls

# Linux - see also LDLIBS below
$DEFINES = 
$SYSTEM  = 
$OPTIMIZ = -Wall -O2
$RANLIB = ls

# MAC/OSX - see also LDLIBS below (XCODE 2.2 files)
DEFINES = 
SYSTEM  = 
OPTIMIZ = -Wall -O2
RANLIB = ls

MAKE = /usr/bin/make
DEPEND = /usr/X11R6/bin/makedepend

#	ar -t libpssm.a for table of contents
AR = ar
RM = rm -f
MV = mv -f 
CP = cp


# C compiler
#CC = /usr/bin/gcc-4.0
CC = /usr/bin/gcc-3.3
#CC = /opt/SUNWspro/bin/cc

#----------------------------------------------------------------------
INCLUDE_DIR = ../include
INCLUDES = -I$(INCLUDE_DIR)


# C Flags to compiler
#CFLAGS = `getconf LFS_CFLAGS` $(OPTIMIZ) $(DEFINES) $(INCLUDES)
CFLAGS = $(OPTIMIZ) $(DEFINES) $(INCLUDES) -I/usr/include/malloc


# Linker Flags
LDFLAGS = $(CFLAGS)
# Red Hat Linux doesn't have ly?
#LDLIBS = -lblimps -ly -lm
LDLIBS = -lblimps -lm
LDOPTIONS = $(LDFLAGS) $(LDDIR)
# cc ld options


#LIBRARY_DIR = ../lib
LIBRARY_DIR = ./
LDDIR = -L$(LIBRARY_DIR)


# source files
SRCS =  blimps-mem.c \
	blimps.c \
	blweight.c \
	blalign.c \
	bldist.c \
	blk2pssm.c \
	rank_matrix.c \
	retblock.c \
	codehop.c \
        htmlize-codehop.c \
        oligo_melt.c \
	mablock.c \
	cobbler.c \
	addseqs.c \
	fastaseqs.c \
	LAMA.c \
	find_biassed_blocks.c \
	makeblockmap.c \
	prints2blocks.c \
	lisblk.c \
	coduse.c \
	narrow.c \
	blk2slx.c \
	blkprob.c \
	blocks.c \
	config.c \
	convert.c \
	errors.c \
	files.c \
	frequency.c \
	gcode.c \
	lists.c \
	matrix.c \
	memory.c \
	pattern.c \
	scores.c \
	scoring.c \
	sequences.c \
	sl.c \
	strutil.c \
	version.c \
	options.c \
	protomat.c  \
#	interpro.c \
	pssmdist.c \
	pssmBL.c \
	papssm.c \
	matrix_logob.c \
	makelogob.c \
	blocks_search.c \
	LAMA_search.c \
	block_vis.c \
	format_block.c \
	biassed_blocks_finder.c \
	htmlize-LAMA.c \
	show_aligned_blocks.c \
	blk2mot.c 

HDRS =  blimps.h \
	blweight.h \
	blimps-mem.h \
	config.h \
	lists.h \
	scores.h \
	scoring.h \
	protomat.h \
	p2c.h


# need the OBJS for blimps dependencies on the .o files.  I don't know a 
# way around this.

OTHER_OBJS_DEBUG =	/usr/lib/debug/malloc.o \
		/usr/lib/debug/mallocmap.o

LIBOBJS = pattern.o \
	files.o \
	frequency.o \
	convert.o \
	blocks.o \
	errors.o \
	gcode.o \
	matrix.o \
	memory.o \
	sequences.o \
	strutil.o \
	sl.o \
	version.o \
	options.o \
	blimps-mem.o \
	config.o \
	lists.o \
	scores.o \
	scoring.o \
	p2clib.o \
	util.o \
        protomat.o


# need malloc.o for malloc_debug() which will have free() raise SIGABRT
# if it is unable to free the space.

LIBRARIES = libblimps.a


########################################################################
########################################################################
#
# main dependencies
#
########################################################################
########################################################################

install: clean all move-lib move-bin

all: lib blimps blweight blalign bldist blk2pssm rank_matrix retblock codehop htmlize-codehop oligo_melt mablock cobbler addseqs fastaseqs LAMA find_biassed_blocks makeblockmap prints2blocks lisblk coduse narrow blk2slx blkprob pssmdist pssmBL papssm matrix_logob makelogob blocks_search LAMA_search block_vis format_block biassed_blocks_finder htmlize-LAMA show_aligned_blocks makelis blk2mot 

blimps: $(LIBRARIES) blimps.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blimps.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

makelis: $(LIBRARIES)  makelis.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  makelis.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blweight: $(LIBRARIES) blweight.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blweight.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blalign: $(LIBRARIES) blalign.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blalign.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

bldist: $(LIBRARIES) bldist.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  bldist.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 
blk2pssm: $(LIBRARIES) blk2pssm.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blk2pssm.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

rank_matrix: $(LIBRARIES) rank_matrix.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  rank_matrix.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

retblock: $(LIBRARIES) retblock.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  retblock.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

codehop: $(LIBRARIES) codehop.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  codehop.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

htmlize-codehop: $(LIBRARIES) htmlize-codehop.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  htmlize-codehop.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

oligo_melt: $(LIBRARIES) oligo_melt.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  oligo_melt.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

mablock: $(LIBRARIES) mablock.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  mablock.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

cobbler: $(LIBRARIES) cobbler.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  cobbler.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

addseqs: $(LIBRARIES) addseqs.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  addseqs.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

fastaseqs: $(LIBRARIES) fastaseqs.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  fastaseqs.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

LAMA: $(LIBRARIES) LAMA.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  LAMA.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

find_biassed_blocks: $(LIBRARIES) find_biassed_blocks.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  find_biassed_blocks.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

makeblockmap: $(LIBRARIES) makeblockmap.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  makeblockmap.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

prints2blocks: $(LIBRARIES) prints2blocks.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  prints2blocks.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

lisblk: $(LIBRARIES) lisblk.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  lisblk.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

coduse: $(LIBRARIES) coduse.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  coduse.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

narrow: $(LIBRARIES) narrow.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  narrow.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blk2slx: $(LIBRARIES) blk2slx.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blk2slx.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blkprob: $(LIBRARIES) blkprob.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blkprob.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

interpro: $(LIBRARIES) interpro.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  interpro.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

pssmdist: $(LIBRARIES) pssmdist.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  pssmdist.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

pssmBL: $(LIBRARIES) pssmBL.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  pssmBL.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

papssm: $(LIBRARIES) papssm.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  papssm.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

matrix_logob: $(LIBRARIES) matrix_logob.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  matrix_logob.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

makelogob: $(LIBRARIES) makelogob.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  makelogob.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blocks_search: $(LIBRARIES) blocks_search.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  blocks_search.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

LAMA_search: $(LIBRARIES) LAMA_search.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  LAMA_search.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

block_vis: $(LIBRARIES) block_vis.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  block_vis.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

format_block: $(LIBRARIES) format_block.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  format_block.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

biassed_blocks_finder: $(LIBRARIES) biassed_blocks_finder.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  biassed_blocks_finder.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

htmlize-LAMA: $(LIBRARIES) htmlize-LAMA.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  htmlize-LAMA.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

show_aligned_blocks: $(LIBRARIES) show_aligned_blocks.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  show_aligned_blocks.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blk2mot: $(LIBRARIES) blk2mot.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  blk2mot.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 


$(LIBOBJS):


########################################################################
########################################################################
#
# include dependencies
#
########################################################################
########################################################################

# none




########################################################################
########################################################################
#
# library dependencies
#
########################################################################
########################################################################

lib: ranlib $(LIBRARIES)

ranlib:
	$(GET_FILES)

#	( cd $(LIBRARY_DIR) ; $(MAKE) $(MFLAGS) )

#
# The libraries.
#

libblimps.a: $(LIBOBJS)
	$(AR) cr $@ $(LIBOBJS) ; $(RANLIB) $@

########################################################################
########################################################################
#
# Local building (for us)
#
########################################################################
########################################################################

#  os = OS_machinename_version
local: clean clean-include clean-lib 
	echo " " ; \
	echo "Making directories..." ; \
	echo " " ; \
	os="`uname -sr | tr ' ' '_'`" ; \
	osdir="../$$os" ; \
	rm -rf $$osdir ; \
	mkdir $$osdir $$osdir/bin $$osdir/include $$osdir/lib ; \
	echo " " ; \
	echo "Running 'make depend' and 'make all'..." ; \
	echo " " ; \
	make depend ; make all	; \
	echo " " ; \
	echo "Copying libraries..." ; \
	echo " " ; \
	cp ../lib/*.a $$osdir/lib ; \
	echo " " ; \
	echo "Copying header files..." ; \
	echo " " ; \
	cp ../include/*.h $$osdir/include ; \
	echo " " ; \
	echo "Copying binary..." ; \
	echo " " ; \
	cp blimps $$osdir/bin





########################################################################
########################################################################
#
# Maintenance dependencies
#
########################################################################
########################################################################


tags: 
	etags ./*.[ch] $(INCLUDE_DIR)/*.[ch]


depend: 
	 $(DEPEND) -- $(CFLAGS) -- -s "# DO NOT DELETE" -- $(SRCS)


clean::
	$(RM) blimps blweight blalign bldist blk2pssm rank_matrix retblock codehop htmlize-codehop oligo_melt mablock makeblockmap prints2blocks lisblk coduse narrow blkprob blk2slx LAMA find_biassed_blocks fastaseqs addseqs cobbler interpro pssmdist pssmBL papssm matrix_logob makelogob blocks_search LAMA_search block_vis format_block biassed_blocks_finder htmlize-LAMA show_aligned_blocks makelis blk2mot 
	$(RM) *.a *.o *~ 
	@echo " "

move-lib:
	$(MV) lib*.a ../lib

move-bin:
	$(MV) blimps ../bin
	$(MV) blweight ../bin
	$(MV) blalign ../bin
	$(MV) bldist ../bin
	$(MV) blk2pssm ../bin
	$(MV) rank_matrix ../bin
	$(MV) retblock ../bin
	$(MV) codehop ../bin
	$(MV) htmlize-codehop ../bin
	$(MV) oligo_melt ../bin
	$(MV) mablock ../bin
	$(MV) makeblockmap ../bin
	$(MV) prints2blocks ../bin
	$(MV) lisblk ../bin
	$(MV) coduse ../bin
	$(MV) narrow ../bin
	$(MV) blkprob ../bin
	$(MV) blk2slx ../bin
	$(MV) LAMA ../bin
	$(MV) find_biassed_blocks ../bin
	$(MV) fastaseqs ../bin
	$(MV) addseqs ../bin
	$(MV) cobbler ../bin
#	$(MV) interpro ../bin
	$(MV) pssmdist ../bin
	$(MV) pssmBL ../bin
	$(MV) papssm ../bin
	$(MV) matrix_logob ../bin
	$(MV) makelogob ../bin
	$(MV) blocks_search ../bin
	$(MV) LAMA_search ../bin
	$(MV) block_vis ../bin
	$(MV) format_block ../bin
	$(MV) biassed_blocks_finder ../bin
	$(MV) htmlize-LAMA ../bin
	$(MV) show_aligned_blocks ../bin
	$(MV) makelis ../bin
	$(MV) blk2mot ../bin


##########
##########
#
# Distribution dependencies
#
##########
##########

SOURCEDIR  = /lab/billa/blimps/dev
BUILDDIR   = /lab/billa/blimps/build-local
DISTRIBDIR = /lab/billa/blimps/distrib
VERSIONDISTRIB = $(DISTRIBDIR).$(VERSION)
BLIMPSDIR  = $(DISTRIBDIR)/blimps
FTPDIR     = /lab/ftp/blimps

TXTVER = `echo  $(VERSION) | \
	 awk -F. '{printf("%d.%d%c", $$1, $$2 / 1000 , \
	 ( $$2 % 1000 ) / 100 + 65)}'`

#
# REMEMBER: each line executes in the directory make started in
#

local-binary: clean-local-binary
	@if [ "$(VERSION)" = "" ] ; then \
		echo "No version specified, bailing out." ; \
		echo "use as: make [ target ... ] VERSION=1.1001" ; \
		echo "    ex: make distrib VERSION=1.1001" ; \
		bail-out-here ; \
	fi
	
	@echo Building local binary for distribution . . .
	@echo " "
	
	@echo Making local build directory . . .
	@mkdir -p $(BUILDDIR)
	
	@echo Making blimps, lib, and include subdirectories . . .
	@mkdir -p $(BUILDDIR)/blimps
	@mkdir -p $(BUILDDIR)/lib
	@mkdir -p $(BUILDDIR)/include
	
	@echo Copying Makefiles over . . .
	@echo REMOVING RCS SUBDIR DEPENDENCY BY THE GREP > /dev/null
	@cat $(SOURCEDIR)/blimps/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BUILDDIR)/blimps/Makefile
	@cat $(SOURCEDIR)/lib/Makefile | grep -v 'RCS/\$$\$$\@,v' >    $(BUILDDIR)/lib/Makefile
	@cat $(SOURCEDIR)/include/Makefile | grep -v 'RCS/\$$\$$\@,v' >$(BUILDDIR)/include/Makefile
	
	@ln -s $(SOURCEDIR)/blimps/RCS  $(BUILDDIR)/blimps/RCS
	@ln -s $(SOURCEDIR)/lib/RCS     $(BUILDDIR)/lib/RCS
	@ln -s $(SOURCEDIR)/include/RCS $(BUILDDIR)/include/RCS
	
	@echo Making local version dependencies . . .
	cd $(BUILDDIR)/blimps ; make VERSION="$(VERSION)" clean ; make VERSION="$(VERSION)" depend 
	
	@echo Removing RCS files to test distrib compilation
	@rm -f $(BUILDDIR)/blimps/RCS
	@rm -f $(BUILDDIR)/lib/RCS
	@rm -f $(BUILDDIR)/include/RCS
	
	@echo Making local version . . .
	cd $(BUILDDIR)/blimps ; make VERSION="$(VERSION)" blimps
	
	@echo Moving local binary into distribution directory . . .
	@mv $(BUILDDIR)/blimps/blimps $(SOURCEDIR)/bin/blimps.$(SYSTEM)
	@echo " "

clean-local-binary:
	@echo Cleaning local build directory \($(BUILDDIR)\) . . .
	rm -rf $(BUILDDIR)
	@echo " "


distrib: local-binary clean-distrib
	@if [ "$(VERSION)" = "" ] ; then \
		echo "No version specified, bailing out." ; \
		echo "use as: make [ target ... ] VERSION=1.1001" ; \
		echo "    ex: make distrib VERSION=1.1001" ; \
		bail-out-here ; \
	fi
	
	@echo Making distribution . . .
	@echo " "
	
	@echo Making distribution directories . . .
	@mkdir -p $(DISTRIBDIR)
	@mkdir -p $(BLIMPSDIR) \
		  $(BLIMPSDIR)/docs \
		  $(BLIMPSDIR)/blimps \
		  $(BLIMPSDIR)/lib \
		  $(BLIMPSDIR)/include \
		  $(BLIMPSDIR)/bin
	@ln -s $(SOURCEDIR)/blimps/RCS  $(BLIMPSDIR)/blimps/RCS
	@ln -s $(SOURCEDIR)/lib/RCS     $(BLIMPSDIR)/lib/RCS
	@ln -s $(SOURCEDIR)/include/RCS $(BLIMPSDIR)/include/RCS
	@ln -s $(SOURCEDIR)/docs/RCS    $(BLIMPSDIR)/docs/RCS
	
	@echo Copying Makefiles over . . .
	@cat $(SOURCEDIR)/blimps/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BLIMPSDIR)/blimps/Makefile
	@cat $(SOURCEDIR)/lib/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BLIMPSDIR)/lib/Makefile
	@cat $(SOURCEDIR)/include/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BLIMPSDIR)/include/Makefile
	
	@echo Making depend on the Makefiles to checkout the files
	cd $(BLIMPSDIR)/blimps ; make VERSION="$(VERSION)" depend
	@rm -f $(BLIMPSDIR)/blimps/RCS
	@rm -f $(BLIMPSDIR)/lib/RCS
	@rm -f $(BLIMPSDIR)/include/RCS
	
	@echo Copying distribution documents of version $(VERSION) into docs directory . . .
	@cd $(BLIMPSDIR)/docs ; co -q -r$(VERSION) RCS/*
	@rm -f $(BLIMPSDIR)/docs/RCS
	@cd $(BLIMPSDIR)/docs ; cp README INSTALL ..
	
	@echo Copying pre-compiled binaries into bin directory . . .
	@cp $(SOURCEDIR)/bin/* $(BLIMPSDIR)/bin/
	
	@echo Moving blimps to blimps.$(TXTVER)
	@mv $(BLIMPSDIR) $(DISTRIBDIR)/blimps.$(TXTVER)
	@echo " "
	
	@echo Making tar file . . .
	@cd $(DISTRIBDIR) ; tar cf blimps.$(TXTVER).tar blimps.$(TXTVER)
	
	@echo Compressing tar file . . .
	@cd $(DISTRIBDIR) ; compress blimps.$(TXTVER).tar
	@echo " "
	
	@echo Moving distrib dir to distrib.$(VERSION)
	@mv $(DISTRIBDIR) $(VERSIONDISTRIB)

clean-distrib:
	@echo  Cleaning distribution directories:
	@echo "     $(DISTRIBDIR)"
	@echo "     $(VERSIONDISTRIB)"
	@echo " . . . "
	rm -rf $(DISTRIBDIR) $(VERSIONDISTRIB)
	@echo " "

$(VERSIONDISTRIB):	distrib

ftp:	$(VERSIONDISTRIB)
	@echo Moving files to the ftp directory . . .
	@echo " "
	
	@echo Copying tar file to the ftp directory . . .
	@cp $(VERSIONDISTRIB)/blimps.$(TXTVER).tar.Z $(FTPDIR)
	@echo " "
	
	@echo Copying README and INSTALL files to the ftp directory . . .
	@rm -f $(FTPDIR)/README $(FTPDIR)/INSTALL 
	@cp $(VERSIONDISTRIB)/blimps.$(TXTVER)/docs/README \
	  $(VERSIONDISTRIB)/blimps.$(TXTVER)/docs/INSTALL $(FTPDIR)
	@echo " "



###########################################################################

 
###########################################################################
# dependencies generated by makedepend
 
# DO NOT DELETE

blimps-mem.o: ../include/global.h /usr/include/stdlib.h
blimps-mem.o: /usr/include/sys/cdefs.h /usr/include/_types.h
blimps-mem.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
blimps-mem.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
blimps-mem.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
blimps-mem.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
blimps-mem.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
blimps-mem.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
blimps-mem.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
blimps-mem.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
blimps-mem.o: /usr/include/machine/types.h /usr/include/ppc/types.h
blimps-mem.o: /usr/include/stdio.h /usr/include/string.h
blimps-mem.o: /usr/include/stddef.h /usr/include/ctype.h
blimps-mem.o: /usr/include/runetype.h /usr/include/malloc/malloc.h
blimps-mem.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
blimps-mem.o: /usr/include/mach/message.h /usr/include/mach/port.h
blimps-mem.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
blimps-mem.o: /usr/include/mach/ppc/boolean.h
blimps-mem.o: /usr/include/mach/machine/vm_types.h
blimps-mem.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
blimps-mem.o: /usr/include/mach/kern_return.h
blimps-mem.o: /usr/include/mach/machine/kern_return.h
blimps-mem.o: /usr/include/mach/ppc/kern_return.h
blimps-mem.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
blimps-mem.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
blimps-mem.o: /usr/include/mach/host_special_ports.h
blimps-mem.o: /usr/include/mach/memory_object_types.h
blimps-mem.o: /usr/include/mach/vm_types.h
blimps-mem.o: /usr/include/mach/exception_types.h
blimps-mem.o: /usr/include/mach/machine/exception.h
blimps-mem.o: /usr/include/mach/ppc/exception.h
blimps-mem.o: /usr/include/mach/thread_status.h
blimps-mem.o: /usr/include/mach/machine/thread_status.h
blimps-mem.o: /usr/include/mach/ppc/thread_status.h
blimps-mem.o: /usr/include/mach/ppc/_types.h
blimps-mem.o: /usr/include/mach/machine/thread_state.h
blimps-mem.o: /usr/include/mach/ppc/thread_state.h
blimps-mem.o: /usr/include/mach/processor_info.h
blimps-mem.o: /usr/include/mach/machine/processor_info.h
blimps-mem.o: /usr/include/mach/ppc/processor_info.h
blimps-mem.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
blimps-mem.o: /usr/include/mach/task_policy.h
blimps-mem.o: /usr/include/mach/task_special_ports.h
blimps-mem.o: /usr/include/mach/thread_info.h
blimps-mem.o: /usr/include/mach/thread_policy.h
blimps-mem.o: /usr/include/mach/thread_special_ports.h
blimps-mem.o: /usr/include/mach/clock_types.h
blimps-mem.o: /usr/include/mach/vm_attributes.h
blimps-mem.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
blimps-mem.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
blimps-mem.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
blimps-mem.o: /usr/include/mach/machine/vm_param.h
blimps-mem.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
blimps-mem.o: /usr/include/mach/std_types.h ../include/license.h
blimps-mem.o: ../include/strutil.h ../include/errors.h ../include/memory.h
blimps-mem.o: blimps-mem.h blimps.h lists.h ../include/skiplist.h
blimps.o: /usr/include/math.h /usr/include/architecture/ppc/math.h
blimps.o: /usr/include/sys/cdefs.h /usr/include/signal.h
blimps.o: /usr/include/_types.h /usr/include/sys/_types.h
blimps.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
blimps.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
blimps.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
blimps.o: ../include/global.h /usr/include/stdlib.h /usr/include/sys/wait.h
blimps.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
blimps.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
blimps.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
blimps.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
blimps.o: /usr/include/machine/types.h /usr/include/ppc/types.h
blimps.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
blimps.o: /usr/include/ctype.h /usr/include/runetype.h
blimps.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
blimps.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
blimps.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
blimps.o: /usr/include/mach/machine/boolean.h /usr/include/mach/ppc/boolean.h
blimps.o: /usr/include/mach/machine/vm_types.h
blimps.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
blimps.o: /usr/include/mach/kern_return.h
blimps.o: /usr/include/mach/machine/kern_return.h
blimps.o: /usr/include/mach/ppc/kern_return.h
blimps.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
blimps.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
blimps.o: /usr/include/mach/host_special_ports.h
blimps.o: /usr/include/mach/memory_object_types.h
blimps.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
blimps.o: /usr/include/mach/machine/exception.h
blimps.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
blimps.o: /usr/include/mach/machine/thread_status.h
blimps.o: /usr/include/mach/ppc/thread_status.h
blimps.o: /usr/include/mach/ppc/_types.h
blimps.o: /usr/include/mach/machine/thread_state.h
blimps.o: /usr/include/mach/ppc/thread_state.h
blimps.o: /usr/include/mach/processor_info.h
blimps.o: /usr/include/mach/machine/processor_info.h
blimps.o: /usr/include/mach/ppc/processor_info.h
blimps.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
blimps.o: /usr/include/mach/task_policy.h
blimps.o: /usr/include/mach/task_special_ports.h
blimps.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
blimps.o: /usr/include/mach/thread_special_ports.h
blimps.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
blimps.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
blimps.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
blimps.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
blimps.o: /usr/include/mach/machine/vm_param.h
blimps.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
blimps.o: /usr/include/mach/std_types.h ../include/license.h
blimps.o: ../include/strutil.h ../include/errors.h ../include/memory.h
blimps.o: ../include/version.h ../include/residues.h ../include/blastapp.h
blimps.o: /usr/include/limits.h /usr/include/machine/limits.h
blimps.o: /usr/include/ppc/limits.h /usr/include/ppc/_limits.h
blimps.o: /usr/include/sys/syslimits.h ../include/alphabet.h
blimps.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
blimps.o: ../include/files.h ../include/blocks.h ../include/output.h
blimps.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blimps.o: ../include/convert.h ../include/frequency.h ../include/options.h
blimps.o: blimps.h blimps-mem.h config.h scores.h scoring.h lists.h
blimps.o: ../include/skiplist.h
blweight.o: ../include/blocksprogs.h /usr/include/stdlib.h
blweight.o: /usr/include/sys/cdefs.h /usr/include/_types.h
blweight.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
blweight.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
blweight.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
blweight.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
blweight.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
blweight.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
blweight.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
blweight.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
blweight.o: /usr/include/machine/types.h /usr/include/ppc/types.h
blweight.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
blweight.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
blweight.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
blweight.o: /usr/include/sys/types.h /usr/include/signal.h
blweight.o: /usr/include/sys/time.h /usr/include/time.h
blweight.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
blweight.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
blweight.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
blweight.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
blweight.o: /usr/include/mach/message.h /usr/include/mach/port.h
blweight.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
blweight.o: /usr/include/mach/ppc/boolean.h
blweight.o: /usr/include/mach/machine/vm_types.h
blweight.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
blweight.o: /usr/include/mach/kern_return.h
blweight.o: /usr/include/mach/machine/kern_return.h
blweight.o: /usr/include/mach/ppc/kern_return.h
blweight.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
blweight.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
blweight.o: /usr/include/mach/host_special_ports.h
blweight.o: /usr/include/mach/memory_object_types.h
blweight.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
blweight.o: /usr/include/mach/machine/exception.h
blweight.o: /usr/include/mach/ppc/exception.h
blweight.o: /usr/include/mach/thread_status.h
blweight.o: /usr/include/mach/machine/thread_status.h
blweight.o: /usr/include/mach/ppc/thread_status.h
blweight.o: /usr/include/mach/ppc/_types.h
blweight.o: /usr/include/mach/machine/thread_state.h
blweight.o: /usr/include/mach/ppc/thread_state.h
blweight.o: /usr/include/mach/processor_info.h
blweight.o: /usr/include/mach/machine/processor_info.h
blweight.o: /usr/include/mach/ppc/processor_info.h
blweight.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
blweight.o: /usr/include/mach/task_policy.h
blweight.o: /usr/include/mach/task_special_ports.h
blweight.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
blweight.o: /usr/include/mach/thread_special_ports.h
blweight.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
blweight.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
blweight.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
blweight.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
blweight.o: /usr/include/mach/machine/vm_param.h
blweight.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
blweight.o: /usr/include/mach/std_types.h ../include/license.h
blweight.o: ../include/strutil.h ../include/errors.h ../include/memory.h
blweight.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
blweight.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
blweight.o: /usr/include/sys/syslimits.h ../include/alphabet.h
blweight.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
blweight.o: ../include/blocks.h ../include/output.h ../include/sequences.h
blweight.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
blweight.o: ../include/frequency.h ../include/files.h ../include/protomat.h
blalign.o: ../include/blocksprogs.h /usr/include/stdlib.h
blalign.o: /usr/include/sys/cdefs.h /usr/include/_types.h
blalign.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
blalign.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
blalign.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
blalign.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
blalign.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
blalign.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
blalign.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
blalign.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
blalign.o: /usr/include/machine/types.h /usr/include/ppc/types.h
blalign.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
blalign.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
blalign.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
blalign.o: /usr/include/sys/types.h /usr/include/signal.h
blalign.o: /usr/include/sys/time.h /usr/include/time.h
blalign.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
blalign.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
blalign.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
blalign.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
blalign.o: /usr/include/mach/message.h /usr/include/mach/port.h
blalign.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
blalign.o: /usr/include/mach/ppc/boolean.h
blalign.o: /usr/include/mach/machine/vm_types.h
blalign.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
blalign.o: /usr/include/mach/kern_return.h
blalign.o: /usr/include/mach/machine/kern_return.h
blalign.o: /usr/include/mach/ppc/kern_return.h
blalign.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
blalign.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
blalign.o: /usr/include/mach/host_special_ports.h
blalign.o: /usr/include/mach/memory_object_types.h
blalign.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
blalign.o: /usr/include/mach/machine/exception.h
blalign.o: /usr/include/mach/ppc/exception.h
blalign.o: /usr/include/mach/thread_status.h
blalign.o: /usr/include/mach/machine/thread_status.h
blalign.o: /usr/include/mach/ppc/thread_status.h
blalign.o: /usr/include/mach/ppc/_types.h
blalign.o: /usr/include/mach/machine/thread_state.h
blalign.o: /usr/include/mach/ppc/thread_state.h
blalign.o: /usr/include/mach/processor_info.h
blalign.o: /usr/include/mach/machine/processor_info.h
blalign.o: /usr/include/mach/ppc/processor_info.h
blalign.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
blalign.o: /usr/include/mach/task_policy.h
blalign.o: /usr/include/mach/task_special_ports.h
blalign.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
blalign.o: /usr/include/mach/thread_special_ports.h
blalign.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
blalign.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
blalign.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
blalign.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
blalign.o: /usr/include/mach/machine/vm_param.h
blalign.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
blalign.o: /usr/include/mach/std_types.h ../include/license.h
blalign.o: ../include/strutil.h ../include/errors.h ../include/memory.h
blalign.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
blalign.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
blalign.o: /usr/include/sys/syslimits.h ../include/alphabet.h
blalign.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
blalign.o: ../include/blocks.h ../include/output.h ../include/sequences.h
blalign.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
blalign.o: ../include/frequency.h ../include/files.h ../include/protomat.h
bldist.o: ../include/blocksprogs.h /usr/include/stdlib.h
bldist.o: /usr/include/sys/cdefs.h /usr/include/_types.h
bldist.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
bldist.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
bldist.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
bldist.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
bldist.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
bldist.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
bldist.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
bldist.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
bldist.o: /usr/include/machine/types.h /usr/include/ppc/types.h
bldist.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
bldist.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
bldist.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
bldist.o: /usr/include/sys/types.h /usr/include/signal.h
bldist.o: /usr/include/sys/time.h /usr/include/time.h
bldist.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
bldist.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
bldist.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
bldist.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
bldist.o: /usr/include/mach/message.h /usr/include/mach/port.h
bldist.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
bldist.o: /usr/include/mach/ppc/boolean.h
bldist.o: /usr/include/mach/machine/vm_types.h
bldist.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
bldist.o: /usr/include/mach/kern_return.h
bldist.o: /usr/include/mach/machine/kern_return.h
bldist.o: /usr/include/mach/ppc/kern_return.h
bldist.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
bldist.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
bldist.o: /usr/include/mach/host_special_ports.h
bldist.o: /usr/include/mach/memory_object_types.h
bldist.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
bldist.o: /usr/include/mach/machine/exception.h
bldist.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
bldist.o: /usr/include/mach/machine/thread_status.h
bldist.o: /usr/include/mach/ppc/thread_status.h
bldist.o: /usr/include/mach/ppc/_types.h
bldist.o: /usr/include/mach/machine/thread_state.h
bldist.o: /usr/include/mach/ppc/thread_state.h
bldist.o: /usr/include/mach/processor_info.h
bldist.o: /usr/include/mach/machine/processor_info.h
bldist.o: /usr/include/mach/ppc/processor_info.h
bldist.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
bldist.o: /usr/include/mach/task_policy.h
bldist.o: /usr/include/mach/task_special_ports.h
bldist.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
bldist.o: /usr/include/mach/thread_special_ports.h
bldist.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
bldist.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
bldist.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
bldist.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
bldist.o: /usr/include/mach/machine/vm_param.h
bldist.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
bldist.o: /usr/include/mach/std_types.h ../include/license.h
bldist.o: ../include/strutil.h ../include/errors.h ../include/memory.h
bldist.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
bldist.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
bldist.o: /usr/include/sys/syslimits.h ../include/alphabet.h
bldist.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
bldist.o: ../include/blocks.h ../include/output.h ../include/sequences.h
bldist.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
bldist.o: ../include/frequency.h ../include/files.h ../include/protomat.h
blk2pssm.o: ../include/blocksprogs.h /usr/include/stdlib.h
blk2pssm.o: /usr/include/sys/cdefs.h /usr/include/_types.h
blk2pssm.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
blk2pssm.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
blk2pssm.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
blk2pssm.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
blk2pssm.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
blk2pssm.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
blk2pssm.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
blk2pssm.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
blk2pssm.o: /usr/include/machine/types.h /usr/include/ppc/types.h
blk2pssm.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
blk2pssm.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
blk2pssm.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
blk2pssm.o: /usr/include/sys/types.h /usr/include/signal.h
blk2pssm.o: /usr/include/sys/time.h /usr/include/time.h
blk2pssm.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
blk2pssm.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
blk2pssm.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
blk2pssm.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
blk2pssm.o: /usr/include/mach/message.h /usr/include/mach/port.h
blk2pssm.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
blk2pssm.o: /usr/include/mach/ppc/boolean.h
blk2pssm.o: /usr/include/mach/machine/vm_types.h
blk2pssm.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
blk2pssm.o: /usr/include/mach/kern_return.h
blk2pssm.o: /usr/include/mach/machine/kern_return.h
blk2pssm.o: /usr/include/mach/ppc/kern_return.h
blk2pssm.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
blk2pssm.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
blk2pssm.o: /usr/include/mach/host_special_ports.h
blk2pssm.o: /usr/include/mach/memory_object_types.h
blk2pssm.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
blk2pssm.o: /usr/include/mach/machine/exception.h
blk2pssm.o: /usr/include/mach/ppc/exception.h
blk2pssm.o: /usr/include/mach/thread_status.h
blk2pssm.o: /usr/include/mach/machine/thread_status.h
blk2pssm.o: /usr/include/mach/ppc/thread_status.h
blk2pssm.o: /usr/include/mach/ppc/_types.h
blk2pssm.o: /usr/include/mach/machine/thread_state.h
blk2pssm.o: /usr/include/mach/ppc/thread_state.h
blk2pssm.o: /usr/include/mach/processor_info.h
blk2pssm.o: /usr/include/mach/machine/processor_info.h
blk2pssm.o: /usr/include/mach/ppc/processor_info.h
blk2pssm.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
blk2pssm.o: /usr/include/mach/task_policy.h
blk2pssm.o: /usr/include/mach/task_special_ports.h
blk2pssm.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
blk2pssm.o: /usr/include/mach/thread_special_ports.h
blk2pssm.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
blk2pssm.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
blk2pssm.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
blk2pssm.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
blk2pssm.o: /usr/include/mach/machine/vm_param.h
blk2pssm.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
blk2pssm.o: /usr/include/mach/std_types.h ../include/license.h
blk2pssm.o: ../include/strutil.h ../include/errors.h ../include/memory.h
blk2pssm.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
blk2pssm.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
blk2pssm.o: /usr/include/sys/syslimits.h ../include/alphabet.h
blk2pssm.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
blk2pssm.o: ../include/blocks.h ../include/output.h ../include/sequences.h
blk2pssm.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
blk2pssm.o: ../include/frequency.h ../include/files.h ../include/protomat.h
rank_matrix.o: ../include/blocksprogs.h /usr/include/stdlib.h
rank_matrix.o: /usr/include/sys/cdefs.h /usr/include/_types.h
rank_matrix.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
rank_matrix.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
rank_matrix.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
rank_matrix.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
rank_matrix.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
rank_matrix.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
rank_matrix.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
rank_matrix.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
rank_matrix.o: /usr/include/machine/types.h /usr/include/ppc/types.h
rank_matrix.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
rank_matrix.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
rank_matrix.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
rank_matrix.o: /usr/include/sys/types.h /usr/include/signal.h
rank_matrix.o: /usr/include/sys/time.h /usr/include/time.h
rank_matrix.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
rank_matrix.o: /usr/include/ctype.h /usr/include/runetype.h
rank_matrix.o: ../include/global.h /usr/include/stddef.h
rank_matrix.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
rank_matrix.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
rank_matrix.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
rank_matrix.o: /usr/include/mach/machine/boolean.h
rank_matrix.o: /usr/include/mach/ppc/boolean.h
rank_matrix.o: /usr/include/mach/machine/vm_types.h
rank_matrix.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
rank_matrix.o: /usr/include/mach/kern_return.h
rank_matrix.o: /usr/include/mach/machine/kern_return.h
rank_matrix.o: /usr/include/mach/ppc/kern_return.h
rank_matrix.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
rank_matrix.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
rank_matrix.o: /usr/include/mach/host_special_ports.h
rank_matrix.o: /usr/include/mach/memory_object_types.h
rank_matrix.o: /usr/include/mach/vm_types.h
rank_matrix.o: /usr/include/mach/exception_types.h
rank_matrix.o: /usr/include/mach/machine/exception.h
rank_matrix.o: /usr/include/mach/ppc/exception.h
rank_matrix.o: /usr/include/mach/thread_status.h
rank_matrix.o: /usr/include/mach/machine/thread_status.h
rank_matrix.o: /usr/include/mach/ppc/thread_status.h
rank_matrix.o: /usr/include/mach/ppc/_types.h
rank_matrix.o: /usr/include/mach/machine/thread_state.h
rank_matrix.o: /usr/include/mach/ppc/thread_state.h
rank_matrix.o: /usr/include/mach/processor_info.h
rank_matrix.o: /usr/include/mach/machine/processor_info.h
rank_matrix.o: /usr/include/mach/ppc/processor_info.h
rank_matrix.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
rank_matrix.o: /usr/include/mach/task_policy.h
rank_matrix.o: /usr/include/mach/task_special_ports.h
rank_matrix.o: /usr/include/mach/thread_info.h
rank_matrix.o: /usr/include/mach/thread_policy.h
rank_matrix.o: /usr/include/mach/thread_special_ports.h
rank_matrix.o: /usr/include/mach/clock_types.h
rank_matrix.o: /usr/include/mach/vm_attributes.h
rank_matrix.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
rank_matrix.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
rank_matrix.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
rank_matrix.o: /usr/include/mach/machine/vm_param.h
rank_matrix.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
rank_matrix.o: /usr/include/mach/std_types.h ../include/license.h
rank_matrix.o: ../include/strutil.h ../include/errors.h ../include/memory.h
rank_matrix.o: ../include/residues.h ../include/blastapp.h
rank_matrix.o: /usr/include/limits.h /usr/include/machine/limits.h
rank_matrix.o: /usr/include/ppc/limits.h /usr/include/sys/syslimits.h
rank_matrix.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
rank_matrix.o: ../include/gcode.h ../include/blocks.h ../include/output.h
rank_matrix.o: ../include/sequences.h ../include/matrix.h
rank_matrix.o: ../include/pattern.h ../include/convert.h
rank_matrix.o: ../include/frequency.h ../include/files.h
rank_matrix.o: ../include/protomat.h
retblock.o: ../include/blocksprogs.h /usr/include/stdlib.h
retblock.o: /usr/include/sys/cdefs.h /usr/include/_types.h
retblock.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
retblock.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
retblock.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
retblock.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
retblock.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
retblock.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
retblock.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
retblock.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
retblock.o: /usr/include/machine/types.h /usr/include/ppc/types.h
retblock.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
retblock.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
retblock.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
retblock.o: /usr/include/sys/types.h /usr/include/signal.h
retblock.o: /usr/include/sys/time.h /usr/include/time.h
retblock.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
retblock.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
retblock.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
retblock.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
retblock.o: /usr/include/mach/message.h /usr/include/mach/port.h
retblock.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
retblock.o: /usr/include/mach/ppc/boolean.h
retblock.o: /usr/include/mach/machine/vm_types.h
retblock.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
retblock.o: /usr/include/mach/kern_return.h
retblock.o: /usr/include/mach/machine/kern_return.h
retblock.o: /usr/include/mach/ppc/kern_return.h
retblock.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
retblock.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
retblock.o: /usr/include/mach/host_special_ports.h
retblock.o: /usr/include/mach/memory_object_types.h
retblock.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
retblock.o: /usr/include/mach/machine/exception.h
retblock.o: /usr/include/mach/ppc/exception.h
retblock.o: /usr/include/mach/thread_status.h
retblock.o: /usr/include/mach/machine/thread_status.h
retblock.o: /usr/include/mach/ppc/thread_status.h
retblock.o: /usr/include/mach/ppc/_types.h
retblock.o: /usr/include/mach/machine/thread_state.h
retblock.o: /usr/include/mach/ppc/thread_state.h
retblock.o: /usr/include/mach/processor_info.h
retblock.o: /usr/include/mach/machine/processor_info.h
retblock.o: /usr/include/mach/ppc/processor_info.h
retblock.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
retblock.o: /usr/include/mach/task_policy.h
retblock.o: /usr/include/mach/task_special_ports.h
retblock.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
retblock.o: /usr/include/mach/thread_special_ports.h
retblock.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
retblock.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
retblock.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
retblock.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
retblock.o: /usr/include/mach/machine/vm_param.h
retblock.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
retblock.o: /usr/include/mach/std_types.h ../include/license.h
retblock.o: ../include/strutil.h ../include/errors.h ../include/memory.h
retblock.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
retblock.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
retblock.o: /usr/include/sys/syslimits.h ../include/alphabet.h
retblock.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
retblock.o: ../include/blocks.h ../include/output.h ../include/sequences.h
retblock.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
retblock.o: ../include/frequency.h ../include/files.h ../include/protomat.h
codehop.o: ../include/blocksprogs.h /usr/include/stdlib.h
codehop.o: /usr/include/sys/cdefs.h /usr/include/_types.h
codehop.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
codehop.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
codehop.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
codehop.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
codehop.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
codehop.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
codehop.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
codehop.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
codehop.o: /usr/include/machine/types.h /usr/include/ppc/types.h
codehop.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
codehop.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
codehop.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
codehop.o: /usr/include/sys/types.h /usr/include/signal.h
codehop.o: /usr/include/sys/time.h /usr/include/time.h
codehop.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
codehop.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
codehop.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
codehop.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
codehop.o: /usr/include/mach/message.h /usr/include/mach/port.h
codehop.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
codehop.o: /usr/include/mach/ppc/boolean.h
codehop.o: /usr/include/mach/machine/vm_types.h
codehop.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
codehop.o: /usr/include/mach/kern_return.h
codehop.o: /usr/include/mach/machine/kern_return.h
codehop.o: /usr/include/mach/ppc/kern_return.h
codehop.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
codehop.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
codehop.o: /usr/include/mach/host_special_ports.h
codehop.o: /usr/include/mach/memory_object_types.h
codehop.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
codehop.o: /usr/include/mach/machine/exception.h
codehop.o: /usr/include/mach/ppc/exception.h
codehop.o: /usr/include/mach/thread_status.h
codehop.o: /usr/include/mach/machine/thread_status.h
codehop.o: /usr/include/mach/ppc/thread_status.h
codehop.o: /usr/include/mach/ppc/_types.h
codehop.o: /usr/include/mach/machine/thread_state.h
codehop.o: /usr/include/mach/ppc/thread_state.h
codehop.o: /usr/include/mach/processor_info.h
codehop.o: /usr/include/mach/machine/processor_info.h
codehop.o: /usr/include/mach/ppc/processor_info.h
codehop.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
codehop.o: /usr/include/mach/task_policy.h
codehop.o: /usr/include/mach/task_special_ports.h
codehop.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
codehop.o: /usr/include/mach/thread_special_ports.h
codehop.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
codehop.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
codehop.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
codehop.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
codehop.o: /usr/include/mach/machine/vm_param.h
codehop.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
codehop.o: /usr/include/mach/std_types.h ../include/license.h
codehop.o: ../include/strutil.h ../include/errors.h ../include/memory.h
codehop.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
codehop.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
codehop.o: /usr/include/sys/syslimits.h ../include/alphabet.h
codehop.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
codehop.o: ../include/blocks.h ../include/output.h ../include/sequences.h
codehop.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
codehop.o: ../include/frequency.h ../include/files.h ../include/protomat.h
codehop.o: codehop.h
htmlize-codehop.o: /usr/include/stdio.h /usr/include/_types.h
htmlize-codehop.o: /usr/include/sys/_types.h /usr/include/sys/cdefs.h
htmlize-codehop.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
htmlize-codehop.o: /usr/include/string.h /usr/include/stdlib.h
htmlize-codehop.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
htmlize-codehop.o: /usr/include/sys/appleapiopts.h
htmlize-codehop.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
htmlize-codehop.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
htmlize-codehop.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
htmlize-codehop.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
htmlize-codehop.o: /usr/include/libkern/ppc/OSByteOrder.h
htmlize-codehop.o: /usr/include/alloca.h /usr/include/machine/types.h
htmlize-codehop.o: /usr/include/ppc/types.h
oligo_melt.o: ../include/blocksprogs.h /usr/include/stdlib.h
oligo_melt.o: /usr/include/sys/cdefs.h /usr/include/_types.h
oligo_melt.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
oligo_melt.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
oligo_melt.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
oligo_melt.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
oligo_melt.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
oligo_melt.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
oligo_melt.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
oligo_melt.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
oligo_melt.o: /usr/include/machine/types.h /usr/include/ppc/types.h
oligo_melt.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
oligo_melt.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
oligo_melt.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
oligo_melt.o: /usr/include/sys/types.h /usr/include/signal.h
oligo_melt.o: /usr/include/sys/time.h /usr/include/time.h
oligo_melt.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
oligo_melt.o: /usr/include/ctype.h /usr/include/runetype.h
oligo_melt.o: ../include/global.h /usr/include/stddef.h
oligo_melt.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
oligo_melt.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
oligo_melt.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
oligo_melt.o: /usr/include/mach/machine/boolean.h
oligo_melt.o: /usr/include/mach/ppc/boolean.h
oligo_melt.o: /usr/include/mach/machine/vm_types.h
oligo_melt.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
oligo_melt.o: /usr/include/mach/kern_return.h
oligo_melt.o: /usr/include/mach/machine/kern_return.h
oligo_melt.o: /usr/include/mach/ppc/kern_return.h
oligo_melt.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
oligo_melt.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
oligo_melt.o: /usr/include/mach/host_special_ports.h
oligo_melt.o: /usr/include/mach/memory_object_types.h
oligo_melt.o: /usr/include/mach/vm_types.h
oligo_melt.o: /usr/include/mach/exception_types.h
oligo_melt.o: /usr/include/mach/machine/exception.h
oligo_melt.o: /usr/include/mach/ppc/exception.h
oligo_melt.o: /usr/include/mach/thread_status.h
oligo_melt.o: /usr/include/mach/machine/thread_status.h
oligo_melt.o: /usr/include/mach/ppc/thread_status.h
oligo_melt.o: /usr/include/mach/ppc/_types.h
oligo_melt.o: /usr/include/mach/machine/thread_state.h
oligo_melt.o: /usr/include/mach/ppc/thread_state.h
oligo_melt.o: /usr/include/mach/processor_info.h
oligo_melt.o: /usr/include/mach/machine/processor_info.h
oligo_melt.o: /usr/include/mach/ppc/processor_info.h
oligo_melt.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
oligo_melt.o: /usr/include/mach/task_policy.h
oligo_melt.o: /usr/include/mach/task_special_ports.h
oligo_melt.o: /usr/include/mach/thread_info.h
oligo_melt.o: /usr/include/mach/thread_policy.h
oligo_melt.o: /usr/include/mach/thread_special_ports.h
oligo_melt.o: /usr/include/mach/clock_types.h
oligo_melt.o: /usr/include/mach/vm_attributes.h
oligo_melt.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
oligo_melt.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
oligo_melt.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
oligo_melt.o: /usr/include/mach/machine/vm_param.h
oligo_melt.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
oligo_melt.o: /usr/include/mach/std_types.h ../include/license.h
oligo_melt.o: ../include/strutil.h ../include/errors.h ../include/memory.h
oligo_melt.o: ../include/residues.h ../include/blastapp.h
oligo_melt.o: /usr/include/limits.h /usr/include/machine/limits.h
oligo_melt.o: /usr/include/ppc/limits.h /usr/include/sys/syslimits.h
oligo_melt.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
oligo_melt.o: ../include/gcode.h ../include/blocks.h ../include/output.h
oligo_melt.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
oligo_melt.o: ../include/convert.h ../include/frequency.h ../include/files.h
oligo_melt.o: ../include/protomat.h
mablock.o: ../include/blocksprogs.h /usr/include/stdlib.h
mablock.o: /usr/include/sys/cdefs.h /usr/include/_types.h
mablock.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
mablock.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
mablock.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
mablock.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
mablock.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
mablock.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
mablock.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
mablock.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
mablock.o: /usr/include/machine/types.h /usr/include/ppc/types.h
mablock.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
mablock.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
mablock.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
mablock.o: /usr/include/sys/types.h /usr/include/signal.h
mablock.o: /usr/include/sys/time.h /usr/include/time.h
mablock.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
mablock.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
mablock.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
mablock.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
mablock.o: /usr/include/mach/message.h /usr/include/mach/port.h
mablock.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
mablock.o: /usr/include/mach/ppc/boolean.h
mablock.o: /usr/include/mach/machine/vm_types.h
mablock.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
mablock.o: /usr/include/mach/kern_return.h
mablock.o: /usr/include/mach/machine/kern_return.h
mablock.o: /usr/include/mach/ppc/kern_return.h
mablock.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
mablock.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
mablock.o: /usr/include/mach/host_special_ports.h
mablock.o: /usr/include/mach/memory_object_types.h
mablock.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
mablock.o: /usr/include/mach/machine/exception.h
mablock.o: /usr/include/mach/ppc/exception.h
mablock.o: /usr/include/mach/thread_status.h
mablock.o: /usr/include/mach/machine/thread_status.h
mablock.o: /usr/include/mach/ppc/thread_status.h
mablock.o: /usr/include/mach/ppc/_types.h
mablock.o: /usr/include/mach/machine/thread_state.h
mablock.o: /usr/include/mach/ppc/thread_state.h
mablock.o: /usr/include/mach/processor_info.h
mablock.o: /usr/include/mach/machine/processor_info.h
mablock.o: /usr/include/mach/ppc/processor_info.h
mablock.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
mablock.o: /usr/include/mach/task_policy.h
mablock.o: /usr/include/mach/task_special_ports.h
mablock.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
mablock.o: /usr/include/mach/thread_special_ports.h
mablock.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
mablock.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
mablock.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
mablock.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
mablock.o: /usr/include/mach/machine/vm_param.h
mablock.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
mablock.o: /usr/include/mach/std_types.h ../include/license.h
mablock.o: ../include/strutil.h ../include/errors.h ../include/memory.h
mablock.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
mablock.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
mablock.o: /usr/include/sys/syslimits.h ../include/alphabet.h
mablock.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
mablock.o: ../include/blocks.h ../include/output.h ../include/sequences.h
mablock.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
mablock.o: ../include/frequency.h ../include/files.h ../include/protomat.h
cobbler.o: ../include/blocksprogs.h /usr/include/stdlib.h
cobbler.o: /usr/include/sys/cdefs.h /usr/include/_types.h
cobbler.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
cobbler.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
cobbler.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
cobbler.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
cobbler.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
cobbler.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
cobbler.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
cobbler.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
cobbler.o: /usr/include/machine/types.h /usr/include/ppc/types.h
cobbler.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
cobbler.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
cobbler.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
cobbler.o: /usr/include/sys/types.h /usr/include/signal.h
cobbler.o: /usr/include/sys/time.h /usr/include/time.h
cobbler.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
cobbler.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
cobbler.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
cobbler.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
cobbler.o: /usr/include/mach/message.h /usr/include/mach/port.h
cobbler.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
cobbler.o: /usr/include/mach/ppc/boolean.h
cobbler.o: /usr/include/mach/machine/vm_types.h
cobbler.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
cobbler.o: /usr/include/mach/kern_return.h
cobbler.o: /usr/include/mach/machine/kern_return.h
cobbler.o: /usr/include/mach/ppc/kern_return.h
cobbler.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
cobbler.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
cobbler.o: /usr/include/mach/host_special_ports.h
cobbler.o: /usr/include/mach/memory_object_types.h
cobbler.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
cobbler.o: /usr/include/mach/machine/exception.h
cobbler.o: /usr/include/mach/ppc/exception.h
cobbler.o: /usr/include/mach/thread_status.h
cobbler.o: /usr/include/mach/machine/thread_status.h
cobbler.o: /usr/include/mach/ppc/thread_status.h
cobbler.o: /usr/include/mach/ppc/_types.h
cobbler.o: /usr/include/mach/machine/thread_state.h
cobbler.o: /usr/include/mach/ppc/thread_state.h
cobbler.o: /usr/include/mach/processor_info.h
cobbler.o: /usr/include/mach/machine/processor_info.h
cobbler.o: /usr/include/mach/ppc/processor_info.h
cobbler.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
cobbler.o: /usr/include/mach/task_policy.h
cobbler.o: /usr/include/mach/task_special_ports.h
cobbler.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
cobbler.o: /usr/include/mach/thread_special_ports.h
cobbler.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
cobbler.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
cobbler.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
cobbler.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
cobbler.o: /usr/include/mach/machine/vm_param.h
cobbler.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
cobbler.o: /usr/include/mach/std_types.h ../include/license.h
cobbler.o: ../include/strutil.h ../include/errors.h ../include/memory.h
cobbler.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
cobbler.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
cobbler.o: /usr/include/sys/syslimits.h ../include/alphabet.h
cobbler.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
cobbler.o: ../include/blocks.h ../include/output.h ../include/sequences.h
cobbler.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
cobbler.o: ../include/frequency.h ../include/files.h ../include/protomat.h
addseqs.o: ../include/blocksprogs.h /usr/include/stdlib.h
addseqs.o: /usr/include/sys/cdefs.h /usr/include/_types.h
addseqs.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
addseqs.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
addseqs.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
addseqs.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
addseqs.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
addseqs.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
addseqs.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
addseqs.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
addseqs.o: /usr/include/machine/types.h /usr/include/ppc/types.h
addseqs.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
addseqs.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
addseqs.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
addseqs.o: /usr/include/sys/types.h /usr/include/signal.h
addseqs.o: /usr/include/sys/time.h /usr/include/time.h
addseqs.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
addseqs.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
addseqs.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
addseqs.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
addseqs.o: /usr/include/mach/message.h /usr/include/mach/port.h
addseqs.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
addseqs.o: /usr/include/mach/ppc/boolean.h
addseqs.o: /usr/include/mach/machine/vm_types.h
addseqs.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
addseqs.o: /usr/include/mach/kern_return.h
addseqs.o: /usr/include/mach/machine/kern_return.h
addseqs.o: /usr/include/mach/ppc/kern_return.h
addseqs.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
addseqs.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
addseqs.o: /usr/include/mach/host_special_ports.h
addseqs.o: /usr/include/mach/memory_object_types.h
addseqs.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
addseqs.o: /usr/include/mach/machine/exception.h
addseqs.o: /usr/include/mach/ppc/exception.h
addseqs.o: /usr/include/mach/thread_status.h
addseqs.o: /usr/include/mach/machine/thread_status.h
addseqs.o: /usr/include/mach/ppc/thread_status.h
addseqs.o: /usr/include/mach/ppc/_types.h
addseqs.o: /usr/include/mach/machine/thread_state.h
addseqs.o: /usr/include/mach/ppc/thread_state.h
addseqs.o: /usr/include/mach/processor_info.h
addseqs.o: /usr/include/mach/machine/processor_info.h
addseqs.o: /usr/include/mach/ppc/processor_info.h
addseqs.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
addseqs.o: /usr/include/mach/task_policy.h
addseqs.o: /usr/include/mach/task_special_ports.h
addseqs.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
addseqs.o: /usr/include/mach/thread_special_ports.h
addseqs.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
addseqs.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
addseqs.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
addseqs.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
addseqs.o: /usr/include/mach/machine/vm_param.h
addseqs.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
addseqs.o: /usr/include/mach/std_types.h ../include/license.h
addseqs.o: ../include/strutil.h ../include/errors.h ../include/memory.h
addseqs.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
addseqs.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
addseqs.o: /usr/include/sys/syslimits.h ../include/alphabet.h
addseqs.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
addseqs.o: ../include/blocks.h ../include/output.h ../include/sequences.h
addseqs.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
addseqs.o: ../include/frequency.h ../include/files.h ../include/protomat.h
fastaseqs.o: ../include/blocksprogs.h /usr/include/stdlib.h
fastaseqs.o: /usr/include/sys/cdefs.h /usr/include/_types.h
fastaseqs.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
fastaseqs.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
fastaseqs.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
fastaseqs.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
fastaseqs.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
fastaseqs.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
fastaseqs.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
fastaseqs.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
fastaseqs.o: /usr/include/machine/types.h /usr/include/ppc/types.h
fastaseqs.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
fastaseqs.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
fastaseqs.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
fastaseqs.o: /usr/include/sys/types.h /usr/include/signal.h
fastaseqs.o: /usr/include/sys/time.h /usr/include/time.h
fastaseqs.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
fastaseqs.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
fastaseqs.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
fastaseqs.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
fastaseqs.o: /usr/include/mach/message.h /usr/include/mach/port.h
fastaseqs.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
fastaseqs.o: /usr/include/mach/ppc/boolean.h
fastaseqs.o: /usr/include/mach/machine/vm_types.h
fastaseqs.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
fastaseqs.o: /usr/include/mach/kern_return.h
fastaseqs.o: /usr/include/mach/machine/kern_return.h
fastaseqs.o: /usr/include/mach/ppc/kern_return.h
fastaseqs.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
fastaseqs.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
fastaseqs.o: /usr/include/mach/host_special_ports.h
fastaseqs.o: /usr/include/mach/memory_object_types.h
fastaseqs.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
fastaseqs.o: /usr/include/mach/machine/exception.h
fastaseqs.o: /usr/include/mach/ppc/exception.h
fastaseqs.o: /usr/include/mach/thread_status.h
fastaseqs.o: /usr/include/mach/machine/thread_status.h
fastaseqs.o: /usr/include/mach/ppc/thread_status.h
fastaseqs.o: /usr/include/mach/ppc/_types.h
fastaseqs.o: /usr/include/mach/machine/thread_state.h
fastaseqs.o: /usr/include/mach/ppc/thread_state.h
fastaseqs.o: /usr/include/mach/processor_info.h
fastaseqs.o: /usr/include/mach/machine/processor_info.h
fastaseqs.o: /usr/include/mach/ppc/processor_info.h
fastaseqs.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
fastaseqs.o: /usr/include/mach/task_policy.h
fastaseqs.o: /usr/include/mach/task_special_ports.h
fastaseqs.o: /usr/include/mach/thread_info.h
fastaseqs.o: /usr/include/mach/thread_policy.h
fastaseqs.o: /usr/include/mach/thread_special_ports.h
fastaseqs.o: /usr/include/mach/clock_types.h
fastaseqs.o: /usr/include/mach/vm_attributes.h /usr/include/mach/vm_inherit.h
fastaseqs.o: /usr/include/mach/vm_purgable.h /usr/include/mach/vm_behavior.h
fastaseqs.o: /usr/include/mach/vm_prot.h /usr/include/mach/vm_sync.h
fastaseqs.o: /usr/include/mach/vm_region.h
fastaseqs.o: /usr/include/mach/machine/vm_param.h
fastaseqs.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
fastaseqs.o: /usr/include/mach/std_types.h ../include/license.h
fastaseqs.o: ../include/strutil.h ../include/errors.h ../include/memory.h
fastaseqs.o: ../include/residues.h ../include/blastapp.h
fastaseqs.o: /usr/include/limits.h /usr/include/machine/limits.h
fastaseqs.o: /usr/include/ppc/limits.h /usr/include/sys/syslimits.h
fastaseqs.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
fastaseqs.o: ../include/gcode.h ../include/blocks.h ../include/output.h
fastaseqs.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
fastaseqs.o: ../include/convert.h ../include/frequency.h ../include/files.h
fastaseqs.o: ../include/protomat.h
LAMA.o: ../include/blocksprogs.h /usr/include/stdlib.h
LAMA.o: /usr/include/sys/cdefs.h /usr/include/_types.h
LAMA.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
LAMA.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
LAMA.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
LAMA.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
LAMA.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
LAMA.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
LAMA.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
LAMA.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
LAMA.o: /usr/include/machine/types.h /usr/include/ppc/types.h
LAMA.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
LAMA.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
LAMA.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
LAMA.o: /usr/include/sys/types.h /usr/include/signal.h
LAMA.o: /usr/include/sys/time.h /usr/include/time.h
LAMA.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
LAMA.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
LAMA.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
LAMA.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
LAMA.o: /usr/include/mach/message.h /usr/include/mach/port.h
LAMA.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
LAMA.o: /usr/include/mach/ppc/boolean.h /usr/include/mach/machine/vm_types.h
LAMA.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
LAMA.o: /usr/include/mach/kern_return.h
LAMA.o: /usr/include/mach/machine/kern_return.h
LAMA.o: /usr/include/mach/ppc/kern_return.h /usr/include/mach/vm_statistics.h
LAMA.o: /usr/include/mach/machine.h /usr/include/mach/time_value.h
LAMA.o: /usr/include/mach/host_notify.h
LAMA.o: /usr/include/mach/host_special_ports.h
LAMA.o: /usr/include/mach/memory_object_types.h /usr/include/mach/vm_types.h
LAMA.o: /usr/include/mach/exception_types.h
LAMA.o: /usr/include/mach/machine/exception.h
LAMA.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
LAMA.o: /usr/include/mach/machine/thread_status.h
LAMA.o: /usr/include/mach/ppc/thread_status.h /usr/include/mach/ppc/_types.h
LAMA.o: /usr/include/mach/machine/thread_state.h
LAMA.o: /usr/include/mach/ppc/thread_state.h
LAMA.o: /usr/include/mach/processor_info.h
LAMA.o: /usr/include/mach/machine/processor_info.h
LAMA.o: /usr/include/mach/ppc/processor_info.h /usr/include/mach/task_info.h
LAMA.o: /usr/include/mach/policy.h /usr/include/mach/task_policy.h
LAMA.o: /usr/include/mach/task_special_ports.h
LAMA.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
LAMA.o: /usr/include/mach/thread_special_ports.h
LAMA.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
LAMA.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
LAMA.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
LAMA.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
LAMA.o: /usr/include/mach/machine/vm_param.h /usr/include/mach/ppc/vm_param.h
LAMA.o: /usr/include/mach/kmod.h /usr/include/mach/std_types.h
LAMA.o: ../include/license.h ../include/strutil.h ../include/errors.h
LAMA.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
LAMA.o: /usr/include/limits.h /usr/include/machine/limits.h
LAMA.o: /usr/include/ppc/limits.h /usr/include/sys/syslimits.h
LAMA.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
LAMA.o: ../include/gcode.h ../include/blocks.h ../include/output.h
LAMA.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
LAMA.o: ../include/convert.h ../include/frequency.h ../include/files.h
LAMA.o: ../include/protomat.h LAMA.h
find_biassed_blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h
find_biassed_blocks.o: /usr/include/sys/cdefs.h /usr/include/_types.h
find_biassed_blocks.o: /usr/include/sys/_types.h
find_biassed_blocks.o: /usr/include/machine/_types.h
find_biassed_blocks.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
find_biassed_blocks.o: /usr/include/sys/signal.h
find_biassed_blocks.o: /usr/include/sys/appleapiopts.h
find_biassed_blocks.o: /usr/include/machine/signal.h
find_biassed_blocks.o: /usr/include/ppc/signal.h /usr/include/sys/resource.h
find_biassed_blocks.o: /usr/include/machine/endian.h
find_biassed_blocks.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
find_biassed_blocks.o: /usr/include/stdint.h
find_biassed_blocks.o: /usr/include/libkern/OSByteOrder.h
find_biassed_blocks.o: /usr/include/libkern/ppc/OSByteOrder.h
find_biassed_blocks.o: /usr/include/alloca.h /usr/include/machine/types.h
find_biassed_blocks.o: /usr/include/ppc/types.h /usr/include/stdio.h
find_biassed_blocks.o: /usr/include/string.h /usr/include/math.h
find_biassed_blocks.o: /usr/include/architecture/ppc/math.h
find_biassed_blocks.o: /usr/include/unistd.h /usr/include/sys/unistd.h
find_biassed_blocks.o: /usr/include/sys/select.h /usr/include/sys/types.h
find_biassed_blocks.o: /usr/include/signal.h /usr/include/sys/time.h
find_biassed_blocks.o: /usr/include/time.h /usr/include/machine/_limits.h
find_biassed_blocks.o: /usr/include/ppc/_limits.h /usr/include/ctype.h
find_biassed_blocks.o: /usr/include/runetype.h ../include/global.h
find_biassed_blocks.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
find_biassed_blocks.o: /usr/include/mach/mach_types.h
find_biassed_blocks.o: /usr/include/mach/host_info.h
find_biassed_blocks.o: /usr/include/mach/message.h /usr/include/mach/port.h
find_biassed_blocks.o: /usr/include/mach/boolean.h
find_biassed_blocks.o: /usr/include/mach/machine/boolean.h
find_biassed_blocks.o: /usr/include/mach/ppc/boolean.h
find_biassed_blocks.o: /usr/include/mach/machine/vm_types.h
find_biassed_blocks.o: /usr/include/mach/ppc/vm_types.h
find_biassed_blocks.o: /usr/include/ppc/vmparam.h
find_biassed_blocks.o: /usr/include/mach/kern_return.h
find_biassed_blocks.o: /usr/include/mach/machine/kern_return.h
find_biassed_blocks.o: /usr/include/mach/ppc/kern_return.h
find_biassed_blocks.o: /usr/include/mach/vm_statistics.h
find_biassed_blocks.o: /usr/include/mach/machine.h
find_biassed_blocks.o: /usr/include/mach/time_value.h
find_biassed_blocks.o: /usr/include/mach/host_notify.h
find_biassed_blocks.o: /usr/include/mach/host_special_ports.h
find_biassed_blocks.o: /usr/include/mach/memory_object_types.h
find_biassed_blocks.o: /usr/include/mach/vm_types.h
find_biassed_blocks.o: /usr/include/mach/exception_types.h
find_biassed_blocks.o: /usr/include/mach/machine/exception.h
find_biassed_blocks.o: /usr/include/mach/ppc/exception.h
find_biassed_blocks.o: /usr/include/mach/thread_status.h
find_biassed_blocks.o: /usr/include/mach/machine/thread_status.h
find_biassed_blocks.o: /usr/include/mach/ppc/thread_status.h
find_biassed_blocks.o: /usr/include/mach/ppc/_types.h
find_biassed_blocks.o: /usr/include/mach/machine/thread_state.h
find_biassed_blocks.o: /usr/include/mach/ppc/thread_state.h
find_biassed_blocks.o: /usr/include/mach/processor_info.h
find_biassed_blocks.o: /usr/include/mach/machine/processor_info.h
find_biassed_blocks.o: /usr/include/mach/ppc/processor_info.h
find_biassed_blocks.o: /usr/include/mach/task_info.h
find_biassed_blocks.o: /usr/include/mach/policy.h
find_biassed_blocks.o: /usr/include/mach/task_policy.h
find_biassed_blocks.o: /usr/include/mach/task_special_ports.h
find_biassed_blocks.o: /usr/include/mach/thread_info.h
find_biassed_blocks.o: /usr/include/mach/thread_policy.h
find_biassed_blocks.o: /usr/include/mach/thread_special_ports.h
find_biassed_blocks.o: /usr/include/mach/clock_types.h
find_biassed_blocks.o: /usr/include/mach/vm_attributes.h
find_biassed_blocks.o: /usr/include/mach/vm_inherit.h
find_biassed_blocks.o: /usr/include/mach/vm_purgable.h
find_biassed_blocks.o: /usr/include/mach/vm_behavior.h
find_biassed_blocks.o: /usr/include/mach/vm_prot.h
find_biassed_blocks.o: /usr/include/mach/vm_sync.h
find_biassed_blocks.o: /usr/include/mach/vm_region.h
find_biassed_blocks.o: /usr/include/mach/machine/vm_param.h
find_biassed_blocks.o: /usr/include/mach/ppc/vm_param.h
find_biassed_blocks.o: /usr/include/mach/kmod.h /usr/include/mach/std_types.h
find_biassed_blocks.o: ../include/license.h ../include/strutil.h
find_biassed_blocks.o: ../include/errors.h ../include/memory.h
find_biassed_blocks.o: ../include/residues.h ../include/blastapp.h
find_biassed_blocks.o: /usr/include/limits.h /usr/include/machine/limits.h
find_biassed_blocks.o: /usr/include/ppc/limits.h /usr/include/sys/syslimits.h
find_biassed_blocks.o: ../include/alphabet.h ../include/aabet.h
find_biassed_blocks.o: ../include/ntbet.h ../include/gcode.h
find_biassed_blocks.o: ../include/blocks.h ../include/output.h
find_biassed_blocks.o: ../include/sequences.h ../include/matrix.h
find_biassed_blocks.o: ../include/pattern.h ../include/convert.h
find_biassed_blocks.o: ../include/frequency.h ../include/files.h
find_biassed_blocks.o: ../include/protomat.h blkvblk.h
makeblockmap.o: ../include/blocksprogs.h /usr/include/stdlib.h
makeblockmap.o: /usr/include/sys/cdefs.h /usr/include/_types.h
makeblockmap.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
makeblockmap.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
makeblockmap.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
makeblockmap.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
makeblockmap.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
makeblockmap.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
makeblockmap.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
makeblockmap.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
makeblockmap.o: /usr/include/machine/types.h /usr/include/ppc/types.h
makeblockmap.o: /usr/include/stdio.h /usr/include/string.h
makeblockmap.o: /usr/include/math.h /usr/include/architecture/ppc/math.h
makeblockmap.o: /usr/include/unistd.h /usr/include/sys/unistd.h
makeblockmap.o: /usr/include/sys/select.h /usr/include/sys/types.h
makeblockmap.o: /usr/include/signal.h /usr/include/sys/time.h
makeblockmap.o: /usr/include/time.h /usr/include/machine/_limits.h
makeblockmap.o: /usr/include/ppc/_limits.h /usr/include/ctype.h
makeblockmap.o: /usr/include/runetype.h ../include/global.h
makeblockmap.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
makeblockmap.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
makeblockmap.o: /usr/include/mach/message.h /usr/include/mach/port.h
makeblockmap.o: /usr/include/mach/boolean.h
makeblockmap.o: /usr/include/mach/machine/boolean.h
makeblockmap.o: /usr/include/mach/ppc/boolean.h
makeblockmap.o: /usr/include/mach/machine/vm_types.h
makeblockmap.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
makeblockmap.o: /usr/include/mach/kern_return.h
makeblockmap.o: /usr/include/mach/machine/kern_return.h
makeblockmap.o: /usr/include/mach/ppc/kern_return.h
makeblockmap.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
makeblockmap.o: /usr/include/mach/time_value.h
makeblockmap.o: /usr/include/mach/host_notify.h
makeblockmap.o: /usr/include/mach/host_special_ports.h
makeblockmap.o: /usr/include/mach/memory_object_types.h
makeblockmap.o: /usr/include/mach/vm_types.h
makeblockmap.o: /usr/include/mach/exception_types.h
makeblockmap.o: /usr/include/mach/machine/exception.h
makeblockmap.o: /usr/include/mach/ppc/exception.h
makeblockmap.o: /usr/include/mach/thread_status.h
makeblockmap.o: /usr/include/mach/machine/thread_status.h
makeblockmap.o: /usr/include/mach/ppc/thread_status.h
makeblockmap.o: /usr/include/mach/ppc/_types.h
makeblockmap.o: /usr/include/mach/machine/thread_state.h
makeblockmap.o: /usr/include/mach/ppc/thread_state.h
makeblockmap.o: /usr/include/mach/processor_info.h
makeblockmap.o: /usr/include/mach/machine/processor_info.h
makeblockmap.o: /usr/include/mach/ppc/processor_info.h
makeblockmap.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
makeblockmap.o: /usr/include/mach/task_policy.h
makeblockmap.o: /usr/include/mach/task_special_ports.h
makeblockmap.o: /usr/include/mach/thread_info.h
makeblockmap.o: /usr/include/mach/thread_policy.h
makeblockmap.o: /usr/include/mach/thread_special_ports.h
makeblockmap.o: /usr/include/mach/clock_types.h
makeblockmap.o: /usr/include/mach/vm_attributes.h
makeblockmap.o: /usr/include/mach/vm_inherit.h
makeblockmap.o: /usr/include/mach/vm_purgable.h
makeblockmap.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
makeblockmap.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
makeblockmap.o: /usr/include/mach/machine/vm_param.h
makeblockmap.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
makeblockmap.o: /usr/include/mach/std_types.h ../include/license.h
makeblockmap.o: ../include/strutil.h ../include/errors.h ../include/memory.h
makeblockmap.o: ../include/residues.h ../include/blastapp.h
makeblockmap.o: /usr/include/limits.h /usr/include/machine/limits.h
makeblockmap.o: /usr/include/ppc/limits.h /usr/include/sys/syslimits.h
makeblockmap.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
makeblockmap.o: ../include/gcode.h ../include/blocks.h ../include/output.h
makeblockmap.o: ../include/sequences.h ../include/matrix.h
makeblockmap.o: ../include/pattern.h ../include/convert.h
makeblockmap.o: ../include/frequency.h ../include/files.h
makeblockmap.o: ../include/protomat.h blockmap.h
prints2blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h
prints2blocks.o: /usr/include/sys/cdefs.h /usr/include/_types.h
prints2blocks.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
prints2blocks.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
prints2blocks.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
prints2blocks.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
prints2blocks.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
prints2blocks.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
prints2blocks.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
prints2blocks.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
prints2blocks.o: /usr/include/machine/types.h /usr/include/ppc/types.h
prints2blocks.o: /usr/include/stdio.h /usr/include/string.h
prints2blocks.o: /usr/include/math.h /usr/include/architecture/ppc/math.h
prints2blocks.o: /usr/include/unistd.h /usr/include/sys/unistd.h
prints2blocks.o: /usr/include/sys/select.h /usr/include/sys/types.h
prints2blocks.o: /usr/include/signal.h /usr/include/sys/time.h
prints2blocks.o: /usr/include/time.h /usr/include/machine/_limits.h
prints2blocks.o: /usr/include/ppc/_limits.h /usr/include/ctype.h
prints2blocks.o: /usr/include/runetype.h ../include/global.h
prints2blocks.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
prints2blocks.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
prints2blocks.o: /usr/include/mach/message.h /usr/include/mach/port.h
prints2blocks.o: /usr/include/mach/boolean.h
prints2blocks.o: /usr/include/mach/machine/boolean.h
prints2blocks.o: /usr/include/mach/ppc/boolean.h
prints2blocks.o: /usr/include/mach/machine/vm_types.h
prints2blocks.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
prints2blocks.o: /usr/include/mach/kern_return.h
prints2blocks.o: /usr/include/mach/machine/kern_return.h
prints2blocks.o: /usr/include/mach/ppc/kern_return.h
prints2blocks.o: /usr/include/mach/vm_statistics.h
prints2blocks.o: /usr/include/mach/machine.h /usr/include/mach/time_value.h
prints2blocks.o: /usr/include/mach/host_notify.h
prints2blocks.o: /usr/include/mach/host_special_ports.h
prints2blocks.o: /usr/include/mach/memory_object_types.h
prints2blocks.o: /usr/include/mach/vm_types.h
prints2blocks.o: /usr/include/mach/exception_types.h
prints2blocks.o: /usr/include/mach/machine/exception.h
prints2blocks.o: /usr/include/mach/ppc/exception.h
prints2blocks.o: /usr/include/mach/thread_status.h
prints2blocks.o: /usr/include/mach/machine/thread_status.h
prints2blocks.o: /usr/include/mach/ppc/thread_status.h
prints2blocks.o: /usr/include/mach/ppc/_types.h
prints2blocks.o: /usr/include/mach/machine/thread_state.h
prints2blocks.o: /usr/include/mach/ppc/thread_state.h
prints2blocks.o: /usr/include/mach/processor_info.h
prints2blocks.o: /usr/include/mach/machine/processor_info.h
prints2blocks.o: /usr/include/mach/ppc/processor_info.h
prints2blocks.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
prints2blocks.o: /usr/include/mach/task_policy.h
prints2blocks.o: /usr/include/mach/task_special_ports.h
prints2blocks.o: /usr/include/mach/thread_info.h
prints2blocks.o: /usr/include/mach/thread_policy.h
prints2blocks.o: /usr/include/mach/thread_special_ports.h
prints2blocks.o: /usr/include/mach/clock_types.h
prints2blocks.o: /usr/include/mach/vm_attributes.h
prints2blocks.o: /usr/include/mach/vm_inherit.h
prints2blocks.o: /usr/include/mach/vm_purgable.h
prints2blocks.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
prints2blocks.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
prints2blocks.o: /usr/include/mach/machine/vm_param.h
prints2blocks.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
prints2blocks.o: /usr/include/mach/std_types.h ../include/license.h
prints2blocks.o: ../include/strutil.h ../include/errors.h ../include/memory.h
prints2blocks.o: ../include/residues.h ../include/blastapp.h
prints2blocks.o: /usr/include/limits.h /usr/include/machine/limits.h
prints2blocks.o: /usr/include/ppc/limits.h /usr/include/sys/syslimits.h
prints2blocks.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
prints2blocks.o: ../include/gcode.h ../include/blocks.h ../include/output.h
prints2blocks.o: ../include/sequences.h ../include/matrix.h
prints2blocks.o: ../include/pattern.h ../include/convert.h
prints2blocks.o: ../include/frequency.h ../include/files.h
prints2blocks.o: ../include/protomat.h
lisblk.o: ../include/blocksprogs.h /usr/include/stdlib.h
lisblk.o: /usr/include/sys/cdefs.h /usr/include/_types.h
lisblk.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
lisblk.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
lisblk.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
lisblk.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
lisblk.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
lisblk.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
lisblk.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
lisblk.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
lisblk.o: /usr/include/machine/types.h /usr/include/ppc/types.h
lisblk.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
lisblk.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
lisblk.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
lisblk.o: /usr/include/sys/types.h /usr/include/signal.h
lisblk.o: /usr/include/sys/time.h /usr/include/time.h
lisblk.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
lisblk.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
lisblk.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
lisblk.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
lisblk.o: /usr/include/mach/message.h /usr/include/mach/port.h
lisblk.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
lisblk.o: /usr/include/mach/ppc/boolean.h
lisblk.o: /usr/include/mach/machine/vm_types.h
lisblk.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
lisblk.o: /usr/include/mach/kern_return.h
lisblk.o: /usr/include/mach/machine/kern_return.h
lisblk.o: /usr/include/mach/ppc/kern_return.h
lisblk.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
lisblk.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
lisblk.o: /usr/include/mach/host_special_ports.h
lisblk.o: /usr/include/mach/memory_object_types.h
lisblk.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
lisblk.o: /usr/include/mach/machine/exception.h
lisblk.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
lisblk.o: /usr/include/mach/machine/thread_status.h
lisblk.o: /usr/include/mach/ppc/thread_status.h
lisblk.o: /usr/include/mach/ppc/_types.h
lisblk.o: /usr/include/mach/machine/thread_state.h
lisblk.o: /usr/include/mach/ppc/thread_state.h
lisblk.o: /usr/include/mach/processor_info.h
lisblk.o: /usr/include/mach/machine/processor_info.h
lisblk.o: /usr/include/mach/ppc/processor_info.h
lisblk.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
lisblk.o: /usr/include/mach/task_policy.h
lisblk.o: /usr/include/mach/task_special_ports.h
lisblk.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
lisblk.o: /usr/include/mach/thread_special_ports.h
lisblk.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
lisblk.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
lisblk.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
lisblk.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
lisblk.o: /usr/include/mach/machine/vm_param.h
lisblk.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
lisblk.o: /usr/include/mach/std_types.h ../include/license.h
lisblk.o: ../include/strutil.h ../include/errors.h ../include/memory.h
lisblk.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
lisblk.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
lisblk.o: /usr/include/sys/syslimits.h ../include/alphabet.h
lisblk.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
lisblk.o: ../include/blocks.h ../include/output.h ../include/sequences.h
lisblk.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
lisblk.o: ../include/frequency.h ../include/files.h ../include/protomat.h
coduse.o: ../include/blocksprogs.h /usr/include/stdlib.h
coduse.o: /usr/include/sys/cdefs.h /usr/include/_types.h
coduse.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
coduse.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
coduse.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
coduse.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
coduse.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
coduse.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
coduse.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
coduse.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
coduse.o: /usr/include/machine/types.h /usr/include/ppc/types.h
coduse.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
coduse.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
coduse.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
coduse.o: /usr/include/sys/types.h /usr/include/signal.h
coduse.o: /usr/include/sys/time.h /usr/include/time.h
coduse.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
coduse.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
coduse.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
coduse.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
coduse.o: /usr/include/mach/message.h /usr/include/mach/port.h
coduse.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
coduse.o: /usr/include/mach/ppc/boolean.h
coduse.o: /usr/include/mach/machine/vm_types.h
coduse.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
coduse.o: /usr/include/mach/kern_return.h
coduse.o: /usr/include/mach/machine/kern_return.h
coduse.o: /usr/include/mach/ppc/kern_return.h
coduse.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
coduse.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
coduse.o: /usr/include/mach/host_special_ports.h
coduse.o: /usr/include/mach/memory_object_types.h
coduse.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
coduse.o: /usr/include/mach/machine/exception.h
coduse.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
coduse.o: /usr/include/mach/machine/thread_status.h
coduse.o: /usr/include/mach/ppc/thread_status.h
coduse.o: /usr/include/mach/ppc/_types.h
coduse.o: /usr/include/mach/machine/thread_state.h
coduse.o: /usr/include/mach/ppc/thread_state.h
coduse.o: /usr/include/mach/processor_info.h
coduse.o: /usr/include/mach/machine/processor_info.h
coduse.o: /usr/include/mach/ppc/processor_info.h
coduse.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
coduse.o: /usr/include/mach/task_policy.h
coduse.o: /usr/include/mach/task_special_ports.h
coduse.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
coduse.o: /usr/include/mach/thread_special_ports.h
coduse.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
coduse.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
coduse.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
coduse.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
coduse.o: /usr/include/mach/machine/vm_param.h
coduse.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
coduse.o: /usr/include/mach/std_types.h ../include/license.h
coduse.o: ../include/strutil.h ../include/errors.h ../include/memory.h
coduse.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
coduse.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
coduse.o: /usr/include/sys/syslimits.h ../include/alphabet.h
coduse.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
coduse.o: ../include/blocks.h ../include/output.h ../include/sequences.h
coduse.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
coduse.o: ../include/frequency.h ../include/files.h ../include/protomat.h
narrow.o: ../include/blocksprogs.h /usr/include/stdlib.h
narrow.o: /usr/include/sys/cdefs.h /usr/include/_types.h
narrow.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
narrow.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
narrow.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
narrow.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
narrow.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
narrow.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
narrow.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
narrow.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
narrow.o: /usr/include/machine/types.h /usr/include/ppc/types.h
narrow.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
narrow.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
narrow.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
narrow.o: /usr/include/sys/types.h /usr/include/signal.h
narrow.o: /usr/include/sys/time.h /usr/include/time.h
narrow.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
narrow.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
narrow.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
narrow.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
narrow.o: /usr/include/mach/message.h /usr/include/mach/port.h
narrow.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
narrow.o: /usr/include/mach/ppc/boolean.h
narrow.o: /usr/include/mach/machine/vm_types.h
narrow.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
narrow.o: /usr/include/mach/kern_return.h
narrow.o: /usr/include/mach/machine/kern_return.h
narrow.o: /usr/include/mach/ppc/kern_return.h
narrow.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
narrow.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
narrow.o: /usr/include/mach/host_special_ports.h
narrow.o: /usr/include/mach/memory_object_types.h
narrow.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
narrow.o: /usr/include/mach/machine/exception.h
narrow.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
narrow.o: /usr/include/mach/machine/thread_status.h
narrow.o: /usr/include/mach/ppc/thread_status.h
narrow.o: /usr/include/mach/ppc/_types.h
narrow.o: /usr/include/mach/machine/thread_state.h
narrow.o: /usr/include/mach/ppc/thread_state.h
narrow.o: /usr/include/mach/processor_info.h
narrow.o: /usr/include/mach/machine/processor_info.h
narrow.o: /usr/include/mach/ppc/processor_info.h
narrow.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
narrow.o: /usr/include/mach/task_policy.h
narrow.o: /usr/include/mach/task_special_ports.h
narrow.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
narrow.o: /usr/include/mach/thread_special_ports.h
narrow.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
narrow.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
narrow.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
narrow.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
narrow.o: /usr/include/mach/machine/vm_param.h
narrow.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
narrow.o: /usr/include/mach/std_types.h ../include/license.h
narrow.o: ../include/strutil.h ../include/errors.h ../include/memory.h
narrow.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
narrow.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
narrow.o: /usr/include/sys/syslimits.h ../include/alphabet.h
narrow.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
narrow.o: ../include/blocks.h ../include/output.h ../include/sequences.h
narrow.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
narrow.o: ../include/frequency.h ../include/files.h ../include/protomat.h
blk2slx.o: ../include/blocksprogs.h /usr/include/stdlib.h
blk2slx.o: /usr/include/sys/cdefs.h /usr/include/_types.h
blk2slx.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
blk2slx.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
blk2slx.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
blk2slx.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
blk2slx.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
blk2slx.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
blk2slx.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
blk2slx.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
blk2slx.o: /usr/include/machine/types.h /usr/include/ppc/types.h
blk2slx.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
blk2slx.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
blk2slx.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
blk2slx.o: /usr/include/sys/types.h /usr/include/signal.h
blk2slx.o: /usr/include/sys/time.h /usr/include/time.h
blk2slx.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
blk2slx.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
blk2slx.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
blk2slx.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
blk2slx.o: /usr/include/mach/message.h /usr/include/mach/port.h
blk2slx.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
blk2slx.o: /usr/include/mach/ppc/boolean.h
blk2slx.o: /usr/include/mach/machine/vm_types.h
blk2slx.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
blk2slx.o: /usr/include/mach/kern_return.h
blk2slx.o: /usr/include/mach/machine/kern_return.h
blk2slx.o: /usr/include/mach/ppc/kern_return.h
blk2slx.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
blk2slx.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
blk2slx.o: /usr/include/mach/host_special_ports.h
blk2slx.o: /usr/include/mach/memory_object_types.h
blk2slx.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
blk2slx.o: /usr/include/mach/machine/exception.h
blk2slx.o: /usr/include/mach/ppc/exception.h
blk2slx.o: /usr/include/mach/thread_status.h
blk2slx.o: /usr/include/mach/machine/thread_status.h
blk2slx.o: /usr/include/mach/ppc/thread_status.h
blk2slx.o: /usr/include/mach/ppc/_types.h
blk2slx.o: /usr/include/mach/machine/thread_state.h
blk2slx.o: /usr/include/mach/ppc/thread_state.h
blk2slx.o: /usr/include/mach/processor_info.h
blk2slx.o: /usr/include/mach/machine/processor_info.h
blk2slx.o: /usr/include/mach/ppc/processor_info.h
blk2slx.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
blk2slx.o: /usr/include/mach/task_policy.h
blk2slx.o: /usr/include/mach/task_special_ports.h
blk2slx.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
blk2slx.o: /usr/include/mach/thread_special_ports.h
blk2slx.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
blk2slx.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
blk2slx.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
blk2slx.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
blk2slx.o: /usr/include/mach/machine/vm_param.h
blk2slx.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
blk2slx.o: /usr/include/mach/std_types.h ../include/license.h
blk2slx.o: ../include/strutil.h ../include/errors.h ../include/memory.h
blk2slx.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
blk2slx.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
blk2slx.o: /usr/include/sys/syslimits.h ../include/alphabet.h
blk2slx.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
blk2slx.o: ../include/blocks.h ../include/output.h ../include/sequences.h
blk2slx.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
blk2slx.o: ../include/frequency.h ../include/files.h ../include/protomat.h
blkprob.o: ../include/blocksprogs.h /usr/include/stdlib.h
blkprob.o: /usr/include/sys/cdefs.h /usr/include/_types.h
blkprob.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
blkprob.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
blkprob.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
blkprob.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
blkprob.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
blkprob.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
blkprob.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
blkprob.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
blkprob.o: /usr/include/machine/types.h /usr/include/ppc/types.h
blkprob.o: /usr/include/stdio.h /usr/include/string.h /usr/include/math.h
blkprob.o: /usr/include/architecture/ppc/math.h /usr/include/unistd.h
blkprob.o: /usr/include/sys/unistd.h /usr/include/sys/select.h
blkprob.o: /usr/include/sys/types.h /usr/include/signal.h
blkprob.o: /usr/include/sys/time.h /usr/include/time.h
blkprob.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
blkprob.o: /usr/include/ctype.h /usr/include/runetype.h ../include/global.h
blkprob.o: /usr/include/stddef.h /usr/include/malloc/malloc.h
blkprob.o: /usr/include/mach/mach_types.h /usr/include/mach/host_info.h
blkprob.o: /usr/include/mach/message.h /usr/include/mach/port.h
blkprob.o: /usr/include/mach/boolean.h /usr/include/mach/machine/boolean.h
blkprob.o: /usr/include/mach/ppc/boolean.h
blkprob.o: /usr/include/mach/machine/vm_types.h
blkprob.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
blkprob.o: /usr/include/mach/kern_return.h
blkprob.o: /usr/include/mach/machine/kern_return.h
blkprob.o: /usr/include/mach/ppc/kern_return.h
blkprob.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
blkprob.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
blkprob.o: /usr/include/mach/host_special_ports.h
blkprob.o: /usr/include/mach/memory_object_types.h
blkprob.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
blkprob.o: /usr/include/mach/machine/exception.h
blkprob.o: /usr/include/mach/ppc/exception.h
blkprob.o: /usr/include/mach/thread_status.h
blkprob.o: /usr/include/mach/machine/thread_status.h
blkprob.o: /usr/include/mach/ppc/thread_status.h
blkprob.o: /usr/include/mach/ppc/_types.h
blkprob.o: /usr/include/mach/machine/thread_state.h
blkprob.o: /usr/include/mach/ppc/thread_state.h
blkprob.o: /usr/include/mach/processor_info.h
blkprob.o: /usr/include/mach/machine/processor_info.h
blkprob.o: /usr/include/mach/ppc/processor_info.h
blkprob.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
blkprob.o: /usr/include/mach/task_policy.h
blkprob.o: /usr/include/mach/task_special_ports.h
blkprob.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
blkprob.o: /usr/include/mach/thread_special_ports.h
blkprob.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
blkprob.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
blkprob.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
blkprob.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
blkprob.o: /usr/include/mach/machine/vm_param.h
blkprob.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
blkprob.o: /usr/include/mach/std_types.h ../include/license.h
blkprob.o: ../include/strutil.h ../include/errors.h ../include/memory.h
blkprob.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
blkprob.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
blkprob.o: /usr/include/sys/syslimits.h ../include/alphabet.h
blkprob.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
blkprob.o: ../include/blocks.h ../include/output.h ../include/sequences.h
blkprob.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
blkprob.o: ../include/frequency.h ../include/files.h ../include/protomat.h
blocks.o: ../include/global.h /usr/include/stdlib.h /usr/include/sys/cdefs.h
blocks.o: /usr/include/_types.h /usr/include/sys/_types.h
blocks.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
blocks.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
blocks.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
blocks.o: /usr/include/ppc/signal.h /usr/include/sys/resource.h
blocks.o: /usr/include/machine/endian.h /usr/include/ppc/endian.h
blocks.o: /usr/include/sys/_endian.h /usr/include/stdint.h
blocks.o: /usr/include/libkern/OSByteOrder.h
blocks.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
blocks.o: /usr/include/machine/types.h /usr/include/ppc/types.h
blocks.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
blocks.o: /usr/include/ctype.h /usr/include/runetype.h
blocks.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
blocks.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
blocks.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
blocks.o: /usr/include/mach/machine/boolean.h /usr/include/mach/ppc/boolean.h
blocks.o: /usr/include/mach/machine/vm_types.h
blocks.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
blocks.o: /usr/include/mach/kern_return.h
blocks.o: /usr/include/mach/machine/kern_return.h
blocks.o: /usr/include/mach/ppc/kern_return.h
blocks.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
blocks.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
blocks.o: /usr/include/mach/host_special_ports.h
blocks.o: /usr/include/mach/memory_object_types.h
blocks.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
blocks.o: /usr/include/mach/machine/exception.h
blocks.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
blocks.o: /usr/include/mach/machine/thread_status.h
blocks.o: /usr/include/mach/ppc/thread_status.h
blocks.o: /usr/include/mach/ppc/_types.h
blocks.o: /usr/include/mach/machine/thread_state.h
blocks.o: /usr/include/mach/ppc/thread_state.h
blocks.o: /usr/include/mach/processor_info.h
blocks.o: /usr/include/mach/machine/processor_info.h
blocks.o: /usr/include/mach/ppc/processor_info.h
blocks.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
blocks.o: /usr/include/mach/task_policy.h
blocks.o: /usr/include/mach/task_special_ports.h
blocks.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
blocks.o: /usr/include/mach/thread_special_ports.h
blocks.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
blocks.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
blocks.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
blocks.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
blocks.o: /usr/include/mach/machine/vm_param.h
blocks.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
blocks.o: /usr/include/mach/std_types.h ../include/license.h
blocks.o: ../include/strutil.h ../include/errors.h ../include/memory.h
blocks.o: ../include/blocks.h ../include/output.h ../include/sequences.h
blocks.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
blocks.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
blocks.o: /usr/include/ppc/_limits.h /usr/include/sys/syslimits.h
blocks.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blocks.o: ../include/gcode.h
config.o: ../include/global.h /usr/include/stdlib.h /usr/include/sys/cdefs.h
config.o: /usr/include/_types.h /usr/include/sys/_types.h
config.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
config.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
config.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
config.o: /usr/include/ppc/signal.h /usr/include/sys/resource.h
config.o: /usr/include/machine/endian.h /usr/include/ppc/endian.h
config.o: /usr/include/sys/_endian.h /usr/include/stdint.h
config.o: /usr/include/libkern/OSByteOrder.h
config.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
config.o: /usr/include/machine/types.h /usr/include/ppc/types.h
config.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
config.o: /usr/include/ctype.h /usr/include/runetype.h
config.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
config.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
config.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
config.o: /usr/include/mach/machine/boolean.h /usr/include/mach/ppc/boolean.h
config.o: /usr/include/mach/machine/vm_types.h
config.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
config.o: /usr/include/mach/kern_return.h
config.o: /usr/include/mach/machine/kern_return.h
config.o: /usr/include/mach/ppc/kern_return.h
config.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
config.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
config.o: /usr/include/mach/host_special_ports.h
config.o: /usr/include/mach/memory_object_types.h
config.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
config.o: /usr/include/mach/machine/exception.h
config.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
config.o: /usr/include/mach/machine/thread_status.h
config.o: /usr/include/mach/ppc/thread_status.h
config.o: /usr/include/mach/ppc/_types.h
config.o: /usr/include/mach/machine/thread_state.h
config.o: /usr/include/mach/ppc/thread_state.h
config.o: /usr/include/mach/processor_info.h
config.o: /usr/include/mach/machine/processor_info.h
config.o: /usr/include/mach/ppc/processor_info.h
config.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
config.o: /usr/include/mach/task_policy.h
config.o: /usr/include/mach/task_special_ports.h
config.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
config.o: /usr/include/mach/thread_special_ports.h
config.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
config.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
config.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
config.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
config.o: /usr/include/mach/machine/vm_param.h
config.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
config.o: /usr/include/mach/std_types.h ../include/license.h
config.o: ../include/strutil.h ../include/errors.h ../include/memory.h
config.o: ../include/files.h ../include/sequences.h ../include/pattern.h
config.o: ../include/options.h config.h blimps.h scoring.h lists.h
config.o: ../include/skiplist.h
convert.o: /usr/include/assert.h /usr/include/sys/cdefs.h /usr/include/math.h
convert.o: /usr/include/architecture/ppc/math.h ../include/global.h
convert.o: /usr/include/stdlib.h /usr/include/_types.h
convert.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
convert.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
convert.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
convert.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
convert.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
convert.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
convert.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
convert.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
convert.o: /usr/include/machine/types.h /usr/include/ppc/types.h
convert.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
convert.o: /usr/include/ctype.h /usr/include/runetype.h
convert.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
convert.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
convert.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
convert.o: /usr/include/mach/machine/boolean.h
convert.o: /usr/include/mach/ppc/boolean.h
convert.o: /usr/include/mach/machine/vm_types.h
convert.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
convert.o: /usr/include/mach/kern_return.h
convert.o: /usr/include/mach/machine/kern_return.h
convert.o: /usr/include/mach/ppc/kern_return.h
convert.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
convert.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
convert.o: /usr/include/mach/host_special_ports.h
convert.o: /usr/include/mach/memory_object_types.h
convert.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
convert.o: /usr/include/mach/machine/exception.h
convert.o: /usr/include/mach/ppc/exception.h
convert.o: /usr/include/mach/thread_status.h
convert.o: /usr/include/mach/machine/thread_status.h
convert.o: /usr/include/mach/ppc/thread_status.h
convert.o: /usr/include/mach/ppc/_types.h
convert.o: /usr/include/mach/machine/thread_state.h
convert.o: /usr/include/mach/ppc/thread_state.h
convert.o: /usr/include/mach/processor_info.h
convert.o: /usr/include/mach/machine/processor_info.h
convert.o: /usr/include/mach/ppc/processor_info.h
convert.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
convert.o: /usr/include/mach/task_policy.h
convert.o: /usr/include/mach/task_special_ports.h
convert.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
convert.o: /usr/include/mach/thread_special_ports.h
convert.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
convert.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
convert.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
convert.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
convert.o: /usr/include/mach/machine/vm_param.h
convert.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
convert.o: /usr/include/mach/std_types.h ../include/license.h
convert.o: ../include/strutil.h ../include/errors.h ../include/memory.h
convert.o: ../include/options.h ../include/blocks.h ../include/output.h
convert.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
convert.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
convert.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
convert.o: /usr/include/ppc/_limits.h /usr/include/sys/syslimits.h
convert.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
convert.o: ../include/gcode.h ../include/frequency.h ../include/protomat.h
convert.o: ../include/convert.h blimps.h
errors.o: ../include/global.h /usr/include/stdlib.h /usr/include/sys/cdefs.h
errors.o: /usr/include/_types.h /usr/include/sys/_types.h
errors.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
errors.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
errors.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
errors.o: /usr/include/ppc/signal.h /usr/include/sys/resource.h
errors.o: /usr/include/machine/endian.h /usr/include/ppc/endian.h
errors.o: /usr/include/sys/_endian.h /usr/include/stdint.h
errors.o: /usr/include/libkern/OSByteOrder.h
errors.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
errors.o: /usr/include/machine/types.h /usr/include/ppc/types.h
errors.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
errors.o: /usr/include/ctype.h /usr/include/runetype.h
errors.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
errors.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
errors.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
errors.o: /usr/include/mach/machine/boolean.h /usr/include/mach/ppc/boolean.h
errors.o: /usr/include/mach/machine/vm_types.h
errors.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
errors.o: /usr/include/mach/kern_return.h
errors.o: /usr/include/mach/machine/kern_return.h
errors.o: /usr/include/mach/ppc/kern_return.h
errors.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
errors.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
errors.o: /usr/include/mach/host_special_ports.h
errors.o: /usr/include/mach/memory_object_types.h
errors.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
errors.o: /usr/include/mach/machine/exception.h
errors.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
errors.o: /usr/include/mach/machine/thread_status.h
errors.o: /usr/include/mach/ppc/thread_status.h
errors.o: /usr/include/mach/ppc/_types.h
errors.o: /usr/include/mach/machine/thread_state.h
errors.o: /usr/include/mach/ppc/thread_state.h
errors.o: /usr/include/mach/processor_info.h
errors.o: /usr/include/mach/machine/processor_info.h
errors.o: /usr/include/mach/ppc/processor_info.h
errors.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
errors.o: /usr/include/mach/task_policy.h
errors.o: /usr/include/mach/task_special_ports.h
errors.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
errors.o: /usr/include/mach/thread_special_ports.h
errors.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
errors.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
errors.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
errors.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
errors.o: /usr/include/mach/machine/vm_param.h
errors.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
errors.o: /usr/include/mach/std_types.h ../include/license.h
errors.o: ../include/strutil.h ../include/errors.h ../include/memory.h
files.o: ../include/global.h /usr/include/stdlib.h /usr/include/sys/cdefs.h
files.o: /usr/include/_types.h /usr/include/sys/_types.h
files.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
files.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
files.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
files.o: /usr/include/ppc/signal.h /usr/include/sys/resource.h
files.o: /usr/include/machine/endian.h /usr/include/ppc/endian.h
files.o: /usr/include/sys/_endian.h /usr/include/stdint.h
files.o: /usr/include/libkern/OSByteOrder.h
files.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
files.o: /usr/include/machine/types.h /usr/include/ppc/types.h
files.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
files.o: /usr/include/ctype.h /usr/include/runetype.h
files.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
files.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
files.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
files.o: /usr/include/mach/machine/boolean.h /usr/include/mach/ppc/boolean.h
files.o: /usr/include/mach/machine/vm_types.h
files.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
files.o: /usr/include/mach/kern_return.h
files.o: /usr/include/mach/machine/kern_return.h
files.o: /usr/include/mach/ppc/kern_return.h
files.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
files.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
files.o: /usr/include/mach/host_special_ports.h
files.o: /usr/include/mach/memory_object_types.h /usr/include/mach/vm_types.h
files.o: /usr/include/mach/exception_types.h
files.o: /usr/include/mach/machine/exception.h
files.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
files.o: /usr/include/mach/machine/thread_status.h
files.o: /usr/include/mach/ppc/thread_status.h /usr/include/mach/ppc/_types.h
files.o: /usr/include/mach/machine/thread_state.h
files.o: /usr/include/mach/ppc/thread_state.h
files.o: /usr/include/mach/processor_info.h
files.o: /usr/include/mach/machine/processor_info.h
files.o: /usr/include/mach/ppc/processor_info.h /usr/include/mach/task_info.h
files.o: /usr/include/mach/policy.h /usr/include/mach/task_policy.h
files.o: /usr/include/mach/task_special_ports.h
files.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
files.o: /usr/include/mach/thread_special_ports.h
files.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
files.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
files.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
files.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
files.o: /usr/include/mach/machine/vm_param.h
files.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
files.o: /usr/include/mach/std_types.h ../include/license.h
files.o: ../include/strutil.h ../include/errors.h ../include/memory.h
files.o: ../include/files.h ../include/sequences.h
frequency.o: ../include/global.h /usr/include/stdlib.h
frequency.o: /usr/include/sys/cdefs.h /usr/include/_types.h
frequency.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
frequency.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
frequency.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
frequency.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
frequency.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
frequency.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
frequency.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
frequency.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
frequency.o: /usr/include/machine/types.h /usr/include/ppc/types.h
frequency.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
frequency.o: /usr/include/ctype.h /usr/include/runetype.h
frequency.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
frequency.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
frequency.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
frequency.o: /usr/include/mach/machine/boolean.h
frequency.o: /usr/include/mach/ppc/boolean.h
frequency.o: /usr/include/mach/machine/vm_types.h
frequency.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
frequency.o: /usr/include/mach/kern_return.h
frequency.o: /usr/include/mach/machine/kern_return.h
frequency.o: /usr/include/mach/ppc/kern_return.h
frequency.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
frequency.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
frequency.o: /usr/include/mach/host_special_ports.h
frequency.o: /usr/include/mach/memory_object_types.h
frequency.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
frequency.o: /usr/include/mach/machine/exception.h
frequency.o: /usr/include/mach/ppc/exception.h
frequency.o: /usr/include/mach/thread_status.h
frequency.o: /usr/include/mach/machine/thread_status.h
frequency.o: /usr/include/mach/ppc/thread_status.h
frequency.o: /usr/include/mach/ppc/_types.h
frequency.o: /usr/include/mach/machine/thread_state.h
frequency.o: /usr/include/mach/ppc/thread_state.h
frequency.o: /usr/include/mach/processor_info.h
frequency.o: /usr/include/mach/machine/processor_info.h
frequency.o: /usr/include/mach/ppc/processor_info.h
frequency.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
frequency.o: /usr/include/mach/task_policy.h
frequency.o: /usr/include/mach/task_special_ports.h
frequency.o: /usr/include/mach/thread_info.h
frequency.o: /usr/include/mach/thread_policy.h
frequency.o: /usr/include/mach/thread_special_ports.h
frequency.o: /usr/include/mach/clock_types.h
frequency.o: /usr/include/mach/vm_attributes.h /usr/include/mach/vm_inherit.h
frequency.o: /usr/include/mach/vm_purgable.h /usr/include/mach/vm_behavior.h
frequency.o: /usr/include/mach/vm_prot.h /usr/include/mach/vm_sync.h
frequency.o: /usr/include/mach/vm_region.h
frequency.o: /usr/include/mach/machine/vm_param.h
frequency.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
frequency.o: /usr/include/mach/std_types.h ../include/license.h
frequency.o: ../include/strutil.h ../include/errors.h ../include/memory.h
frequency.o: ../include/blocks.h ../include/output.h ../include/sequences.h
frequency.o: ../include/matrix.h ../include/pattern.h ../include/frequency.h
frequency.o: ../include/convert.h ../include/files.h ../include/residues.h
frequency.o: ../include/blastapp.h /usr/include/limits.h
frequency.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
frequency.o: /usr/include/ppc/_limits.h /usr/include/sys/syslimits.h
frequency.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
frequency.o: ../include/gcode.h
gcode.o: ../include/global.h /usr/include/stdlib.h /usr/include/sys/cdefs.h
gcode.o: /usr/include/_types.h /usr/include/sys/_types.h
gcode.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
gcode.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
gcode.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
gcode.o: /usr/include/ppc/signal.h /usr/include/sys/resource.h
gcode.o: /usr/include/machine/endian.h /usr/include/ppc/endian.h
gcode.o: /usr/include/sys/_endian.h /usr/include/stdint.h
gcode.o: /usr/include/libkern/OSByteOrder.h
gcode.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
gcode.o: /usr/include/machine/types.h /usr/include/ppc/types.h
gcode.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
gcode.o: /usr/include/ctype.h /usr/include/runetype.h
gcode.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
gcode.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
gcode.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
gcode.o: /usr/include/mach/machine/boolean.h /usr/include/mach/ppc/boolean.h
gcode.o: /usr/include/mach/machine/vm_types.h
gcode.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
gcode.o: /usr/include/mach/kern_return.h
gcode.o: /usr/include/mach/machine/kern_return.h
gcode.o: /usr/include/mach/ppc/kern_return.h
gcode.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
gcode.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
gcode.o: /usr/include/mach/host_special_ports.h
gcode.o: /usr/include/mach/memory_object_types.h /usr/include/mach/vm_types.h
gcode.o: /usr/include/mach/exception_types.h
gcode.o: /usr/include/mach/machine/exception.h
gcode.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
gcode.o: /usr/include/mach/machine/thread_status.h
gcode.o: /usr/include/mach/ppc/thread_status.h /usr/include/mach/ppc/_types.h
gcode.o: /usr/include/mach/machine/thread_state.h
gcode.o: /usr/include/mach/ppc/thread_state.h
gcode.o: /usr/include/mach/processor_info.h
gcode.o: /usr/include/mach/machine/processor_info.h
gcode.o: /usr/include/mach/ppc/processor_info.h /usr/include/mach/task_info.h
gcode.o: /usr/include/mach/policy.h /usr/include/mach/task_policy.h
gcode.o: /usr/include/mach/task_special_ports.h
gcode.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
gcode.o: /usr/include/mach/thread_special_ports.h
gcode.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
gcode.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
gcode.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
gcode.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
gcode.o: /usr/include/mach/machine/vm_param.h
gcode.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
gcode.o: /usr/include/mach/std_types.h ../include/license.h
gcode.o: ../include/strutil.h ../include/errors.h ../include/memory.h
gcode.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
gcode.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
gcode.o: /usr/include/ppc/_limits.h /usr/include/sys/syslimits.h
gcode.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
gcode.o: ../include/gcode.h ../include/sequences.h
lists.o: ../include/global.h /usr/include/stdlib.h /usr/include/sys/cdefs.h
lists.o: /usr/include/_types.h /usr/include/sys/_types.h
lists.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
lists.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
lists.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
lists.o: /usr/include/ppc/signal.h /usr/include/sys/resource.h
lists.o: /usr/include/machine/endian.h /usr/include/ppc/endian.h
lists.o: /usr/include/sys/_endian.h /usr/include/stdint.h
lists.o: /usr/include/libkern/OSByteOrder.h
lists.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
lists.o: /usr/include/machine/types.h /usr/include/ppc/types.h
lists.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
lists.o: /usr/include/ctype.h /usr/include/runetype.h
lists.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
lists.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
lists.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
lists.o: /usr/include/mach/machine/boolean.h /usr/include/mach/ppc/boolean.h
lists.o: /usr/include/mach/machine/vm_types.h
lists.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
lists.o: /usr/include/mach/kern_return.h
lists.o: /usr/include/mach/machine/kern_return.h
lists.o: /usr/include/mach/ppc/kern_return.h
lists.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
lists.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
lists.o: /usr/include/mach/host_special_ports.h
lists.o: /usr/include/mach/memory_object_types.h /usr/include/mach/vm_types.h
lists.o: /usr/include/mach/exception_types.h
lists.o: /usr/include/mach/machine/exception.h
lists.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
lists.o: /usr/include/mach/machine/thread_status.h
lists.o: /usr/include/mach/ppc/thread_status.h /usr/include/mach/ppc/_types.h
lists.o: /usr/include/mach/machine/thread_state.h
lists.o: /usr/include/mach/ppc/thread_state.h
lists.o: /usr/include/mach/processor_info.h
lists.o: /usr/include/mach/machine/processor_info.h
lists.o: /usr/include/mach/ppc/processor_info.h /usr/include/mach/task_info.h
lists.o: /usr/include/mach/policy.h /usr/include/mach/task_policy.h
lists.o: /usr/include/mach/task_special_ports.h
lists.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
lists.o: /usr/include/mach/thread_special_ports.h
lists.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
lists.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
lists.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
lists.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
lists.o: /usr/include/mach/machine/vm_param.h
lists.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
lists.o: /usr/include/mach/std_types.h ../include/license.h
lists.o: ../include/strutil.h ../include/errors.h ../include/memory.h
lists.o: ../include/blocks.h ../include/output.h ../include/sequences.h
lists.o: ../include/matrix.h ../include/pattern.h lists.h
lists.o: ../include/skiplist.h blimps.h scores.h
matrix.o: ../include/global.h /usr/include/stdlib.h /usr/include/sys/cdefs.h
matrix.o: /usr/include/_types.h /usr/include/sys/_types.h
matrix.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
matrix.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
matrix.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
matrix.o: /usr/include/ppc/signal.h /usr/include/sys/resource.h
matrix.o: /usr/include/machine/endian.h /usr/include/ppc/endian.h
matrix.o: /usr/include/sys/_endian.h /usr/include/stdint.h
matrix.o: /usr/include/libkern/OSByteOrder.h
matrix.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
matrix.o: /usr/include/machine/types.h /usr/include/ppc/types.h
matrix.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
matrix.o: /usr/include/ctype.h /usr/include/runetype.h
matrix.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
matrix.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
matrix.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
matrix.o: /usr/include/mach/machine/boolean.h /usr/include/mach/ppc/boolean.h
matrix.o: /usr/include/mach/machine/vm_types.h
matrix.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
matrix.o: /usr/include/mach/kern_return.h
matrix.o: /usr/include/mach/machine/kern_return.h
matrix.o: /usr/include/mach/ppc/kern_return.h
matrix.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
matrix.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
matrix.o: /usr/include/mach/host_special_ports.h
matrix.o: /usr/include/mach/memory_object_types.h
matrix.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
matrix.o: /usr/include/mach/machine/exception.h
matrix.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
matrix.o: /usr/include/mach/machine/thread_status.h
matrix.o: /usr/include/mach/ppc/thread_status.h
matrix.o: /usr/include/mach/ppc/_types.h
matrix.o: /usr/include/mach/machine/thread_state.h
matrix.o: /usr/include/mach/ppc/thread_state.h
matrix.o: /usr/include/mach/processor_info.h
matrix.o: /usr/include/mach/machine/processor_info.h
matrix.o: /usr/include/mach/ppc/processor_info.h
matrix.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
matrix.o: /usr/include/mach/task_policy.h
matrix.o: /usr/include/mach/task_special_ports.h
matrix.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
matrix.o: /usr/include/mach/thread_special_ports.h
matrix.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
matrix.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
matrix.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
matrix.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
matrix.o: /usr/include/mach/machine/vm_param.h
matrix.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
matrix.o: /usr/include/mach/std_types.h ../include/license.h
matrix.o: ../include/strutil.h ../include/errors.h ../include/memory.h
matrix.o: ../include/blocks.h ../include/output.h ../include/sequences.h
matrix.o: ../include/matrix.h ../include/pattern.h ../include/residues.h
matrix.o: ../include/blastapp.h /usr/include/limits.h
matrix.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
matrix.o: /usr/include/ppc/_limits.h /usr/include/sys/syslimits.h
matrix.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
matrix.o: ../include/gcode.h
memory.o: ../include/global.h /usr/include/stdlib.h /usr/include/sys/cdefs.h
memory.o: /usr/include/_types.h /usr/include/sys/_types.h
memory.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
memory.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
memory.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
memory.o: /usr/include/ppc/signal.h /usr/include/sys/resource.h
memory.o: /usr/include/machine/endian.h /usr/include/ppc/endian.h
memory.o: /usr/include/sys/_endian.h /usr/include/stdint.h
memory.o: /usr/include/libkern/OSByteOrder.h
memory.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
memory.o: /usr/include/machine/types.h /usr/include/ppc/types.h
memory.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
memory.o: /usr/include/ctype.h /usr/include/runetype.h
memory.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
memory.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
memory.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
memory.o: /usr/include/mach/machine/boolean.h /usr/include/mach/ppc/boolean.h
memory.o: /usr/include/mach/machine/vm_types.h
memory.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
memory.o: /usr/include/mach/kern_return.h
memory.o: /usr/include/mach/machine/kern_return.h
memory.o: /usr/include/mach/ppc/kern_return.h
memory.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
memory.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
memory.o: /usr/include/mach/host_special_ports.h
memory.o: /usr/include/mach/memory_object_types.h
memory.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
memory.o: /usr/include/mach/machine/exception.h
memory.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
memory.o: /usr/include/mach/machine/thread_status.h
memory.o: /usr/include/mach/ppc/thread_status.h
memory.o: /usr/include/mach/ppc/_types.h
memory.o: /usr/include/mach/machine/thread_state.h
memory.o: /usr/include/mach/ppc/thread_state.h
memory.o: /usr/include/mach/processor_info.h
memory.o: /usr/include/mach/machine/processor_info.h
memory.o: /usr/include/mach/ppc/processor_info.h
memory.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
memory.o: /usr/include/mach/task_policy.h
memory.o: /usr/include/mach/task_special_ports.h
memory.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
memory.o: /usr/include/mach/thread_special_ports.h
memory.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
memory.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
memory.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
memory.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
memory.o: /usr/include/mach/machine/vm_param.h
memory.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
memory.o: /usr/include/mach/std_types.h ../include/license.h
memory.o: ../include/strutil.h ../include/errors.h ../include/memory.h
pattern.o: /usr/include/assert.h /usr/include/sys/cdefs.h ../include/global.h
pattern.o: /usr/include/stdlib.h /usr/include/_types.h
pattern.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
pattern.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
pattern.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
pattern.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
pattern.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
pattern.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
pattern.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
pattern.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
pattern.o: /usr/include/machine/types.h /usr/include/ppc/types.h
pattern.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
pattern.o: /usr/include/ctype.h /usr/include/runetype.h
pattern.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
pattern.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
pattern.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
pattern.o: /usr/include/mach/machine/boolean.h
pattern.o: /usr/include/mach/ppc/boolean.h
pattern.o: /usr/include/mach/machine/vm_types.h
pattern.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
pattern.o: /usr/include/mach/kern_return.h
pattern.o: /usr/include/mach/machine/kern_return.h
pattern.o: /usr/include/mach/ppc/kern_return.h
pattern.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
pattern.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
pattern.o: /usr/include/mach/host_special_ports.h
pattern.o: /usr/include/mach/memory_object_types.h
pattern.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
pattern.o: /usr/include/mach/machine/exception.h
pattern.o: /usr/include/mach/ppc/exception.h
pattern.o: /usr/include/mach/thread_status.h
pattern.o: /usr/include/mach/machine/thread_status.h
pattern.o: /usr/include/mach/ppc/thread_status.h
pattern.o: /usr/include/mach/ppc/_types.h
pattern.o: /usr/include/mach/machine/thread_state.h
pattern.o: /usr/include/mach/ppc/thread_state.h
pattern.o: /usr/include/mach/processor_info.h
pattern.o: /usr/include/mach/machine/processor_info.h
pattern.o: /usr/include/mach/ppc/processor_info.h
pattern.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
pattern.o: /usr/include/mach/task_policy.h
pattern.o: /usr/include/mach/task_special_ports.h
pattern.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
pattern.o: /usr/include/mach/thread_special_ports.h
pattern.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
pattern.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
pattern.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
pattern.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
pattern.o: /usr/include/mach/machine/vm_param.h
pattern.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
pattern.o: /usr/include/mach/std_types.h ../include/license.h
pattern.o: ../include/strutil.h ../include/errors.h ../include/memory.h
pattern.o: ../include/files.h ../include/blocks.h ../include/output.h
pattern.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
pattern.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
pattern.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
pattern.o: /usr/include/ppc/_limits.h /usr/include/sys/syslimits.h
pattern.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
pattern.o: ../include/gcode.h ../include/skiplist.h
scores.o: /usr/include/math.h /usr/include/architecture/ppc/math.h
scores.o: /usr/include/sys/cdefs.h ../include/global.h /usr/include/stdlib.h
scores.o: /usr/include/_types.h /usr/include/sys/_types.h
scores.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
scores.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
scores.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
scores.o: /usr/include/ppc/signal.h /usr/include/sys/resource.h
scores.o: /usr/include/machine/endian.h /usr/include/ppc/endian.h
scores.o: /usr/include/sys/_endian.h /usr/include/stdint.h
scores.o: /usr/include/libkern/OSByteOrder.h
scores.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
scores.o: /usr/include/machine/types.h /usr/include/ppc/types.h
scores.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
scores.o: /usr/include/ctype.h /usr/include/runetype.h
scores.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
scores.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
scores.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
scores.o: /usr/include/mach/machine/boolean.h /usr/include/mach/ppc/boolean.h
scores.o: /usr/include/mach/machine/vm_types.h
scores.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
scores.o: /usr/include/mach/kern_return.h
scores.o: /usr/include/mach/machine/kern_return.h
scores.o: /usr/include/mach/ppc/kern_return.h
scores.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
scores.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
scores.o: /usr/include/mach/host_special_ports.h
scores.o: /usr/include/mach/memory_object_types.h
scores.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
scores.o: /usr/include/mach/machine/exception.h
scores.o: /usr/include/mach/ppc/exception.h /usr/include/mach/thread_status.h
scores.o: /usr/include/mach/machine/thread_status.h
scores.o: /usr/include/mach/ppc/thread_status.h
scores.o: /usr/include/mach/ppc/_types.h
scores.o: /usr/include/mach/machine/thread_state.h
scores.o: /usr/include/mach/ppc/thread_state.h
scores.o: /usr/include/mach/processor_info.h
scores.o: /usr/include/mach/machine/processor_info.h
scores.o: /usr/include/mach/ppc/processor_info.h
scores.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
scores.o: /usr/include/mach/task_policy.h
scores.o: /usr/include/mach/task_special_ports.h
scores.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
scores.o: /usr/include/mach/thread_special_ports.h
scores.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
scores.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
scores.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
scores.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
scores.o: /usr/include/mach/machine/vm_param.h
scores.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
scores.o: /usr/include/mach/std_types.h ../include/license.h
scores.o: ../include/strutil.h ../include/errors.h ../include/memory.h
scores.o: ../include/blocks.h ../include/output.h ../include/sequences.h
scores.o: ../include/matrix.h ../include/pattern.h scores.h blimps.h
scores.o: scoring.h lists.h ../include/skiplist.h
scoring.o: /usr/include/math.h /usr/include/architecture/ppc/math.h
scoring.o: /usr/include/sys/cdefs.h ../include/global.h /usr/include/stdlib.h
scoring.o: /usr/include/_types.h /usr/include/sys/_types.h
scoring.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
scoring.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
scoring.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
scoring.o: /usr/include/ppc/signal.h /usr/include/sys/resource.h
scoring.o: /usr/include/machine/endian.h /usr/include/ppc/endian.h
scoring.o: /usr/include/sys/_endian.h /usr/include/stdint.h
scoring.o: /usr/include/libkern/OSByteOrder.h
scoring.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
scoring.o: /usr/include/machine/types.h /usr/include/ppc/types.h
scoring.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
scoring.o: /usr/include/ctype.h /usr/include/runetype.h
scoring.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
scoring.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
scoring.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
scoring.o: /usr/include/mach/machine/boolean.h
scoring.o: /usr/include/mach/ppc/boolean.h
scoring.o: /usr/include/mach/machine/vm_types.h
scoring.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
scoring.o: /usr/include/mach/kern_return.h
scoring.o: /usr/include/mach/machine/kern_return.h
scoring.o: /usr/include/mach/ppc/kern_return.h
scoring.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
scoring.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
scoring.o: /usr/include/mach/host_special_ports.h
scoring.o: /usr/include/mach/memory_object_types.h
scoring.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
scoring.o: /usr/include/mach/machine/exception.h
scoring.o: /usr/include/mach/ppc/exception.h
scoring.o: /usr/include/mach/thread_status.h
scoring.o: /usr/include/mach/machine/thread_status.h
scoring.o: /usr/include/mach/ppc/thread_status.h
scoring.o: /usr/include/mach/ppc/_types.h
scoring.o: /usr/include/mach/machine/thread_state.h
scoring.o: /usr/include/mach/ppc/thread_state.h
scoring.o: /usr/include/mach/processor_info.h
scoring.o: /usr/include/mach/machine/processor_info.h
scoring.o: /usr/include/mach/ppc/processor_info.h
scoring.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
scoring.o: /usr/include/mach/task_policy.h
scoring.o: /usr/include/mach/task_special_ports.h
scoring.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
scoring.o: /usr/include/mach/thread_special_ports.h
scoring.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
scoring.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
scoring.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
scoring.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
scoring.o: /usr/include/mach/machine/vm_param.h
scoring.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
scoring.o: /usr/include/mach/std_types.h ../include/license.h
scoring.o: ../include/strutil.h ../include/errors.h ../include/memory.h
scoring.o: ../include/blocks.h ../include/output.h ../include/sequences.h
scoring.o: ../include/matrix.h ../include/pattern.h ../include/residues.h
scoring.o: ../include/blastapp.h /usr/include/limits.h
scoring.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
scoring.o: /usr/include/ppc/_limits.h /usr/include/sys/syslimits.h
scoring.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
scoring.o: ../include/gcode.h scoring.h blimps.h scores.h lists.h
scoring.o: ../include/skiplist.h
sequences.o: ../include/global.h /usr/include/stdlib.h
sequences.o: /usr/include/sys/cdefs.h /usr/include/_types.h
sequences.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
sequences.o: /usr/include/ppc/_types.h /usr/include/sys/wait.h
sequences.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
sequences.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
sequences.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
sequences.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
sequences.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
sequences.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
sequences.o: /usr/include/machine/types.h /usr/include/ppc/types.h
sequences.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
sequences.o: /usr/include/ctype.h /usr/include/runetype.h
sequences.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
sequences.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
sequences.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
sequences.o: /usr/include/mach/machine/boolean.h
sequences.o: /usr/include/mach/ppc/boolean.h
sequences.o: /usr/include/mach/machine/vm_types.h
sequences.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
sequences.o: /usr/include/mach/kern_return.h
sequences.o: /usr/include/mach/machine/kern_return.h
sequences.o: /usr/include/mach/ppc/kern_return.h
sequences.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
sequences.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
sequences.o: /usr/include/mach/host_special_ports.h
sequences.o: /usr/include/mach/memory_object_types.h
sequences.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
sequences.o: /usr/include/mach/machine/exception.h
sequences.o: /usr/include/mach/ppc/exception.h
sequences.o: /usr/include/mach/thread_status.h
sequences.o: /usr/include/mach/machine/thread_status.h
sequences.o: /usr/include/mach/ppc/thread_status.h
sequences.o: /usr/include/mach/ppc/_types.h
sequences.o: /usr/include/mach/machine/thread_state.h
sequences.o: /usr/include/mach/ppc/thread_state.h
sequences.o: /usr/include/mach/processor_info.h
sequences.o: /usr/include/mach/machine/processor_info.h
sequences.o: /usr/include/mach/ppc/processor_info.h
sequences.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
sequences.o: /usr/include/mach/task_policy.h
sequences.o: /usr/include/mach/task_special_ports.h
sequences.o: /usr/include/mach/thread_info.h
sequences.o: /usr/include/mach/thread_policy.h
sequences.o: /usr/include/mach/thread_special_ports.h
sequences.o: /usr/include/mach/clock_types.h
sequences.o: /usr/include/mach/vm_attributes.h /usr/include/mach/vm_inherit.h
sequences.o: /usr/include/mach/vm_purgable.h /usr/include/mach/vm_behavior.h
sequences.o: /usr/include/mach/vm_prot.h /usr/include/mach/vm_sync.h
sequences.o: /usr/include/mach/vm_region.h
sequences.o: /usr/include/mach/machine/vm_param.h
sequences.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
sequences.o: /usr/include/mach/std_types.h ../include/license.h
sequences.o: ../include/strutil.h ../include/errors.h ../include/memory.h
sequences.o: ../include/sequences.h ../include/residues.h
sequences.o: ../include/blastapp.h /usr/include/limits.h
sequences.o: /usr/include/machine/limits.h /usr/include/ppc/limits.h
sequences.o: /usr/include/ppc/_limits.h /usr/include/sys/syslimits.h
sequences.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
sequences.o: ../include/gcode.h
sl.o: /usr/include/assert.h /usr/include/sys/cdefs.h /usr/include/time.h
sl.o: /usr/include/_types.h /usr/include/sys/_types.h
sl.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
sl.o: /usr/include/machine/_limits.h /usr/include/ppc/_limits.h
sl.o: ../include/global.h /usr/include/stdlib.h /usr/include/sys/wait.h
sl.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
sl.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
sl.o: /usr/include/sys/resource.h /usr/include/machine/endian.h
sl.o: /usr/include/ppc/endian.h /usr/include/sys/_endian.h
sl.o: /usr/include/stdint.h /usr/include/libkern/OSByteOrder.h
sl.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
sl.o: /usr/include/machine/types.h /usr/include/ppc/types.h
sl.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
sl.o: /usr/include/ctype.h /usr/include/runetype.h
sl.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
sl.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
sl.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
sl.o: /usr/include/mach/machine/boolean.h /usr/include/mach/ppc/boolean.h
sl.o: /usr/include/mach/machine/vm_types.h /usr/include/mach/ppc/vm_types.h
sl.o: /usr/include/ppc/vmparam.h /usr/include/mach/kern_return.h
sl.o: /usr/include/mach/machine/kern_return.h
sl.o: /usr/include/mach/ppc/kern_return.h /usr/include/mach/vm_statistics.h
sl.o: /usr/include/mach/machine.h /usr/include/mach/time_value.h
sl.o: /usr/include/mach/host_notify.h /usr/include/mach/host_special_ports.h
sl.o: /usr/include/mach/memory_object_types.h /usr/include/mach/vm_types.h
sl.o: /usr/include/mach/exception_types.h
sl.o: /usr/include/mach/machine/exception.h /usr/include/mach/ppc/exception.h
sl.o: /usr/include/mach/thread_status.h
sl.o: /usr/include/mach/machine/thread_status.h
sl.o: /usr/include/mach/ppc/thread_status.h /usr/include/mach/ppc/_types.h
sl.o: /usr/include/mach/machine/thread_state.h
sl.o: /usr/include/mach/ppc/thread_state.h /usr/include/mach/processor_info.h
sl.o: /usr/include/mach/machine/processor_info.h
sl.o: /usr/include/mach/ppc/processor_info.h /usr/include/mach/task_info.h
sl.o: /usr/include/mach/policy.h /usr/include/mach/task_policy.h
sl.o: /usr/include/mach/task_special_ports.h /usr/include/mach/thread_info.h
sl.o: /usr/include/mach/thread_policy.h
sl.o: /usr/include/mach/thread_special_ports.h
sl.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
sl.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
sl.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
sl.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
sl.o: /usr/include/mach/machine/vm_param.h /usr/include/mach/ppc/vm_param.h
sl.o: /usr/include/mach/kmod.h /usr/include/mach/std_types.h
sl.o: ../include/license.h ../include/strutil.h ../include/errors.h
sl.o: ../include/memory.h ../include/skiplist.h
strutil.o: ../include/global.h /usr/include/stdlib.h /usr/include/sys/cdefs.h
strutil.o: /usr/include/_types.h /usr/include/sys/_types.h
strutil.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
strutil.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
strutil.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
strutil.o: /usr/include/ppc/signal.h /usr/include/sys/resource.h
strutil.o: /usr/include/machine/endian.h /usr/include/ppc/endian.h
strutil.o: /usr/include/sys/_endian.h /usr/include/stdint.h
strutil.o: /usr/include/libkern/OSByteOrder.h
strutil.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
strutil.o: /usr/include/machine/types.h /usr/include/ppc/types.h
strutil.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
strutil.o: /usr/include/ctype.h /usr/include/runetype.h
strutil.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
strutil.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
strutil.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
strutil.o: /usr/include/mach/machine/boolean.h
strutil.o: /usr/include/mach/ppc/boolean.h
strutil.o: /usr/include/mach/machine/vm_types.h
strutil.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
strutil.o: /usr/include/mach/kern_return.h
strutil.o: /usr/include/mach/machine/kern_return.h
strutil.o: /usr/include/mach/ppc/kern_return.h
strutil.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
strutil.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
strutil.o: /usr/include/mach/host_special_ports.h
strutil.o: /usr/include/mach/memory_object_types.h
strutil.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
strutil.o: /usr/include/mach/machine/exception.h
strutil.o: /usr/include/mach/ppc/exception.h
strutil.o: /usr/include/mach/thread_status.h
strutil.o: /usr/include/mach/machine/thread_status.h
strutil.o: /usr/include/mach/ppc/thread_status.h
strutil.o: /usr/include/mach/ppc/_types.h
strutil.o: /usr/include/mach/machine/thread_state.h
strutil.o: /usr/include/mach/ppc/thread_state.h
strutil.o: /usr/include/mach/processor_info.h
strutil.o: /usr/include/mach/machine/processor_info.h
strutil.o: /usr/include/mach/ppc/processor_info.h
strutil.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
strutil.o: /usr/include/mach/task_policy.h
strutil.o: /usr/include/mach/task_special_ports.h
strutil.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
strutil.o: /usr/include/mach/thread_special_ports.h
strutil.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
strutil.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
strutil.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
strutil.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
strutil.o: /usr/include/mach/machine/vm_param.h
strutil.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
strutil.o: /usr/include/mach/std_types.h ../include/license.h
strutil.o: ../include/strutil.h ../include/errors.h ../include/memory.h
version.o: ../include/global.h /usr/include/stdlib.h /usr/include/sys/cdefs.h
version.o: /usr/include/_types.h /usr/include/sys/_types.h
version.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
version.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
version.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
version.o: /usr/include/ppc/signal.h /usr/include/sys/resource.h
version.o: /usr/include/machine/endian.h /usr/include/ppc/endian.h
version.o: /usr/include/sys/_endian.h /usr/include/stdint.h
version.o: /usr/include/libkern/OSByteOrder.h
version.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
version.o: /usr/include/machine/types.h /usr/include/ppc/types.h
version.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
version.o: /usr/include/ctype.h /usr/include/runetype.h
version.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
version.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
version.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
version.o: /usr/include/mach/machine/boolean.h
version.o: /usr/include/mach/ppc/boolean.h
version.o: /usr/include/mach/machine/vm_types.h
version.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
version.o: /usr/include/mach/kern_return.h
version.o: /usr/include/mach/machine/kern_return.h
version.o: /usr/include/mach/ppc/kern_return.h
version.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
version.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
version.o: /usr/include/mach/host_special_ports.h
version.o: /usr/include/mach/memory_object_types.h
version.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
version.o: /usr/include/mach/machine/exception.h
version.o: /usr/include/mach/ppc/exception.h
version.o: /usr/include/mach/thread_status.h
version.o: /usr/include/mach/machine/thread_status.h
version.o: /usr/include/mach/ppc/thread_status.h
version.o: /usr/include/mach/ppc/_types.h
version.o: /usr/include/mach/machine/thread_state.h
version.o: /usr/include/mach/ppc/thread_state.h
version.o: /usr/include/mach/processor_info.h
version.o: /usr/include/mach/machine/processor_info.h
version.o: /usr/include/mach/ppc/processor_info.h
version.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
version.o: /usr/include/mach/task_policy.h
version.o: /usr/include/mach/task_special_ports.h
version.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
version.o: /usr/include/mach/thread_special_ports.h
version.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
version.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
version.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
version.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
version.o: /usr/include/mach/machine/vm_param.h
version.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
version.o: /usr/include/mach/std_types.h ../include/license.h
version.o: ../include/strutil.h ../include/errors.h ../include/memory.h
version.o: ../include/version.h
options.o: ../include/global.h /usr/include/stdlib.h /usr/include/sys/cdefs.h
options.o: /usr/include/_types.h /usr/include/sys/_types.h
options.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
options.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
options.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
options.o: /usr/include/ppc/signal.h /usr/include/sys/resource.h
options.o: /usr/include/machine/endian.h /usr/include/ppc/endian.h
options.o: /usr/include/sys/_endian.h /usr/include/stdint.h
options.o: /usr/include/libkern/OSByteOrder.h
options.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/alloca.h
options.o: /usr/include/machine/types.h /usr/include/ppc/types.h
options.o: /usr/include/stdio.h /usr/include/string.h /usr/include/stddef.h
options.o: /usr/include/ctype.h /usr/include/runetype.h
options.o: /usr/include/malloc/malloc.h /usr/include/mach/mach_types.h
options.o: /usr/include/mach/host_info.h /usr/include/mach/message.h
options.o: /usr/include/mach/port.h /usr/include/mach/boolean.h
options.o: /usr/include/mach/machine/boolean.h
options.o: /usr/include/mach/ppc/boolean.h
options.o: /usr/include/mach/machine/vm_types.h
options.o: /usr/include/mach/ppc/vm_types.h /usr/include/ppc/vmparam.h
options.o: /usr/include/mach/kern_return.h
options.o: /usr/include/mach/machine/kern_return.h
options.o: /usr/include/mach/ppc/kern_return.h
options.o: /usr/include/mach/vm_statistics.h /usr/include/mach/machine.h
options.o: /usr/include/mach/time_value.h /usr/include/mach/host_notify.h
options.o: /usr/include/mach/host_special_ports.h
options.o: /usr/include/mach/memory_object_types.h
options.o: /usr/include/mach/vm_types.h /usr/include/mach/exception_types.h
options.o: /usr/include/mach/machine/exception.h
options.o: /usr/include/mach/ppc/exception.h
options.o: /usr/include/mach/thread_status.h
options.o: /usr/include/mach/machine/thread_status.h
options.o: /usr/include/mach/ppc/thread_status.h
options.o: /usr/include/mach/ppc/_types.h
options.o: /usr/include/mach/machine/thread_state.h
options.o: /usr/include/mach/ppc/thread_state.h
options.o: /usr/include/mach/processor_info.h
options.o: /usr/include/mach/machine/processor_info.h
options.o: /usr/include/mach/ppc/processor_info.h
options.o: /usr/include/mach/task_info.h /usr/include/mach/policy.h
options.o: /usr/include/mach/task_policy.h
options.o: /usr/include/mach/task_special_ports.h
options.o: /usr/include/mach/thread_info.h /usr/include/mach/thread_policy.h
options.o: /usr/include/mach/thread_special_ports.h
options.o: /usr/include/mach/clock_types.h /usr/include/mach/vm_attributes.h
options.o: /usr/include/mach/vm_inherit.h /usr/include/mach/vm_purgable.h
options.o: /usr/include/mach/vm_behavior.h /usr/include/mach/vm_prot.h
options.o: /usr/include/mach/vm_sync.h /usr/include/mach/vm_region.h
options.o: /usr/include/mach/machine/vm_param.h
options.o: /usr/include/mach/ppc/vm_param.h /usr/include/mach/kmod.h
options.o: /usr/include/mach/std_types.h ../include/license.h
options.o: ../include/strutil.h ../include/errors.h ../include/memory.h
options.o: ../include/options.h
protomat.o: /usr/include/sys/types.h /usr/include/sys/appleapiopts.h
protomat.o: /usr/include/sys/cdefs.h /usr/include/machine/types.h
protomat.o: /usr/include/ppc/types.h /usr/include/ppc/_types.h
protomat.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
protomat.o: /usr/include/machine/endian.h /usr/include/ppc/endian.h
protomat.o: /usr/include/sys/_endian.h /usr/include/stdint.h
protomat.o: /usr/include/libkern/OSByteOrder.h
protomat.o: /usr/include/libkern/ppc/OSByteOrder.h /usr/include/dirent.h
protomat.o: /usr/include/_types.h /usr/include/sys/dirent.h
protomat.o: /usr/include/ctype.h /usr/include/runetype.h
protomat.o: ../include/protomat.h /usr/include/stdlib.h
protomat.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
protomat.o: /usr/include/machine/signal.h /usr/include/ppc/signal.h
protomat.o: /usr/include/sys/resource.h /usr/include/alloca.h
protomat.o: /usr/include/stdio.h /usr/include/string.h
lobal.h /usr/include/stdlib.h /usr/include/sys/cdefs.h
strutil.o: /usr/include/_types.h /usr/include/sys/_types.h
strutil.o: /usr/include/machine/_types.h /usr/include/ppc/_types.h
strutil.o: /usr/include/sys/wait.h /usr/include/sys/signal.h
strutil.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
stblimps-3.9/blimps/README.OSX000064400001460000012000000007101042724502600157640ustar00jorjastaff000004000000275/6/2006 Mac/OSX compile notes
----------------------------------------------------------------------------
Darwin 8.2.0 Darwin Kernel Version 8.2.0: Fri Jun 24 17:46:54 PDT 2005; root:xnu-792.2.4.obj~3/RELEASE_PPC Power Macintosh powerpc
-----------------------------------------------------------------------
gcc-3.3:
Reading specs from /usr/libexec/gcc/darwin/ppc/3.3/specs
Thread model: posix
gcc version 3.3 20030304 (Apple Computer, Inc. build 1809)
blimps-3.9/blimps/Makefile.Sun_intel000064400001460000012000003127271062462107200200470ustar00jorjastaff00000400000027# Makefile: makefile for BLIMPS blocks searcher
# Written by: Bill Alford
# (C) Copyright 1993-9, Fred Hutchinson Cancer Research Center 
# Use, modification or distribution of these programs is subject to 
# the terms of the non-commercial licensing agreement in license.h. 

# Instructions for use:
# 1. Change DEFINES, SYSTEM, OPTIMIZ, RANLIB, CC for your system
# 2. make depend
# 3. make install (updates ../bin and ../lib)


# System defines.  The main reason for this is that on the Sun there is a 
# function malloc_debug() wich will raise a signal if there are problems
# with memory.  The problem is that there is no function like that on other
# machines, at least that I've seen.  Defines are set up so that the
# malloc_debug call is only in the Sun code.

# Generic -- Should work on most systems not listed below.
#DEFINES = -DNO_STRDUP
#SYSTEM  = generic 
#OPTIMIZ =
#RANLIB = ../bin/ranlib

# SunOS
#DEFINES = 
#SYSTEM  = sun4.1.3
#OPTIMIZ = -O
#RANLIB = /bin/ranlib
## For debugging.
# DEFINES = -DMALLOC_DEBUG
# OTHER_OBJS = /usr/lib/debug/malloc.o 

# Sun Solaris
#DEFINES = 
#SYSTEM = solaris
#	Some programs don't give the same results when compiled with -fast,
#	e.g. codehop.c; offending options -fsimple=2
#OPTIMIZ = -fast
#OPTIMIZ = -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=2 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit 
#OPTIMIZ = -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit
#OPTIMIZ = -g
#	RANLIB is obsolete under Solaris 2.5; just put something here
#	so the Makefile continues to work.

# Linux
DEFINES = 
SYSTEM  = 
OPTIMIZ = -Wall -O2
RANLIB = ls

MAKE = make
DEPEND = makedepend

#	ar -t libpssm.a for table of contents
AR = ar
RM = rm -f
MV = mv -f 
CP = cp


# C compiler
CC = /usr/sfw/bin/gcc
#	Version from sunfreeware.com
#CC = /usr/local/bin/gcc
#CC = /opt/SUNWspro/bin/cc

# Optimization level (or debugging)
#OPTIMIZ = -g
#OPTIMIZ = -g -O $(WARNS) $(XWARN)
#OPTIMIZ = -p
WARNS = -W \
	-Wreturn-type \
	-Wswitch \
	-Wcomment \
	-Wtrigraphs \
	-Wformat \
	-Wparentheses 

# like -Wall but without 
#   -Wimplicit  -- gets all the printf's etc..
#   -Wunused    -- gets all the rcsid and 3 funcs. I know about
#   -Wchar-subscripts -- gets all ??_atob arrays (ascii to binary residue)
#   -Wuninitialized -- Caught 4 places which are tricky cases but are OK.

WARNS2 = -Wall
XWARN = -Wshadow \
	-Wcast-qual \
	-Wcast-align \
	-Wpointer-arith \
	-Waggregate-return \
	-Wredundant-decls \
	-Wnested-externs \
	-Winline

#    -Wtraditional -- gets printf, fprintf, etc.
#    -Wid-clash-16 -- causes lots of warnings.
#    -Wwrite-strings -- causes a LOT of warnings, think all are needed.
#    -Wconversion  -- causes a lot of warnings, but they look like they 
#                       should be OK.
#    -Wstrict-prototypes -Wmissing-prototypes -- too many to count...

XXWARN = -Werror

INCLUDE_DIR = ../include
INCLUDES = -I$(INCLUDE_DIR)


# C Flags to compiler
#CFLAGS = `getconf LFS_CFLAGS` $(OPTIMIZ) $(DEFINES) $(INCLUDES)
CFLAGS = $(OPTIMIZ) $(DEFINES) $(INCLUDES)


# Linker Flags
LDFLAGS = $(CFLAGS)
LDLIBS = -lblimps -lm
LDOPTIONS = $(LDFLAGS) $(LDDIR)
# cc ld options


#LIBRARY_DIR = ../lib
LIBRARY_DIR = ./
LDDIR = -L$(LIBRARY_DIR)


# source files
SRCS =  blimps-mem.c \
	blimps.c \
	blweight.c \
	blalign.c \
	bldist.c \
	blk2pssm.c \
	rank_matrix.c \
	retblock.c \
	codehop.c \
        htmlize-codehop.c \
        oligo_melt.c \
	mablock.c \
	cobbler.c \
	addseqs.c \
	fastaseqs.c \
	LAMA.c \
	find_biassed_blocks.c \
	makeblockmap.c \
	prints2blocks.c \
	lisblk.c \
	coduse.c \
	narrow.c \
	blk2slx.c \
	blkprob.c \
	blocks.c \
	config.c \
	convert.c \
	errors.c \
	files.c \
	frequency.c \
	gcode.c \
	lists.c \
	matrix.c \
	memory.c \
	pattern.c \
	scores.c \
	scoring.c \
	sequences.c \
	sl.c \
	strutil.c \
	version.c \
	options.c \
	protomat.c  \
	interpro.c \
	pssmdist.c \
	pssmBL.c \
	papssm.c \
	matrix_logob.c \
	makelogob.c \
	blocks_search.c \
	LAMA_search.c \
	block_vis.c \
	format_block.c \
	biassed_blocks_finder.c \
	htmlize-LAMA.c \
	show_aligned_blocks.c \
	blk2mot.c 

HDRS =  blimps.h \
	blweight.h \
	blimps-mem.h \
	config.h \
	lists.h \
	scores.h \
	scoring.h \
	protomat.h \
	p2c.h


# need the OBJS for blimps dependencies on the .o files.  I don't know a 
# way around this.

OTHER_OBJS_DEBUG =	/usr/lib/debug/malloc.o \
		/usr/lib/debug/mallocmap.o

LIBOBJS = pattern.o \
	files.o \
	frequency.o \
	convert.o \
	blocks.o \
	errors.o \
	gcode.o \
	matrix.o \
	memory.o \
	sequences.o \
	strutil.o \
	sl.o \
	version.o \
	options.o \
	blimps-mem.o \
	config.o \
	lists.o \
	scores.o \
	scoring.o \
	p2clib.o \
	util.o \
        protomat.o


# need malloc.o for malloc_debug() which will have free() raise SIGABRT
# if it is unable to free the space.

LIBRARIES = libblimps.a


########################################################################
########################################################################
#
# main dependencies
#
########################################################################
########################################################################

install: clean all move-lib move-bin

all: lib blimps blweight blalign bldist blk2pssm rank_matrix retblock codehop htmlize-codehop oligo_melt mablock cobbler addseqs fastaseqs LAMA find_biassed_blocks makeblockmap prints2blocks lisblk coduse narrow blk2slx blkprob interpro pssmdist pssmBL papssm matrix_logob makelogob blocks_search LAMA_search block_vis format_block biassed_blocks_finder htmlize-LAMA show_aligned_blocks makelis blk2mot 

blimps: $(LIBRARIES) blimps.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blimps.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

makelis: $(LIBRARIES)  makelis.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  makelis.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blweight: $(LIBRARIES) blweight.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blweight.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blalign: $(LIBRARIES) blalign.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blalign.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

bldist: $(LIBRARIES) bldist.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  bldist.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 
blk2pssm: $(LIBRARIES) blk2pssm.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blk2pssm.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

rank_matrix: $(LIBRARIES) rank_matrix.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  rank_matrix.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

retblock: $(LIBRARIES) retblock.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  retblock.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

codehop: $(LIBRARIES) codehop.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  codehop.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

htmlize-codehop: $(LIBRARIES) htmlize-codehop.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  htmlize-codehop.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

oligo_melt: $(LIBRARIES) oligo_melt.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  oligo_melt.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

mablock: $(LIBRARIES) mablock.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  mablock.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

cobbler: $(LIBRARIES) cobbler.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  cobbler.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

addseqs: $(LIBRARIES) addseqs.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  addseqs.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

fastaseqs: $(LIBRARIES) fastaseqs.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  fastaseqs.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

LAMA: $(LIBRARIES) LAMA.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  LAMA.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

find_biassed_blocks: $(LIBRARIES) find_biassed_blocks.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  find_biassed_blocks.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

makeblockmap: $(LIBRARIES) makeblockmap.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  makeblockmap.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

prints2blocks: $(LIBRARIES) prints2blocks.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  prints2blocks.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

lisblk: $(LIBRARIES) lisblk.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  lisblk.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

coduse: $(LIBRARIES) coduse.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  coduse.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

narrow: $(LIBRARIES) narrow.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  narrow.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blk2slx: $(LIBRARIES) blk2slx.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blk2slx.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blkprob: $(LIBRARIES) blkprob.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blkprob.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

interpro: $(LIBRARIES) interpro.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  interpro.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

pssmdist: $(LIBRARIES) pssmdist.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  pssmdist.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

pssmBL: $(LIBRARIES) pssmBL.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  pssmBL.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

papssm: $(LIBRARIES) papssm.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  papssm.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

matrix_logob: $(LIBRARIES) matrix_logob.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  matrix_logob.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

makelogob: $(LIBRARIES) makelogob.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  makelogob.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blocks_search: $(LIBRARIES) blocks_search.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  blocks_search.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

LAMA_search: $(LIBRARIES) LAMA_search.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  LAMA_search.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

block_vis: $(LIBRARIES) block_vis.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  block_vis.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

format_block: $(LIBRARIES) format_block.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  format_block.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

biassed_blocks_finder: $(LIBRARIES) biassed_blocks_finder.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  biassed_blocks_finder.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

htmlize-LAMA: $(LIBRARIES) htmlize-LAMA.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  htmlize-LAMA.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

show_aligned_blocks: $(LIBRARIES) show_aligned_blocks.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  show_aligned_blocks.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blk2mot: $(LIBRARIES) blk2mot.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  blk2mot.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 


$(LIBOBJS):


########################################################################
########################################################################
#
# include dependencies
#
########################################################################
########################################################################

# none




########################################################################
########################################################################
#
# library dependencies
#
########################################################################
########################################################################

lib: ranlib $(LIBRARIES)

ranlib:
	$(GET_FILES)

#	( cd $(LIBRARY_DIR) ; $(MAKE) $(MFLAGS) )

#
# The libraries.
#

libblimps.a: $(LIBOBJS)
	$(AR) cr $@ $(LIBOBJS) ; $(RANLIB) $@

########################################################################
########################################################################
#
# Local building (for us)
#
########################################################################
########################################################################

#  os = OS_machinename_version
local: clean clean-include clean-lib 
	echo " " ; \
	echo "Making directories..." ; \
	echo " " ; \
	os="`uname -sr | tr ' ' '_'`" ; \
	osdir="../$$os" ; \
	rm -rf $$osdir ; \
	mkdir $$osdir $$osdir/bin $$osdir/include $$osdir/lib ; \
	echo " " ; \
	echo "Running 'make depend' and 'make all'..." ; \
	echo " " ; \
	make depend ; make all	; \
	echo " " ; \
	echo "Copying libraries..." ; \
	echo " " ; \
	cp ../lib/*.a $$osdir/lib ; \
	echo " " ; \
	echo "Copying header files..." ; \
	echo " " ; \
	cp ../include/*.h $$osdir/include ; \
	echo " " ; \
	echo "Copying binary..." ; \
	echo " " ; \
	cp blimps $$osdir/bin





########################################################################
########################################################################
#
# Maintenance dependencies
#
########################################################################
########################################################################


tags: 
	etags ./*.[ch] $(INCLUDE_DIR)/*.[ch]


depend: 
	 $(DEPEND) -- $(CFLAGS) -- -s "# DO NOT DELETE" -- $(SRCS)


clean::
	$(RM) blimps blweight blalign bldist blk2pssm rank_matrix retblock codehop htmlize-codehop oligo_melt mablock makeblockmap prints2blocks lisblk coduse narrow blkprob blk2slx LAMA find_biassed_blocks fastaseqs addseqs cobbler interpro pssmdist pssmBL papssm matrix_logob makelogob blocks_search LAMA_search block_vis format_block biassed_blocks_finder htmlize-LAMA show_aligned_blocks makelis blk2mot 
	$(RM) *.a *.o *~ 
	@echo " "

move-lib:
	$(MV) lib*.a ../lib

move-bin:
	$(MV) blimps ../bin
	$(MV) blweight ../bin
	$(MV) blalign ../bin
	$(MV) bldist ../bin
	$(MV) blk2pssm ../bin
	$(MV) rank_matrix ../bin
	$(MV) retblock ../bin
	$(MV) codehop ../bin
	$(MV) htmlize-codehop ../bin
	$(MV) oligo_melt ../bin
	$(MV) mablock ../bin
	$(MV) makeblockmap ../bin
	$(MV) prints2blocks ../bin
	$(MV) lisblk ../bin
	$(MV) coduse ../bin
	$(MV) narrow ../bin
	$(MV) blkprob ../bin
	$(MV) blk2slx ../bin
	$(MV) LAMA ../bin
	$(MV) find_biassed_blocks ../bin
	$(MV) fastaseqs ../bin
	$(MV) addseqs ../bin
	$(MV) cobbler ../bin
	$(MV) interpro ../bin
	$(MV) pssmdist ../bin
	$(MV) pssmBL ../bin
	$(MV) papssm ../bin
	$(MV) matrix_logob ../bin
	$(MV) makelogob ../bin
	$(MV) blocks_search ../bin
	$(MV) LAMA_search ../bin
	$(MV) block_vis ../bin
	$(MV) format_block ../bin
	$(MV) biassed_blocks_finder ../bin
	$(MV) htmlize-LAMA ../bin
	$(MV) show_aligned_blocks ../bin
	$(MV) makelis ../bin
	$(MV) blk2mot ../bin


##########
##########
#
# Distribution dependencies
#
##########
##########

SOURCEDIR  = /lab/billa/blimps/dev
BUILDDIR   = /lab/billa/blimps/build-local
DISTRIBDIR = /lab/billa/blimps/distrib
VERSIONDISTRIB = $(DISTRIBDIR).$(VERSION)
BLIMPSDIR  = $(DISTRIBDIR)/blimps
FTPDIR     = /lab/ftp/blimps

TXTVER = `echo  $(VERSION) | \
	 awk -F. '{printf("%d.%d%c", $$1, $$2 / 1000 , \
	 ( $$2 % 1000 ) / 100 + 65)}'`

#
# REMEMBER: each line executes in the directory make started in
#

local-binary: clean-local-binary
	@if [ "$(VERSION)" = "" ] ; then \
		echo "No version specified, bailing out." ; \
		echo "use as: make [ target ... ] VERSION=1.1001" ; \
		echo "    ex: make distrib VERSION=1.1001" ; \
		bail-out-here ; \
	fi
	
	@echo Building local binary for distribution . . .
	@echo " "
	
	@echo Making local build directory . . .
	@mkdir -p $(BUILDDIR)
	
	@echo Making blimps, lib, and include subdirectories . . .
	@mkdir -p $(BUILDDIR)/blimps
	@mkdir -p $(BUILDDIR)/lib
	@mkdir -p $(BUILDDIR)/include
	
	@echo Copying Makefiles over . . .
	@echo REMOVING RCS SUBDIR DEPENDENCY BY THE GREP > /dev/null
	@cat $(SOURCEDIR)/blimps/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BUILDDIR)/blimps/Makefile
	@cat $(SOURCEDIR)/lib/Makefile | grep -v 'RCS/\$$\$$\@,v' >    $(BUILDDIR)/lib/Makefile
	@cat $(SOURCEDIR)/include/Makefile | grep -v 'RCS/\$$\$$\@,v' >$(BUILDDIR)/include/Makefile
	
	@ln -s $(SOURCEDIR)/blimps/RCS  $(BUILDDIR)/blimps/RCS
	@ln -s $(SOURCEDIR)/lib/RCS     $(BUILDDIR)/lib/RCS
	@ln -s $(SOURCEDIR)/include/RCS $(BUILDDIR)/include/RCS
	
	@echo Making local version dependencies . . .
	cd $(BUILDDIR)/blimps ; make VERSION="$(VERSION)" clean ; make VERSION="$(VERSION)" depend 
	
	@echo Removing RCS files to test distrib compilation
	@rm -f $(BUILDDIR)/blimps/RCS
	@rm -f $(BUILDDIR)/lib/RCS
	@rm -f $(BUILDDIR)/include/RCS
	
	@echo Making local version . . .
	cd $(BUILDDIR)/blimps ; make VERSION="$(VERSION)" blimps
	
	@echo Moving local binary into distribution directory . . .
	@mv $(BUILDDIR)/blimps/blimps $(SOURCEDIR)/bin/blimps.$(SYSTEM)
	@echo " "

clean-local-binary:
	@echo Cleaning local build directory \($(BUILDDIR)\) . . .
	rm -rf $(BUILDDIR)
	@echo " "


distrib: local-binary clean-distrib
	@if [ "$(VERSION)" = "" ] ; then \
		echo "No version specified, bailing out." ; \
		echo "use as: make [ target ... ] VERSION=1.1001" ; \
		echo "    ex: make distrib VERSION=1.1001" ; \
		bail-out-here ; \
	fi
	
	@echo Making distribution . . .
	@echo " "
	
	@echo Making distribution directories . . .
	@mkdir -p $(DISTRIBDIR)
	@mkdir -p $(BLIMPSDIR) \
		  $(BLIMPSDIR)/docs \
		  $(BLIMPSDIR)/blimps \
		  $(BLIMPSDIR)/lib \
		  $(BLIMPSDIR)/include \
		  $(BLIMPSDIR)/bin
	@ln -s $(SOURCEDIR)/blimps/RCS  $(BLIMPSDIR)/blimps/RCS
	@ln -s $(SOURCEDIR)/lib/RCS     $(BLIMPSDIR)/lib/RCS
	@ln -s $(SOURCEDIR)/include/RCS $(BLIMPSDIR)/include/RCS
	@ln -s $(SOURCEDIR)/docs/RCS    $(BLIMPSDIR)/docs/RCS
	
	@echo Copying Makefiles over . . .
	@cat $(SOURCEDIR)/blimps/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BLIMPSDIR)/blimps/Makefile
	@cat $(SOURCEDIR)/lib/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BLIMPSDIR)/lib/Makefile
	@cat $(SOURCEDIR)/include/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BLIMPSDIR)/include/Makefile
	
	@echo Making depend on the Makefiles to checkout the files
	cd $(BLIMPSDIR)/blimps ; make VERSION="$(VERSION)" depend
	@rm -f $(BLIMPSDIR)/blimps/RCS
	@rm -f $(BLIMPSDIR)/lib/RCS
	@rm -f $(BLIMPSDIR)/include/RCS
	
	@echo Copying distribution documents of version $(VERSION) into docs directory . . .
	@cd $(BLIMPSDIR)/docs ; co -q -r$(VERSION) RCS/*
	@rm -f $(BLIMPSDIR)/docs/RCS
	@cd $(BLIMPSDIR)/docs ; cp README INSTALL ..
	
	@echo Copying pre-compiled binaries into bin directory . . .
	@cp $(SOURCEDIR)/bin/* $(BLIMPSDIR)/bin/
	
	@echo Moving blimps to blimps.$(TXTVER)
	@mv $(BLIMPSDIR) $(DISTRIBDIR)/blimps.$(TXTVER)
	@echo " "
	
	@echo Making tar file . . .
	@cd $(DISTRIBDIR) ; tar cf blimps.$(TXTVER).tar blimps.$(TXTVER)
	
	@echo Compressing tar file . . .
	@cd $(DISTRIBDIR) ; compress blimps.$(TXTVER).tar
	@echo " "
	
	@echo Moving distrib dir to distrib.$(VERSION)
	@mv $(DISTRIBDIR) $(VERSIONDISTRIB)

clean-distrib:
	@echo  Cleaning distribution directories:
	@echo "     $(DISTRIBDIR)"
	@echo "     $(VERSIONDISTRIB)"
	@echo " . . . "
	rm -rf $(DISTRIBDIR) $(VERSIONDISTRIB)
	@echo " "

$(VERSIONDISTRIB):	distrib

ftp:	$(VERSIONDISTRIB)
	@echo Moving files to the ftp directory . . .
	@echo " "
	
	@echo Copying tar file to the ftp directory . . .
	@cp $(VERSIONDISTRIB)/blimps.$(TXTVER).tar.Z $(FTPDIR)
	@echo " "
	
	@echo Copying README and INSTALL files to the ftp directory . . .
	@rm -f $(FTPDIR)/README $(FTPDIR)/INSTALL 
	@cp $(VERSIONDISTRIB)/blimps.$(TXTVER)/docs/README \
	  $(VERSIONDISTRIB)/blimps.$(TXTVER)/docs/INSTALL $(FTPDIR)
	@echo " "



###########################################################################

 
###########################################################################
# dependencies generated by makedepend
 
# DO NOT DELETE

blimps-mem.o: ../include/global.h /usr/include/stdlib.h
blimps-mem.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blimps-mem.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
blimps-mem.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
blimps-mem.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blimps-mem.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blimps-mem.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
blimps-mem.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
blimps-mem.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
blimps-mem.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
blimps-mem.o: /usr/include/malloc.h /usr/include/sys/types.h
blimps-mem.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
blimps-mem.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
blimps-mem.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
blimps-mem.o: /usr/include/sys/time.h ../include/license.h
blimps-mem.o: ../include/strutil.h ../include/errors.h ../include/memory.h
blimps-mem.o: blimps-mem.h blimps.h lists.h ../include/skiplist.h
blimps.o: /usr/include/math.h /usr/include/iso/math_iso.h
blimps.o: /usr/include/sys/feature_tests.h /usr/include/sys/ccompile.h
blimps.o: /usr/include/sys/isa_defs.h /usr/include/iso/math_c99.h
blimps.o: /usr/include/signal.h /usr/include/iso/signal_iso.h
blimps.o: /usr/include/sys/iso/signal_iso.h /usr/include/sys/unistd.h
blimps.o: /usr/include/sys/signal.h ../include/global.h /usr/include/stdlib.h
blimps.o: /usr/include/iso/stdlib_iso.h /usr/include/iso/stdlib_c99.h
blimps.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
blimps.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
blimps.o: /usr/include/stdio_impl.h /usr/include/iso/stdio_c99.h
blimps.o: /usr/include/string.h /usr/include/iso/string_iso.h
blimps.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
blimps.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blimps.o: /usr/include/iso/ctype_c99.h /usr/include/malloc.h
blimps.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
blimps.o: /usr/include/ia32/sys/machtypes.h /usr/include/sys/int_types.h
blimps.o: /usr/include/sys/select.h /usr/include/sys/time_impl.h
blimps.o: /usr/include/sys/time.h /usr/include/sys/time.h
blimps.o: ../include/license.h ../include/strutil.h ../include/errors.h
blimps.o: ../include/memory.h ../include/version.h ../include/residues.h
blimps.o: ../include/blastapp.h /usr/include/limits.h
blimps.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
blimps.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
blimps.o: ../include/files.h ../include/blocks.h ../include/output.h
blimps.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blimps.o: ../include/convert.h ../include/frequency.h ../include/options.h
blimps.o: blimps.h blimps-mem.h config.h scores.h scoring.h lists.h
blimps.o: ../include/skiplist.h
blweight.o: ../include/blocksprogs.h /usr/include/stdlib.h
blweight.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blweight.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
blweight.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
blweight.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blweight.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blweight.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
blweight.o: /usr/include/iso/string_iso.h /usr/include/math.h
blweight.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
blweight.o: /usr/include/unistd.h /usr/include/sys/types.h
blweight.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
blweight.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
blweight.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
blweight.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
blweight.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blweight.o: /usr/include/iso/ctype_c99.h ../include/global.h
blweight.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
blweight.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
blweight.o: ../include/errors.h ../include/memory.h ../include/residues.h
blweight.o: ../include/blastapp.h /usr/include/limits.h
blweight.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
blweight.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
blweight.o: ../include/blocks.h ../include/output.h ../include/sequences.h
blweight.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
blweight.o: ../include/frequency.h ../include/files.h ../include/protomat.h
blalign.o: ../include/blocksprogs.h /usr/include/stdlib.h
blalign.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blalign.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
blalign.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
blalign.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blalign.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blalign.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
blalign.o: /usr/include/iso/string_iso.h /usr/include/math.h
blalign.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
blalign.o: /usr/include/unistd.h /usr/include/sys/types.h
blalign.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
blalign.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
blalign.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
blalign.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
blalign.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blalign.o: /usr/include/iso/ctype_c99.h ../include/global.h
blalign.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
blalign.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
blalign.o: ../include/errors.h ../include/memory.h ../include/residues.h
blalign.o: ../include/blastapp.h /usr/include/limits.h
blalign.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
blalign.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
blalign.o: ../include/blocks.h ../include/output.h ../include/sequences.h
blalign.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
blalign.o: ../include/frequency.h ../include/files.h ../include/protomat.h
bldist.o: ../include/blocksprogs.h /usr/include/stdlib.h
bldist.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
bldist.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
bldist.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
bldist.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
bldist.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
bldist.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
bldist.o: /usr/include/iso/string_iso.h /usr/include/math.h
bldist.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
bldist.o: /usr/include/unistd.h /usr/include/sys/types.h
bldist.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
bldist.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
bldist.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
bldist.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
bldist.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
bldist.o: /usr/include/iso/ctype_c99.h ../include/global.h
bldist.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
bldist.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
bldist.o: ../include/errors.h ../include/memory.h ../include/residues.h
bldist.o: ../include/blastapp.h /usr/include/limits.h
bldist.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
bldist.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
bldist.o: ../include/blocks.h ../include/output.h ../include/sequences.h
bldist.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
bldist.o: ../include/frequency.h ../include/files.h ../include/protomat.h
blk2pssm.o: ../include/blocksprogs.h /usr/include/stdlib.h
blk2pssm.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blk2pssm.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
blk2pssm.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
blk2pssm.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blk2pssm.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blk2pssm.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
blk2pssm.o: /usr/include/iso/string_iso.h /usr/include/math.h
blk2pssm.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
blk2pssm.o: /usr/include/unistd.h /usr/include/sys/types.h
blk2pssm.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
blk2pssm.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
blk2pssm.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
blk2pssm.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
blk2pssm.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blk2pssm.o: /usr/include/iso/ctype_c99.h ../include/global.h
blk2pssm.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
blk2pssm.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
blk2pssm.o: ../include/errors.h ../include/memory.h ../include/residues.h
blk2pssm.o: ../include/blastapp.h /usr/include/limits.h
blk2pssm.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
blk2pssm.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
blk2pssm.o: ../include/blocks.h ../include/output.h ../include/sequences.h
blk2pssm.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
blk2pssm.o: ../include/frequency.h ../include/files.h ../include/protomat.h
rank_matrix.o: ../include/blocksprogs.h /usr/include/stdlib.h
rank_matrix.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
rank_matrix.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
rank_matrix.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
rank_matrix.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
rank_matrix.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
rank_matrix.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
rank_matrix.o: /usr/include/iso/string_iso.h /usr/include/math.h
rank_matrix.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
rank_matrix.o: /usr/include/unistd.h /usr/include/sys/types.h
rank_matrix.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
rank_matrix.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
rank_matrix.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
rank_matrix.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
rank_matrix.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
rank_matrix.o: /usr/include/iso/ctype_c99.h ../include/global.h
rank_matrix.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
rank_matrix.o: /usr/include/malloc.h ../include/license.h
rank_matrix.o: ../include/strutil.h ../include/errors.h ../include/memory.h
rank_matrix.o: ../include/residues.h ../include/blastapp.h
rank_matrix.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
rank_matrix.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
rank_matrix.o: ../include/gcode.h ../include/blocks.h ../include/output.h
rank_matrix.o: ../include/sequences.h ../include/matrix.h
rank_matrix.o: ../include/pattern.h ../include/convert.h
rank_matrix.o: ../include/frequency.h ../include/files.h
rank_matrix.o: ../include/protomat.h
retblock.o: ../include/blocksprogs.h /usr/include/stdlib.h
retblock.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
retblock.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
retblock.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
retblock.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
retblock.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
retblock.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
retblock.o: /usr/include/iso/string_iso.h /usr/include/math.h
retblock.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
retblock.o: /usr/include/unistd.h /usr/include/sys/types.h
retblock.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
retblock.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
retblock.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
retblock.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
retblock.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
retblock.o: /usr/include/iso/ctype_c99.h ../include/global.h
retblock.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
retblock.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
retblock.o: ../include/errors.h ../include/memory.h ../include/residues.h
retblock.o: ../include/blastapp.h /usr/include/limits.h
retblock.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
retblock.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
retblock.o: ../include/blocks.h ../include/output.h ../include/sequences.h
retblock.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
retblock.o: ../include/frequency.h ../include/files.h ../include/protomat.h
codehop.o: ../include/blocksprogs.h /usr/include/stdlib.h
codehop.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
codehop.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
codehop.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
codehop.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
codehop.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
codehop.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
codehop.o: /usr/include/iso/string_iso.h /usr/include/math.h
codehop.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
codehop.o: /usr/include/unistd.h /usr/include/sys/types.h
codehop.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
codehop.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
codehop.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
codehop.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
codehop.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
codehop.o: /usr/include/iso/ctype_c99.h ../include/global.h
codehop.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
codehop.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
codehop.o: ../include/errors.h ../include/memory.h ../include/residues.h
codehop.o: ../include/blastapp.h /usr/include/limits.h
codehop.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
codehop.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
codehop.o: ../include/blocks.h ../include/output.h ../include/sequences.h
codehop.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
codehop.o: ../include/frequency.h ../include/files.h ../include/protomat.h
codehop.o: codehop.h
htmlize-codehop.o: /usr/include/stdio.h /usr/include/sys/feature_tests.h
htmlize-codehop.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
htmlize-codehop.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
htmlize-codehop.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
htmlize-codehop.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
htmlize-codehop.o: /usr/include/iso/string_iso.h /usr/include/stdlib.h
htmlize-codehop.o: /usr/include/iso/stdlib_iso.h
htmlize-codehop.o: /usr/include/iso/stdlib_c99.h
oligo_melt.o: ../include/blocksprogs.h /usr/include/stdlib.h
oligo_melt.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
oligo_melt.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
oligo_melt.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
oligo_melt.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
oligo_melt.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
oligo_melt.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
oligo_melt.o: /usr/include/iso/string_iso.h /usr/include/math.h
oligo_melt.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
oligo_melt.o: /usr/include/unistd.h /usr/include/sys/types.h
oligo_melt.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
oligo_melt.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
oligo_melt.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
oligo_melt.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
oligo_melt.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
oligo_melt.o: /usr/include/iso/ctype_c99.h ../include/global.h
oligo_melt.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
oligo_melt.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
oligo_melt.o: ../include/errors.h ../include/memory.h ../include/residues.h
oligo_melt.o: ../include/blastapp.h /usr/include/limits.h
oligo_melt.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
oligo_melt.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
oligo_melt.o: ../include/blocks.h ../include/output.h ../include/sequences.h
oligo_melt.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
oligo_melt.o: ../include/frequency.h ../include/files.h ../include/protomat.h
mablock.o: ../include/blocksprogs.h /usr/include/stdlib.h
mablock.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
mablock.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
mablock.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
mablock.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
mablock.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
mablock.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
mablock.o: /usr/include/iso/string_iso.h /usr/include/math.h
mablock.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
mablock.o: /usr/include/unistd.h /usr/include/sys/types.h
mablock.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
mablock.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
mablock.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
mablock.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
mablock.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
mablock.o: /usr/include/iso/ctype_c99.h ../include/global.h
mablock.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
mablock.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
mablock.o: ../include/errors.h ../include/memory.h ../include/residues.h
mablock.o: ../include/blastapp.h /usr/include/limits.h
mablock.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
mablock.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
mablock.o: ../include/blocks.h ../include/output.h ../include/sequences.h
mablock.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
mablock.o: ../include/frequency.h ../include/files.h ../include/protomat.h
cobbler.o: ../include/blocksprogs.h /usr/include/stdlib.h
cobbler.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
cobbler.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
cobbler.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
cobbler.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
cobbler.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
cobbler.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
cobbler.o: /usr/include/iso/string_iso.h /usr/include/math.h
cobbler.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
cobbler.o: /usr/include/unistd.h /usr/include/sys/types.h
cobbler.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
cobbler.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
cobbler.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
cobbler.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
cobbler.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
cobbler.o: /usr/include/iso/ctype_c99.h ../include/global.h
cobbler.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
cobbler.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
cobbler.o: ../include/errors.h ../include/memory.h ../include/residues.h
cobbler.o: ../include/blastapp.h /usr/include/limits.h
cobbler.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
cobbler.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
cobbler.o: ../include/blocks.h ../include/output.h ../include/sequences.h
cobbler.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
cobbler.o: ../include/frequency.h ../include/files.h ../include/protomat.h
addseqs.o: ../include/blocksprogs.h /usr/include/stdlib.h
addseqs.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
addseqs.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
addseqs.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
addseqs.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
addseqs.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
addseqs.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
addseqs.o: /usr/include/iso/string_iso.h /usr/include/math.h
addseqs.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
addseqs.o: /usr/include/unistd.h /usr/include/sys/types.h
addseqs.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
addseqs.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
addseqs.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
addseqs.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
addseqs.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
addseqs.o: /usr/include/iso/ctype_c99.h ../include/global.h
addseqs.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
addseqs.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
addseqs.o: ../include/errors.h ../include/memory.h ../include/residues.h
addseqs.o: ../include/blastapp.h /usr/include/limits.h
addseqs.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
addseqs.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
addseqs.o: ../include/blocks.h ../include/output.h ../include/sequences.h
addseqs.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
addseqs.o: ../include/frequency.h ../include/files.h ../include/protomat.h
fastaseqs.o: ../include/blocksprogs.h /usr/include/stdlib.h
fastaseqs.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
fastaseqs.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
fastaseqs.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
fastaseqs.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
fastaseqs.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
fastaseqs.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
fastaseqs.o: /usr/include/iso/string_iso.h /usr/include/math.h
fastaseqs.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
fastaseqs.o: /usr/include/unistd.h /usr/include/sys/types.h
fastaseqs.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
fastaseqs.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
fastaseqs.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
fastaseqs.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
fastaseqs.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
fastaseqs.o: /usr/include/iso/ctype_c99.h ../include/global.h
fastaseqs.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
fastaseqs.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
fastaseqs.o: ../include/errors.h ../include/memory.h ../include/residues.h
fastaseqs.o: ../include/blastapp.h /usr/include/limits.h
fastaseqs.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
fastaseqs.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
fastaseqs.o: ../include/blocks.h ../include/output.h ../include/sequences.h
fastaseqs.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
fastaseqs.o: ../include/frequency.h ../include/files.h ../include/protomat.h
LAMA.o: ../include/blocksprogs.h /usr/include/stdlib.h
LAMA.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
LAMA.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
LAMA.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
LAMA.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
LAMA.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
LAMA.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
LAMA.o: /usr/include/iso/string_iso.h /usr/include/math.h
LAMA.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
LAMA.o: /usr/include/unistd.h /usr/include/sys/types.h
LAMA.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
LAMA.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
LAMA.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
LAMA.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
LAMA.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
LAMA.o: /usr/include/iso/ctype_c99.h ../include/global.h
LAMA.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
LAMA.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
LAMA.o: ../include/errors.h ../include/memory.h ../include/residues.h
LAMA.o: ../include/blastapp.h /usr/include/limits.h
LAMA.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
LAMA.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
LAMA.o: ../include/blocks.h ../include/output.h ../include/sequences.h
LAMA.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
LAMA.o: ../include/frequency.h ../include/files.h ../include/protomat.h
LAMA.o: LAMA.h
find_biassed_blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h
find_biassed_blocks.o: /usr/include/iso/stdlib_iso.h
find_biassed_blocks.o: /usr/include/sys/feature_tests.h
find_biassed_blocks.o: /usr/include/sys/ccompile.h
find_biassed_blocks.o: /usr/include/sys/isa_defs.h
find_biassed_blocks.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
find_biassed_blocks.o: /usr/include/iso/stdio_iso.h
find_biassed_blocks.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
find_biassed_blocks.o: /usr/include/stdio_impl.h /usr/include/iso/stdio_c99.h
find_biassed_blocks.o: /usr/include/string.h /usr/include/iso/string_iso.h
find_biassed_blocks.o: /usr/include/math.h /usr/include/iso/math_iso.h
find_biassed_blocks.o: /usr/include/iso/math_c99.h /usr/include/unistd.h
find_biassed_blocks.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
find_biassed_blocks.o: /usr/include/ia32/sys/machtypes.h
find_biassed_blocks.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
find_biassed_blocks.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
find_biassed_blocks.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
find_biassed_blocks.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
find_biassed_blocks.o: /usr/include/iso/ctype_c99.h ../include/global.h
find_biassed_blocks.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
find_biassed_blocks.o: /usr/include/malloc.h ../include/license.h
find_biassed_blocks.o: ../include/strutil.h ../include/errors.h
find_biassed_blocks.o: ../include/memory.h ../include/residues.h
find_biassed_blocks.o: ../include/blastapp.h /usr/include/limits.h
find_biassed_blocks.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
find_biassed_blocks.o: ../include/aabet.h ../include/ntbet.h
find_biassed_blocks.o: ../include/gcode.h ../include/blocks.h
find_biassed_blocks.o: ../include/output.h ../include/sequences.h
find_biassed_blocks.o: ../include/matrix.h ../include/pattern.h
find_biassed_blocks.o: ../include/convert.h ../include/frequency.h
find_biassed_blocks.o: ../include/files.h ../include/protomat.h blkvblk.h
makeblockmap.o: ../include/blocksprogs.h /usr/include/stdlib.h
makeblockmap.o: /usr/include/iso/stdlib_iso.h
makeblockmap.o: /usr/include/sys/feature_tests.h /usr/include/sys/ccompile.h
makeblockmap.o: /usr/include/sys/isa_defs.h /usr/include/iso/stdlib_c99.h
makeblockmap.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
makeblockmap.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
makeblockmap.o: /usr/include/stdio_impl.h /usr/include/iso/stdio_c99.h
makeblockmap.o: /usr/include/string.h /usr/include/iso/string_iso.h
makeblockmap.o: /usr/include/math.h /usr/include/iso/math_iso.h
makeblockmap.o: /usr/include/iso/math_c99.h /usr/include/unistd.h
makeblockmap.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
makeblockmap.o: /usr/include/ia32/sys/machtypes.h
makeblockmap.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
makeblockmap.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
makeblockmap.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
makeblockmap.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
makeblockmap.o: /usr/include/iso/ctype_c99.h ../include/global.h
makeblockmap.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
makeblockmap.o: /usr/include/malloc.h ../include/license.h
makeblockmap.o: ../include/strutil.h ../include/errors.h ../include/memory.h
makeblockmap.o: ../include/residues.h ../include/blastapp.h
makeblockmap.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
makeblockmap.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
makeblockmap.o: ../include/gcode.h ../include/blocks.h ../include/output.h
makeblockmap.o: ../include/sequences.h ../include/matrix.h
makeblockmap.o: ../include/pattern.h ../include/convert.h
makeblockmap.o: ../include/frequency.h ../include/files.h
makeblockmap.o: ../include/protomat.h blockmap.h
prints2blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h
prints2blocks.o: /usr/include/iso/stdlib_iso.h
prints2blocks.o: /usr/include/sys/feature_tests.h /usr/include/sys/ccompile.h
prints2blocks.o: /usr/include/sys/isa_defs.h /usr/include/iso/stdlib_c99.h
prints2blocks.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
prints2blocks.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
prints2blocks.o: /usr/include/stdio_impl.h /usr/include/iso/stdio_c99.h
prints2blocks.o: /usr/include/string.h /usr/include/iso/string_iso.h
prints2blocks.o: /usr/include/math.h /usr/include/iso/math_iso.h
prints2blocks.o: /usr/include/iso/math_c99.h /usr/include/unistd.h
prints2blocks.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
prints2blocks.o: /usr/include/ia32/sys/machtypes.h
prints2blocks.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
prints2blocks.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
prints2blocks.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
prints2blocks.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
prints2blocks.o: /usr/include/iso/ctype_c99.h ../include/global.h
prints2blocks.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
prints2blocks.o: /usr/include/malloc.h ../include/license.h
prints2blocks.o: ../include/strutil.h ../include/errors.h ../include/memory.h
prints2blocks.o: ../include/residues.h ../include/blastapp.h
prints2blocks.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
prints2blocks.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
prints2blocks.o: ../include/gcode.h ../include/blocks.h ../include/output.h
prints2blocks.o: ../include/sequences.h ../include/matrix.h
prints2blocks.o: ../include/pattern.h ../include/convert.h
prints2blocks.o: ../include/frequency.h ../include/files.h
prints2blocks.o: ../include/protomat.h
lisblk.o: ../include/blocksprogs.h /usr/include/stdlib.h
lisblk.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
lisblk.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
lisblk.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
lisblk.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
lisblk.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
lisblk.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
lisblk.o: /usr/include/iso/string_iso.h /usr/include/math.h
lisblk.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
lisblk.o: /usr/include/unistd.h /usr/include/sys/types.h
lisblk.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
lisblk.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
lisblk.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
lisblk.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
lisblk.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
lisblk.o: /usr/include/iso/ctype_c99.h ../include/global.h
lisblk.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
lisblk.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
lisblk.o: ../include/errors.h ../include/memory.h ../include/residues.h
lisblk.o: ../include/blastapp.h /usr/include/limits.h
lisblk.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
lisblk.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
lisblk.o: ../include/blocks.h ../include/output.h ../include/sequences.h
lisblk.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
lisblk.o: ../include/frequency.h ../include/files.h ../include/protomat.h
coduse.o: ../include/blocksprogs.h /usr/include/stdlib.h
coduse.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
coduse.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
coduse.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
coduse.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
coduse.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
coduse.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
coduse.o: /usr/include/iso/string_iso.h /usr/include/math.h
coduse.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
coduse.o: /usr/include/unistd.h /usr/include/sys/types.h
coduse.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
coduse.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
coduse.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
coduse.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
coduse.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
coduse.o: /usr/include/iso/ctype_c99.h ../include/global.h
coduse.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
coduse.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
coduse.o: ../include/errors.h ../include/memory.h ../include/residues.h
coduse.o: ../include/blastapp.h /usr/include/limits.h
coduse.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
coduse.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
coduse.o: ../include/blocks.h ../include/output.h ../include/sequences.h
coduse.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
coduse.o: ../include/frequency.h ../include/files.h ../include/protomat.h
narrow.o: ../include/blocksprogs.h /usr/include/stdlib.h
narrow.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
narrow.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
narrow.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
narrow.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
narrow.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
narrow.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
narrow.o: /usr/include/iso/string_iso.h /usr/include/math.h
narrow.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
narrow.o: /usr/include/unistd.h /usr/include/sys/types.h
narrow.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
narrow.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
narrow.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
narrow.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
narrow.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
narrow.o: /usr/include/iso/ctype_c99.h ../include/global.h
narrow.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
narrow.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
narrow.o: ../include/errors.h ../include/memory.h ../include/residues.h
narrow.o: ../include/blastapp.h /usr/include/limits.h
narrow.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
narrow.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
narrow.o: ../include/blocks.h ../include/output.h ../include/sequences.h
narrow.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
narrow.o: ../include/frequency.h ../include/files.h ../include/protomat.h
blk2slx.o: ../include/blocksprogs.h /usr/include/stdlib.h
blk2slx.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blk2slx.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
blk2slx.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
blk2slx.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blk2slx.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blk2slx.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
blk2slx.o: /usr/include/iso/string_iso.h /usr/include/math.h
blk2slx.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
blk2slx.o: /usr/include/unistd.h /usr/include/sys/types.h
blk2slx.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
blk2slx.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
blk2slx.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
blk2slx.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
blk2slx.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blk2slx.o: /usr/include/iso/ctype_c99.h ../include/global.h
blk2slx.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
blk2slx.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
blk2slx.o: ../include/errors.h ../include/memory.h ../include/residues.h
blk2slx.o: ../include/blastapp.h /usr/include/limits.h
blk2slx.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
blk2slx.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
blk2slx.o: ../include/blocks.h ../include/output.h ../include/sequences.h
blk2slx.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
blk2slx.o: ../include/frequency.h ../include/files.h ../include/protomat.h
blkprob.o: ../include/blocksprogs.h /usr/include/stdlib.h
blkprob.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blkprob.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
blkprob.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
blkprob.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blkprob.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blkprob.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
blkprob.o: /usr/include/iso/string_iso.h /usr/include/math.h
blkprob.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
blkprob.o: /usr/include/unistd.h /usr/include/sys/types.h
blkprob.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
blkprob.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
blkprob.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
blkprob.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
blkprob.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blkprob.o: /usr/include/iso/ctype_c99.h ../include/global.h
blkprob.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
blkprob.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
blkprob.o: ../include/errors.h ../include/memory.h ../include/residues.h
blkprob.o: ../include/blastapp.h /usr/include/limits.h
blkprob.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
blkprob.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
blkprob.o: ../include/blocks.h ../include/output.h ../include/sequences.h
blkprob.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
blkprob.o: ../include/frequency.h ../include/files.h ../include/protomat.h
blocks.o: ../include/global.h /usr/include/stdlib.h
blocks.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blocks.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
blocks.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
blocks.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blocks.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blocks.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
blocks.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
blocks.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
blocks.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
blocks.o: /usr/include/malloc.h /usr/include/sys/types.h
blocks.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
blocks.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
blocks.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
blocks.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
blocks.o: ../include/errors.h ../include/memory.h ../include/blocks.h
blocks.o: ../include/output.h ../include/sequences.h ../include/residues.h
blocks.o: ../include/blastapp.h /usr/include/limits.h
blocks.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
blocks.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
config.o: ../include/global.h /usr/include/stdlib.h
config.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
config.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
config.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
config.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
config.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
config.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
config.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
config.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
config.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
config.o: /usr/include/malloc.h /usr/include/sys/types.h
config.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
config.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
config.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
config.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
config.o: ../include/errors.h ../include/memory.h ../include/files.h
config.o: ../include/sequences.h ../include/pattern.h ../include/options.h
config.o: config.h blimps.h scoring.h lists.h ../include/skiplist.h
convert.o: /usr/include/assert.h /usr/include/math.h
convert.o: /usr/include/iso/math_iso.h /usr/include/sys/feature_tests.h
convert.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
convert.o: /usr/include/iso/math_c99.h ../include/global.h
convert.o: /usr/include/stdlib.h /usr/include/iso/stdlib_iso.h
convert.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
convert.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
convert.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
convert.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
convert.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
convert.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
convert.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
convert.o: /usr/include/malloc.h /usr/include/sys/types.h
convert.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
convert.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
convert.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
convert.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
convert.o: ../include/errors.h ../include/memory.h ../include/options.h
convert.o: ../include/blocks.h ../include/output.h ../include/sequences.h
convert.o: ../include/matrix.h ../include/pattern.h ../include/residues.h
convert.o: ../include/blastapp.h /usr/include/limits.h
convert.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
convert.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
convert.o: ../include/frequency.h ../include/protomat.h ../include/convert.h
convert.o: blimps.h
errors.o: ../include/global.h /usr/include/stdlib.h
errors.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
errors.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
errors.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
errors.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
errors.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
errors.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
errors.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
errors.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
errors.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
errors.o: /usr/include/malloc.h /usr/include/sys/types.h
errors.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
errors.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
errors.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
errors.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
errors.o: ../include/errors.h ../include/memory.h
files.o: ../include/global.h /usr/include/stdlib.h
files.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
files.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
files.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
files.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
files.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
files.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
files.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
files.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
files.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
files.o: /usr/include/malloc.h /usr/include/sys/types.h
files.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
files.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
files.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
files.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
files.o: ../include/errors.h ../include/memory.h ../include/files.h
files.o: ../include/sequences.h
frequency.o: ../include/global.h /usr/include/stdlib.h
frequency.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
frequency.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
frequency.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
frequency.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
frequency.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
frequency.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
frequency.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
frequency.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
frequency.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
frequency.o: /usr/include/malloc.h /usr/include/sys/types.h
frequency.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
frequency.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
frequency.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
frequency.o: /usr/include/sys/time.h ../include/license.h
frequency.o: ../include/strutil.h ../include/errors.h ../include/memory.h
frequency.o: ../include/blocks.h ../include/output.h ../include/sequences.h
frequency.o: ../include/matrix.h ../include/pattern.h ../include/frequency.h
frequency.o: ../include/convert.h ../include/files.h ../include/residues.h
frequency.o: ../include/blastapp.h /usr/include/limits.h
frequency.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
frequency.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
gcode.o: ../include/global.h /usr/include/stdlib.h
gcode.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
gcode.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
gcode.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
gcode.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
gcode.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
gcode.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
gcode.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
gcode.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
gcode.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
gcode.o: /usr/include/malloc.h /usr/include/sys/types.h
gcode.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
gcode.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
gcode.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
gcode.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
gcode.o: ../include/errors.h ../include/memory.h ../include/residues.h
gcode.o: ../include/blastapp.h /usr/include/limits.h
gcode.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
gcode.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
gcode.o: ../include/sequences.h
lists.o: ../include/global.h /usr/include/stdlib.h
lists.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
lists.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
lists.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
lists.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
lists.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
lists.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
lists.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
lists.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
lists.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
lists.o: /usr/include/malloc.h /usr/include/sys/types.h
lists.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
lists.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
lists.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
lists.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
lists.o: ../include/errors.h ../include/memory.h ../include/blocks.h
lists.o: ../include/output.h ../include/sequences.h ../include/matrix.h
lists.o: ../include/pattern.h lists.h ../include/skiplist.h blimps.h scores.h
matrix.o: ../include/global.h /usr/include/stdlib.h
matrix.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
matrix.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
matrix.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
matrix.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
matrix.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
matrix.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
matrix.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
matrix.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
matrix.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
matrix.o: /usr/include/malloc.h /usr/include/sys/types.h
matrix.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
matrix.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
matrix.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
matrix.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
matrix.o: ../include/errors.h ../include/memory.h ../include/blocks.h
matrix.o: ../include/output.h ../include/sequences.h ../include/matrix.h
matrix.o: ../include/pattern.h ../include/residues.h ../include/blastapp.h
matrix.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
matrix.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
matrix.o: ../include/gcode.h
memory.o: ../include/global.h /usr/include/stdlib.h
memory.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
memory.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
memory.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
memory.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
memory.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
memory.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
memory.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
memory.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
memory.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
memory.o: /usr/include/malloc.h /usr/include/sys/types.h
memory.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
memory.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
memory.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
memory.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
memory.o: ../include/errors.h ../include/memory.h
pattern.o: /usr/include/assert.h ../include/global.h /usr/include/stdlib.h
pattern.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
pattern.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
pattern.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
pattern.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
pattern.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
pattern.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
pattern.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
pattern.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
pattern.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
pattern.o: /usr/include/malloc.h /usr/include/sys/types.h
pattern.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
pattern.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
pattern.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
pattern.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
pattern.o: ../include/errors.h ../include/memory.h ../include/files.h
pattern.o: ../include/blocks.h ../include/output.h ../include/sequences.h
pattern.o: ../include/matrix.h ../include/pattern.h ../include/residues.h
pattern.o: ../include/blastapp.h /usr/include/limits.h
pattern.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
pattern.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
pattern.o: ../include/skiplist.h
scores.o: /usr/include/math.h /usr/include/iso/math_iso.h
scores.o: /usr/include/sys/feature_tests.h /usr/include/sys/ccompile.h
scores.o: /usr/include/sys/isa_defs.h /usr/include/iso/math_c99.h
scores.o: ../include/global.h /usr/include/stdlib.h
scores.o: /usr/include/iso/stdlib_iso.h /usr/include/iso/stdlib_c99.h
scores.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
scores.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
scores.o: /usr/include/stdio_impl.h /usr/include/iso/stdio_c99.h
scores.o: /usr/include/string.h /usr/include/iso/string_iso.h
scores.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
scores.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
scores.o: /usr/include/iso/ctype_c99.h /usr/include/malloc.h
scores.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
scores.o: /usr/include/ia32/sys/machtypes.h /usr/include/sys/int_types.h
scores.o: /usr/include/sys/select.h /usr/include/sys/time_impl.h
scores.o: /usr/include/sys/time.h /usr/include/sys/time.h
scores.o: ../include/license.h ../include/strutil.h ../include/errors.h
scores.o: ../include/memory.h ../include/blocks.h ../include/output.h
scores.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
scores.o: scores.h blimps.h scoring.h lists.h ../include/skiplist.h
scoring.o: /usr/include/math.h /usr/include/iso/math_iso.h
scoring.o: /usr/include/sys/feature_tests.h /usr/include/sys/ccompile.h
scoring.o: /usr/include/sys/isa_defs.h /usr/include/iso/math_c99.h
scoring.o: ../include/global.h /usr/include/stdlib.h
scoring.o: /usr/include/iso/stdlib_iso.h /usr/include/iso/stdlib_c99.h
scoring.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
scoring.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
scoring.o: /usr/include/stdio_impl.h /usr/include/iso/stdio_c99.h
scoring.o: /usr/include/string.h /usr/include/iso/string_iso.h
scoring.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
scoring.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
scoring.o: /usr/include/iso/ctype_c99.h /usr/include/malloc.h
scoring.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
scoring.o: /usr/include/ia32/sys/machtypes.h /usr/include/sys/int_types.h
scoring.o: /usr/include/sys/select.h /usr/include/sys/time_impl.h
scoring.o: /usr/include/sys/time.h /usr/include/sys/time.h
scoring.o: ../include/license.h ../include/strutil.h ../include/errors.h
scoring.o: ../include/memory.h ../include/blocks.h ../include/output.h
scoring.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
scoring.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
scoring.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
scoring.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h scoring.h
scoring.o: blimps.h scores.h lists.h ../include/skiplist.h
sequences.o: ../include/global.h /usr/include/stdlib.h
sequences.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
sequences.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
sequences.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
sequences.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
sequences.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
sequences.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
sequences.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
sequences.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
sequences.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
sequences.o: /usr/include/malloc.h /usr/include/sys/types.h
sequences.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
sequences.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
sequences.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
sequences.o: /usr/include/sys/time.h ../include/license.h
sequences.o: ../include/strutil.h ../include/errors.h ../include/memory.h
sequences.o: ../include/sequences.h ../include/residues.h
sequences.o: ../include/blastapp.h /usr/include/limits.h
sequences.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
sequences.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
sl.o: /usr/include/assert.h /usr/include/sys/time.h ../include/global.h
sl.o: /usr/include/stdlib.h /usr/include/iso/stdlib_iso.h
sl.o: /usr/include/sys/feature_tests.h /usr/include/sys/ccompile.h
sl.o: /usr/include/sys/isa_defs.h /usr/include/iso/stdlib_c99.h
sl.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
sl.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
sl.o: /usr/include/stdio_impl.h /usr/include/iso/stdio_c99.h
sl.o: /usr/include/string.h /usr/include/iso/string_iso.h
sl.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
sl.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
sl.o: /usr/include/iso/ctype_c99.h /usr/include/malloc.h
sl.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
sl.o: /usr/include/ia32/sys/machtypes.h /usr/include/sys/int_types.h
sl.o: /usr/include/sys/select.h /usr/include/sys/time_impl.h
sl.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
sl.o: ../include/errors.h ../include/memory.h ../include/skiplist.h
strutil.o: ../include/global.h /usr/include/stdlib.h
strutil.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
strutil.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
strutil.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
strutil.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
strutil.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
strutil.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
strutil.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
strutil.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
strutil.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
strutil.o: /usr/include/malloc.h /usr/include/sys/types.h
strutil.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
strutil.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
strutil.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
strutil.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
strutil.o: ../include/errors.h ../include/memory.h
version.o: ../include/global.h /usr/include/stdlib.h
version.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
version.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
version.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
version.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
version.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
version.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
version.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
version.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
version.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
version.o: /usr/include/malloc.h /usr/include/sys/types.h
version.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
version.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
version.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
version.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
version.o: ../include/errors.h ../include/memory.h ../include/version.h
options.o: ../include/global.h /usr/include/stdlib.h
options.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
options.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
options.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
options.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
options.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
options.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
options.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
options.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
options.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
options.o: /usr/include/malloc.h /usr/include/sys/types.h
options.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
options.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
options.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
options.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
options.o: ../include/errors.h ../include/memory.h ../include/options.h
protomat.o: /usr/include/sys/types.h /usr/include/sys/feature_tests.h
protomat.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
protomat.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
protomat.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
protomat.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
protomat.o: /usr/include/sys/time.h /usr/include/dirent.h
protomat.o: /usr/include/sys/dirent.h /usr/include/ctype.h
protomat.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
protomat.o: ../include/protomat.h /usr/include/stdlib.h
protomat.o: /usr/include/iso/stdlib_iso.h /usr/include/iso/stdlib_c99.h
protomat.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
protomat.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
protomat.o: /usr/include/stdio_impl.h /usr/include/iso/stdio_c99.h
protomat.o: /usr/include/string.h /usr/include/iso/string_iso.h
interpro.o: ../include/blocksprogs.h /usr/include/stdlib.h
interpro.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
interpro.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
interpro.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
interpro.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
interpro.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
interpro.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
interpro.o: /usr/include/iso/string_iso.h /usr/include/math.h
interpro.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
interpro.o: /usr/include/unistd.h /usr/include/sys/types.h
interpro.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
interpro.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
interpro.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
interpro.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
interpro.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
interpro.o: /usr/include/iso/ctype_c99.h ../include/global.h
interpro.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
interpro.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
interpro.o: ../include/errors.h ../include/memory.h ../include/residues.h
interpro.o: ../include/blastapp.h /usr/include/limits.h
interpro.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
interpro.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
interpro.o: ../include/blocks.h ../include/output.h ../include/sequences.h
interpro.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
interpro.o: ../include/frequency.h ../include/files.h ../include/protomat.h
pssmdist.o: ../include/blocksprogs.h /usr/include/stdlib.h
pssmdist.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
pssmdist.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
pssmdist.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
pssmdist.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
pssmdist.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
pssmdist.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
pssmdist.o: /usr/include/iso/string_iso.h /usr/include/math.h
pssmdist.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
pssmdist.o: /usr/include/unistd.h /usr/include/sys/types.h
pssmdist.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
pssmdist.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
pssmdist.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
pssmdist.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
pssmdist.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
pssmdist.o: /usr/include/iso/ctype_c99.h ../include/global.h
pssmdist.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
pssmdist.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
pssmdist.o: ../include/errors.h ../include/memory.h ../include/residues.h
pssmdist.o: ../include/blastapp.h /usr/include/limits.h
pssmdist.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
pssmdist.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
pssmdist.o: ../include/blocks.h ../include/output.h ../include/sequences.h
pssmdist.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
pssmdist.o: ../include/frequency.h ../include/files.h ../include/protomat.h
pssmBL.o: ../include/blocksprogs.h /usr/include/stdlib.h
pssmBL.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
pssmBL.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
pssmBL.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
pssmBL.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
pssmBL.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
pssmBL.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
pssmBL.o: /usr/include/iso/string_iso.h /usr/include/math.h
pssmBL.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
pssmBL.o: /usr/include/unistd.h /usr/include/sys/types.h
pssmBL.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
pssmBL.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
pssmBL.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
pssmBL.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
pssmBL.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
pssmBL.o: /usr/include/iso/ctype_c99.h ../include/global.h
pssmBL.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
pssmBL.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
pssmBL.o: ../include/errors.h ../include/memory.h ../include/residues.h
pssmBL.o: ../include/blastapp.h /usr/include/limits.h
pssmBL.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
pssmBL.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
pssmBL.o: ../include/blocks.h ../include/output.h ../include/sequences.h
pssmBL.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
pssmBL.o: ../include/frequency.h ../include/files.h ../include/protomat.h
papssm.o: ../include/blocksprogs.h /usr/include/stdlib.h
papssm.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
papssm.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
papssm.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
papssm.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
papssm.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
papssm.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
papssm.o: /usr/include/iso/string_iso.h /usr/include/math.h
papssm.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
papssm.o: /usr/include/unistd.h /usr/include/sys/types.h
papssm.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
papssm.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
papssm.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
papssm.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
papssm.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
papssm.o: /usr/include/iso/ctype_c99.h ../include/global.h
papssm.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
papssm.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
papssm.o: ../include/errors.h ../include/memory.h ../include/residues.h
papssm.o: ../include/blastapp.h /usr/include/limits.h
papssm.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
papssm.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
papssm.o: ../include/blocks.h ../include/output.h ../include/sequences.h
papssm.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
papssm.o: ../include/frequency.h ../include/files.h ../include/protomat.h
papssm.o: blimps.h
matrix_logob.o: /usr/include/sys/types.h /usr/include/sys/feature_tests.h
matrix_logob.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
matrix_logob.o: /usr/include/sys/machtypes.h
matrix_logob.o: /usr/include/ia32/sys/machtypes.h
matrix_logob.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
matrix_logob.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
matrix_logob.o: /usr/include/sys/time.h /usr/include/sys/stat.h
matrix_logob.o: /usr/include/sys/stat_impl.h ../include/blocksprogs.h
matrix_logob.o: /usr/include/stdlib.h /usr/include/iso/stdlib_iso.h
matrix_logob.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
matrix_logob.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
matrix_logob.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
matrix_logob.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
matrix_logob.o: /usr/include/iso/string_iso.h /usr/include/math.h
matrix_logob.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
matrix_logob.o: /usr/include/unistd.h /usr/include/sys/unistd.h
matrix_logob.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
matrix_logob.o: /usr/include/iso/ctype_c99.h ../include/global.h
matrix_logob.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
matrix_logob.o: /usr/include/malloc.h ../include/license.h
matrix_logob.o: ../include/strutil.h ../include/errors.h ../include/memory.h
matrix_logob.o: ../include/residues.h ../include/blastapp.h
matrix_logob.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
matrix_logob.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
matrix_logob.o: ../include/gcode.h ../include/blocks.h ../include/output.h
matrix_logob.o: ../include/sequences.h ../include/matrix.h
matrix_logob.o: ../include/pattern.h ../include/convert.h
matrix_logob.o: ../include/frequency.h ../include/files.h
matrix_logob.o: ../include/protomat.h
makelogob.o: p2c.h /usr/include/stdio.h /usr/include/sys/feature_tests.h
makelogob.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
makelogob.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
makelogob.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
makelogob.o: /usr/include/iso/stdio_c99.h /usr/include/stddef.h
makelogob.o: /usr/include/iso/stddef_iso.h /usr/include/stdlib.h
makelogob.o: /usr/include/iso/stdlib_iso.h /usr/include/iso/stdlib_c99.h
makelogob.o: /usr/include/string.h /usr/include/iso/string_iso.h
makelogob.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
makelogob.o: /usr/include/iso/ctype_c99.h /usr/include/math.h
makelogob.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
makelogob.o: /usr/include/setjmp.h /usr/include/iso/setjmp_iso.h
makelogob.o: /usr/include/assert.h
blocks_search.o: /usr/include/stdio.h /usr/include/sys/feature_tests.h
blocks_search.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
blocks_search.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blocks_search.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blocks_search.o: /usr/include/iso/stdio_c99.h /usr/include/stdlib.h
blocks_search.o: /usr/include/iso/stdlib_iso.h /usr/include/iso/stdlib_c99.h
blocks_search.o: ../include/global.h /usr/include/string.h
blocks_search.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
blocks_search.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
blocks_search.o: /usr/include/iso/ctype_iso.h /usr/include/iso/ctype_c99.h
blocks_search.o: /usr/include/malloc.h /usr/include/sys/types.h
blocks_search.o: /usr/include/sys/machtypes.h
blocks_search.o: /usr/include/ia32/sys/machtypes.h
blocks_search.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
blocks_search.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
blocks_search.o: /usr/include/sys/time.h ../include/license.h
blocks_search.o: ../include/strutil.h ../include/errors.h ../include/memory.h
blocks_search.o: /usr/include/unistd.h /usr/include/sys/unistd.h
LAMA_search.o: ../include/blocksprogs.h /usr/include/stdlib.h
LAMA_search.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
LAMA_search.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
LAMA_search.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
LAMA_search.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
LAMA_search.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
LAMA_search.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
LAMA_search.o: /usr/include/iso/string_iso.h /usr/include/math.h
LAMA_search.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
LAMA_search.o: /usr/include/unistd.h /usr/include/sys/types.h
LAMA_search.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
LAMA_search.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
LAMA_search.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
LAMA_search.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
LAMA_search.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
LAMA_search.o: /usr/include/iso/ctype_c99.h ../include/global.h
LAMA_search.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
LAMA_search.o: /usr/include/malloc.h ../include/license.h
LAMA_search.o: ../include/strutil.h ../include/errors.h ../include/memory.h
LAMA_search.o: ../include/residues.h ../include/blastapp.h
LAMA_search.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
LAMA_search.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
LAMA_search.o: ../include/gcode.h ../include/blocks.h ../include/output.h
LAMA_search.o: ../include/sequences.h ../include/matrix.h
LAMA_search.o: ../include/pattern.h ../include/convert.h
LAMA_search.o: ../include/frequency.h ../include/files.h
LAMA_search.o: ../include/protomat.h
block_vis.o: ../include/blocksprogs.h /usr/include/stdlib.h
block_vis.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
block_vis.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
block_vis.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
block_vis.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
block_vis.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
block_vis.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
block_vis.o: /usr/include/iso/string_iso.h /usr/include/math.h
block_vis.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
block_vis.o: /usr/include/unistd.h /usr/include/sys/types.h
block_vis.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
block_vis.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
block_vis.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
block_vis.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
block_vis.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
block_vis.o: /usr/include/iso/ctype_c99.h ../include/global.h
block_vis.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
block_vis.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
block_vis.o: ../include/errors.h ../include/memory.h ../include/residues.h
block_vis.o: ../include/blastapp.h /usr/include/limits.h
block_vis.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
block_vis.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
block_vis.o: ../include/blocks.h ../include/output.h ../include/sequences.h
block_vis.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
block_vis.o: ../include/frequency.h ../include/files.h ../include/protomat.h
block_vis.o: blockmap.h
format_block.o: ../include/blocksprogs.h /usr/include/stdlib.h
format_block.o: /usr/include/iso/stdlib_iso.h
format_block.o: /usr/include/sys/feature_tests.h /usr/include/sys/ccompile.h
format_block.o: /usr/include/sys/isa_defs.h /usr/include/iso/stdlib_c99.h
format_block.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
format_block.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
format_block.o: /usr/include/stdio_impl.h /usr/include/iso/stdio_c99.h
format_block.o: /usr/include/string.h /usr/include/iso/string_iso.h
format_block.o: /usr/include/math.h /usr/include/iso/math_iso.h
format_block.o: /usr/include/iso/math_c99.h /usr/include/unistd.h
format_block.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
format_block.o: /usr/include/ia32/sys/machtypes.h
format_block.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
format_block.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
format_block.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
format_block.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
format_block.o: /usr/include/iso/ctype_c99.h ../include/global.h
format_block.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
format_block.o: /usr/include/malloc.h ../include/license.h
format_block.o: ../include/strutil.h ../include/errors.h ../include/memory.h
format_block.o: ../include/residues.h ../include/blastapp.h
format_block.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
format_block.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
format_block.o: ../include/gcode.h ../include/blocks.h ../include/output.h
format_block.o: ../include/sequences.h ../include/matrix.h
format_block.o: ../include/pattern.h ../include/convert.h
format_block.o: ../include/frequency.h ../include/files.h
format_block.o: ../include/protomat.h
biassed_blocks_finder.o: ../include/blocksprogs.h /usr/include/stdlib.h
biassed_blocks_finder.o: /usr/include/iso/stdlib_iso.h
biassed_blocks_finder.o: /usr/include/sys/feature_tests.h
biassed_blocks_finder.o: /usr/include/sys/ccompile.h
biassed_blocks_finder.o: /usr/include/sys/isa_defs.h
biassed_blocks_finder.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
biassed_blocks_finder.o: /usr/include/iso/stdio_iso.h
biassed_blocks_finder.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
biassed_blocks_finder.o: /usr/include/stdio_impl.h
biassed_blocks_finder.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
biassed_blocks_finder.o: /usr/include/iso/string_iso.h /usr/include/math.h
biassed_blocks_finder.o: /usr/include/iso/math_iso.h
biassed_blocks_finder.o: /usr/include/iso/math_c99.h /usr/include/unistd.h
biassed_blocks_finder.o: /usr/include/sys/types.h
biassed_blocks_finder.o: /usr/include/sys/machtypes.h
biassed_blocks_finder.o: /usr/include/ia32/sys/machtypes.h
biassed_blocks_finder.o: /usr/include/sys/int_types.h
biassed_blocks_finder.o: /usr/include/sys/select.h
biassed_blocks_finder.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
biassed_blocks_finder.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
biassed_blocks_finder.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
biassed_blocks_finder.o: /usr/include/iso/ctype_c99.h ../include/global.h
biassed_blocks_finder.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
biassed_blocks_finder.o: /usr/include/malloc.h ../include/license.h
biassed_blocks_finder.o: ../include/strutil.h ../include/errors.h
biassed_blocks_finder.o: ../include/memory.h ../include/residues.h
biassed_blocks_finder.o: ../include/blastapp.h /usr/include/limits.h
biassed_blocks_finder.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
biassed_blocks_finder.o: ../include/aabet.h ../include/ntbet.h
biassed_blocks_finder.o: ../include/gcode.h ../include/blocks.h
biassed_blocks_finder.o: ../include/output.h ../include/sequences.h
biassed_blocks_finder.o: ../include/matrix.h ../include/pattern.h
biassed_blocks_finder.o: ../include/convert.h ../include/frequency.h
biassed_blocks_finder.o: ../include/files.h ../include/protomat.h
htmlize-LAMA.o: /usr/include/stdlib.h /usr/include/iso/stdlib_iso.h
htmlize-LAMA.o: /usr/include/sys/feature_tests.h /usr/include/sys/ccompile.h
htmlize-LAMA.o: /usr/include/sys/isa_defs.h /usr/include/iso/stdlib_c99.h
htmlize-LAMA.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
htmlize-LAMA.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
htmlize-LAMA.o: /usr/include/stdio_impl.h /usr/include/iso/stdio_c99.h
show_aligned_blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h
show_aligned_blocks.o: /usr/include/iso/stdlib_iso.h
show_aligned_blocks.o: /usr/include/sys/feature_tests.h
show_aligned_blocks.o: /usr/include/sys/ccompile.h
show_aligned_blocks.o: /usr/include/sys/isa_defs.h
show_aligned_blocks.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
show_aligned_blocks.o: /usr/include/iso/stdio_iso.h
show_aligned_blocks.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
show_aligned_blocks.o: /usr/include/stdio_impl.h /usr/include/iso/stdio_c99.h
show_aligned_blocks.o: /usr/include/string.h /usr/include/iso/string_iso.h
show_aligned_blocks.o: /usr/include/math.h /usr/include/iso/math_iso.h
show_aligned_blocks.o: /usr/include/iso/math_c99.h /usr/include/unistd.h
show_aligned_blocks.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
show_aligned_blocks.o: /usr/include/ia32/sys/machtypes.h
show_aligned_blocks.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
show_aligned_blocks.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
show_aligned_blocks.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
show_aligned_blocks.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
show_aligned_blocks.o: /usr/include/iso/ctype_c99.h ../include/global.h
show_aligned_blocks.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
show_aligned_blocks.o: /usr/include/malloc.h ../include/license.h
show_aligned_blocks.o: ../include/strutil.h ../include/errors.h
show_aligned_blocks.o: ../include/memory.h ../include/residues.h
show_aligned_blocks.o: ../include/blastapp.h /usr/include/limits.h
show_aligned_blocks.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
show_aligned_blocks.o: ../include/aabet.h ../include/ntbet.h
show_aligned_blocks.o: ../include/gcode.h ../include/blocks.h
show_aligned_blocks.o: ../include/output.h ../include/sequences.h
show_aligned_blocks.o: ../include/matrix.h ../include/pattern.h
show_aligned_blocks.o: ../include/convert.h ../include/frequency.h
show_aligned_blocks.o: ../include/files.h ../include/protomat.h
blk2mot.o: ../include/blocksprogs.h /usr/include/stdlib.h
blk2mot.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blk2mot.o: /usr/include/sys/ccompile.h /usr/include/sys/isa_defs.h
blk2mot.o: /usr/include/iso/stdlib_c99.h /usr/include/stdio.h
blk2mot.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blk2mot.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blk2mot.o: /usr/include/iso/stdio_c99.h /usr/include/string.h
blk2mot.o: /usr/include/iso/string_iso.h /usr/include/math.h
blk2mot.o: /usr/include/iso/math_iso.h /usr/include/iso/math_c99.h
blk2mot.o: /usr/include/unistd.h /usr/include/sys/types.h
blk2mot.o: /usr/include/sys/machtypes.h /usr/include/ia32/sys/machtypes.h
blk2mot.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
blk2mot.o: /usr/include/sys/time_impl.h /usr/include/sys/time.h
blk2mot.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
blk2mot.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blk2mot.o: /usr/include/iso/ctype_c99.h ../include/global.h
blk2mot.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
blk2mot.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
blk2mot.o: ../include/errors.h ../include/memory.h ../include/residues.h
blk2mot.o: ../include/blastapp.h /usr/include/limits.h
blk2mot.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
blk2mot.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
blk2mot.o: ../include/blocks.h ../include/output.h ../include/sequences.h
blk2mot.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
blk2mot.o: ../include/frequency.h ../include/files.h ../include/protomat.h
/include/alphabet.h ../include/aabet.h ..blimps-3.9/blimps/cccb000075500001460000012000000003311054700066200152510ustar00jorjastaff00000400000027#      Compile one program with blimps
#	Usage to compile program.c:   cccb 
set b = ../
set CC = /opt/SUNWspro/bin/cc
#set CC = /opt/sfw/bin/gcc
$CC -fast -I$b/include -L$b/lib -o $1 $1.c -lblimps -lm

exit
blimps-3.9/blimps/cccbg000075500001460000012000000003261056472650700154400ustar00jorjastaff00000400000027#      Compile one program with blimps
#	Usage to compile program.c:   cccb 
set b = ../
set CC = /opt/SUNWspro/bin/cc
#set CC = /opt/sfw/bin/gcc
$CC -g -I$b/include -L$b/lib -o $1 $1.c -lblimps -lm

exit
blimps-3.9/blimps/Makefile.Sun_sparc000064400001460000012000002605271054326150500200450ustar00jorjastaff00000400000027# Makefile: makefile for BLIMPS blocks searcher
# Written by: Bill Alford
# (C) Copyright 1993-9, Fred Hutchinson Cancer Research Center 
# Use, modification or distribution of these programs is subject to 
# the terms of the non-commercial licensing agreement in license.h. 

# Instructions for use:
# 1. Change DEFINES, SYSTEM, OPTIMIZ, RANLIB, CC for your system
# 2. make depend
# 3. make install (updates ../bin and ../lib)


# System defines.  The main reason for this is that on the Sun there is a 
# function malloc_debug() wich will raise a signal if there are problems
# with memory.  The problem is that there is no function like that on other
# machines, at least that I've seen.  Defines are set up so that the
# malloc_debug call is only in the Sun code.

# Generic -- Should work on most systems not listed below.
#DEFINES = -DNO_STRDUP
#SYSTEM  = generic 
#OPTIMIZ =
#RANLIB = ../bin/ranlib

# SunOS
#DEFINES = 
#SYSTEM  = sun4.1.3
#OPTIMIZ = -O
#RANLIB = /bin/ranlib
## For debugging.
# DEFINES = -DMALLOC_DEBUG
# OTHER_OBJS = /usr/lib/debug/malloc.o 

# Sun Solaris
DEFINES = 
SYSTEM = solaris
#	Some programs don't give the same results when compiled with -fast,
#	e.g. codehop.c; offending options -fsimple=2
#OPTIMIZ = -fast
#OPTIMIZ = -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=2 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit 
OPTIMIZ = -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit
#OPTIMIZ = -g
#	RANLIB is obsolete under Solaris 2.5; just put something here
#	so the Makefile continues to work.
RANLIB = ls

# Linux
#DEFINES = 
#SYSTEM  = 
#OPTIMIZ = -Wall -O2
#RANLIB = ls

MAKE = make
DEPEND = makedepend

#	ar -t libpssm.a for table of contents
AR = ar
RM = rm -f
MV = mv -f 
CP = cp


# C compiler
#CC = gcc
CC = /opt/SUNWspro/bin/cc

# Optimization level (or debugging)
#OPTIMIZ = -g
#OPTIMIZ = -g -O $(WARNS) $(XWARN)
#OPTIMIZ = -p
WARNS = -W \
	-Wreturn-type \
	-Wswitch \
	-Wcomment \
	-Wtrigraphs \
	-Wformat \
	-Wparentheses 

# like -Wall but without 
#   -Wimplicit  -- gets all the printf's etc..
#   -Wunused    -- gets all the rcsid and 3 funcs. I know about
#   -Wchar-subscripts -- gets all ??_atob arrays (ascii to binary residue)
#   -Wuninitialized -- Caught 4 places which are tricky cases but are OK.

WARNS2 = -Wall
XWARN = -Wshadow \
	-Wcast-qual \
	-Wcast-align \
	-Wpointer-arith \
	-Waggregate-return \
	-Wredundant-decls \
	-Wnested-externs \
	-Winline

#    -Wtraditional -- gets printf, fprintf, etc.
#    -Wid-clash-16 -- causes lots of warnings.
#    -Wwrite-strings -- causes a LOT of warnings, think all are needed.
#    -Wconversion  -- causes a lot of warnings, but they look like they 
#                       should be OK.
#    -Wstrict-prototypes -Wmissing-prototypes -- too many to count...

XXWARN = -Werror

INCLUDE_DIR = ../include
INCLUDES = -I$(INCLUDE_DIR)


# C Flags to compiler
#CFLAGS = `getconf LFS_CFLAGS` $(OPTIMIZ) $(DEFINES) $(INCLUDES)
CFLAGS = $(OPTIMIZ) $(DEFINES) $(INCLUDES)


# Linker Flags
LDFLAGS = $(CFLAGS)
LDLIBS = -lblimps -ly -lm
LDOPTIONS = $(LDFLAGS) $(LDDIR)
# cc ld options


#LIBRARY_DIR = ../lib
LIBRARY_DIR = ./
LDDIR = -L$(LIBRARY_DIR)


# source files
SRCS =  blimps-mem.c \
	blimps.c \
	blweight.c \
	blalign.c \
	bldist.c \
	blk2pssm.c \
	rank_matrix.c \
	retblock.c \
	codehop.c \
        htmlize-codehop.c \
        oligo_melt.c \
	mablock.c \
	cobbler.c \
	addseqs.c \
	fastaseqs.c \
	LAMA.c \
	find_biassed_blocks.c \
	makeblockmap.c \
	prints2blocks.c \
	lisblk.c \
	coduse.c \
	narrow.c \
	blk2slx.c \
	blkprob.c \
	blocks.c \
	config.c \
	convert.c \
	errors.c \
	files.c \
	frequency.c \
	gcode.c \
	lists.c \
	matrix.c \
	memory.c \
	pattern.c \
	scores.c \
	scoring.c \
	sequences.c \
	sl.c \
	strutil.c \
	version.c \
	options.c \
	protomat.c  \
	interpro.c \
	pssmdist.c \
	pssmBL.c \
	papssm.c \
	matrix_logob.c \
	makelogob.c \
	blocks_search.c \
	LAMA_search.c \
	block_vis.c \
	format_block.c \
	biassed_blocks_finder.c \
	htmlize-LAMA.c \
	show_aligned_blocks.c \
	blk2mot.c 

HDRS =  blimps.h \
	blweight.h \
	blimps-mem.h \
	config.h \
	lists.h \
	scores.h \
	scoring.h \
	protomat.h \
	p2c.h


# need the OBJS for blimps dependencies on the .o files.  I don't know a 
# way around this.

OTHER_OBJS_DEBUG =	/usr/lib/debug/malloc.o \
		/usr/lib/debug/mallocmap.o

LIBOBJS = pattern.o \
	files.o \
	frequency.o \
	convert.o \
	blocks.o \
	errors.o \
	gcode.o \
	matrix.o \
	memory.o \
	sequences.o \
	strutil.o \
	sl.o \
	version.o \
	options.o \
	blimps-mem.o \
	config.o \
	lists.o \
	scores.o \
	scoring.o \
	p2clib.o \
	util.o \
        protomat.o


# need malloc.o for malloc_debug() which will have free() raise SIGABRT
# if it is unable to free the space.

LIBRARIES = libblimps.a


########################################################################
########################################################################
#
# main dependencies
#
########################################################################
########################################################################

install: clean all move-lib move-bin

all: lib blimps blweight blalign bldist blk2pssm rank_matrix retblock codehop htmlize-codehop oligo_melt mablock cobbler addseqs fastaseqs LAMA find_biassed_blocks makeblockmap prints2blocks lisblk coduse narrow blk2slx blkprob interpro pssmdist pssmBL papssm matrix_logob makelogob blocks_search LAMA_search block_vis format_block biassed_blocks_finder htmlize-LAMA show_aligned_blocks makelis blk2mot 

blimps: $(LIBRARIES) blimps.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blimps.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

makelis: $(LIBRARIES)  makelis.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  makelis.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blweight: $(LIBRARIES) blweight.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blweight.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blalign: $(LIBRARIES) blalign.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blalign.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

bldist: $(LIBRARIES) bldist.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  bldist.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 
blk2pssm: $(LIBRARIES) blk2pssm.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blk2pssm.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

rank_matrix: $(LIBRARIES) rank_matrix.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  rank_matrix.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

retblock: $(LIBRARIES) retblock.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  retblock.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

codehop: $(LIBRARIES) codehop.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  codehop.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

htmlize-codehop: $(LIBRARIES) htmlize-codehop.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  htmlize-codehop.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

oligo_melt: $(LIBRARIES) oligo_melt.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  oligo_melt.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

mablock: $(LIBRARIES) mablock.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  mablock.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

cobbler: $(LIBRARIES) cobbler.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  cobbler.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

addseqs: $(LIBRARIES) addseqs.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  addseqs.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

fastaseqs: $(LIBRARIES) fastaseqs.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  fastaseqs.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

LAMA: $(LIBRARIES) LAMA.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  LAMA.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

find_biassed_blocks: $(LIBRARIES) find_biassed_blocks.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  find_biassed_blocks.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

makeblockmap: $(LIBRARIES) makeblockmap.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  makeblockmap.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

prints2blocks: $(LIBRARIES) prints2blocks.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  prints2blocks.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

lisblk: $(LIBRARIES) lisblk.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  lisblk.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

coduse: $(LIBRARIES) coduse.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  coduse.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

narrow: $(LIBRARIES) narrow.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  narrow.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blk2slx: $(LIBRARIES) blk2slx.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blk2slx.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blkprob: $(LIBRARIES) blkprob.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  blkprob.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

interpro: $(LIBRARIES) interpro.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  interpro.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

pssmdist: $(LIBRARIES) pssmdist.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  pssmdist.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

pssmBL: $(LIBRARIES) pssmBL.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  pssmBL.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

papssm: $(LIBRARIES) papssm.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  papssm.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

matrix_logob: $(LIBRARIES) matrix_logob.o $(LIBOBJS) 
	$(RM) $@
	$(CC) -o $@  matrix_logob.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

makelogob: $(LIBRARIES) makelogob.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  makelogob.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blocks_search: $(LIBRARIES) blocks_search.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  blocks_search.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

LAMA_search: $(LIBRARIES) LAMA_search.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  LAMA_search.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

block_vis: $(LIBRARIES) block_vis.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  block_vis.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

format_block: $(LIBRARIES) format_block.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  format_block.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

biassed_blocks_finder: $(LIBRARIES) biassed_blocks_finder.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  biassed_blocks_finder.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

htmlize-LAMA: $(LIBRARIES) htmlize-LAMA.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  htmlize-LAMA.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

show_aligned_blocks: $(LIBRARIES) show_aligned_blocks.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  show_aligned_blocks.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 

blk2mot: $(LIBRARIES) blk2mot.o $(LIBOBJS)
	$(RM) $@
	$(CC) -o $@  blk2mot.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 


$(LIBOBJS):


########################################################################
########################################################################
#
# include dependencies
#
########################################################################
########################################################################

# none




########################################################################
########################################################################
#
# library dependencies
#
########################################################################
########################################################################

lib: ranlib $(LIBRARIES)

ranlib:
	$(GET_FILES)

#	( cd $(LIBRARY_DIR) ; $(MAKE) $(MFLAGS) )

#
# The libraries.
#

libblimps.a: $(LIBOBJS)
	$(AR) cr $@ $(LIBOBJS) ; $(RANLIB) $@

########################################################################
########################################################################
#
# Local building (for us)
#
########################################################################
########################################################################

#  os = OS_machinename_version
local: clean clean-include clean-lib 
	echo " " ; \
	echo "Making directories..." ; \
	echo " " ; \
	os="`uname -sr | tr ' ' '_'`" ; \
	osdir="../$$os" ; \
	rm -rf $$osdir ; \
	mkdir $$osdir $$osdir/bin $$osdir/include $$osdir/lib ; \
	echo " " ; \
	echo "Running 'make depend' and 'make all'..." ; \
	echo " " ; \
	make depend ; make all	; \
	echo " " ; \
	echo "Copying libraries..." ; \
	echo " " ; \
	cp ../lib/*.a $$osdir/lib ; \
	echo " " ; \
	echo "Copying header files..." ; \
	echo " " ; \
	cp ../include/*.h $$osdir/include ; \
	echo " " ; \
	echo "Copying binary..." ; \
	echo " " ; \
	cp blimps $$osdir/bin





########################################################################
########################################################################
#
# Maintenance dependencies
#
########################################################################
########################################################################


tags: 
	etags ./*.[ch] $(INCLUDE_DIR)/*.[ch]


depend: 
	 $(DEPEND) -- $(CFLAGS) -- -s "# DO NOT DELETE" -- $(SRCS)


clean::
	$(RM) blimps blweight blalign bldist blk2pssm rank_matrix retblock codehop htmlize-codehop oligo_melt mablock makeblockmap prints2blocks lisblk coduse narrow blkprob blk2slx LAMA find_biassed_blocks fastaseqs addseqs cobbler interpro pssmdist pssmBL papssm matrix_logob makelogob blocks_search LAMA_search block_vis format_block biassed_blocks_finder htmlize-LAMA show_aligned_blocks makelis blk2mot 
	$(RM) *.a *.o *~ 
	@echo " "

move-lib:
	$(MV) lib*.a ../lib

move-bin:
	$(MV) blimps ../bin
	$(MV) blweight ../bin
	$(MV) blalign ../bin
	$(MV) bldist ../bin
	$(MV) blk2pssm ../bin
	$(MV) rank_matrix ../bin
	$(MV) retblock ../bin
	$(MV) codehop ../bin
	$(MV) htmlize-codehop ../bin
	$(MV) oligo_melt ../bin
	$(MV) mablock ../bin
	$(MV) makeblockmap ../bin
	$(MV) prints2blocks ../bin
	$(MV) lisblk ../bin
	$(MV) coduse ../bin
	$(MV) narrow ../bin
	$(MV) blkprob ../bin
	$(MV) blk2slx ../bin
	$(MV) LAMA ../bin
	$(MV) find_biassed_blocks ../bin
	$(MV) fastaseqs ../bin
	$(MV) addseqs ../bin
	$(MV) cobbler ../bin
	$(MV) interpro ../bin
	$(MV) pssmdist ../bin
	$(MV) pssmBL ../bin
	$(MV) papssm ../bin
	$(MV) matrix_logob ../bin
	$(MV) makelogob ../bin
	$(MV) blocks_search ../bin
	$(MV) LAMA_search ../bin
	$(MV) block_vis ../bin
	$(MV) format_block ../bin
	$(MV) biassed_blocks_finder ../bin
	$(MV) htmlize-LAMA ../bin
	$(MV) show_aligned_blocks ../bin
	$(MV) makelis ../bin
	$(MV) blk2mot ../bin


##########
##########
#
# Distribution dependencies
#
##########
##########

SOURCEDIR  = /lab/billa/blimps/dev
BUILDDIR   = /lab/billa/blimps/build-local
DISTRIBDIR = /lab/billa/blimps/distrib
VERSIONDISTRIB = $(DISTRIBDIR).$(VERSION)
BLIMPSDIR  = $(DISTRIBDIR)/blimps
FTPDIR     = /lab/ftp/blimps

TXTVER = `echo  $(VERSION) | \
	 awk -F. '{printf("%d.%d%c", $$1, $$2 / 1000 , \
	 ( $$2 % 1000 ) / 100 + 65)}'`

#
# REMEMBER: each line executes in the directory make started in
#

local-binary: clean-local-binary
	@if [ "$(VERSION)" = "" ] ; then \
		echo "No version specified, bailing out." ; \
		echo "use as: make [ target ... ] VERSION=1.1001" ; \
		echo "    ex: make distrib VERSION=1.1001" ; \
		bail-out-here ; \
	fi
	
	@echo Building local binary for distribution . . .
	@echo " "
	
	@echo Making local build directory . . .
	@mkdir -p $(BUILDDIR)
	
	@echo Making blimps, lib, and include subdirectories . . .
	@mkdir -p $(BUILDDIR)/blimps
	@mkdir -p $(BUILDDIR)/lib
	@mkdir -p $(BUILDDIR)/include
	
	@echo Copying Makefiles over . . .
	@echo REMOVING RCS SUBDIR DEPENDENCY BY THE GREP > /dev/null
	@cat $(SOURCEDIR)/blimps/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BUILDDIR)/blimps/Makefile
	@cat $(SOURCEDIR)/lib/Makefile | grep -v 'RCS/\$$\$$\@,v' >    $(BUILDDIR)/lib/Makefile
	@cat $(SOURCEDIR)/include/Makefile | grep -v 'RCS/\$$\$$\@,v' >$(BUILDDIR)/include/Makefile
	
	@ln -s $(SOURCEDIR)/blimps/RCS  $(BUILDDIR)/blimps/RCS
	@ln -s $(SOURCEDIR)/lib/RCS     $(BUILDDIR)/lib/RCS
	@ln -s $(SOURCEDIR)/include/RCS $(BUILDDIR)/include/RCS
	
	@echo Making local version dependencies . . .
	cd $(BUILDDIR)/blimps ; make VERSION="$(VERSION)" clean ; make VERSION="$(VERSION)" depend 
	
	@echo Removing RCS files to test distrib compilation
	@rm -f $(BUILDDIR)/blimps/RCS
	@rm -f $(BUILDDIR)/lib/RCS
	@rm -f $(BUILDDIR)/include/RCS
	
	@echo Making local version . . .
	cd $(BUILDDIR)/blimps ; make VERSION="$(VERSION)" blimps
	
	@echo Moving local binary into distribution directory . . .
	@mv $(BUILDDIR)/blimps/blimps $(SOURCEDIR)/bin/blimps.$(SYSTEM)
	@echo " "

clean-local-binary:
	@echo Cleaning local build directory \($(BUILDDIR)\) . . .
	rm -rf $(BUILDDIR)
	@echo " "


distrib: local-binary clean-distrib
	@if [ "$(VERSION)" = "" ] ; then \
		echo "No version specified, bailing out." ; \
		echo "use as: make [ target ... ] VERSION=1.1001" ; \
		echo "    ex: make distrib VERSION=1.1001" ; \
		bail-out-here ; \
	fi
	
	@echo Making distribution . . .
	@echo " "
	
	@echo Making distribution directories . . .
	@mkdir -p $(DISTRIBDIR)
	@mkdir -p $(BLIMPSDIR) \
		  $(BLIMPSDIR)/docs \
		  $(BLIMPSDIR)/blimps \
		  $(BLIMPSDIR)/lib \
		  $(BLIMPSDIR)/include \
		  $(BLIMPSDIR)/bin
	@ln -s $(SOURCEDIR)/blimps/RCS  $(BLIMPSDIR)/blimps/RCS
	@ln -s $(SOURCEDIR)/lib/RCS     $(BLIMPSDIR)/lib/RCS
	@ln -s $(SOURCEDIR)/include/RCS $(BLIMPSDIR)/include/RCS
	@ln -s $(SOURCEDIR)/docs/RCS    $(BLIMPSDIR)/docs/RCS
	
	@echo Copying Makefiles over . . .
	@cat $(SOURCEDIR)/blimps/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BLIMPSDIR)/blimps/Makefile
	@cat $(SOURCEDIR)/lib/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BLIMPSDIR)/lib/Makefile
	@cat $(SOURCEDIR)/include/Makefile | grep -v 'RCS/\$$\$$\@,v' > $(BLIMPSDIR)/include/Makefile
	
	@echo Making depend on the Makefiles to checkout the files
	cd $(BLIMPSDIR)/blimps ; make VERSION="$(VERSION)" depend
	@rm -f $(BLIMPSDIR)/blimps/RCS
	@rm -f $(BLIMPSDIR)/lib/RCS
	@rm -f $(BLIMPSDIR)/include/RCS
	
	@echo Copying distribution documents of version $(VERSION) into docs directory . . .
	@cd $(BLIMPSDIR)/docs ; co -q -r$(VERSION) RCS/*
	@rm -f $(BLIMPSDIR)/docs/RCS
	@cd $(BLIMPSDIR)/docs ; cp README INSTALL ..
	
	@echo Copying pre-compiled binaries into bin directory . . .
	@cp $(SOURCEDIR)/bin/* $(BLIMPSDIR)/bin/
	
	@echo Moving blimps to blimps.$(TXTVER)
	@mv $(BLIMPSDIR) $(DISTRIBDIR)/blimps.$(TXTVER)
	@echo " "
	
	@echo Making tar file . . .
	@cd $(DISTRIBDIR) ; tar cf blimps.$(TXTVER).tar blimps.$(TXTVER)
	
	@echo Compressing tar file . . .
	@cd $(DISTRIBDIR) ; compress blimps.$(TXTVER).tar
	@echo " "
	
	@echo Moving distrib dir to distrib.$(VERSION)
	@mv $(DISTRIBDIR) $(VERSIONDISTRIB)

clean-distrib:
	@echo  Cleaning distribution directories:
	@echo "     $(DISTRIBDIR)"
	@echo "     $(VERSIONDISTRIB)"
	@echo " . . . "
	rm -rf $(DISTRIBDIR) $(VERSIONDISTRIB)
	@echo " "

$(VERSIONDISTRIB):	distrib

ftp:	$(VERSIONDISTRIB)
	@echo Moving files to the ftp directory . . .
	@echo " "
	
	@echo Copying tar file to the ftp directory . . .
	@cp $(VERSIONDISTRIB)/blimps.$(TXTVER).tar.Z $(FTPDIR)
	@echo " "
	
	@echo Copying README and INSTALL files to the ftp directory . . .
	@rm -f $(FTPDIR)/README $(FTPDIR)/INSTALL 
	@cp $(VERSIONDISTRIB)/blimps.$(TXTVER)/docs/README \
	  $(VERSIONDISTRIB)/blimps.$(TXTVER)/docs/INSTALL $(FTPDIR)
	@echo " "



###########################################################################

 
###########################################################################
# dependencies generated by makedepend
 
# DO NOT DELETE

blimps-mem.o: ../include/global.h /usr/include/stdlib.h
blimps-mem.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blimps-mem.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
blimps-mem.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blimps-mem.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blimps-mem.o: /usr/include/string.h /usr/include/iso/string_iso.h
blimps-mem.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
blimps-mem.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blimps-mem.o: /usr/include/malloc.h /usr/include/sys/types.h
blimps-mem.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
blimps-mem.o: /usr/include/sys/select.h /usr/include/sys/time.h
blimps-mem.o: /usr/include/sys/time.h ../include/license.h
blimps-mem.o: ../include/strutil.h ../include/errors.h ../include/memory.h
blimps-mem.o: blimps-mem.h blimps.h lists.h ../include/skiplist.h
blimps.o: /usr/include/math.h /usr/include/iso/math_iso.h
blimps.o: /usr/include/signal.h /usr/include/sys/feature_tests.h
blimps.o: /usr/include/sys/isa_defs.h /usr/include/iso/signal_iso.h
blimps.o: /usr/include/sys/iso/signal_iso.h /usr/include/sys/unistd.h
blimps.o: /usr/include/sys/signal.h ../include/global.h /usr/include/stdlib.h
blimps.o: /usr/include/iso/stdlib_iso.h /usr/include/stdio.h
blimps.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blimps.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blimps.o: /usr/include/string.h /usr/include/iso/string_iso.h
blimps.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
blimps.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blimps.o: /usr/include/malloc.h /usr/include/sys/types.h
blimps.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
blimps.o: /usr/include/sys/select.h /usr/include/sys/time.h
blimps.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
blimps.o: ../include/errors.h ../include/memory.h ../include/version.h
blimps.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
blimps.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
blimps.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
blimps.o: ../include/files.h ../include/blocks.h ../include/output.h
blimps.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blimps.o: ../include/convert.h ../include/frequency.h ../include/options.h
blimps.o: blimps.h blimps-mem.h config.h scores.h scoring.h lists.h
blimps.o: ../include/skiplist.h
blweight.o: ../include/blocksprogs.h /usr/include/stdlib.h
blweight.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blweight.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
blweight.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blweight.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blweight.o: /usr/include/string.h /usr/include/iso/string_iso.h
blweight.o: /usr/include/math.h /usr/include/iso/math_iso.h
blweight.o: /usr/include/unistd.h /usr/include/sys/types.h
blweight.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
blweight.o: /usr/include/sys/select.h /usr/include/sys/time.h
blweight.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
blweight.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blweight.o: ../include/global.h /usr/include/stddef.h
blweight.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
blweight.o: ../include/license.h ../include/strutil.h ../include/errors.h
blweight.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
blweight.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
blweight.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blweight.o: ../include/gcode.h ../include/blocks.h ../include/output.h
blweight.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blweight.o: ../include/convert.h ../include/frequency.h ../include/files.h
blweight.o: ../include/protomat.h
blalign.o: ../include/blocksprogs.h /usr/include/stdlib.h
blalign.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blalign.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
blalign.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blalign.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blalign.o: /usr/include/string.h /usr/include/iso/string_iso.h
blalign.o: /usr/include/math.h /usr/include/iso/math_iso.h
blalign.o: /usr/include/unistd.h /usr/include/sys/types.h
blalign.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
blalign.o: /usr/include/sys/select.h /usr/include/sys/time.h
blalign.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
blalign.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blalign.o: ../include/global.h /usr/include/stddef.h
blalign.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
blalign.o: ../include/license.h ../include/strutil.h ../include/errors.h
blalign.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
blalign.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
blalign.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blalign.o: ../include/gcode.h ../include/blocks.h ../include/output.h
blalign.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blalign.o: ../include/convert.h ../include/frequency.h ../include/files.h
blalign.o: ../include/protomat.h
bldist.o: ../include/blocksprogs.h /usr/include/stdlib.h
bldist.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
bldist.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
bldist.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
bldist.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
bldist.o: /usr/include/string.h /usr/include/iso/string_iso.h
bldist.o: /usr/include/math.h /usr/include/iso/math_iso.h
bldist.o: /usr/include/unistd.h /usr/include/sys/types.h
bldist.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
bldist.o: /usr/include/sys/select.h /usr/include/sys/time.h
bldist.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
bldist.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
bldist.o: ../include/global.h /usr/include/stddef.h
bldist.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
bldist.o: ../include/license.h ../include/strutil.h ../include/errors.h
bldist.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
bldist.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
bldist.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
bldist.o: ../include/gcode.h ../include/blocks.h ../include/output.h
bldist.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
bldist.o: ../include/convert.h ../include/frequency.h ../include/files.h
bldist.o: ../include/protomat.h
blk2pssm.o: ../include/blocksprogs.h /usr/include/stdlib.h
blk2pssm.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blk2pssm.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
blk2pssm.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blk2pssm.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blk2pssm.o: /usr/include/string.h /usr/include/iso/string_iso.h
blk2pssm.o: /usr/include/math.h /usr/include/iso/math_iso.h
blk2pssm.o: /usr/include/unistd.h /usr/include/sys/types.h
blk2pssm.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
blk2pssm.o: /usr/include/sys/select.h /usr/include/sys/time.h
blk2pssm.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
blk2pssm.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blk2pssm.o: ../include/global.h /usr/include/stddef.h
blk2pssm.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
blk2pssm.o: ../include/license.h ../include/strutil.h ../include/errors.h
blk2pssm.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
blk2pssm.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
blk2pssm.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blk2pssm.o: ../include/gcode.h ../include/blocks.h ../include/output.h
blk2pssm.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blk2pssm.o: ../include/convert.h ../include/frequency.h ../include/files.h
blk2pssm.o: ../include/protomat.h
rank_matrix.o: ../include/blocksprogs.h /usr/include/stdlib.h
rank_matrix.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
rank_matrix.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
rank_matrix.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
rank_matrix.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
rank_matrix.o: /usr/include/string.h /usr/include/iso/string_iso.h
rank_matrix.o: /usr/include/math.h /usr/include/iso/math_iso.h
rank_matrix.o: /usr/include/unistd.h /usr/include/sys/types.h
rank_matrix.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
rank_matrix.o: /usr/include/sys/select.h /usr/include/sys/time.h
rank_matrix.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
rank_matrix.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
rank_matrix.o: ../include/global.h /usr/include/stddef.h
rank_matrix.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
rank_matrix.o: ../include/license.h ../include/strutil.h ../include/errors.h
rank_matrix.o: ../include/memory.h ../include/residues.h
rank_matrix.o: ../include/blastapp.h /usr/include/limits.h
rank_matrix.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
rank_matrix.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
rank_matrix.o: ../include/blocks.h ../include/output.h ../include/sequences.h
rank_matrix.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
rank_matrix.o: ../include/frequency.h ../include/files.h
rank_matrix.o: ../include/protomat.h
retblock.o: ../include/blocksprogs.h /usr/include/stdlib.h
retblock.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
retblock.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
retblock.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
retblock.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
retblock.o: /usr/include/string.h /usr/include/iso/string_iso.h
retblock.o: /usr/include/math.h /usr/include/iso/math_iso.h
retblock.o: /usr/include/unistd.h /usr/include/sys/types.h
retblock.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
retblock.o: /usr/include/sys/select.h /usr/include/sys/time.h
retblock.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
retblock.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
retblock.o: ../include/global.h /usr/include/stddef.h
retblock.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
retblock.o: ../include/license.h ../include/strutil.h ../include/errors.h
retblock.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
retblock.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
retblock.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
retblock.o: ../include/gcode.h ../include/blocks.h ../include/output.h
retblock.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
retblock.o: ../include/convert.h ../include/frequency.h ../include/files.h
retblock.o: ../include/protomat.h
codehop.o: ../include/blocksprogs.h /usr/include/stdlib.h
codehop.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
codehop.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
codehop.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
codehop.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
codehop.o: /usr/include/string.h /usr/include/iso/string_iso.h
codehop.o: /usr/include/math.h /usr/include/iso/math_iso.h
codehop.o: /usr/include/unistd.h /usr/include/sys/types.h
codehop.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
codehop.o: /usr/include/sys/select.h /usr/include/sys/time.h
codehop.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
codehop.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
codehop.o: ../include/global.h /usr/include/stddef.h
codehop.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
codehop.o: ../include/license.h ../include/strutil.h ../include/errors.h
codehop.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
codehop.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
codehop.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
codehop.o: ../include/gcode.h ../include/blocks.h ../include/output.h
codehop.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
codehop.o: ../include/convert.h ../include/frequency.h ../include/files.h
codehop.o: ../include/protomat.h codehop.h
htmlize-codehop.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
htmlize-codehop.o: /usr/include/sys/feature_tests.h
htmlize-codehop.o: /usr/include/sys/isa_defs.h /usr/include/sys/va_list.h
htmlize-codehop.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
htmlize-codehop.o: /usr/include/string.h /usr/include/iso/string_iso.h
htmlize-codehop.o: /usr/include/stdlib.h /usr/include/iso/stdlib_iso.h
oligo_melt.o: ../include/blocksprogs.h /usr/include/stdlib.h
oligo_melt.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
oligo_melt.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
oligo_melt.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
oligo_melt.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
oligo_melt.o: /usr/include/string.h /usr/include/iso/string_iso.h
oligo_melt.o: /usr/include/math.h /usr/include/iso/math_iso.h
oligo_melt.o: /usr/include/unistd.h /usr/include/sys/types.h
oligo_melt.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
oligo_melt.o: /usr/include/sys/select.h /usr/include/sys/time.h
oligo_melt.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
oligo_melt.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
oligo_melt.o: ../include/global.h /usr/include/stddef.h
oligo_melt.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
oligo_melt.o: ../include/license.h ../include/strutil.h ../include/errors.h
oligo_melt.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
oligo_melt.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
oligo_melt.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
oligo_melt.o: ../include/gcode.h ../include/blocks.h ../include/output.h
oligo_melt.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
oligo_melt.o: ../include/convert.h ../include/frequency.h ../include/files.h
oligo_melt.o: ../include/protomat.h
mablock.o: ../include/blocksprogs.h /usr/include/stdlib.h
mablock.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
mablock.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
mablock.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
mablock.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
mablock.o: /usr/include/string.h /usr/include/iso/string_iso.h
mablock.o: /usr/include/math.h /usr/include/iso/math_iso.h
mablock.o: /usr/include/unistd.h /usr/include/sys/types.h
mablock.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
mablock.o: /usr/include/sys/select.h /usr/include/sys/time.h
mablock.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
mablock.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
mablock.o: ../include/global.h /usr/include/stddef.h
mablock.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
mablock.o: ../include/license.h ../include/strutil.h ../include/errors.h
mablock.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
mablock.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
mablock.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
mablock.o: ../include/gcode.h ../include/blocks.h ../include/output.h
mablock.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
mablock.o: ../include/convert.h ../include/frequency.h ../include/files.h
mablock.o: ../include/protomat.h
cobbler.o: ../include/blocksprogs.h /usr/include/stdlib.h
cobbler.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
cobbler.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
cobbler.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
cobbler.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
cobbler.o: /usr/include/string.h /usr/include/iso/string_iso.h
cobbler.o: /usr/include/math.h /usr/include/iso/math_iso.h
cobbler.o: /usr/include/unistd.h /usr/include/sys/types.h
cobbler.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
cobbler.o: /usr/include/sys/select.h /usr/include/sys/time.h
cobbler.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
cobbler.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
cobbler.o: ../include/global.h /usr/include/stddef.h
cobbler.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
cobbler.o: ../include/license.h ../include/strutil.h ../include/errors.h
cobbler.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
cobbler.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
cobbler.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
cobbler.o: ../include/gcode.h ../include/blocks.h ../include/output.h
cobbler.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
cobbler.o: ../include/convert.h ../include/frequency.h ../include/files.h
cobbler.o: ../include/protomat.h
addseqs.o: ../include/blocksprogs.h /usr/include/stdlib.h
addseqs.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
addseqs.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
addseqs.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
addseqs.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
addseqs.o: /usr/include/string.h /usr/include/iso/string_iso.h
addseqs.o: /usr/include/math.h /usr/include/iso/math_iso.h
addseqs.o: /usr/include/unistd.h /usr/include/sys/types.h
addseqs.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
addseqs.o: /usr/include/sys/select.h /usr/include/sys/time.h
addseqs.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
addseqs.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
addseqs.o: ../include/global.h /usr/include/stddef.h
addseqs.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
addseqs.o: ../include/license.h ../include/strutil.h ../include/errors.h
addseqs.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
addseqs.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
addseqs.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
addseqs.o: ../include/gcode.h ../include/blocks.h ../include/output.h
addseqs.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
addseqs.o: ../include/convert.h ../include/frequency.h ../include/files.h
addseqs.o: ../include/protomat.h
fastaseqs.o: ../include/blocksprogs.h /usr/include/stdlib.h
fastaseqs.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
fastaseqs.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
fastaseqs.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
fastaseqs.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
fastaseqs.o: /usr/include/string.h /usr/include/iso/string_iso.h
fastaseqs.o: /usr/include/math.h /usr/include/iso/math_iso.h
fastaseqs.o: /usr/include/unistd.h /usr/include/sys/types.h
fastaseqs.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
fastaseqs.o: /usr/include/sys/select.h /usr/include/sys/time.h
fastaseqs.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
fastaseqs.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
fastaseqs.o: ../include/global.h /usr/include/stddef.h
fastaseqs.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
fastaseqs.o: ../include/license.h ../include/strutil.h ../include/errors.h
fastaseqs.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
fastaseqs.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
fastaseqs.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
fastaseqs.o: ../include/gcode.h ../include/blocks.h ../include/output.h
fastaseqs.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
fastaseqs.o: ../include/convert.h ../include/frequency.h ../include/files.h
fastaseqs.o: ../include/protomat.h
LAMA.o: ../include/blocksprogs.h /usr/include/stdlib.h
LAMA.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
LAMA.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
LAMA.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
LAMA.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
LAMA.o: /usr/include/string.h /usr/include/iso/string_iso.h
LAMA.o: /usr/include/math.h /usr/include/iso/math_iso.h /usr/include/unistd.h
LAMA.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
LAMA.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
LAMA.o: /usr/include/sys/time.h /usr/include/sys/time.h
LAMA.o: /usr/include/sys/unistd.h /usr/include/ctype.h
LAMA.o: /usr/include/iso/ctype_iso.h ../include/global.h
LAMA.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
LAMA.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
LAMA.o: ../include/errors.h ../include/memory.h ../include/residues.h
LAMA.o: ../include/blastapp.h /usr/include/limits.h
LAMA.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
LAMA.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
LAMA.o: ../include/blocks.h ../include/output.h ../include/sequences.h
LAMA.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
LAMA.o: ../include/frequency.h ../include/files.h ../include/protomat.h
LAMA.o: LAMA.h
find_biassed_blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h
find_biassed_blocks.o: /usr/include/iso/stdlib_iso.h
find_biassed_blocks.o: /usr/include/sys/feature_tests.h
find_biassed_blocks.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
find_biassed_blocks.o: /usr/include/iso/stdio_iso.h
find_biassed_blocks.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
find_biassed_blocks.o: /usr/include/stdio_impl.h /usr/include/string.h
find_biassed_blocks.o: /usr/include/iso/string_iso.h /usr/include/math.h
find_biassed_blocks.o: /usr/include/iso/math_iso.h /usr/include/unistd.h
find_biassed_blocks.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
find_biassed_blocks.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
find_biassed_blocks.o: /usr/include/sys/time.h /usr/include/sys/time.h
find_biassed_blocks.o: /usr/include/sys/unistd.h /usr/include/ctype.h
find_biassed_blocks.o: /usr/include/iso/ctype_iso.h ../include/global.h
find_biassed_blocks.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
find_biassed_blocks.o: /usr/include/malloc.h ../include/license.h
find_biassed_blocks.o: ../include/strutil.h ../include/errors.h
find_biassed_blocks.o: ../include/memory.h ../include/residues.h
find_biassed_blocks.o: ../include/blastapp.h /usr/include/limits.h
find_biassed_blocks.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
find_biassed_blocks.o: ../include/aabet.h ../include/ntbet.h
find_biassed_blocks.o: ../include/gcode.h ../include/blocks.h
find_biassed_blocks.o: ../include/output.h ../include/sequences.h
find_biassed_blocks.o: ../include/matrix.h ../include/pattern.h
find_biassed_blocks.o: ../include/convert.h ../include/frequency.h
find_biassed_blocks.o: ../include/files.h ../include/protomat.h blkvblk.h
makeblockmap.o: ../include/blocksprogs.h /usr/include/stdlib.h
makeblockmap.o: /usr/include/iso/stdlib_iso.h
makeblockmap.o: /usr/include/sys/feature_tests.h /usr/include/sys/isa_defs.h
makeblockmap.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
makeblockmap.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
makeblockmap.o: /usr/include/stdio_impl.h /usr/include/string.h
makeblockmap.o: /usr/include/iso/string_iso.h /usr/include/math.h
makeblockmap.o: /usr/include/iso/math_iso.h /usr/include/unistd.h
makeblockmap.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
makeblockmap.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
makeblockmap.o: /usr/include/sys/time.h /usr/include/sys/time.h
makeblockmap.o: /usr/include/sys/unistd.h /usr/include/ctype.h
makeblockmap.o: /usr/include/iso/ctype_iso.h ../include/global.h
makeblockmap.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
makeblockmap.o: /usr/include/malloc.h ../include/license.h
makeblockmap.o: ../include/strutil.h ../include/errors.h ../include/memory.h
makeblockmap.o: ../include/residues.h ../include/blastapp.h
makeblockmap.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
makeblockmap.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
makeblockmap.o: ../include/gcode.h ../include/blocks.h ../include/output.h
makeblockmap.o: ../include/sequences.h ../include/matrix.h
makeblockmap.o: ../include/pattern.h ../include/convert.h
makeblockmap.o: ../include/frequency.h ../include/files.h
makeblockmap.o: ../include/protomat.h blockmap.h
prints2blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h
prints2blocks.o: /usr/include/iso/stdlib_iso.h
prints2blocks.o: /usr/include/sys/feature_tests.h /usr/include/sys/isa_defs.h
prints2blocks.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
prints2blocks.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
prints2blocks.o: /usr/include/stdio_impl.h /usr/include/string.h
prints2blocks.o: /usr/include/iso/string_iso.h /usr/include/math.h
prints2blocks.o: /usr/include/iso/math_iso.h /usr/include/unistd.h
prints2blocks.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
prints2blocks.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
prints2blocks.o: /usr/include/sys/time.h /usr/include/sys/time.h
prints2blocks.o: /usr/include/sys/unistd.h /usr/include/ctype.h
prints2blocks.o: /usr/include/iso/ctype_iso.h ../include/global.h
prints2blocks.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
prints2blocks.o: /usr/include/malloc.h ../include/license.h
prints2blocks.o: ../include/strutil.h ../include/errors.h ../include/memory.h
prints2blocks.o: ../include/residues.h ../include/blastapp.h
prints2blocks.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
prints2blocks.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
prints2blocks.o: ../include/gcode.h ../include/blocks.h ../include/output.h
prints2blocks.o: ../include/sequences.h ../include/matrix.h
prints2blocks.o: ../include/pattern.h ../include/convert.h
prints2blocks.o: ../include/frequency.h ../include/files.h
prints2blocks.o: ../include/protomat.h
lisblk.o: ../include/blocksprogs.h /usr/include/stdlib.h
lisblk.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
lisblk.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
lisblk.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
lisblk.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
lisblk.o: /usr/include/string.h /usr/include/iso/string_iso.h
lisblk.o: /usr/include/math.h /usr/include/iso/math_iso.h
lisblk.o: /usr/include/unistd.h /usr/include/sys/types.h
lisblk.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
lisblk.o: /usr/include/sys/select.h /usr/include/sys/time.h
lisblk.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
lisblk.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
lisblk.o: ../include/global.h /usr/include/stddef.h
lisblk.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
lisblk.o: ../include/license.h ../include/strutil.h ../include/errors.h
lisblk.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
lisblk.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
lisblk.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
lisblk.o: ../include/gcode.h ../include/blocks.h ../include/output.h
lisblk.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
lisblk.o: ../include/convert.h ../include/frequency.h ../include/files.h
lisblk.o: ../include/protomat.h
coduse.o: ../include/blocksprogs.h /usr/include/stdlib.h
coduse.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
coduse.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
coduse.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
coduse.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
coduse.o: /usr/include/string.h /usr/include/iso/string_iso.h
coduse.o: /usr/include/math.h /usr/include/iso/math_iso.h
coduse.o: /usr/include/unistd.h /usr/include/sys/types.h
coduse.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
coduse.o: /usr/include/sys/select.h /usr/include/sys/time.h
coduse.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
coduse.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
coduse.o: ../include/global.h /usr/include/stddef.h
coduse.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
coduse.o: ../include/license.h ../include/strutil.h ../include/errors.h
coduse.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
coduse.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
coduse.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
coduse.o: ../include/gcode.h ../include/blocks.h ../include/output.h
coduse.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
coduse.o: ../include/convert.h ../include/frequency.h ../include/files.h
coduse.o: ../include/protomat.h
narrow.o: ../include/blocksprogs.h /usr/include/stdlib.h
narrow.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
narrow.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
narrow.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
narrow.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
narrow.o: /usr/include/string.h /usr/include/iso/string_iso.h
narrow.o: /usr/include/math.h /usr/include/iso/math_iso.h
narrow.o: /usr/include/unistd.h /usr/include/sys/types.h
narrow.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
narrow.o: /usr/include/sys/select.h /usr/include/sys/time.h
narrow.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
narrow.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
narrow.o: ../include/global.h /usr/include/stddef.h
narrow.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
narrow.o: ../include/license.h ../include/strutil.h ../include/errors.h
narrow.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
narrow.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
narrow.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
narrow.o: ../include/gcode.h ../include/blocks.h ../include/output.h
narrow.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
narrow.o: ../include/convert.h ../include/frequency.h ../include/files.h
narrow.o: ../include/protomat.h
blk2slx.o: ../include/blocksprogs.h /usr/include/stdlib.h
blk2slx.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blk2slx.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
blk2slx.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blk2slx.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blk2slx.o: /usr/include/string.h /usr/include/iso/string_iso.h
blk2slx.o: /usr/include/math.h /usr/include/iso/math_iso.h
blk2slx.o: /usr/include/unistd.h /usr/include/sys/types.h
blk2slx.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
blk2slx.o: /usr/include/sys/select.h /usr/include/sys/time.h
blk2slx.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
blk2slx.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blk2slx.o: ../include/global.h /usr/include/stddef.h
blk2slx.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
blk2slx.o: ../include/license.h ../include/strutil.h ../include/errors.h
blk2slx.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
blk2slx.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
blk2slx.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blk2slx.o: ../include/gcode.h ../include/blocks.h ../include/output.h
blk2slx.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blk2slx.o: ../include/convert.h ../include/frequency.h ../include/files.h
blk2slx.o: ../include/protomat.h
blkprob.o: ../include/blocksprogs.h /usr/include/stdlib.h
blkprob.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blkprob.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
blkprob.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blkprob.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blkprob.o: /usr/include/string.h /usr/include/iso/string_iso.h
blkprob.o: /usr/include/math.h /usr/include/iso/math_iso.h
blkprob.o: /usr/include/unistd.h /usr/include/sys/types.h
blkprob.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
blkprob.o: /usr/include/sys/select.h /usr/include/sys/time.h
blkprob.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
blkprob.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blkprob.o: ../include/global.h /usr/include/stddef.h
blkprob.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
blkprob.o: ../include/license.h ../include/strutil.h ../include/errors.h
blkprob.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
blkprob.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
blkprob.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blkprob.o: ../include/gcode.h ../include/blocks.h ../include/output.h
blkprob.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blkprob.o: ../include/convert.h ../include/frequency.h ../include/files.h
blkprob.o: ../include/protomat.h
blocks.o: ../include/global.h /usr/include/stdlib.h
blocks.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blocks.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
blocks.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blocks.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blocks.o: /usr/include/string.h /usr/include/iso/string_iso.h
blocks.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
blocks.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blocks.o: /usr/include/malloc.h /usr/include/sys/types.h
blocks.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
blocks.o: /usr/include/sys/select.h /usr/include/sys/time.h
blocks.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
blocks.o: ../include/errors.h ../include/memory.h ../include/blocks.h
blocks.o: ../include/output.h ../include/sequences.h ../include/residues.h
blocks.o: ../include/blastapp.h /usr/include/limits.h
blocks.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
blocks.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
config.o: ../include/global.h /usr/include/stdlib.h
config.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
config.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
config.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
config.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
config.o: /usr/include/string.h /usr/include/iso/string_iso.h
config.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
config.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
config.o: /usr/include/malloc.h /usr/include/sys/types.h
config.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
config.o: /usr/include/sys/select.h /usr/include/sys/time.h
config.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
config.o: ../include/errors.h ../include/memory.h ../include/files.h
config.o: ../include/sequences.h ../include/pattern.h ../include/options.h
config.o: config.h blimps.h scoring.h lists.h ../include/skiplist.h
convert.o: /usr/include/assert.h /usr/include/math.h
convert.o: /usr/include/iso/math_iso.h ../include/global.h
convert.o: /usr/include/stdlib.h /usr/include/iso/stdlib_iso.h
convert.o: /usr/include/sys/feature_tests.h /usr/include/sys/isa_defs.h
convert.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
convert.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
convert.o: /usr/include/stdio_impl.h /usr/include/string.h
convert.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
convert.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
convert.o: /usr/include/iso/ctype_iso.h /usr/include/malloc.h
convert.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
convert.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
convert.o: /usr/include/sys/time.h /usr/include/sys/time.h
convert.o: ../include/license.h ../include/strutil.h ../include/errors.h
convert.o: ../include/memory.h ../include/options.h ../include/blocks.h
convert.o: ../include/output.h ../include/sequences.h ../include/matrix.h
convert.o: ../include/pattern.h ../include/residues.h ../include/blastapp.h
convert.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
convert.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
convert.o: ../include/gcode.h ../include/frequency.h ../include/protomat.h
convert.o: ../include/convert.h blimps.h
errors.o: ../include/global.h /usr/include/stdlib.h
errors.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
errors.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
errors.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
errors.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
errors.o: /usr/include/string.h /usr/include/iso/string_iso.h
errors.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
errors.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
errors.o: /usr/include/malloc.h /usr/include/sys/types.h
errors.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
errors.o: /usr/include/sys/select.h /usr/include/sys/time.h
errors.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
errors.o: ../include/errors.h ../include/memory.h
files.o: ../include/global.h /usr/include/stdlib.h
files.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
files.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
files.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
files.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
files.o: /usr/include/string.h /usr/include/iso/string_iso.h
files.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
files.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
files.o: /usr/include/malloc.h /usr/include/sys/types.h
files.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
files.o: /usr/include/sys/select.h /usr/include/sys/time.h
files.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
files.o: ../include/errors.h ../include/memory.h ../include/files.h
files.o: ../include/sequences.h
frequency.o: ../include/global.h /usr/include/stdlib.h
frequency.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
frequency.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
frequency.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
frequency.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
frequency.o: /usr/include/string.h /usr/include/iso/string_iso.h
frequency.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
frequency.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
frequency.o: /usr/include/malloc.h /usr/include/sys/types.h
frequency.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
frequency.o: /usr/include/sys/select.h /usr/include/sys/time.h
frequency.o: /usr/include/sys/time.h ../include/license.h
frequency.o: ../include/strutil.h ../include/errors.h ../include/memory.h
frequency.o: ../include/blocks.h ../include/output.h ../include/sequences.h
frequency.o: ../include/matrix.h ../include/pattern.h ../include/frequency.h
frequency.o: ../include/convert.h ../include/files.h ../include/residues.h
frequency.o: ../include/blastapp.h /usr/include/limits.h
frequency.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
frequency.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
gcode.o: ../include/global.h /usr/include/stdlib.h
gcode.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
gcode.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
gcode.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
gcode.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
gcode.o: /usr/include/string.h /usr/include/iso/string_iso.h
gcode.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
gcode.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
gcode.o: /usr/include/malloc.h /usr/include/sys/types.h
gcode.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
gcode.o: /usr/include/sys/select.h /usr/include/sys/time.h
gcode.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
gcode.o: ../include/errors.h ../include/memory.h ../include/residues.h
gcode.o: ../include/blastapp.h /usr/include/limits.h
gcode.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
gcode.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
gcode.o: ../include/sequences.h
lists.o: ../include/global.h /usr/include/stdlib.h
lists.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
lists.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
lists.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
lists.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
lists.o: /usr/include/string.h /usr/include/iso/string_iso.h
lists.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
lists.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
lists.o: /usr/include/malloc.h /usr/include/sys/types.h
lists.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
lists.o: /usr/include/sys/select.h /usr/include/sys/time.h
lists.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
lists.o: ../include/errors.h ../include/memory.h ../include/blocks.h
lists.o: ../include/output.h ../include/sequences.h ../include/matrix.h
lists.o: ../include/pattern.h lists.h ../include/skiplist.h blimps.h scores.h
matrix.o: ../include/global.h /usr/include/stdlib.h
matrix.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
matrix.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
matrix.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
matrix.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
matrix.o: /usr/include/string.h /usr/include/iso/string_iso.h
matrix.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
matrix.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
matrix.o: /usr/include/malloc.h /usr/include/sys/types.h
matrix.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
matrix.o: /usr/include/sys/select.h /usr/include/sys/time.h
matrix.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
matrix.o: ../include/errors.h ../include/memory.h ../include/blocks.h
matrix.o: ../include/output.h ../include/sequences.h ../include/matrix.h
matrix.o: ../include/pattern.h ../include/residues.h ../include/blastapp.h
matrix.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
matrix.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
matrix.o: ../include/gcode.h
memory.o: ../include/global.h /usr/include/stdlib.h
memory.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
memory.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
memory.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
memory.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
memory.o: /usr/include/string.h /usr/include/iso/string_iso.h
memory.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
memory.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
memory.o: /usr/include/malloc.h /usr/include/sys/types.h
memory.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
memory.o: /usr/include/sys/select.h /usr/include/sys/time.h
memory.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
memory.o: ../include/errors.h ../include/memory.h
pattern.o: /usr/include/assert.h ../include/global.h /usr/include/stdlib.h
pattern.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
pattern.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
pattern.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
pattern.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
pattern.o: /usr/include/string.h /usr/include/iso/string_iso.h
pattern.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
pattern.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
pattern.o: /usr/include/malloc.h /usr/include/sys/types.h
pattern.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
pattern.o: /usr/include/sys/select.h /usr/include/sys/time.h
pattern.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
pattern.o: ../include/errors.h ../include/memory.h ../include/files.h
pattern.o: ../include/blocks.h ../include/output.h ../include/sequences.h
pattern.o: ../include/matrix.h ../include/pattern.h ../include/residues.h
pattern.o: ../include/blastapp.h /usr/include/limits.h
pattern.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
pattern.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
pattern.o: ../include/skiplist.h
scores.o: /usr/include/math.h /usr/include/iso/math_iso.h ../include/global.h
scores.o: /usr/include/stdlib.h /usr/include/iso/stdlib_iso.h
scores.o: /usr/include/sys/feature_tests.h /usr/include/sys/isa_defs.h
scores.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
scores.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
scores.o: /usr/include/stdio_impl.h /usr/include/string.h
scores.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
scores.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
scores.o: /usr/include/iso/ctype_iso.h /usr/include/malloc.h
scores.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
scores.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
scores.o: /usr/include/sys/time.h /usr/include/sys/time.h
scores.o: ../include/license.h ../include/strutil.h ../include/errors.h
scores.o: ../include/memory.h ../include/blocks.h ../include/output.h
scores.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
scores.o: scores.h blimps.h scoring.h lists.h ../include/skiplist.h
scoring.o: /usr/include/math.h /usr/include/iso/math_iso.h
scoring.o: ../include/global.h /usr/include/stdlib.h
scoring.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
scoring.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
scoring.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
scoring.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
scoring.o: /usr/include/string.h /usr/include/iso/string_iso.h
scoring.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
scoring.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
scoring.o: /usr/include/malloc.h /usr/include/sys/types.h
scoring.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
scoring.o: /usr/include/sys/select.h /usr/include/sys/time.h
scoring.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
scoring.o: ../include/errors.h ../include/memory.h ../include/blocks.h
scoring.o: ../include/output.h ../include/sequences.h ../include/matrix.h
scoring.o: ../include/pattern.h ../include/residues.h ../include/blastapp.h
scoring.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
scoring.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
scoring.o: ../include/gcode.h scoring.h blimps.h scores.h lists.h
scoring.o: ../include/skiplist.h
sequences.o: ../include/global.h /usr/include/stdlib.h
sequences.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
sequences.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
sequences.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
sequences.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
sequences.o: /usr/include/string.h /usr/include/iso/string_iso.h
sequences.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
sequences.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
sequences.o: /usr/include/malloc.h /usr/include/sys/types.h
sequences.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
sequences.o: /usr/include/sys/select.h /usr/include/sys/time.h
sequences.o: /usr/include/sys/time.h ../include/license.h
sequences.o: ../include/strutil.h ../include/errors.h ../include/memory.h
sequences.o: ../include/sequences.h ../include/residues.h
sequences.o: ../include/blastapp.h /usr/include/limits.h
sequences.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
sequences.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
sl.o: /usr/include/assert.h /usr/include/sys/time.h ../include/global.h
sl.o: /usr/include/stdlib.h /usr/include/iso/stdlib_iso.h
sl.o: /usr/include/sys/feature_tests.h /usr/include/sys/isa_defs.h
sl.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
sl.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
sl.o: /usr/include/stdio_impl.h /usr/include/string.h
sl.o: /usr/include/iso/string_iso.h /usr/include/stddef.h
sl.o: /usr/include/iso/stddef_iso.h /usr/include/ctype.h
sl.o: /usr/include/iso/ctype_iso.h /usr/include/malloc.h
sl.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
sl.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
sl.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
sl.o: ../include/errors.h ../include/memory.h ../include/skiplist.h
strutil.o: ../include/global.h /usr/include/stdlib.h
strutil.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
strutil.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
strutil.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
strutil.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
strutil.o: /usr/include/string.h /usr/include/iso/string_iso.h
strutil.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
strutil.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
strutil.o: /usr/include/malloc.h /usr/include/sys/types.h
strutil.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
strutil.o: /usr/include/sys/select.h /usr/include/sys/time.h
strutil.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
strutil.o: ../include/errors.h ../include/memory.h
version.o: ../include/global.h /usr/include/stdlib.h
version.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
version.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
version.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
version.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
version.o: /usr/include/string.h /usr/include/iso/string_iso.h
version.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
version.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
version.o: /usr/include/malloc.h /usr/include/sys/types.h
version.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
version.o: /usr/include/sys/select.h /usr/include/sys/time.h
version.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
version.o: ../include/errors.h ../include/memory.h ../include/version.h
options.o: ../include/global.h /usr/include/stdlib.h
options.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
options.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
options.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
options.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
options.o: /usr/include/string.h /usr/include/iso/string_iso.h
options.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
options.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
options.o: /usr/include/malloc.h /usr/include/sys/types.h
options.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
options.o: /usr/include/sys/select.h /usr/include/sys/time.h
options.o: /usr/include/sys/time.h ../include/license.h ../include/strutil.h
options.o: ../include/errors.h ../include/memory.h ../include/options.h
protomat.o: /usr/include/sys/types.h /usr/include/sys/isa_defs.h
protomat.o: /usr/include/sys/feature_tests.h /usr/include/sys/machtypes.h
protomat.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
protomat.o: /usr/include/sys/time.h /usr/include/sys/time.h
protomat.o: /usr/include/dirent.h /usr/include/sys/dirent.h
protomat.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
protomat.o: ../include/protomat.h /usr/include/stdlib.h
protomat.o: /usr/include/iso/stdlib_iso.h /usr/include/stdio.h
protomat.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
protomat.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
protomat.o: /usr/include/string.h /usr/include/iso/string_iso.h
interpro.o: ../include/blocksprogs.h /usr/include/stdlib.h
interpro.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
interpro.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
interpro.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
interpro.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
interpro.o: /usr/include/string.h /usr/include/iso/string_iso.h
interpro.o: /usr/include/math.h /usr/include/iso/math_iso.h
interpro.o: /usr/include/unistd.h /usr/include/sys/types.h
interpro.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
interpro.o: /usr/include/sys/select.h /usr/include/sys/time.h
interpro.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
interpro.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
interpro.o: ../include/global.h /usr/include/stddef.h
interpro.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
interpro.o: ../include/license.h ../include/strutil.h ../include/errors.h
interpro.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
interpro.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
interpro.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
interpro.o: ../include/gcode.h ../include/blocks.h ../include/output.h
interpro.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
interpro.o: ../include/convert.h ../include/frequency.h ../include/files.h
interpro.o: ../include/protomat.h
pssmdist.o: ../include/blocksprogs.h /usr/include/stdlib.h
pssmdist.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
pssmdist.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
pssmdist.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
pssmdist.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
pssmdist.o: /usr/include/string.h /usr/include/iso/string_iso.h
pssmdist.o: /usr/include/math.h /usr/include/iso/math_iso.h
pssmdist.o: /usr/include/unistd.h /usr/include/sys/types.h
pssmdist.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
pssmdist.o: /usr/include/sys/select.h /usr/include/sys/time.h
pssmdist.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
pssmdist.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
pssmdist.o: ../include/global.h /usr/include/stddef.h
pssmdist.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
pssmdist.o: ../include/license.h ../include/strutil.h ../include/errors.h
pssmdist.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
pssmdist.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
pssmdist.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
pssmdist.o: ../include/gcode.h ../include/blocks.h ../include/output.h
pssmdist.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
pssmdist.o: ../include/convert.h ../include/frequency.h ../include/files.h
pssmdist.o: ../include/protomat.h
pssmBL.o: ../include/blocksprogs.h /usr/include/stdlib.h
pssmBL.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
pssmBL.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
pssmBL.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
pssmBL.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
pssmBL.o: /usr/include/string.h /usr/include/iso/string_iso.h
pssmBL.o: /usr/include/math.h /usr/include/iso/math_iso.h
pssmBL.o: /usr/include/unistd.h /usr/include/sys/types.h
pssmBL.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
pssmBL.o: /usr/include/sys/select.h /usr/include/sys/time.h
pssmBL.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
pssmBL.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
pssmBL.o: ../include/global.h /usr/include/stddef.h
pssmBL.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
pssmBL.o: ../include/license.h ../include/strutil.h ../include/errors.h
pssmBL.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
pssmBL.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
pssmBL.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
pssmBL.o: ../include/gcode.h ../include/blocks.h ../include/output.h
pssmBL.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
pssmBL.o: ../include/convert.h ../include/frequency.h ../include/files.h
pssmBL.o: ../include/protomat.h
papssm.o: ../include/blocksprogs.h /usr/include/stdlib.h
papssm.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
papssm.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
papssm.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
papssm.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
papssm.o: /usr/include/string.h /usr/include/iso/string_iso.h
papssm.o: /usr/include/math.h /usr/include/iso/math_iso.h
papssm.o: /usr/include/unistd.h /usr/include/sys/types.h
papssm.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
papssm.o: /usr/include/sys/select.h /usr/include/sys/time.h
papssm.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
papssm.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
papssm.o: ../include/global.h /usr/include/stddef.h
papssm.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
papssm.o: ../include/license.h ../include/strutil.h ../include/errors.h
papssm.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
papssm.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
papssm.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
papssm.o: ../include/gcode.h ../include/blocks.h ../include/output.h
papssm.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
papssm.o: ../include/convert.h ../include/frequency.h ../include/files.h
papssm.o: ../include/protomat.h blimps.h
matrix_logob.o: /usr/include/sys/types.h /usr/include/sys/isa_defs.h
matrix_logob.o: /usr/include/sys/feature_tests.h /usr/include/sys/machtypes.h
matrix_logob.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
matrix_logob.o: /usr/include/sys/time.h /usr/include/sys/time.h
matrix_logob.o: /usr/include/sys/stat.h /usr/include/sys/time_impl.h
matrix_logob.o: /usr/include/sys/stat_impl.h ../include/blocksprogs.h
matrix_logob.o: /usr/include/stdlib.h /usr/include/iso/stdlib_iso.h
matrix_logob.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
matrix_logob.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
matrix_logob.o: /usr/include/stdio_impl.h /usr/include/string.h
matrix_logob.o: /usr/include/iso/string_iso.h /usr/include/math.h
matrix_logob.o: /usr/include/iso/math_iso.h /usr/include/unistd.h
matrix_logob.o: /usr/include/sys/unistd.h /usr/include/ctype.h
matrix_logob.o: /usr/include/iso/ctype_iso.h ../include/global.h
matrix_logob.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
matrix_logob.o: /usr/include/malloc.h ../include/license.h
matrix_logob.o: ../include/strutil.h ../include/errors.h ../include/memory.h
matrix_logob.o: ../include/residues.h ../include/blastapp.h
matrix_logob.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
matrix_logob.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
matrix_logob.o: ../include/gcode.h ../include/blocks.h ../include/output.h
matrix_logob.o: ../include/sequences.h ../include/matrix.h
matrix_logob.o: ../include/pattern.h ../include/convert.h
matrix_logob.o: ../include/frequency.h ../include/files.h
matrix_logob.o: ../include/protomat.h
makelogob.o: p2c.h /usr/include/stdio.h /usr/include/iso/stdio_iso.h
makelogob.o: /usr/include/sys/feature_tests.h /usr/include/sys/isa_defs.h
makelogob.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
makelogob.o: /usr/include/stdio_impl.h /usr/include/stddef.h
makelogob.o: /usr/include/iso/stddef_iso.h /usr/include/stdlib.h
makelogob.o: /usr/include/iso/stdlib_iso.h /usr/include/string.h
makelogob.o: /usr/include/iso/string_iso.h /usr/include/ctype.h
makelogob.o: /usr/include/iso/ctype_iso.h /usr/include/math.h
makelogob.o: /usr/include/iso/math_iso.h /usr/include/setjmp.h
makelogob.o: /usr/include/iso/setjmp_iso.h /usr/include/assert.h
blocks_search.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
blocks_search.o: /usr/include/sys/feature_tests.h /usr/include/sys/isa_defs.h
blocks_search.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
blocks_search.o: /usr/include/stdio_impl.h /usr/include/stdlib.h
blocks_search.o: /usr/include/iso/stdlib_iso.h ../include/global.h
blocks_search.o: /usr/include/string.h /usr/include/iso/string_iso.h
blocks_search.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
blocks_search.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blocks_search.o: /usr/include/malloc.h /usr/include/sys/types.h
blocks_search.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
blocks_search.o: /usr/include/sys/select.h /usr/include/sys/time.h
blocks_search.o: /usr/include/sys/time.h ../include/license.h
blocks_search.o: ../include/strutil.h ../include/errors.h ../include/memory.h
blocks_search.o: /usr/include/unistd.h /usr/include/sys/unistd.h
LAMA_search.o: ../include/blocksprogs.h /usr/include/stdlib.h
LAMA_search.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
LAMA_search.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
LAMA_search.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
LAMA_search.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
LAMA_search.o: /usr/include/string.h /usr/include/iso/string_iso.h
LAMA_search.o: /usr/include/math.h /usr/include/iso/math_iso.h
LAMA_search.o: /usr/include/unistd.h /usr/include/sys/types.h
LAMA_search.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
LAMA_search.o: /usr/include/sys/select.h /usr/include/sys/time.h
LAMA_search.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
LAMA_search.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
LAMA_search.o: ../include/global.h /usr/include/stddef.h
LAMA_search.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
LAMA_search.o: ../include/license.h ../include/strutil.h ../include/errors.h
LAMA_search.o: ../include/memory.h ../include/residues.h
LAMA_search.o: ../include/blastapp.h /usr/include/limits.h
LAMA_search.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
LAMA_search.o: ../include/aabet.h ../include/ntbet.h ../include/gcode.h
LAMA_search.o: ../include/blocks.h ../include/output.h ../include/sequences.h
LAMA_search.o: ../include/matrix.h ../include/pattern.h ../include/convert.h
LAMA_search.o: ../include/frequency.h ../include/files.h
LAMA_search.o: ../include/protomat.h
block_vis.o: ../include/blocksprogs.h /usr/include/stdlib.h
block_vis.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
block_vis.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
block_vis.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
block_vis.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
block_vis.o: /usr/include/string.h /usr/include/iso/string_iso.h
block_vis.o: /usr/include/math.h /usr/include/iso/math_iso.h
block_vis.o: /usr/include/unistd.h /usr/include/sys/types.h
block_vis.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
block_vis.o: /usr/include/sys/select.h /usr/include/sys/time.h
block_vis.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
block_vis.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
block_vis.o: ../include/global.h /usr/include/stddef.h
block_vis.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
block_vis.o: ../include/license.h ../include/strutil.h ../include/errors.h
block_vis.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
block_vis.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
block_vis.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
block_vis.o: ../include/gcode.h ../include/blocks.h ../include/output.h
block_vis.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
block_vis.o: ../include/convert.h ../include/frequency.h ../include/files.h
block_vis.o: ../include/protomat.h blockmap.h
format_block.o: ../include/blocksprogs.h /usr/include/stdlib.h
format_block.o: /usr/include/iso/stdlib_iso.h
format_block.o: /usr/include/sys/feature_tests.h /usr/include/sys/isa_defs.h
format_block.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
format_block.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
format_block.o: /usr/include/stdio_impl.h /usr/include/string.h
format_block.o: /usr/include/iso/string_iso.h /usr/include/math.h
format_block.o: /usr/include/iso/math_iso.h /usr/include/unistd.h
format_block.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
format_block.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
format_block.o: /usr/include/sys/time.h /usr/include/sys/time.h
format_block.o: /usr/include/sys/unistd.h /usr/include/ctype.h
format_block.o: /usr/include/iso/ctype_iso.h ../include/global.h
format_block.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
format_block.o: /usr/include/malloc.h ../include/license.h
format_block.o: ../include/strutil.h ../include/errors.h ../include/memory.h
format_block.o: ../include/residues.h ../include/blastapp.h
format_block.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
format_block.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
format_block.o: ../include/gcode.h ../include/blocks.h ../include/output.h
format_block.o: ../include/sequences.h ../include/matrix.h
format_block.o: ../include/pattern.h ../include/convert.h
format_block.o: ../include/frequency.h ../include/files.h
format_block.o: ../include/protomat.h
biassed_blocks_finder.o: ../include/blocksprogs.h /usr/include/stdlib.h
biassed_blocks_finder.o: /usr/include/iso/stdlib_iso.h
biassed_blocks_finder.o: /usr/include/sys/feature_tests.h
biassed_blocks_finder.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
biassed_blocks_finder.o: /usr/include/iso/stdio_iso.h
biassed_blocks_finder.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
biassed_blocks_finder.o: /usr/include/stdio_impl.h /usr/include/string.h
biassed_blocks_finder.o: /usr/include/iso/string_iso.h /usr/include/math.h
biassed_blocks_finder.o: /usr/include/iso/math_iso.h /usr/include/unistd.h
biassed_blocks_finder.o: /usr/include/sys/types.h
biassed_blocks_finder.o: /usr/include/sys/machtypes.h
biassed_blocks_finder.o: /usr/include/sys/int_types.h
biassed_blocks_finder.o: /usr/include/sys/select.h /usr/include/sys/time.h
biassed_blocks_finder.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
biassed_blocks_finder.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
biassed_blocks_finder.o: ../include/global.h /usr/include/stddef.h
biassed_blocks_finder.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
biassed_blocks_finder.o: ../include/license.h ../include/strutil.h
biassed_blocks_finder.o: ../include/errors.h ../include/memory.h
biassed_blocks_finder.o: ../include/residues.h ../include/blastapp.h
biassed_blocks_finder.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
biassed_blocks_finder.o: ../include/alphabet.h ../include/aabet.h
biassed_blocks_finder.o: ../include/ntbet.h ../include/gcode.h
biassed_blocks_finder.o: ../include/blocks.h ../include/output.h
biassed_blocks_finder.o: ../include/sequences.h ../include/matrix.h
biassed_blocks_finder.o: ../include/pattern.h ../include/convert.h
biassed_blocks_finder.o: ../include/frequency.h ../include/files.h
biassed_blocks_finder.o: ../include/protomat.h
htmlize-LAMA.o: /usr/include/stdlib.h /usr/include/iso/stdlib_iso.h
htmlize-LAMA.o: /usr/include/sys/feature_tests.h /usr/include/sys/isa_defs.h
htmlize-LAMA.o: /usr/include/stdio.h /usr/include/iso/stdio_iso.h
htmlize-LAMA.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
htmlize-LAMA.o: /usr/include/stdio_impl.h
show_aligned_blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h
show_aligned_blocks.o: /usr/include/iso/stdlib_iso.h
show_aligned_blocks.o: /usr/include/sys/feature_tests.h
show_aligned_blocks.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
show_aligned_blocks.o: /usr/include/iso/stdio_iso.h
show_aligned_blocks.o: /usr/include/sys/va_list.h /usr/include/stdio_tag.h
show_aligned_blocks.o: /usr/include/stdio_impl.h /usr/include/string.h
show_aligned_blocks.o: /usr/include/iso/string_iso.h /usr/include/math.h
show_aligned_blocks.o: /usr/include/iso/math_iso.h /usr/include/unistd.h
show_aligned_blocks.o: /usr/include/sys/types.h /usr/include/sys/machtypes.h
show_aligned_blocks.o: /usr/include/sys/int_types.h /usr/include/sys/select.h
show_aligned_blocks.o: /usr/include/sys/time.h /usr/include/sys/time.h
show_aligned_blocks.o: /usr/include/sys/unistd.h /usr/include/ctype.h
show_aligned_blocks.o: /usr/include/iso/ctype_iso.h ../include/global.h
show_aligned_blocks.o: /usr/include/stddef.h /usr/include/iso/stddef_iso.h
show_aligned_blocks.o: /usr/include/malloc.h ../include/license.h
show_aligned_blocks.o: ../include/strutil.h ../include/errors.h
show_aligned_blocks.o: ../include/memory.h ../include/residues.h
show_aligned_blocks.o: ../include/blastapp.h /usr/include/limits.h
show_aligned_blocks.o: /usr/include/iso/limits_iso.h ../include/alphabet.h
show_aligned_blocks.o: ../include/aabet.h ../include/ntbet.h
show_aligned_blocks.o: ../include/gcode.h ../include/blocks.h
show_aligned_blocks.o: ../include/output.h ../include/sequences.h
show_aligned_blocks.o: ../include/matrix.h ../include/pattern.h
show_aligned_blocks.o: ../include/convert.h ../include/frequency.h
show_aligned_blocks.o: ../include/files.h ../include/protomat.h
blk2mot.o: ../include/blocksprogs.h /usr/include/stdlib.h
blk2mot.o: /usr/include/iso/stdlib_iso.h /usr/include/sys/feature_tests.h
blk2mot.o: /usr/include/sys/isa_defs.h /usr/include/stdio.h
blk2mot.o: /usr/include/iso/stdio_iso.h /usr/include/sys/va_list.h
blk2mot.o: /usr/include/stdio_tag.h /usr/include/stdio_impl.h
blk2mot.o: /usr/include/string.h /usr/include/iso/string_iso.h
blk2mot.o: /usr/include/math.h /usr/include/iso/math_iso.h
blk2mot.o: /usr/include/unistd.h /usr/include/sys/types.h
blk2mot.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
blk2mot.o: /usr/include/sys/select.h /usr/include/sys/time.h
blk2mot.o: /usr/include/sys/time.h /usr/include/sys/unistd.h
blk2mot.o: /usr/include/ctype.h /usr/include/iso/ctype_iso.h
blk2mot.o: ../include/global.h /usr/include/stddef.h
blk2mot.o: /usr/include/iso/stddef_iso.h /usr/include/malloc.h
blk2mot.o: ../include/license.h ../include/strutil.h ../include/errors.h
blk2mot.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
blk2mot.o: /usr/include/limits.h /usr/include/iso/limits_iso.h
blk2mot.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
blk2mot.o: ../include/gcode.h ../include/blocks.h ../include/output.h
blk2mot.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
blk2mot.o: ../include/convert.h ../include/frequency.h ../include/files.h
blk2mot.o: ../include/protomat.h
clude/malloc.h /usr/include/sys/types.h
blocks_search.o: /usr/include/sys/machtypes.h /usr/include/sys/int_types.h
blocks_search.o: /usr/include/sys/select.h /usr/includblimps-3.9/blimps/protxblk.c000064400001460000012000000042531054700061700164510ustar00jorjastaff00000400000027/*    Copyright 2007 Fred Hutchinson Cancer Research Center

	protxblk  

	Converts blocks to one line per protein with start/end
--------------------------------------------------------------------
  1/ 3/07 J. Henikoff
====================================================================*/

#define PROTXBLK_C_
#define EXTERN
#define MAXNAME 80	/* Maximum file name length */

#include 

/*
 * Local variables and data structures
 */
void output_prot();
/*=======================================================================*/
/*
 * main
 *   controls flow of program
 */

int main(argc, argv)
     int argc;
     char *argv[];
{
  FILE *bfp, *ofp;
  Block *block;
  char bdbname[MAXNAME], conname[MAXNAME];

/* ------------1st arg = blocks database -------------------------------*/
   if (argc > 1)
      strcpy(bdbname, argv[1]);
   else
   {
      printf("\nEnter name of blocks database: ");
      gets(bdbname);
   }
   if ( (bfp=fopen(bdbname, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", bdbname);
      exit(-1);
   }
/* ------------2nd arg = output file ---------------------*/
   if (argc > 2)
      strcpy(conname, argv[2]);
   else
   {
      printf("\nEnter name of output file: ");
      gets(conname);
   }
   if ( (ofp=fopen(conname, "w")) == NULL)
   {
      printf("\nCannot open file %s\n", conname);
      exit(-1);
   }

/*-----------------------------------------------------------------*/

  while ((block = read_a_block(bfp)) != NULL)
  {
     output_prot(block, ofp);
  }
   
  fclose(bfp); fclose(ofp);
  exit(0);

}  /* end of main */
/*===================================================================
     format is sequence name, block name, start, end, weight
====================================================================*/
void output_prot(block, ofp)
Block *block;
FILE *ofp;
{
   int seq, start, end;
   for (seq=0; seq < block->num_sequences; seq++)
   {
      start = block->sequences[seq].position;
      end = start + block->width - 1;
      fprintf(ofp, "%-20s\t%s\t%d\t%d\t%f\n", 
	block->sequences[seq].name, block->number, start, end,
	block->sequences[seq].weight);
   }
}  /* end of output_prot */
blimps-3.9/docs/000075500001460000012000000000001041505754000140775ustar00jorjastaff00000400000027blimps-3.9/docs/arab.codon.use000064400001460000012000000027221012171035700166220ustar00jorjastaff000004000000270.030759	-- [ 0] AAA
0.020932	-- [ 1] AAC
0.032765	-- [ 2] AAG
0.022274	-- [ 3] AAU
0.015655	-- [ 4] ACA
0.010364	-- [ 5] ACC
0.007708	-- [ 6] ACG
0.017626	-- [ 7] ACU
0.018855	-- [ 8] AGA
0.011281	-- [ 9] AGC
0.010937	-- [10] AGG
0.013962	-- [11] AGU
0.012527	-- [12] AUA
0.018588	-- [13] AUC
0.024427	-- [14] AUG
0.021581	-- [15] AUU
0.019338	-- [16] CAA
0.008693	-- [17] CAC
0.015213	-- [18] CAG
0.013720	-- [19] CAU
0.016158	-- [20] CCA
0.005316	-- [21] CCC
0.008576	-- [22] CCG
0.018707	-- [23] CCU
0.006262	-- [24] CGA
0.003765	-- [25] CGC
0.004827	-- [26] CGG
0.009007	-- [27] CGU
0.009861	-- [28] CUA
0.016086	-- [29] CUC
0.009840	-- [30] CUG
0.024165	-- [31] CUU
0.034321	-- [32] GAA
0.017247	-- [33] GAC
0.032298	-- [34] GAG
0.036727	-- [35] GAU
0.017533	-- [36] GCA
0.010396	-- [37] GCC
0.008973	-- [38] GCG
0.028530	-- [39] GCU
0.024278	-- [40] GGA
0.009177	-- [41] GGC
0.010223	-- [42] GGG
0.022375	-- [43] GGU
0.009928	-- [44] GUA
0.012805	-- [45] GUC
0.017400	-- [46] GUG
0.027350	-- [47] GUU
0.000915	-- [48] UAA
0.013830	-- [49] UAC
0.000509	-- [50] UAG
0.014682	-- [51] UAU
0.018124	-- [52] UCA
0.011123	-- [53] UCC
0.009221	-- [54] UCG
0.025087	-- [55] UCU
0.001092	-- [56] UGA
0.007089	-- [57] UGC
0.012469	-- [58] UGG
0.010462	-- [59] UGU
0.012630	-- [60] UUA
0.020723	-- [61] UUC
0.020865	-- [62] UUG
0.021847	-- [63] UUU
---------------------------------------------
arab.codon.use
Codon usage for Arabidopsis thaliana: 66749
 from GB142/gbpln.spsum: 26545376 codons
blimps-3.9/docs/blosum55.iij000064400001460000012000000025560774335060700162710ustar00jorjastaff00000400000027#  BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 55
#  Entropy =   0.5637, Expected =  -0.4179
 A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V  B   Z   X
  5 
 -2   8 
 -2  -1   8 
 -2  -2   2   8 
  0  -4  -3  -4  13 
 -1   1   0   0  -4   7 
 -1   0   0   2  -4   2   7 
  0  -3   0  -2  -3  -2  -3   8 
 -2   0   1  -1  -4   1  -1  -2  11 
 -2  -4  -4  -4  -2  -4  -4  -5  -4   6 
 -2  -3  -4  -5  -2  -3  -4  -5  -3   2   6 
 -1   3   0  -1  -4   2   1  -2   0  -4  -3   6 
 -1  -2  -3  -4  -2   0  -3  -3  -2   2   3  -2   8 
 -3  -3  -4  -5  -3  -4  -4  -4  -1   0   1  -4   0   9 
 -1  -3  -2  -2  -3  -1  -1  -3  -3  -3  -4  -1  -3  -5  10 
  2  -1   1   0  -1   0   0   0  -1  -3  -3   0  -2  -3  -1   5 
  0  -1   0  -1  -1  -1  -1  -2  -2  -1  -2  -1  -1  -3  -1   2   6 
 -4  -3  -5  -5  -4  -2  -3  -3  -3  -3  -3  -4  -2   2  -5  -4  -3  15 
 -2  -2  -2  -3  -3  -1  -2  -4   2  -1  -1  -2  -1   4  -4  -2  -2   3   9 
  0  -3  -4  -4  -1  -3  -3  -4  -4   4   1  -3   1  -1  -3  -2   0  -4  -2   5 
 -2  -1   4   5  -4   0   1  -1   0  -4  -4   0  -3  -5  -2   0  -1  -5  -3  -4   5 
 -1   0   0   1  -4   4   5  -3   0  -4  -3   1  -2  -4  -1   0  -1  -3  -2  -3   0   5 
 -1  -1  -1  -2  -2  -1  -1  -2  -1  -1  -1  -1  -1  -2  -2  -1  -1  -3  -1  -1  -1  -1  -1 
blimps-3.9/docs/blosum55.qij000064400001460000012000000033300774335061400162660ustar00jorjastaff00000400000027#  BLOSUM Clustered Target Frequencies=qij
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 55
   A      R      N      D      C      Q      E      G      H      I      L      K      M      F      P      S      T      W      Y      V   
0.0198 
0.0025 0.0157 
0.0022 0.0019 0.0116 
0.0024 0.0018 0.0035 0.0177 
0.0016 0.0005 0.0005 0.0005 0.0100 
0.0020 0.0025 0.0015 0.0016 0.0003 0.0064 
0.0032 0.0028 0.0023 0.0048 0.0005 0.0034 0.0150 
0.0059 0.0019 0.0030 0.0026 0.0008 0.0015 0.0021 0.0341 
0.0011 0.0013 0.0014 0.0010 0.0003 0.0011 0.0012 0.0010 0.0074 
0.0034 0.0014 0.0012 0.0013 0.0010 0.0010 0.0014 0.0017 0.0006 0.0158 
0.0045 0.0026 0.0016 0.0017 0.0014 0.0018 0.0023 0.0024 0.0011 0.0105 0.0328 
0.0033 0.0062 0.0025 0.0026 0.0005 0.0030 0.0044 0.0027 0.0013 0.0016 0.0025 0.0142 
0.0015 0.0008 0.0006 0.0005 0.0004 0.0008 0.0007 0.0008 0.0004 0.0023 0.0045 0.0009 0.0036 
0.0019 0.0011 0.0008 0.0007 0.0006 0.0006 0.0010 0.0013 0.0008 0.0031 0.0057 0.0011 0.0013 0.0163 
0.0022 0.0010 0.0010 0.0014 0.0004 0.0010 0.0017 0.0016 0.0006 0.0012 0.0016 0.0018 0.0005 0.0006 0.0184 
0.0064 0.0024 0.0031 0.0028 0.0011 0.0020 0.0030 0.0042 0.0011 0.0020 0.0027 0.0032 0.0009 0.0014 0.0018 0.0122 
0.0040 0.0020 0.0025 0.0021 0.0011 0.0015 0.0023 0.0025 0.0008 0.0029 0.0035 0.0025 0.0011 0.0013 0.0016 0.0049 0.0115 
0.0004 0.0003 0.0002 0.0002 0.0001 0.0003 0.0004 0.0005 0.0002 0.0004 0.0007 0.0003 0.0002 0.0009 0.0002 0.0003 0.0003 0.0063 
0.0015 0.0011 0.0008 0.0008 0.0004 0.0008 0.0011 0.0010 0.0013 0.0016 0.0026 0.0011 0.0007 0.0040 0.0006 0.0012 0.0011 0.0010 0.0086 
0.0054 0.0018 0.0013 0.0016 0.0014 0.0013 0.0019 0.0021 0.0007 0.0115 0.0092 0.0021 0.0022 0.0028 0.0015 0.0027 0.0039 0.0004 0.0017 0.0181 
blimps-3.9/docs/blosum62.mat000064400001460000012000000020030774507171300162600ustar00jorjastaff00000400000027 A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   X
  8 
  3   9 
  2   4  10 
  2   2   5  10 
  4   1   1   1  13 
  3   5   4   4   1   9 
  3   4   4   6   0   6   9 
  4   2   4   3   1   2   2  10 
  2   4   5   3   1   4   4   2  12 
  3   1   1   1   3   1   1   0   1   8 
  3   2   1   0   3   2   1   0   1   6   8 
  3   6   4   3   1   5   5   2   3   1   2   9 
  3   3   2   1   3   4   2   1   2   5   6   3   9 
  2   1   1   1   2   1   1   1   3   4   4   1   4  10 
  3   2   2   3   1   3   3   2   2   1   1   3   2   0  11 
  5   3   5   4   3   4   4   4   3   2   2   4   3   2   3   8 
  4   3   4   3   3   3   3   2   2   3   3   3   3   2   3   5   9 
  1   1   0   0   2   2   1   2   2   1   2   1   3   5   0   1   2  15 
  2   2   2   1   2   3   2   1   6   3   3   2   3   7   1   2   2   6  11 
  4   1   1   1   3   2   2   1   1   7   5   2   5   3   2   2   4   1   3   8 
  0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
blimps-3.9/docs/colors000064400001460000012000000034130774505301000153240ustar00jorjastaff00000400000027* Color scheme for logos of proteins (for the MakeLogo program).
* The colors are based on the divisions discussed on the usenet
* and given to me by Irit Orr. Modification according to division of Joel
* Sussman. The differences from Sussman's division are -
* Met in a group by itself (not with Pro), Ala with hydrophobic (not with Gly),
* Tyr with aromatics (not with Asn and Gln), His with Arg and Lys (not by
* itself), and charged aa separated to positive and negative.
* Shmuel Pietrokovski. June 94'
* 
* Red for acidic amino acids; Glu, Asp
D 1 0 0
d 1 0 0
E 1 0 0
e 1 0 0
*
*Blue for basic amino acids; Lys, Arg, His
K 0 0 1 
k 0 0 1 
R 0 0 1 
r 0 0 1 
H 0 0 1 
h 0 0 1 
*
*White for polar OH/SH amino acids; Ser, Thr, Cys
* White would not be seen onthe background so it is light grey
C 0.8 0.8 0.8
c 0.8 0.8 0.8
S 0.8 0.8 0.8
s 0.8 0.8 0.8
T 0.8 0.8 0.8
t 0.8 0.8 0.8
*
*Green for amide amino acids; Asn and Gln
N 0 0.8 0.4
n 0 0.8 0.4
Q 0 0.8 0.4
q 0 0.8 0.4
*
*Yellow (sulphur) for Metionine
M 1 0.9 0
m 1 0.9 0
*
*Black for hydrophobic amino acids; Ala, Val, Leu, Ile
*(Black is the opposite of white and so if white is for hydrophilic
*hydroxyl amino acids black is a natural for hydrophobic ones)
*A
*a
*V
*v
*L
*l
*I
*i
*
*Orange for aromatic amino acids; Tyr, Phe, Trp
*(since "orange" sounds a little like "aromatic" and
*oranges are aromatic (if that suits you better))
Y 1 0.6 0
y 1 0.6 0
F 1 0.6 0
f 1 0.6 0
W 1 0.6 0
w 1 0.6 0
*
*Purple for proline; Pro
*(since both have "prl" in them)
P 0.7 0 1
p 0.7 0 1
*
*Grey for glycine; Gly
*(since both start with "g" and grey is sort of blah-like glycine)
G 0.5 0.5 0.5
g 0.5 0.5 0.5
*
*All other letters light blue so they would stand out
B 0 1 1
b 0 1 1
J 0 1 1
j 0 1 1
O 0 1 1
o 0 1 1
U 0 1 1
u 0 1 1
X 0 1 1
x 0 1 1
Z 0 1 1
z 0 1 1
blimps-3.9/docs/default.amino.frq000064400001460000012000000030530774335153400173520ustar00jorjastaff000004000000270.0             -- [ 0] gap score = -
.07681          -- [ 1] Alanine       (Ala, A)
0.0             -- [21] ambiguity code B = D or N
.01791          -- [ 5] Cysteine      (Cys, C)
.05263          -- [ 4] Aspartic acid (Asp, D)
.06264          -- [ 7] Glutamic acid (Glu, E)
.03991          -- [14] Phenylalanine (Phe, F)
.07081          -- [ 8] Glycine       (Gly, G)
.02251          -- [ 9] Histidine     (His, H)
.05521          -- [10] Isoleucine    (Ile, I)
0.0             -- [25] no code J, 0, U
.05801          -- [12] Lysine        (Lys, K)
.09191          -- [11] Leucine       (Leu, L)
.02351          -- [13] Methionine    (Met, M)
.04434          -- [ 3] Asparagine    (Asn, N)
0.0             -- [25] no code J, 0, U
.05041          -- [15] Proline       (Pro, P)
.04033          -- [ 6] Glutamine     (Gln, Q)
.05251          -- [ 2] Arginine      (Arg, R)
.07061          -- [16] Serine        (Ser, S)
.05831          -- [17] Threonine     (Thr, T)
0.0             -- [25] no code J, 0, U
.06531          -- [20] Valine        (Val, V)
.01311          -- [18] Tryptophan    (Trp, W)
0.0             -- [23] ambiguity code X = any amino acid
.03221          -- [19] Tyrosine      (Tyr, Y)
0.0             -- [22] ambiguity code Z = E or Q
0.0             -- [24] stop codon translation score = *
-- Created from SwissProt 27

------------------------------------------------------------------------
BLIMPS (BLocks IMProved Searcher)
(C) Copyright 1993, Fred Hutchinson Cancer Research Center

default.amino.frq -- The default amino acid frequency file access.
 
blimps-3.9/docs/default.codon.frq000064400001460000012000000024130774335153400173500ustar00jorjastaff000004000000270.0		-- [ 0] gap score = -
.0625		-- [ 1] Alanine       (Ala, A)
0.0		-- [21] ambiguity code B = D or N
.03125		-- [ 5] Cysteine      (Cys, C)
.03125		-- [ 4] Aspartic acid (Asp, D)
.03125		-- [ 7] Glutamic acid (Glu, E)
.03125		-- [14] Phenylalanine (Phe, F)
.0625		-- [ 8] Glycine       (Gly, G)
.03125		-- [ 9] Histidine     (His, H)
.04688		-- [10] Isoleucine    (Ile, I)
0.0		-- [25] no code J, 0, U
.03125		-- [12] Lysine        (Lys, K)
.09375		-- [11] Leucine       (Leu, L)
.01563		-- [13] Methionine    (Met, M)
.03125		-- [ 3] Asparagine    (Asn, N)
0.0		-- [25] no code J, 0, U
.0625		-- [15] Proline       (Pro, P)
.03125		-- [ 6] Glutamine     (Gln, Q)
.09375		-- [ 2] Arginine      (Arg, R)
.09375		-- [16] Serine        (Ser, S)
.0625		-- [17] Threonine     (Thr, T)
0.0		-- [25] no code J, 0, U
.0625		-- [20] Valine        (Val, V)
.0156		-- [18] Tryptophan    (Trp, W)
0.0		-- [23] ambiguity code X = any amino acid
.03125		-- [19] Tyrosine      (Tyr, Y)
0.0		-- [22] ambiguity code Z = E or Q
0.0		-- [24] stop codon translation score = *

------------------------------------------------------------------------
BLIMPS (BLocks IMProved Searcher)
(C) Copyright 1993, Fred Hutchinson Cancer Research Center

default.codon.frq -- The default codon frequency file access.
 
-- [ 8] Glycine       (Gly, G)
.03125		-- [ 9] Histidine     (His, H)
.04688		-- [10] Isoleucine    (Ile, I)
0.0		-- [25] no code J, 0, U
.03125		-- [12] Lysine        (Lys, K)
.09375		-- [11] Leucine       (Leu, L)
.01563		-- [13] Methionine   blimps-3.9/docs/default.codon.use000064400001460000012000000027131012171036100173340ustar00jorjastaff000004000000270.024037	-- [ 0] AAA
0.019172	-- [ 1] AAC
0.032215	-- [ 2] AAG
0.016716	-- [ 3] AAU
0.014914	-- [ 4] ACA
0.019092	-- [ 5] ACC
0.006154	-- [ 6] ACG
0.013013	-- [ 7] ACU
0.011724	-- [ 8] AGA
0.019447	-- [ 9] AGC
0.011709	-- [10] AGG
0.012055	-- [11] AGU
0.007275	-- [12] AUA
0.021067	-- [13] AUC
0.022184	-- [14] AUG
0.015794	-- [15] AUU
0.012034	-- [16] CAA
0.015027	-- [17] CAC
0.034392	-- [18] CAG
0.010687	-- [19] CAU
0.016843	-- [20] CCA
0.020029	-- [21] CCC
0.007037	-- [22] CCG
0.017418	-- [23] CCU
0.006241	-- [24] CGA
0.010679	-- [25] CGC
0.011646	-- [26] CGG
0.004635	-- [27] CGU
0.007045	-- [28] CUA
0.019671	-- [29] CUC
0.040129	-- [30] CUG
0.013007	-- [31] CUU
0.028922	-- [32] GAA
0.025499	-- [33] GAC
0.039982	-- [34] GAG
0.021984	-- [35] GAU
0.016001	-- [36] GCA
0.028282	-- [37] GCC
0.007548	-- [38] GCG
0.018575	-- [39] GCU
0.016417	-- [40] GGA
0.022563	-- [41] GGC
0.016478	-- [42] GGG
0.010795	-- [43] GGU
0.007060	-- [44] GUA
0.014629	-- [45] GUC
0.028556	-- [46] GUG
0.010978	-- [47] GUU
0.000712	-- [48] UAA
0.015408	-- [49] UAC
0.000569	-- [50] UAG
0.012087	-- [51] UAU
0.012001	-- [52] UCA
0.017629	-- [53] UCC
0.004472	-- [54] UCG
0.014894	-- [55] UCU
0.001228	-- [56] UGA
0.012551	-- [57] UGC
0.013054	-- [58] UGG
0.010306	-- [59] UGU
0.007431	-- [60] UUA
0.020387	-- [61] UUC
0.012755	-- [62] UUG
0.017157	-- [63] UUU
---------------------------------------------
human.codon.use
Codon usage for Homo sapiens: 68796
 from GB142/gbpri.spsum: 29547517 codons
blimps-3.9/docs/default.consensus.iij000064400001460000012000000025560774335060700202610ustar00jorjastaff00000400000027#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 62
#  Entropy =   0.6979, Expected =  -0.5209
 A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V  B   Z   X
  4 
 -1   5 
 -2   0   6 
 -2  -2   1   6 
  0  -3  -3  -3   9 
 -1   1   0   0  -3   5 
 -1   0   0   2  -4   2   5 
  0  -2   0  -1  -3  -2  -2   6 
 -2   0   1  -1  -3   0   0  -2   8 
 -1  -3  -3  -3  -1  -3  -3  -4  -3   4 
 -1  -2  -3  -4  -1  -2  -3  -4  -3   2   4 
 -1   2   0  -1  -3   1   1  -2  -1  -3  -2   5 
 -1  -1  -2  -3  -1   0  -2  -3  -2   1   2  -1   5 
 -2  -3  -3  -3  -2  -3  -3  -3  -1   0   0  -3   0   6 
 -1  -2  -2  -1  -3  -1  -1  -2  -2  -3  -3  -1  -2  -4   7 
  1  -1   1   0  -1   0   0   0  -1  -2  -2   0  -1  -2  -1   4 
  0  -1   0  -1  -1  -1  -1  -2  -2  -1  -1  -1  -1  -2  -1   1   5 
 -3  -3  -4  -4  -2  -2  -3  -2  -2  -3  -2  -3  -1   1  -4  -3  -2  11 
 -2  -2  -2  -3  -2  -1  -2  -3   2  -1  -1  -2  -1   3  -3  -2  -2   2   7 
  0  -3  -3  -3  -1  -2  -2  -3  -3   3   1  -2   1  -1  -2  -2   0  -3  -1   4 
 -2  -1   3   4  -3   0   1  -1   0  -3  -4   0  -3  -3  -2   0  -1  -4  -3  -3   4 
 -1   0   0   1  -3   3   4  -2   0  -3  -3   1  -1  -3  -1   0  -1  -3  -2  -2   0   4 
  0  -1  -1  -1  -2  -1  -1  -1  -1  -1  -1  -1  -1  -1  -2   0   0  -2  -1  -1  -1  -1  -1 
blimps-3.9/docs/default.diri000064400001460000012000000101220774762127600164110ustar00jorjastaff00000400000027ClassName = DirichletReg
Name = merge-opt.13comp
Alphabet = ExtAA
Order =  A C D E F G H I K L M N P Q R S T V W Y
AlphaChar= 20
NumDistr= 13

Number= 0
Mixture= 0.109352
Alpha= 1.30226 0.388746 0.0253054 0.0224268 0.026518 0.0367385 0.0241792 0.0322076 0.206244 0.0059514 0.0158113 0.0350778 0.0351076 0.0164858 0.0137612 0.0917171 0.187681 0.0626166 0.00498456 0.0104666 0.0602319 
Comment= A S G , P C >< T V M , Q K R E N D L W F , Y I H

Number= 1
Mixture= 0.0862437
Alpha= 1.81388 0.0517631 0.0177749 0.0127646 0.00631385 0.0133196 0.0271782 0.0132966 0.0103533 0.0104886 0.264004 0.807661 0.0177537 0.175596 0.141159 0.0220077 0.0144998 0.0299289 0.016497 0.0175224 0.143995 
Comment= L M , I , F V >< W , Q C A T P Y H , R K N S , E G , D

Number= 2
Mixture= 0.0914987
Alpha= 1.70395 0.0610492 0.044453 0.368744 0.315694 0.0148718 0.0588252 0.0908927 0.222958 0.0672017 0.006044 0.0135798 0.0877828 0.00485097 0.012609 0.0498296 0.168811 0.0652581 0.00652446 0.0338823 0.010088 
Comment= N , D , H G S >< Q K E P T R Y , A C W , F M , L V I

Number= 3
Mixture= 0.0817738
Alpha= 2.11182 0.0796662 0.475607 0.077247 0.0136208 0.00761021 0.18985 0.110994 0.0563167 0.0713015 0.0341013 0.0808963 0.564383 0.0267238 0.0165387 0.0627218 0.0651016 0.0855045 0.0125425 0.0358879 0.0452026 
Comment= R K , Q , H >< E N T P M , S Y A L W G V I , F C , D

Number= 4
Mixture= 0.0707857
Alpha= 4.96847 0.317696 0.217794 0.192446 0.128582 0.110939 0.183911 0.170879 0.206556 0.339981 0.246824 0.407255 0.181928 0.138334 0.441344 0.127958 0.251084 0.245119 0.115968 0.629135 0.314739 
Comment= Y H F , W M C >< L Q R V I T N S A K P E G , D

Number= 5
Mixture= 0.0472798
Alpha= 3.33809 0.0446044 0.0194969 0.0156684 0.0134169 0.0170118 0.00598883 0.014928 0.0279526 2.74064e-06 1.24306 0.433818 0.0235435 0.0752952 0.0818952 0.00769209 0.0237729 0.0605068 0.00984592 0.039723 1.17986 
Comment= I V ,, L M >< F , Y T C , W A , R K S G N E D , P Q ,,,,,,,,,, H

Number= 6
Mixture= 0.0665499
Alpha= 2.19222 0.142671 0.0377603 0.0560163 0.391867 0.00172471 0.189149 0.796428 0.0507474 0.0337799 0.0169946 0.0315845 0.143701 0.0130077 0.0127552 0.086296 0.0701466 0.0617127 0.00600271 0.0170779 0.0327986 
Comment= E , D Q , K >< P A H N S , T R G M , V Y W L F I ,, C

Number= 7
Mixture= 0.104728
Alpha= 0.0590483 0.00281745 0.00285057 0.00244641 0.00417499 0.00552169 0.00165027 0.00218621 0.00978086 0.00226513 0.00229518 0.00312013 0.000288688 0.00106406 0.00287303 0.00279557 0.00125284 0.00271746 0.00225774 0.00348149 0.00320849 
Comment= C , W G , H Y D F P R >< N M T V Q I L E A , S ,, K

Number= 8
Mixture= 0.0953671
Alpha= 0.0844172 0.00322581 0.00579248 0.00273016 0.00597818 0.00013552 0.00322314 0.00438741 0.0158901 0.00243118 0.00206323 0.00518845 0.00656549 0.000562418 0.00193385 0.0121928 0.00329082 0.00288987 0.00227726 0.00158929 0.00206985 
Comment= P G , W R K H D Q >< E L N S T F Y , A I V M ,, C

Number= 9
Mixture= 0.0525092
Alpha= 2.10287 0.14246 0.038186 0.117688 0.0639103 0.0306225 0.0475692 0.0396449 0.0394262 0.018336 0.0452637 0.0412351 0.0606921 0.0225931 0.0154444 0.0752369 0.50948 0.696177 0.0102097 0.0178433 0.0708571 
Comment= T , S , N >< A P C Q D M , V K H R I W E , G L Y F

Number= 10
Mixture= 0.0384309
Alpha= 1.10699 0.0177105 1.47755e-06 1.47581e-06 0.00274088 0.00908289 1.47629e-06 0.00444563 0.00282536 1.4813e-06 0.0384249 0.0931481 1.47392e-06 0.0186396 0.411122 0.00676848 0.012354 0.0111622 0.0874503 0.35553 0.035578 
Comment= F Y , W ,, L >< M I , V C , A S T P , E , D G ,,,,,,,,,, H Q , N R K

Number= 11
Mixture= 0.0960116
Alpha= 7.12351 0.668982 0.464298 0.437926 0.554692 0.0472318 0.521498 0.890999 0.336612 0.107352 0.16552 0.267021 0.822984 0.0936297 0.0440375 0.242805 0.649512 0.507446 0.0151661 0.0333911 0.252405 
Comment= E K Q S R D N T A >< P H M G V , L I C , F W Y

Number= 12
Mixture= 0.0594692
Alpha= 2.18943 0.304645 0.0248684 0.020799 0.0139475 0.0610182 0.0336194 0.0452959 1.47952e-06 0.0113568 0.308808 0.209537 0.0448228 0.0639208 0.0312398 0.0641272 0.0434541 0.21585 0.0052348 0.00937749 0.677503 
Comment= V , I , A T C M L >< P , Q F K E S , R H N W , Y D ,,,,,,,,,,,,, G
EndClassName = DirichletReg
blimps-3.9/docs/default.embed.iij000064400001460000012000000025560774335060700173150ustar00jorjastaff00000400000027#  BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 55
#  Entropy =   0.5637, Expected =  -0.4179
 A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V  B   Z   X
  5 
 -2   8 
 -2  -1   8 
 -2  -2   2   8 
  0  -4  -3  -4  13 
 -1   1   0   0  -4   7 
 -1   0   0   2  -4   2   7 
  0  -3   0  -2  -3  -2  -3   8 
 -2   0   1  -1  -4   1  -1  -2  11 
 -2  -4  -4  -4  -2  -4  -4  -5  -4   6 
 -2  -3  -4  -5  -2  -3  -4  -5  -3   2   6 
 -1   3   0  -1  -4   2   1  -2   0  -4  -3   6 
 -1  -2  -3  -4  -2   0  -3  -3  -2   2   3  -2   8 
 -3  -3  -4  -5  -3  -4  -4  -4  -1   0   1  -4   0   9 
 -1  -3  -2  -2  -3  -1  -1  -3  -3  -3  -4  -1  -3  -5  10 
  2  -1   1   0  -1   0   0   0  -1  -3  -3   0  -2  -3  -1   5 
  0  -1   0  -1  -1  -1  -1  -2  -2  -1  -2  -1  -1  -3  -1   2   6 
 -4  -3  -5  -5  -4  -2  -3  -3  -3  -3  -3  -4  -2   2  -5  -4  -3  15 
 -2  -2  -2  -3  -3  -1  -2  -4   2  -1  -1  -2  -1   4  -4  -2  -2   3   9 
  0  -3  -4  -4  -1  -3  -3  -4  -4   4   1  -3   1  -1  -3  -2   0  -4  -2   5 
 -2  -1   4   5  -4   0   1  -1   0  -4  -4   0  -3  -5  -2   0  -1  -5  -3  -4   5 
 -1   0   0   1  -4   4   5  -3   0  -4  -3   1  -2  -4  -1   0  -1  -3  -2  -3   0   5 
 -1  -1  -1  -2  -2  -1  -1  -2  -1  -1  -1  -1  -1  -2  -2  -1  -1  -3  -1  -1  -1  -1  -1 
blimps-3.9/docs/default.embed.mat000064400001460000012000000053150774335061700173200ustar00jorjastaff00000400000027ID   BLOSUM55; MATRIX
AC   BLOSUM55; distance from previous block=(0,0)
DE   Blosum55 in PSSM format, rows are -ARNDCQEGHILKMFPSTWYVBZX*
MA   xxx width=25 seqs=1
  A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z   *   -
  0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
  5  -2   0  -2  -1  -3   0  -2  -2  -1  -2  -1  -2  -1  -1  -2   2   0   0  -4  -1  -2  -1   0   0
 -2  -1  -4  -2   0  -3  -3   0  -4   3  -3  -2  -1  -3   1   8  -1  -1  -3  -3  -1  -2   0   0   0
 -2   4  -3   2   0  -4   0   1  -4   0  -4  -3   8  -2   0  -1   1   0  -4  -5  -1  -2   0   0   0
 -2   5  -4   8   2  -5  -2  -1  -4  -1  -5  -4   2  -2   0  -2   0  -1  -4  -5  -2  -3   1   0   0
  0  -4  13  -4  -4  -3  -3  -4  -2  -4  -2  -2  -3  -3  -4  -4  -1  -1  -1  -4  -2  -3  -4   0   0
 -1   0  -4   0   2  -4  -2   1  -4   2  -3   0   0  -1   7   1   0  -1  -3  -2  -1  -1   4   0   0
 -1   1  -4   2   7  -4  -3  -1  -4   1  -4  -3   0  -1   2   0   0  -1  -3  -3  -1  -2   5   0   0
  0  -1  -3  -2  -3  -4   8  -2  -5  -2  -5  -3   0  -3  -2  -3   0  -2  -4  -3  -2  -4  -3   0   0
 -2   0  -4  -1  -1  -1  -2  11  -4   0  -3  -2   1  -3   1   0  -1  -2  -4  -3  -1   2   0   0   0
 -2  -4  -2  -4  -4   0  -5  -4   6  -4   2   2  -4  -3  -4  -4  -3  -1   4  -3  -1  -1  -4   0   0
 -2  -4  -2  -5  -4   1  -5  -3   2  -3   6   3  -4  -4  -3  -3  -3  -2   1  -3  -1  -1  -3   0   0
 -1   0  -4  -1   1  -4  -2   0  -4   6  -3  -2   0  -1   2   3   0  -1  -3  -4  -1  -2   1   0   0
 -1  -3  -2  -4  -3   0  -3  -2   2  -2   3   8  -3  -3   0  -2  -2  -1   1  -2  -1  -1  -2   0   0
 -3  -5  -3  -5  -4   9  -4  -1   0  -4   1   0  -4  -5  -4  -3  -3  -3  -1   2  -2   4  -4   0   0
 -1  -2  -3  -2  -1  -5  -3  -3  -3  -1  -4  -3  -2  10  -1  -3  -1  -1  -3  -5  -2  -4  -1   0   0
  2   0  -1   0   0  -3   0  -1  -3   0  -3  -2   1  -1   0  -1   5   2  -2  -4  -1  -2   0   0   0
  0   0  -1  -1  -1  -3  -2  -2  -1  -1  -2  -1   0  -1  -1  -1   2   6   0  -3  -1  -2  -1   0   0
 -4  -5  -4  -5  -3   2  -3  -3  -3  -4  -3  -2  -5  -5  -2  -3  -4  -3  -4  15  -3   3  -3   0   0
 -2  -3  -3  -3  -2   4  -4   2  -1  -2  -1  -1  -2  -4  -1  -2  -2  -2  -2   3  -1   9  -3   0   0
  0  -4  -1  -4  -3  -1  -4  -4   4  -3   1   1  -4  -3  -3  -3  -2   0   5   -4 -1  -2  -3   0   0
 -2   5  -4   5   1  -5  -1   0  -4   0  -4  -3   4  -2   0  -1   0  -1  -4  -5  -1  -3   0   0   0
 -1   0  -4   1   5  -4  -3   0  -4   1  -3  -2   1  -1   4   0   0  -1  -3  -3  -1  -3   5   0   0
 -1  -1  -2  -2  -1  -2  -2  -1  -1  -1  -1  -1  -1  -2  -1  -1  -1  -1  -1  -3  -1  -1  -1   0   0
  0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
//
blimps-3.9/docs/default.embed.qij000064400001460000012000000033300774335061400173120ustar00jorjastaff00000400000027#  BLOSUM Clustered Target Frequencies=qij
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 55
   A      R      N      D      C      Q      E      G      H      I      L      K      M      F      P      S      T      W      Y      V   
0.0198 
0.0025 0.0157 
0.0022 0.0019 0.0116 
0.0024 0.0018 0.0035 0.0177 
0.0016 0.0005 0.0005 0.0005 0.0100 
0.0020 0.0025 0.0015 0.0016 0.0003 0.0064 
0.0032 0.0028 0.0023 0.0048 0.0005 0.0034 0.0150 
0.0059 0.0019 0.0030 0.0026 0.0008 0.0015 0.0021 0.0341 
0.0011 0.0013 0.0014 0.0010 0.0003 0.0011 0.0012 0.0010 0.0074 
0.0034 0.0014 0.0012 0.0013 0.0010 0.0010 0.0014 0.0017 0.0006 0.0158 
0.0045 0.0026 0.0016 0.0017 0.0014 0.0018 0.0023 0.0024 0.0011 0.0105 0.0328 
0.0033 0.0062 0.0025 0.0026 0.0005 0.0030 0.0044 0.0027 0.0013 0.0016 0.0025 0.0142 
0.0015 0.0008 0.0006 0.0005 0.0004 0.0008 0.0007 0.0008 0.0004 0.0023 0.0045 0.0009 0.0036 
0.0019 0.0011 0.0008 0.0007 0.0006 0.0006 0.0010 0.0013 0.0008 0.0031 0.0057 0.0011 0.0013 0.0163 
0.0022 0.0010 0.0010 0.0014 0.0004 0.0010 0.0017 0.0016 0.0006 0.0012 0.0016 0.0018 0.0005 0.0006 0.0184 
0.0064 0.0024 0.0031 0.0028 0.0011 0.0020 0.0030 0.0042 0.0011 0.0020 0.0027 0.0032 0.0009 0.0014 0.0018 0.0122 
0.0040 0.0020 0.0025 0.0021 0.0011 0.0015 0.0023 0.0025 0.0008 0.0029 0.0035 0.0025 0.0011 0.0013 0.0016 0.0049 0.0115 
0.0004 0.0003 0.0002 0.0002 0.0001 0.0003 0.0004 0.0005 0.0002 0.0004 0.0007 0.0003 0.0002 0.0009 0.0002 0.0003 0.0003 0.0063 
0.0015 0.0011 0.0008 0.0008 0.0004 0.0008 0.0011 0.0010 0.0013 0.0016 0.0026 0.0011 0.0007 0.0040 0.0006 0.0012 0.0011 0.0010 0.0086 
0.0054 0.0018 0.0013 0.0016 0.0014 0.0013 0.0019 0.0021 0.0007 0.0115 0.0092 0.0021 0.0022 0.0028 0.0015 0.0027 0.0039 0.0004 0.0017 0.0181 
blimps-3.9/docs/default.iij000064400001460000012000000025560774335061000162340ustar00jorjastaff00000400000027#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 62
#  Entropy =   0.6979, Expected =  -0.5209
 A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V  B   Z   X
  4 
 -1   5 
 -2   0   6 
 -2  -2   1   6 
  0  -3  -3  -3   9 
 -1   1   0   0  -3   5 
 -1   0   0   2  -4   2   5 
  0  -2   0  -1  -3  -2  -2   6 
 -2   0   1  -1  -3   0   0  -2   8 
 -1  -3  -3  -3  -1  -3  -3  -4  -3   4 
 -1  -2  -3  -4  -1  -2  -3  -4  -3   2   4 
 -1   2   0  -1  -3   1   1  -2  -1  -3  -2   5 
 -1  -1  -2  -3  -1   0  -2  -3  -2   1   2  -1   5 
 -2  -3  -3  -3  -2  -3  -3  -3  -1   0   0  -3   0   6 
 -1  -2  -2  -1  -3  -1  -1  -2  -2  -3  -3  -1  -2  -4   7 
  1  -1   1   0  -1   0   0   0  -1  -2  -2   0  -1  -2  -1   4 
  0  -1   0  -1  -1  -1  -1  -2  -2  -1  -1  -1  -1  -2  -1   1   5 
 -3  -3  -4  -4  -2  -2  -3  -2  -2  -3  -2  -3  -1   1  -4  -3  -2  11 
 -2  -2  -2  -3  -2  -1  -2  -3   2  -1  -1  -2  -1   3  -3  -2  -2   2   7 
  0  -3  -3  -3  -1  -2  -2  -3  -3   3   1  -2   1  -1  -2  -2   0  -3  -1   4 
 -2  -1   3   4  -3   0   1  -1   0  -3  -4   0  -3  -3  -2   0  -1  -4  -3  -3   4 
 -1   0   0   1  -3   3   4  -2   0  -3  -3   1  -1  -3  -1   0  -1  -3  -2  -2   0   4 
  0  -1  -1  -1  -2  -1  -1  -1  -1  -1  -1  -1  -1  -1  -2   0   0  -2  -1  -1  -1  -1  -1 
blimps-3.9/docs/default.mat000064400001460000012000000053150774335061700162450ustar00jorjastaff00000400000027ID   BLOSUM55; MATRIX
AC   BLOSUM55; distance from previous block=(0,0)
DE   Blosum55 in PSSM format, rows are -ARNDCQEGHILKMFPSTWYVBZX*
MA   xxx width=25 seqs=1
  A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z   *   -
  0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
  5  -2   0  -2  -1  -3   0  -2  -2  -1  -2  -1  -2  -1  -1  -2   2   0   0  -4  -1  -2  -1   0   0
 -2  -1  -4  -2   0  -3  -3   0  -4   3  -3  -2  -1  -3   1   8  -1  -1  -3  -3  -1  -2   0   0   0
 -2   4  -3   2   0  -4   0   1  -4   0  -4  -3   8  -2   0  -1   1   0  -4  -5  -1  -2   0   0   0
 -2   5  -4   8   2  -5  -2  -1  -4  -1  -5  -4   2  -2   0  -2   0  -1  -4  -5  -2  -3   1   0   0
  0  -4  13  -4  -4  -3  -3  -4  -2  -4  -2  -2  -3  -3  -4  -4  -1  -1  -1  -4  -2  -3  -4   0   0
 -1   0  -4   0   2  -4  -2   1  -4   2  -3   0   0  -1   7   1   0  -1  -3  -2  -1  -1   4   0   0
 -1   1  -4   2   7  -4  -3  -1  -4   1  -4  -3   0  -1   2   0   0  -1  -3  -3  -1  -2   5   0   0
  0  -1  -3  -2  -3  -4   8  -2  -5  -2  -5  -3   0  -3  -2  -3   0  -2  -4  -3  -2  -4  -3   0   0
 -2   0  -4  -1  -1  -1  -2  11  -4   0  -3  -2   1  -3   1   0  -1  -2  -4  -3  -1   2   0   0   0
 -2  -4  -2  -4  -4   0  -5  -4   6  -4   2   2  -4  -3  -4  -4  -3  -1   4  -3  -1  -1  -4   0   0
 -2  -4  -2  -5  -4   1  -5  -3   2  -3   6   3  -4  -4  -3  -3  -3  -2   1  -3  -1  -1  -3   0   0
 -1   0  -4  -1   1  -4  -2   0  -4   6  -3  -2   0  -1   2   3   0  -1  -3  -4  -1  -2   1   0   0
 -1  -3  -2  -4  -3   0  -3  -2   2  -2   3   8  -3  -3   0  -2  -2  -1   1  -2  -1  -1  -2   0   0
 -3  -5  -3  -5  -4   9  -4  -1   0  -4   1   0  -4  -5  -4  -3  -3  -3  -1   2  -2   4  -4   0   0
 -1  -2  -3  -2  -1  -5  -3  -3  -3  -1  -4  -3  -2  10  -1  -3  -1  -1  -3  -5  -2  -4  -1   0   0
  2   0  -1   0   0  -3   0  -1  -3   0  -3  -2   1  -1   0  -1   5   2  -2  -4  -1  -2   0   0   0
  0   0  -1  -1  -1  -3  -2  -2  -1  -1  -2  -1   0  -1  -1  -1   2   6   0  -3  -1  -2  -1   0   0
 -4  -5  -4  -5  -3   2  -3  -3  -3  -4  -3  -2  -5  -5  -2  -3  -4  -3  -4  15  -3   3  -3   0   0
 -2  -3  -3  -3  -2   4  -4   2  -1  -2  -1  -1  -2  -4  -1  -2  -2  -2  -2   3  -1   9  -3   0   0
  0  -4  -1  -4  -3  -1  -4  -4   4  -3   1   1  -4  -3  -3  -3  -2   0   5   -4 -1  -2  -3   0   0
 -2   5  -4   5   1  -5  -1   0  -4   0  -4  -3   4  -2   0  -1   0  -1  -4  -5  -1  -3   0   0   0
 -1   0  -4   1   5  -4  -3   0  -4   1  -3  -2   1  -1   4   0   0  -1  -3  -3  -1  -3   5   0   0
 -1  -1  -2  -2  -1  -2  -2  -1  -1  -1  -1  -1  -1  -2  -1  -1  -1  -1  -1  -3  -1  -1  -1   0   0
  0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
//
blimps-3.9/docs/default.qij000064400001460000012000000033300774335061400162370ustar00jorjastaff00000400000027#  BLOSUM Clustered Target Frequencies=qij
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 62
   A      R      N      D      C      Q      E      G      H      I      L      K      M      F      P      S      T      W      Y      V   
0.0215 
0.0023 0.0178 
0.0019 0.0020 0.0141 
0.0022 0.0016 0.0037 0.0213 
0.0016 0.0004 0.0004 0.0004 0.0119 
0.0019 0.0025 0.0015 0.0016 0.0003 0.0073 
0.0030 0.0027 0.0022 0.0049 0.0004 0.0035 0.0161 
0.0058 0.0017 0.0029 0.0025 0.0008 0.0014 0.0019 0.0378 
0.0011 0.0012 0.0014 0.0010 0.0002 0.0010 0.0014 0.0010 0.0093 
0.0032 0.0012 0.0010 0.0012 0.0011 0.0009 0.0012 0.0014 0.0006 0.0184 
0.0044 0.0024 0.0014 0.0015 0.0016 0.0016 0.0020 0.0021 0.0010 0.0114 0.0371 
0.0033 0.0062 0.0024 0.0024 0.0005 0.0031 0.0041 0.0025 0.0012 0.0016 0.0025 0.0161 
0.0013 0.0008 0.0005 0.0005 0.0004 0.0007 0.0007 0.0007 0.0004 0.0025 0.0049 0.0009 0.0040 
0.0016 0.0009 0.0008 0.0008 0.0005 0.0005 0.0009 0.0012 0.0008 0.0030 0.0054 0.0009 0.0012 0.0183 
0.0022 0.0010 0.0009 0.0012 0.0004 0.0008 0.0014 0.0014 0.0005 0.0010 0.0014 0.0016 0.0004 0.0005 0.0191 
0.0063 0.0023 0.0031 0.0028 0.0010 0.0019 0.0030 0.0038 0.0011 0.0017 0.0024 0.0031 0.0009 0.0012 0.0017 0.0126 
0.0037 0.0018 0.0022 0.0019 0.0009 0.0014 0.0020 0.0022 0.0007 0.0027 0.0033 0.0023 0.0010 0.0012 0.0014 0.0047 0.0125 
0.0004 0.0003 0.0002 0.0002 0.0001 0.0002 0.0003 0.0004 0.0002 0.0004 0.0007 0.0003 0.0002 0.0008 0.0001 0.0003 0.0003 0.0065 
0.0013 0.0009 0.0007 0.0006 0.0003 0.0007 0.0009 0.0008 0.0015 0.0014 0.0022 0.0010 0.0006 0.0042 0.0005 0.0010 0.0009 0.0009 0.0102 
0.0051 0.0016 0.0012 0.0013 0.0014 0.0012 0.0017 0.0018 0.0006 0.0120 0.0095 0.0019 0.0023 0.0026 0.0012 0.0024 0.0036 0.0004 0.0015 0.0196 
blimps-3.9/docs/default.sij000064400001460000012000000043300774762440600162510ustar00jorjastaff00000400000027#  BLOSUM Clustered Scoring Matrix in Bit Units=sij
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 62
#  Entropy =   0.6979, Expected =  -0.5209
   A        R        N        D        C        Q        E        G        H        I        L        K        M        F        P        S        T        W        Y        V     
  1.9646 
 -0.7068   2.7367 
 -0.7654  -0.2199   2.8266 
 -0.8767  -0.8029   0.6358   2.8871 
 -0.2043  -1.6946  -1.3299  -1.7300   4.2911 
 -0.4020   0.4914   0.0008  -0.1567  -1.4509   2.6426 
 -0.4319  -0.0577  -0.1340   0.7552  -1.8062   0.9273   2.4514 
  0.0798  -1.1521  -0.2114  -0.6568  -1.2502  -0.8926  -1.0551   2.7816 
 -0.8126  -0.1249   0.2892  -0.5595  -1.4939   0.2240  -0.0588  -1.0204   3.7555 
 -0.6609  -1.4951  -1.6085  -1.5606  -0.6138  -1.3848  -1.5972  -1.8624  -1.6158   1.9993 
 -0.7323  -1.0773  -1.6895  -1.8028  -0.6387  -1.0670  -1.4232  -1.8135  -1.3934   0.7608   1.9247 
 -0.3670   1.0544  -0.0895  -0.3509  -1.5182   0.6363   0.3877  -0.7640  -0.3605  -1.3351  -1.2234   2.2523 
 -0.4676  -0.6836  -1.0754  -1.5293  -0.7099  -0.2105  -0.9990  -1.3383  -0.7756   0.5634   0.9959  -0.6774   2.6963 
 -1.1050  -1.3932  -1.4970  -1.7419  -1.1877  -1.5822  -1.5962  -1.5537  -0.6171  -0.0804   0.2074  -1.5393   0.0063   3.0230 
 -0.4071  -1.0543  -1.0002  -0.7401  -1.3976  -0.6410  -0.5581  -1.0668  -1.0805  -1.3783  -1.4300  -0.5068  -1.2382  -1.7986   3.6823 
  0.5579  -0.3824   0.3005  -0.1305  -0.4375  -0.0506  -0.0735  -0.1462  -0.4408  -1.1741  -1.2213  -0.1017  -0.7404  -1.1845  -0.4045   1.9422 
 -0.0227  -0.5612  -0.0230  -0.5254  -0.4333  -0.3377  -0.4316  -0.7877  -0.8429  -0.3588  -0.5987  -0.3348  -0.3331  -1.0538  -0.5376   0.6906   2.2727 
 -1.2634  -1.3397  -1.8480  -2.1072  -1.1521  -0.9732  -1.4177  -1.2457  -1.1711  -1.2903  -0.8159  -1.4782  -0.7124   0.4588  -1.8271  -1.3759  -1.2145   5.2520 
 -0.8820  -0.8469  -1.0409  -1.5325  -1.2036  -0.7105  -1.0102  -1.5199   0.8463  -0.6657  -0.5310  -0.9100  -0.4974   1.4696  -1.4599  -0.8429  -0.8030   1.0771   3.2975 
 -0.0947  -1.2513  -1.4382  -1.5713  -0.4038  -1.0992  -1.2211  -1.5694  -1.5587   1.2735   0.3942  -1.1312   0.3436  -0.4245  -1.1744  -0.8231  -0.0278  -1.4171  -0.6038   1.8845 
blimps-3.9/docs/fontfile000064400001460000012000000134560774507177000156560ustar00jorjastaff00000400000027CA 501 21 18 28
 -1956 1135 -1956 2735 -1442 2442 -12835
CB 502 21 21 28
 -1456 1435 -1456 2356 2655 2754 2852 2850 2748 2647
 2346 -1446 2346 2645 2744 2842 2839 2737 2636 2335
 1435 -13135
CC 503 21 21 28
 -2851 2753 2555 2356 1956 1755 1553 1451 1348 1343
 1440 1538 1736 1935 2335 2536 2738 2840 -13135
CD 504 21 21 28
 -1456 1435 -1456 2156 2455 2653 2751 2848 2843 2740
 2638 2436 2135 1435 -13135
CE 505 21 19 28
 -1456 1435 -1456 2756 -1446 2246 -1435 2735 -12935
CF 506 21 18 28
 -1456 1435 -1456 2756 -1446 2246 -12835
CG 507 21 21 28
 -2851 2753 2555 2356 1956 1755 1553 1451 1348 1343
 1440 1538 1736 1935 2335 2536 2738 2840 2843 -2343
 2843 -13135
CH 508 21 22 28
 -1456 1435 -2856 2835 -1446 2846 -13235
CI 509 21 8 28
 -1456 1435 -11835
CJ 510 21 16 28
 -2256 2240 2137 2036 1835 1635 1436 1337 1240 1242
 -12635
CK 511 21 21 28
 -1456 1435 -2856 1442 -1947 2835 -13135
CL 512 21 17 28
 -1456 1435 -1435 2635 -12735
CM 513 21 24 28
 -1456 1435 -1456 2235 -3056 2235 -3056 3035 -13435
CN 514 21 22 28
 -1456 1435 -1456 2835 -2856 2835 -13235
CO 515 21 22 28
 -1956 1755 1553 1451 1348 1343 1440 1538 1736 1935
 2335 2536 2738 2840 2943 2948 2851 2753 2555 2356
 1956 -13235
CP 516 21 21 28
 -1456 1435 -1456 2356 2655 2754 2852 2849 2747 2646
 2345 1445 -13135
CQ 517 21 22 28
 -1956 1755 1553 1451 1348 1343 1440 1538 1736 1935
 2335 2536 2738 2840 2943 2948 2851 2753 2555 2356
 1956 -2239 2833 -13235
CR 518 21 21 28
 -1456 1435 -1456 2356 2655 2754 2852 2850 2748 2647
 2346 1446 -2146 2835 -13135
CS 519 21 20 28
 -2753 2555 2256 1856 1555 1353 1351 1449 1548 1747
 2345 2544 2643 2741 2738 2536 2235 1835 1536 1338
 -13035
CT 520 21 16 28
 -1856 1835 -1156 2556 -12635
CU 521 21 22 28
 -1456 1441 1538 1736 2035 2235 2536 2738 2841 2856
 -13235
CV 522 21 18 28
 -1156 1935 -2756 1935 -12835
CW 523 21 24 28
 -1256 1735 -2256 1735 -2256 2735 -3256 2735 -13435
CX 524 21 20 28
 -1356 2735 -2756 1335 -13035
CY 525 21 18 28
 -1156 1946 1935 -2756 1946 -12835
CZ 526 21 20 28
 -2756 1335 -1356 2756 -1335 2735 -13035
Ca 601 21 19 28
 -2549 2535 -2546 2348 2149 1849 1648 1446 1343 1341
 1438 1636 1835 2135 2336 2538 -12935
Cb 602 21 19 28
 -1456 1435 -1446 1648 1849 2149 2348 2546 2643 2641
 2538 2336 2135 1835 1636 1438 -12935
Cc 603 21 18 28
 -2546 2348 2149 1849 1648 1446 1343 1341 1438 1636
 1835 2135 2336 2538 -12835
Cd 604 21 19 28
 -2556 2535 -2546 2348 2149 1849 1648 1446 1343 1341
 1438 1636 1835 2135 2336 2538 -12935
Ce 605 21 18 28
 -1343 2543 2545 2447 2348 2149 1849 1648 1446 1343
 1341 1438 1636 1835 2135 2336 2538 -12835
Cf 606 21 12 28
 -2056 1856 1655 1552 1535 -1249 1949 -12235
Cg 607 21 19 28
 -2549 2533 2430 2329 2128 1828 1629 -2546 2348 2149
 1849 1648 1446 1343 1341 1438 1636 1835 2135 2336
 2538 -12935
Ch 608 21 19 28
 -1456 1435 -1445 1748 1949 2249 2448 2545 2535 -12935
Ci 609 21 8 28
 -1356 1455 1556 1457 1356 -1449 1435 -11835
Cj 610 21 10 28
 -1556 1655 1756 1657 1556 -1649 1632 1529 1328 1128
 -12035
Ck 611 21 17 28
 -1456 1435 -2449 1439 -1843 2535 -12735
Cl 612 21 8 28
 -1456 1435 -11835
Cm 613 21 30 28
 -1449 1435 -1445 1748 1949 2249 2448 2545 2535 -2545
 2848 3049 3349 3548 3645 3635 -14035
Cn 614 21 19 28
 -1449 1435 -1445 1748 1949 2249 2448 2545 2535 -12935
Co 615 21 19 28
 -1849 1648 1446 1343 1341 1438 1636 1835 2135 2336
 2538 2641 2643 2546 2348 2149 1849 -12935
Cp 616 21 19 28
 -1449 1428 -1446 1648 1849 2149 2348 2546 2643 2641
 2538 2336 2135 1835 1636 1438 -12935
Cq 617 21 19 28
 -2549 2528 -2546 2348 2149 1849 1648 1446 1343 1341
 1438 1636 1835 2135 2336 2538 -12935
Cr 618 21 13 28
 -1449 1435 -1443 1546 1748 1949 2249 -12335
Cs 619 21 17 28
 -2446 2348 2049 1749 1448 1346 1444 1643 2142 2341
 2439 2438 2336 2035 1735 1436 1338 -12735
Ct 620 21 12 28
 -1556 1539 1636 1835 2035 -1249 1949 -12235
Cu 621 21 19 28
 -1449 1439 1536 1735 2035 2236 2539 -2549 2535 -12935
Cv 622 21 16 28
 -1249 1835 -2449 1835 -12635
Cw 623 21 22 28
 -1349 1735 -2149 1735 -2149 2535 -2949 2535 -13235
Cx 624 21 17 28
 -1349 2435 -2449 1335 -12735
Cy 625 21 16 28
 -1249 1835 -2449 1835 1631 1429 1228 1128 -12635
Cz 626 21 17 28
 -2449 1335 -1349 2449 -1335 2435 -12735
C0 700 21 20 28
 -1956 1655 1452 1347 1344 1439 1636 1935 2135 2436
 2639 2744 2747 2652 2455 2156 1956 -13035
C1 701 21 20 28
 -1652 1853 2156 2135 -13035
C2 702 21 20 28
 -1451 1452 1554 1655 1856 2256 2455 2554 2652 2650
 2548 2345 1335 2735 -13035
C3 703 21 20 28
 -1556 2656 2048 2348 2547 2646 2743 2741 2638 2436
 2135 1835 1536 1437 1339 -13035
C4 704 21 20 28
 -2356 1342 2842 -2356 2335 -13035
C5 705 21 20 28
 -2556 1556 1447 1548 1849 2149 2448 2646 2743 2741
 2638 2436 2135 1835 1536 1437 1339 -13035
C6 706 21 20 28
 -2653 2555 2256 2056 1755 1552 1447 1442 1538 1736
 2035 2135 2436 2638 2741 2742 2645 2447 2148 2048
 1747 1545 1442 -13035
C7 707 21 20 28
 -2756 1735 -1356 2756 -13035
C8 708 21 20 28
 -1856 1555 1453 1451 1549 1748 2147 2446 2644 2742
 2739 2637 2536 2235 1835 1536 1437 1339 1342 1444
 1646 1947 2348 2549 2651 2653 2555 2256 1856 -13035
C9 709 21 20 28
 -2649 2546 2344 2043 1943 1644 1446 1349 1350 1453
 1655 1956 2056 2355 2553 2649 2644 2539 2336 2035
 1835 1536 1438 -13035
C. 710 21 10 28
 -1537 1436 1535 1636 1537 -12035
C, 711 21 10 28
 -1636 1535 1436 1537 1636 1634 1532 1431 -12035
C: 712 21 10 28
 -1549 1448 1547 1648 1549 -1537 1436 1535 1636 1537
 -12035
C; 713 21 10 28
 -1549 1448 1547 1648 1549 -1636 1535 1436 1537 1636
 1634 1532 1431 -12035
C! 714 21 10 28
 -1556 1542 -1537 1436 1535 1636 1537 -12035
C? 715 21 18 28
 -1351 1352 1454 1555 1756 2156 2355 2454 2552 2550
 2448 2347 1945 1942 -1937 1836 1935 2036 1937 -12835
C/ 720 21 22 28
 -3060 1228 -13235
C( 721 21 14 28
 -2160 1958 1755 1551 1446 1442 1537 1733 1930 2128
 -12435
C) 722 21 14 28
 -1360 1558 1755 1951 2046 2042 1937 1733 1530 1328
 -12435
C- 724 21 26 28
 -1444 3244 -13635
C* 728 21 16 28
 -1850 1838 -1347 2341 -2347 1341 -12635
C  699 21 16 28
 -12635

blimps-3.9/docs/identity.frq000064400001460000012000000023430774335153400164560ustar00jorjastaff000004000000270.0		-- [ 0] gap score = -
1.0000		-- [ 1] Alanine       (Ala, A)
0.0		-- [21] ambiguity code B = D or N
1.0000		-- [ 5] Cysteine      (Cys, C)
1.0000		-- [ 4] Aspartic acid (Asp, D)
1.0000		-- [ 7] Glutamic acid (Glu, E)
1.0000		-- [14] Phenylalanine (Phe, F)
1.0000		-- [ 8] Glycine       (Gly, G)
1.0000		-- [ 9] Histidine     (His, H)
1.0000		-- [10] Isoleucine    (Ile, I)
0.0		-- [25] no code J, 0, U
1.0000		-- [12] Lysine        (Lys, K)
1.0000		-- [11] Leucine       (Leu, L)
1.0000		-- [13] Methionine    (Met, M)
1.0000		-- [ 3] Asparagine    (Asn, N)
0.0		-- [25] no code J, 0, U
1.0000		-- [15] Proline       (Pro, P)
1.0000		-- [ 6] Glutamine     (Gln, Q)
1.0000		-- [ 2] Arginine      (Arg, R)
1.0000		-- [16] Serine        (Ser, S)
1.0000		-- [17] Threonine     (Thr, T)
0.0		-- [25] no code J, 0, U
1.0000		-- [20] Valine        (Val, V)
1.0000		-- [18] Tryptophan    (Trp, W)
0.0		-- [23] ambiguity code X = any amino acid
1.0000		-- [19] Tyrosine      (Tyr, Y)
0.0		-- [22] ambiguity code Z = E or Q
0.0		-- [24] stop codon translation score = *

------------------------------------------------------------------------
BLIMPS (BLocks IMProved Searcher)
(C) Copyright 1993, Fred Hutchinson Cancer Research Center

identity.frq --
 
blimps-3.9/docs/single50.mat000064400001460000012000000047300774335061700162470ustar00jorjastaff00000400000027ID   SINGLE; MATRIX
AC   SINGLE; distance from previous block=(3,1095)
DE   Single sequence
MA   xxx width=23 seqs=1
  A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z   *   -
  5  -2   0  -2  -2  -2   0  -2  -1  -1  -2  -1  -2  -2  -1  -2   0  -1   0  -3   0  -2  -2   0   0
 -2   4  -2   6   1  -3  -1  -1  -3  -1  -3  -3   1  -2  -1  -2  -1  -1  -3  -4   0  -2   0   0   0
 -1  -3  10  -3  -3  -2  -2  -2  -2  -3  -2  -1  -2  -4  -3  -3  -2  -1  -1  -4   0  -2  -3   0   0
 -2   4  -2   6   1  -3  -1  -1  -3  -1  -3  -3   1  -2  -1  -2  -1  -1  -3  -4   0  -2   0   0   0
 -1   0  -2   1   5  -2  -2   0  -3   0  -3  -2  -1  -2   1  -1  -1  -1  -2  -2   0  -2   3   0   0
 -2  -3  -2  -4  -3   7  -3  -1   0  -3   0   0  -3  -4  -3  -3  -3  -2  -1   1   0   2  -3   0   0
  0  -1  -2  -1  -3  -2   6  -2  -3  -2  -3  -2  -1  -2  -2  -2  -1  -2  -3  -2   0  -3  -2   0   0
 -2   0  -2  -1  -1  -1  -2   8  -2  -1  -2  -1   0  -3  -1  -1  -2  -2  -3  -2   0   1  -1   0   0
 -2  -3  -2  -4  -3   0  -3  -3   5  -3   1   1  -3  -3  -3  -3  -3  -1   2  -2   0  -1  -3   0   0
 -1  -1  -2  -1   0  -2  -2   0  -2   5  -2  -1   0  -2   0   2  -1  -1  -2  -2   0  -2   0   0   0
 -2  -3  -1  -3  -3   1  -3  -2   1  -3   4   1  -3  -4  -3  -2  -3  -2   1  -2   0  -1  -3   0   0
 -1  -3  -1  -3  -2   0  -2  -1   1  -2   1   7  -2  -3  -1  -2  -2  -1   0  -1   0  -1  -2   0   0
 -2   3  -1   1  -1  -2  -1   1  -2   0  -3  -2   6  -3  -1  -1   0   0  -2  -4   0  -2  -1   0   0
 -2  -2  -2  -2  -1  -3  -2  -2  -2  -1  -3  -2  -2   7  -2  -2  -2  -2  -2  -3   0  -3  -1   0   0
 -1  -1  -2  -1   1  -3  -2   0  -2   1  -2  -1   0  -2   6   0  -1  -1  -2  -2   0  -1   3   0   0
 -2  -1  -2  -2  -1  -2  -2   0  -2   2  -2  -1  -1  -3   0   6  -2  -2  -2  -2   0  -1  -1   0   0
  0   0   0  -1  -1  -2   0  -1  -2  -1  -2  -1   0  -2  -1  -1   4   0  -1  -3   0  -2  -1   0   0
 -1  -1   0  -1  -1  -2  -2  -1  -1  -1  -1  -1   0  -2  -2  -1   0   5   0  -2   0  -2  -1   0   0
 -1  -3  -1  -3  -3   0  -3  -3   2  -2   0   0  -3  -3  -3  -2  -2  -1   5  -2   0  -1  -3   0   0
 -3  -4  -3  -4  -3   1  -2  -2  -2  -3  -2  -1  -4  -4  -2  -2  -4  -3  -2  11   0   1  -3   0   0
  0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
 -2  -2  -2  -2  -2   3  -2   1  -1  -2  -1  -1  -2  -4  -2  -1  -2  -2  -1   1   0   7  -2   0   0
 -1   0  -2   1   5  -2  -2   0  -3   0  -3  -2  -1  -2   1  -1  -1  -1  -2  -2   0  -2   3   0   0
//
blimps-3.9/docs/single55.iij000064400001460000012000000042400774335061000162330ustar00jorjastaff00000400000027  A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
  7  -3   0  -3  -2  -3   0  -3  -2  -2  -3  -2  -3  -3  -3  -3   0  -1   0  -5   0  -3  -3
 -3   6  -3   9   1  -5  -2  -1  -4  -1  -5  -5   1  -3  -2  -3  -2  -2  -4  -6   0  -4   0
 -1  -4  15  -5  -5  -3  -4  -3  -2  -5  -3  -2  -4  -5  -6  -5  -3  -2  -1  -6   0  -4  -6
 -3   6  -3   9   1  -5  -2  -1  -4  -1  -5  -5   1  -3  -2  -3  -2  -2  -4  -6   0  -4   0
 -2   0  -4   1   8  -4  -4  -1  -4   1  -4  -3  -1  -3   1  -1  -2  -2  -4  -3   0  -3   5
 -4  -6  -2  -6  -5  11  -5  -2   0  -5   0   0  -5  -7  -6  -4  -5  -4  -1   1   0   3  -6
 -1  -2  -3  -3  -4  -4   9  -3  -5  -3  -5  -4  -1  -4  -4  -4  -2  -3  -4  -4   0  -5  -4
 -3  -1  -2  -2  -2  -2  -3  13  -4  -1  -4  -2   0  -4   0  -1  -3  -3  -4  -3   0   1  -1
 -3  -5  -2  -5  -5   0  -5  -5   8  -5   2   1  -5  -5  -5  -5  -4  -2   3  -4   0  -2  -5
 -2  -1  -4  -1   0  -4  -3  -1  -4   8  -4  -3  -1  -3   0   2  -2  -2  -3  -5   0  -3   0
 -3  -5  -2  -5  -5   1  -5  -4   2  -4   7   2  -5  -6  -4  -4  -5  -3   1  -3   0  -2  -5
 -2  -4  -1  -5  -4   0  -4  -2   1  -3   2  11  -3  -5  -2  -3  -4  -2   1  -3   0  -1  -3
 -3   5  -3   1  -2  -4  -1   1  -4  -1  -5  -3   9  -4  -1  -2  -1  -1  -4  -5   0  -3  -2
 -2  -3  -3  -3  -3  -5  -3  -3  -4  -2  -4  -4  -3  10  -3  -4  -3  -2  -3  -5   0  -4  -3
 -2  -1  -4  -1   1  -4  -3   1  -4   1  -3  -1  -1  -3   9   1  -2  -2  -3  -3   0  -2   4
 -3  -2  -3  -3  -1  -4  -4   0  -4   2  -3  -3  -2  -5   0   9  -3  -3  -4  -4   0  -3  -1
  1  -1  -1  -1  -2  -3  -1  -2  -3  -1  -4  -3   0  -3  -2  -2   7   1  -2  -5   0  -3  -2
 -1  -1   0  -2  -2  -3  -3  -3  -1  -2  -2  -1  -1  -3  -2  -2   0   8   0  -4   0  -3  -2
 -1  -5  -1  -5  -5  -1  -5  -5   4  -4   1   0  -5  -5  -4  -4  -4  -1   8  -5   0  -2  -5
 -5  -6  -5  -6  -4   1  -4  -3  -4  -5  -3  -3  -6  -6  -3  -5  -6  -5  -4  16   0   3  -4
  0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
 -3  -4  -2  -4  -4   4  -4   2  -1  -3  -1  -1  -3  -5  -3  -3  -4  -3  -2   3   0  11  -3
 -2   0  -4   1   8  -4  -4  -1  -4   1  -4  -3  -1  -3   1  -1  -2  -2  -4  -3   0  -3   5
blimps-3.9/docs/single55.mat000064400001460000012000000121420774335062000162420ustar00jorjastaff00000400000027ID   SINGLE55; MATRIX
AC   SINGLE55; distance from previous block=(0,0)
DE   Single sequence PSSM using blosum55  rows are -ARNDCQEGHILKMFPSTWYVBZX*
MA   xxx width=25 seqs=1
  A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z   *   -
 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000  0.0000 0.0000 0.0000  0.0000
 6.9886 -2.7871 -0.0436 -2.9541 -2.4626 -2.7678 -0.3452 -2.6547 -1.6537 -1.9970 -2.6464 -1.5005 -2.5888 -3.1441 -2.5911 -2.7675  0.0191 -1.1867 -0.3786 -4.6933  0.0000 -2.8632 -2.5129  0.0000  0.0000
-2.7835 -2.1229 -3.4477 -2.5691 -1.4104 -3.5032 -3.6193 -0.3016 -3.8639  2.3625 -3.3906 -2.5910 -1.5933 -4.9266  0.0048  9.0014 -2.5959 -2.5567 -3.5034 -4.3083  0.0000 -2.5754 -0.8561  0.0000  0.0000
-2.5977  4.8661 -2.7087  1.0480 -1.5227 -4.1424 -0.9033  0.7582 -3.7921 -0.8295 -4.7528 -3.0971  9.3980 -4.1875 -1.4670 -1.5861 -0.7492 -0.8518 -4.1727 -5.3242  0.0000 -3.2147 -1.5009  0.0000  0.0000
-2.9602  5.5346 -3.4477  9.3121  0.9224 -5.4594 -2.2618 -1.4371 -4.1847 -1.3988 -5.2295 -4.6253  1.0508 -3.4703 -1.9268 -2.5592 -1.9288 -2.3455 -4.0131 -6.0632  0.0000 -3.9537 -0.1935  0.0000  0.0000
-1.2925 -4.3513  14.6022 -4.6905 -5.4441 -2.7040 -3.9405 -3.2254 -1.8976 -5.1117 -2.6472 -2.1685 -3.9487 -5.4698 -5.7493 -4.6806 -2.5500 -1.7216 -1.1685 -5.6406  0.0000 -3.5312 -5.5636  0.0000  0.0000
-1.9944 -1.1125 -3.9037 -1.3240  1.1848 -4.3717 -2.8875  0.7303 -3.5653  0.9754 -3.2272 -0.8362 -0.8615 -3.1717  8.9874  0.6175 -1.6302 -2.0469 -3.1569 -2.5534  0.0000 -2.1989  4.2408  0.0000  0.0000
-2.0304  0.2439 -3.7631  1.3607  7.9359 -4.2310 -3.5015 -0.9634 -4.1793  0.5628 -4.2365 -3.4843 -1.0817 -2.9453  1.0203 -0.9623 -1.9455 -2.2671 -3.5847 -3.3786  0.0000 -2.8908  5.2273  0.0000  0.0000
-0.6101 -1.8980 -2.9564 -2.5204 -4.1984 -4.3230  8.8898 -2.9800 -4.5665 -2.7783 -5.2799 -4.1339 -1.1593 -4.4352 -3.7490 -3.8681 -1.7168 -3.1338 -4.3791 -3.6403  0.0000 -4.5308 -4.0224  0.0000  0.0000
-3.1482 -0.9194 -2.4700 -1.9245 -1.8890 -1.6929 -3.2087  12.6273 -4.3425 -1.2102 -3.9250 -2.4025  0.2736 -3.9489 -0.3599 -0.7791 -2.7840 -3.3339 -4.4025 -2.8746  0.0000  1.3362 -1.2901  0.0000  0.0000
-2.5114 -4.8555 -1.5065 -5.0363 -5.4691 -0.0776 -5.1594 -4.7067  8.1920 -4.5588  1.5921  0.9209 -4.6409 -5.1962 -5.0197 -4.7057 -4.4438 -2.0072  3.4646 -4.1219  0.0000 -2.0125 -5.2931  0.0000  0.0000
-2.9130 -5.2707 -1.6649 -5.4899 -4.9352  0.9438 -5.2816 -3.6981  2.1833 -4.2420  6.8968  2.2111 -5.0105 -5.5658 -4.0904 -3.6411 -4.7596 -2.8080  0.8841 -3.3146  0.0000 -1.5259 -4.6044  0.0000  0.0000
-2.0730 -1.2071 -3.9388 -1.4686  0.0547 -3.9943 -2.5895 -0.7927 -3.7771  8.0357 -4.0514 -2.5724 -0.8966 -2.8737  0.3028  2.3025 -1.8419 -2.0820 -3.3273 -4.7994  0.0000 -3.0665  0.1519  0.0000  0.0000
-1.8058 -4.2245 -1.2249 -4.9245 -4.2218  0.4084 -4.1745 -2.2143  1.4733 -2.8018  2.1723  10.8460 -3.3936 -4.7380 -1.7382 -2.8804 -3.6525 -1.9556  0.5537 -2.8746  0.0000 -1.3431 -3.2491  0.0000  0.0000
-3.5947 -5.6767 -2.2820 -6.2802 -5.4901  10.5221 -4.8852 -2.0263 -0.0468 -4.7452  0.3834 -0.1131 -4.9605 -6.7609 -5.7953 -4.3141 -4.5522 -4.0445 -1.2145  0.8231  0.0000  3.3886 -5.6096  0.0000  0.0000
-2.3098 -2.9565 -3.3865 -2.6298 -2.5431 -5.0996 -3.3360 -2.6210 -3.5041 -1.9633 -4.4649 -3.5982 -3.3442  10.2908 -2.9340 -4.0762 -2.8140 -2.4954 -3.2654 -5.0362  0.0000 -4.1718 -2.6962  0.0000  0.0000
 0.6756 -0.7254 -0.6445 -1.2661 -1.7211 -3.0687 -0.7954 -1.6339 -2.9295 -1.1094 -3.8365 -2.6905 -0.0837 -2.9918 -1.5703 -1.9234  6.7750  0.7124 -2.3577 -4.9176  0.0000 -2.8081 -1.6620  0.0000  0.0000
-0.8977 -1.3661 -0.1836 -2.0503 -2.4102 -2.9286 -2.5799 -2.5513 -0.8605 -1.7170 -2.2524 -1.3612 -0.5539 -3.0408 -2.3545 -2.2516  0.3449  7.7085 -0.3053 -4.4567  0.0000 -2.7239 -2.3884  0.0000  0.0000
-4.9438 -5.9684 -4.6422 -6.3076 -4.0612  1.3996 -3.6260 -2.6316 -3.5147 -4.9739 -3.2985 -2.8197 -5.5657 -6.1211 -3.4006 -4.5428 -5.8247 -4.9963 -4.2418  16.1932  0.0000  2.7833 -3.8024  0.0000  0.0000
-3.0597 -3.8050 -2.4788 -4.1442 -3.5195  4.0190 -4.4626  1.6331 -1.3513 -3.1871 -1.4558 -1.2343 -3.4023 -5.2027 -2.9921 -2.7560 -3.6612 -3.2094 -1.8160  2.8373  0.0000  10.7248 -3.3129  0.0000  0.0000
-0.9874 -4.6876 -0.5285 -4.6159 -4.6257 -0.9964 -4.7231 -4.5179  3.7135 -3.8602  0.5418  0.2503 -4.7727 -4.7087 -4.3625 -4.0962 -3.6232 -1.2032  7.5252 -4.6002  0.0000 -2.2284 -4.5226  0.0000  0.0000
-2.9602  5.5346 -3.4477  9.3121  0.9224 -5.4594 -2.2618 -1.4371 -4.1847 -1.3988 -5.2295 -4.6253  1.0508 -3.4703 -1.9268 -2.5592 -1.9288 -2.3455 -4.0131 -6.0632  0.0000 -3.9537 -0.1935  0.0000  0.0000
-2.0304  0.2439 -3.7631  1.3607  7.9359 -4.2310 -3.5015 -0.9634 -4.1793  0.5628 -4.2365 -3.4843 -1.0817 -2.9453  1.0203 -0.9623 -1.9455 -2.2671 -3.5847 -3.3786  0.0000 -2.8908  5.2273  0.0000  0.0000
 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000  0.0000 0.0000 0.0000  0.0000
 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000  0.0000 0.0000 0.0000  0.0000
//
blimps-3.9/docs/single55.psi000064400001460000012000000121440774335062500162630ustar00jorjastaff00000400000027ID   SINGLE; MATRIX
AC   SINGLE; distance from previous block=(3,1095)
DE   Single sequence
MA   xxx width=25 seqs=1
  A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z   *   -
 0.0678  0.0483  0.0339  0.0510  0.0552  0.0500  0.0630  0.0331  0.0578  0.0566  0.0829  0.0264  0.0452  0.0444  0.0375  0.0516  0.0566  0.0515  0.0645  0.0309  0.0512  0.0400  0.0484  0.0000  0.0264
 0.3861  0.0256  0.0177  0.0266  0.0355  0.0211  0.0654  0.0122  0.0377  0.0366  0.0499  0.0166  0.0244  0.0244  0.0222  0.0277  0.0709  0.0443  0.0598  0.0044  0.0611  0.0166  0.0304  0.0000  0.0044
 0.0404  0.0298  0.0081  0.0291  0.0452  0.0178  0.0307  0.0210  0.0226  0.1001  0.0420  0.0129  0.0307  0.0161  0.0404  0.4202  0.0388  0.0323  0.0291  0.0048  0.0532  0.0178  0.0434  0.0000  0.0048
 0.0421  0.2142  0.0096  0.0670  0.0441  0.0153  0.0575  0.0268  0.0230  0.0479  0.0307  0.0115  0.3889  0.0192  0.0287  0.0364  0.0594  0.0479  0.0249  0.0038  0.0510  0.0153  0.0382  0.0000  0.0038
 0.0388  0.2714  0.0081  0.4525  0.0775  0.0113  0.0420  0.0161  0.0210  0.0420  0.0275  0.0081  0.0565  0.0226  0.0258  0.0291  0.0452  0.0339  0.0258  0.0032  0.0539  0.0129  0.0577  0.0000  0.0032
 0.0570  0.0178  0.5228  0.0178  0.0178  0.0214  0.0285  0.0107  0.0356  0.0178  0.0499  0.0142  0.0178  0.0142  0.0107  0.0178  0.0392  0.0392  0.0499  0.0036  0.0347  0.0142  0.0151  0.0000  0.0036
 0.0484  0.0377  0.0073  0.0388  0.0824  0.0145  0.0363  0.0266  0.0242  0.0727  0.0436  0.0194  0.0363  0.0242  0.3217  0.0606  0.0484  0.0363  0.0315  0.0073  0.0500  0.0194  0.1743  0.0000  0.0073
 0.0480  0.0549  0.0075  0.0721  0.3919  0.0150  0.0315  0.0180  0.0210  0.0661  0.0345  0.0105  0.0345  0.0255  0.0511  0.0420  0.0450  0.0345  0.0285  0.0060  0.0572  0.0165  0.2610  0.0000  0.0060
 0.0667  0.0315  0.0090  0.0294  0.0237  0.0147  0.5522  0.0113  0.0192  0.0305  0.0271  0.0090  0.0339  0.0181  0.0170  0.0215  0.0475  0.0283  0.0237  0.0057  0.0623  0.0113  0.0211  0.0000  0.0057
 0.0371  0.0399  0.0101  0.0337  0.0405  0.0270  0.0337  0.4163  0.0202  0.0439  0.0371  0.0135  0.0472  0.0202  0.0371  0.0439  0.0371  0.0270  0.0236  0.0067  0.0402  0.0439  0.0392  0.0000  0.0067
 0.0430  0.0159  0.0126  0.0164  0.0177  0.0392  0.0215  0.0076  0.3665  0.0202  0.1328  0.0291  0.0152  0.0152  0.0126  0.0177  0.0253  0.0367  0.1454  0.0051  0.0519  0.0202  0.0158  0.0000  0.0051
 0.0392  0.0144  0.0122  0.0148  0.0200  0.0496  0.0209  0.0096  0.0914  0.0218  0.4523  0.0392  0.0139  0.0139  0.0157  0.0226  0.0235  0.0305  0.0801  0.0061  0.0664  0.0226  0.0184  0.0000  0.0061
 0.0476  0.0368  0.0072  0.0375  0.0634  0.0159  0.0389  0.0187  0.0231  0.3714  0.0360  0.0130  0.0360  0.0260  0.0433  0.0894  0.0461  0.0360  0.0303  0.0043  0.0558  0.0159  0.0557  0.0000  0.0043
 0.0506  0.0184  0.0135  0.0169  0.0236  0.0439  0.0270  0.0135  0.0776  0.0304  0.1518  0.2881  0.0202  0.0169  0.0270  0.0270  0.0304  0.0371  0.0742  0.0067  0.0472  0.0236  0.0249  0.0000  0.0067
 0.0335  0.0131  0.0106  0.0123  0.0176  0.4538  0.0229  0.0141  0.0546  0.0194  0.1004  0.0229  0.0141  0.0106  0.0106  0.0194  0.0247  0.0229  0.0493  0.0159  0.0474  0.0705  0.0149  0.0000  0.0106
 0.0450  0.0249  0.0082  0.0287  0.0348  0.0123  0.0328  0.0123  0.0246  0.0369  0.0328  0.0102  0.0205  0.5434  0.0205  0.0205  0.0369  0.0328  0.0307  0.0041  0.0516  0.0123  0.0293  0.0000  0.0041
 0.0898  0.0412  0.0154  0.0393  0.0421  0.0196  0.0589  0.0154  0.0281  0.0449  0.0379  0.0126  0.0435  0.0253  0.0281  0.0337  0.3378  0.0687  0.0379  0.0042  0.0598  0.0168  0.0367  0.0000  0.0042
 0.0624  0.0356  0.0172  0.0328  0.0359  0.0203  0.0390  0.0125  0.0453  0.0390  0.0546  0.0172  0.0390  0.0250  0.0234  0.0312  0.0765  0.3461  0.0609  0.0047  0.0546  0.0172  0.0311  0.0000  0.0047
 0.0245  0.0123  0.0061  0.0123  0.0245  0.0551  0.0306  0.0123  0.0245  0.0184  0.0429  0.0123  0.0123  0.0123  0.0184  0.0184  0.0184  0.0184  0.0245  0.5527  0.0296  0.0613  0.0222  0.0000  0.0061
 0.0379  0.0202  0.0101  0.0202  0.0278  0.1010  0.0253  0.0328  0.0404  0.0278  0.0657  0.0177  0.0202  0.0152  0.0202  0.0278  0.0303  0.0278  0.0429  0.0253  0.0433  0.3838  0.0249  0.0000  0.0101
 0.0611  0.0166  0.0159  0.0181  0.0215  0.0317  0.0238  0.0079  0.1302  0.0238  0.1042  0.0249  0.0147  0.0170  0.0147  0.0204  0.0306  0.0442  0.3716  0.0045  0.0382  0.0192  0.0189  0.0000  0.0045
 0.0388  0.2714  0.0081  0.4525  0.0775  0.0113  0.0420  0.0161  0.0210  0.0420  0.0275  0.0081  0.0565  0.0226  0.0258  0.0291  0.0452  0.0339  0.0258  0.0032  0.0539  0.0129  0.0577  0.0000  0.0032
 0.0480  0.0549  0.0075  0.0721  0.3919  0.0150  0.0315  0.0180  0.0210  0.0661  0.0345  0.0105  0.0345  0.0255  0.0511  0.0420  0.0450  0.0345  0.0285  0.0060  0.0572  0.0165  0.2610  0.0000  0.0060
 0.0678  0.0483  0.0339  0.0510  0.0552  0.0500  0.0630  0.0331  0.0578  0.0566  0.0829  0.0264  0.0452  0.0444  0.0375  0.0516  0.0566  0.0515  0.0645  0.0309  0.0512  0.0400  0.0484  0.0000  0.0264
 0.0678  0.0483  0.0339  0.0510  0.0552  0.0500  0.0630  0.0331  0.0578  0.0566  0.0829  0.0264  0.0452  0.0444  0.0375  0.0516  0.0566  0.0515  0.0645  0.0309  0.0512  0.0400  0.0484  0.0000  0.0264
//
blimps-3.9/docs/single62.iij000064400001460000012000000042400774335061000162310ustar00jorjastaff00000400000027  A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
  5  -2   0  -2  -2  -2   0  -2  -1  -1  -2  -1  -2  -2  -2  -2   0  -1   0  -3   0  -2  -2
 -2   4  -3   6   1  -3  -2  -1  -3  -1  -4  -3   1  -3  -1  -2  -1  -2  -3  -4   0  -4   0
 -1  -4  10  -4  -4  -2  -3  -3  -1  -4  -2  -2  -3  -4  -4  -4  -2  -2  -1  -4   0  -3  -4
 -2   4  -3   6   1  -3  -2  -1  -3  -1  -4  -3   1  -3  -1  -2  -1  -2  -3  -4   0  -4   0
 -1   0  -3   1   5  -3  -3   0  -3   0  -3  -2  -1  -2   1  -1  -1  -2  -3  -3   0  -2   4
 -3  -4  -2  -4  -4   7  -3  -1   0  -4   0   0  -3  -5  -4  -3  -3  -3  -1   0   0   2  -4
  0  -1  -2  -2  -3  -3   6  -2  -4  -2  -4  -3  -1  -3  -3  -3  -1  -2  -3  -3   0  -4  -3
 -2  -1  -3  -1  -1  -1  -2   9  -3  -1  -3  -2   0  -3  -1  -1  -2  -3  -4  -2   0   1  -1
 -2  -4  -1  -4  -4   0  -4  -3   6  -3   1   1  -4  -4  -4  -4  -4  -2   2  -3   0  -2  -4
 -1  -1  -3  -1   0  -3  -2  -1  -3   6  -3  -2  -1  -2   0   2  -1  -2  -3  -3   0  -2   0
 -2  -4  -1  -4  -4   0  -4  -3   2  -3   5   2  -4  -4  -3  -3  -4  -2   1  -2   0  -2  -4
 -2  -3  -1  -3  -3   0  -3  -1   1  -2   2   7  -3  -4  -2  -2  -2  -2   0  -2   0  -1  -2
 -2   3  -3   1  -1  -3  -1   0  -3  -1  -4  -3   7  -3  -1  -1  -1  -1  -3  -4   0  -3  -1
 -1  -2  -2  -2  -2  -4  -2  -2  -3  -2  -3  -3  -2   7  -2  -3  -2  -2  -3  -5   0  -3  -2
 -1  -1  -3  -1   1  -3  -2   0  -3   1  -2  -1  -1  -3   6   0  -1  -2  -2  -3   0  -2   3
 -2  -2  -3  -2  -1  -3  -3   0  -3   2  -2  -2  -1  -3   0   6  -2  -2  -3  -3   0  -2  -1
  1   0  -1  -1  -1  -2  -1  -1  -2  -1  -3  -2   0  -2  -1  -1   5   0  -2  -3   0  -2  -1
 -1  -1  -1  -2  -2  -2  -2  -2  -1  -1  -2  -1  -1  -2  -2  -2   0   5   0  -3   0  -2  -2
 -1  -4   0  -4  -3  -1  -4  -3   3  -3   0   0  -3  -4  -3  -3  -3  -1   5  -3   0  -2  -3
 -3  -4  -3  -4  -3   1  -3  -2  -2  -3  -2  -2  -4  -6  -3  -3  -4  -3  -3  11   0   2  -3
  0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
 -2  -3  -2  -4  -3   3  -4   2  -1  -2  -1  -1  -3  -4  -2  -2  -3  -3  -1   2   0   7  -3
 -1   0  -3   1   5  -3  -3   0  -3   0  -3  -2  -1  -2   1  -1  -1  -2  -3  -3   0  -2   4
blimps-3.9/docs/single62.mat000064400001460000012000000121460774335062000162440ustar00jorjastaff00000400000027ID   SINGLE; MATRIX
AC   SINGLE; distance from previous block=(3,1095)
DE   Single sequence
MA   xxx width=25 seqs=1
  A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z   *   -
-0.3872  0.0344  2.2084 -0.0297 -0.4651  0.5879 -0.2819  1.3273  0.0158 -0.1489 -0.3558  0.3251  0.1105 -0.3466 -0.1876 -0.0002 -0.7393 -0.4124 -0.1240  2.7194 -0.0631  0.6885 -0.3585 -0.7393 -0.7393
 4.8572 -2.1589  0.2222 -2.1911 -1.8370 -2.3734 -0.1400 -1.7209 -1.3856 -1.3654 -1.8598 -1.4012 -2.1207 -1.9752 -1.7918 -1.9960 -0.0170 -0.8964 -0.3994 -2.9164 -0.9023 -2.2476 -1.8196 -2.9164 -2.9164
-2.0607 -1.5456 -2.7336 -2.0657 -1.0968 -2.9894 -2.6368 -0.4256 -3.1714  1.4984 -2.5645 -1.7579 -0.9285 -3.2060  0.0443  6.2720 -1.8803 -1.9312 -2.7001 -2.7022 -1.2944 -2.2645 -0.6586 -3.2060 -3.2060
-2.1849  3.4172 -2.3065  0.7803 -1.2606 -2.9021 -0.6687  0.4463 -3.2704 -0.8129 -3.6926 -2.6869  6.5458 -3.0829 -1.0025 -0.9279 -0.5919 -0.9251 -3.1030 -3.4450 -1.2148 -2.5625 -1.1615 -3.6926 -3.6926
-2.2987  3.8481 -2.8433  6.4702  0.5131 -3.4390 -1.6338 -1.0614 -3.2812 -1.3498 -4.0304 -3.2237  0.7369 -2.7897 -1.3532 -2.1086 -1.4224 -1.8849 -3.4089 -3.9819 -1.4886 -3.5441 -0.2036 -4.0304 -4.0304
-0.9704 -3.7026  10.1919 -3.9283 -4.4691 -2.5480 -2.6743 -3.4581 -1.2851 -3.6287 -1.5970 -1.6205 -3.4349 -3.7125 -3.9361 -3.8615 -2.1461 -1.7938 -0.9479 -3.7347 -2.3388 -3.2970 -4.2644 -4.4691 -4.4691
-1.4083 -0.7215 -2.3600 -0.8620  0.8557 -3.4817 -1.9934  0.2520 -2.7978  0.7021 -2.5307 -0.9395 -0.5549 -2.6462  6.2393  0.4925 -1.2279 -1.4527 -2.3265 -2.6685 -0.9333 -1.7859  2.9232 -3.4817 -3.4817
-1.4413  0.1855 -2.8808  1.0165  5.3956 -3.1366 -2.4631 -0.1280 -3.3186  0.1580 -3.2377 -2.2903 -0.8006 -2.3824  0.8680 -0.6363 -1.2608 -1.7744 -2.6723 -2.8494 -1.0563 -2.4116  3.6568 -3.3186 -3.3186
-0.4361 -1.4007 -1.7778 -1.8222 -3.1549 -3.2035  6.2230 -1.9959 -3.7709 -2.1665 -3.9940 -3.1874 -0.9006 -3.2794 -2.6729 -2.8682 -1.4758 -2.3964 -3.4044 -2.9164 -1.7598 -3.6485 -2.9698 -3.9940 -3.9940
-2.2334 -0.7966 -2.7780 -1.4662 -1.0362 -1.3736 -2.2123  8.7278 -3.2158 -1.2844 -3.1349 -1.8023 -0.0020 -3.2504 -0.6440 -0.8734 -2.0529 -2.7008 -3.5745 -1.9166 -1.4895  1.1651 -0.8856 -3.2504 -3.2504
-1.9000 -3.7028 -0.6068 -3.6879 -4.2287 -0.3075 -3.9891 -3.2177  5.5086 -3.2021  1.1393  0.7378 -3.7205 -3.9981 -3.6957 -3.6211 -3.5446 -1.5534  2.3216 -2.6642 -1.8487 -1.7817 -4.0240 -4.2287 -4.2287
-2.0633 -3.9916 -0.6079 -4.1262 -3.8370  0.3063 -3.9014 -2.8260  1.4501 -2.9966  4.6939  1.5973 -3.8319 -4.1095 -3.1177 -2.7033 -3.6318 -2.0566  0.5654 -2.1317 -1.6489 -1.5597 -3.5608 -4.1262 -4.1262
-1.3515 -1.0025 -2.4221 -1.2282 -0.2238 -3.3218 -1.8564 -0.7580 -2.6737  5.4830 -2.7791 -1.7504 -0.7348 -2.1823  0.3326  1.5771 -1.3514 -1.5563 -2.5366 -3.0346 -0.9751 -2.2928 -0.0102 -3.3218 -3.3218
-1.6045 -3.0937 -0.6311 -3.3194 -2.8894 -0.0569 -3.0946 -1.4931  1.0488 -1.9677  1.5975  7.3219 -2.8260 -3.7475 -1.5263 -1.8965 -2.4851 -1.5248  0.4495 -1.7697 -1.2678 -1.3319 -2.3659 -3.7475 -3.7475
-2.8568 -3.5890 -1.8387 -3.8146 -4.0157  7.1555 -3.3908 -1.3445 -0.2765 -3.8191  0.0264 -0.3369 -3.3212 -4.9550 -4.3485 -3.4080 -3.5064 -2.8501 -1.0481  0.3789 -1.9931  2.4314 -4.1435 -4.9550 -4.9550
-1.3589 -2.2197 -1.9035 -2.0657 -2.1618 -3.8553 -2.3670 -2.1216 -2.8674 -1.5799 -3.2896 -2.9278 -2.4024  7.1167 -2.4134 -2.5250 -1.9224 -1.8263 -2.7001 -5.0421 -1.7772 -3.1304 -2.2584 -5.0421 -5.0421
 0.5444 -0.3934 -0.3921 -0.7533 -1.0951 -2.4616 -0.6182 -0.9790 -2.4688 -0.8039 -2.8668 -1.7204  0.0338 -1.9773 -1.0499 -1.2541  4.5913  0.5358 -1.8325 -3.0046 -0.6963 -2.2628 -1.0778 -3.0046 -3.0046
-0.6382 -1.1000 -0.3430 -1.5191 -1.9119 -2.1085 -1.8421 -1.9300 -0.7808 -1.3121 -1.5948 -1.0633 -0.6027 -2.1844 -1.5780 -1.6083  0.2325  5.4252 -0.3094 -2.6515 -0.8700 -2.2137 -1.7837 -2.6515 -2.6515
-3.1742 -3.9064 -2.7999 -4.1320 -3.5030  0.6044 -2.8781 -1.6619 -2.4077 -3.3064 -2.1860 -1.8242 -3.6386 -5.9162 -3.3098 -2.8953 -3.8238 -3.1675 -2.7664  11.0897 -2.5210  1.6692 -3.4288 -5.9162 -5.9162
-2.3374 -3.0971 -2.1941 -3.5262 -2.8971  2.8250 -3.4422  1.5878 -1.3571 -2.3965 -1.4459 -1.2184 -2.5880 -3.8365 -2.2591 -2.2895 -2.9139 -2.5616 -1.5167  1.8373 -1.6588  7.5188 -2.6521 -3.8365 -3.8365
-0.7601 -3.5419 -0.1160 -3.6619 -3.4287 -0.9255 -3.4690 -3.4227  2.4753 -2.9112  0.4082  0.2921 -3.3995 -3.6771 -3.0706 -2.9960 -2.7546 -0.9283  5.1369 -2.8693 -1.7583 -1.7876 -3.2912 -3.6771 -3.6771
-2.2987  3.8481 -2.8433  6.4702  0.5131 -3.4390 -1.6338 -1.0614 -3.2812 -1.3498 -4.0304 -3.2237  0.7369 -2.7897 -1.3532 -2.1086 -1.4224 -1.8849 -3.4089 -3.9819 -1.4886 -3.5441 -0.2036 -4.0304 -4.0304
-1.4413  0.1855 -2.8808  1.0165  5.3956 -3.1366 -2.4631 -0.1280 -3.3186  0.1580 -3.2377 -2.2903 -0.8006 -2.3824  0.8680 -0.6363 -1.2608 -1.7744 -2.6723 -2.8494 -1.0563 -2.4116  3.6568 -3.3186 -3.3186
-0.3872  0.0344  2.2084 -0.0297 -0.4651  0.5879 -0.2819  1.3273  0.0158 -0.1489 -0.3558  0.3251  0.1105 -0.3466 -0.1876 -0.0002 -0.7393 -0.4124 -0.1240  2.7194 -0.0631  0.6885 -0.3585 -0.7393 -0.7393
-0.3872  0.0344  2.2084 -0.0297 -0.4651  0.5879 -0.2819  1.3273  0.0158 -0.1489 -0.3558  0.3251  0.1105 -0.3466 -0.1876 -0.0002 -0.7393 -0.4124 -0.1240  2.7194 -0.0631  0.6885 -0.3585 -0.7393 -0.7393
//
blimps-3.9/docs/single62.psi000064400001460000012000000121440774335062500162610ustar00jorjastaff00000400000027ID   SINGLE; MATRIX
AC   SINGLE; distance from previous block=(3,1095)
DE   Single sequence
MA   xxx width=25 seqs=1
  A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z   *   -
 0.0663  0.0496  0.0358  0.0523  0.0543  0.0502  0.0621  0.0356  0.0585  0.0566  0.0833  0.0266  0.0463  0.0435  0.0373  0.0517  0.0552  0.0492  0.0631  0.0317  0.0510  0.0404  0.0477  0.0000  0.0266
 0.4085  0.0232  0.0180  0.0247  0.0337  0.0180  0.0652  0.0124  0.0360  0.0371  0.0495  0.0146  0.0214  0.0247  0.0214  0.0259  0.0709  0.0416  0.0574  0.0045  0.0618  0.0146  0.0290  0.0000  0.0045
 0.0371  0.0288  0.0065  0.0258  0.0436  0.0145  0.0275  0.0194  0.0194  0.1001  0.0388  0.0129  0.0323  0.0161  0.0404  0.4541  0.0371  0.0291  0.0258  0.0048  0.0532  0.0145  0.0424  0.0000  0.0048
 0.0356  0.2346  0.0075  0.0693  0.0412  0.0150  0.0543  0.0262  0.0187  0.0449  0.0262  0.0094  0.4307  0.0169  0.0281  0.0375  0.0581  0.0412  0.0225  0.0037  0.0505  0.0131  0.0362  0.0000  0.0037
 0.0342  0.2965  0.0062  0.4978  0.0762  0.0124  0.0389  0.0155  0.0187  0.0373  0.0233  0.0078  0.0575  0.0187  0.0249  0.0249  0.0435  0.0295  0.0202  0.0031  0.0540  0.0093  0.0565  0.0000  0.0031
 0.0542  0.0136  0.5698  0.0136  0.0136  0.0169  0.0271  0.0068  0.0373  0.0169  0.0542  0.0136  0.0136  0.0136  0.0102  0.0136  0.0339  0.0305  0.0474  0.0034  0.0334  0.0102  0.0122  0.0000  0.0034
 0.0466  0.0381  0.0074  0.0392  0.0858  0.0123  0.0343  0.0245  0.0221  0.0760  0.0392  0.0172  0.0368  0.0196  0.3456  0.0613  0.0466  0.0343  0.0294  0.0049  0.0499  0.0172  0.1856  0.0000  0.0049
 0.0460  0.0562  0.0061  0.0752  0.4138  0.0138  0.0292  0.0215  0.0184  0.0629  0.0307  0.0107  0.0338  0.0215  0.0537  0.0414  0.0460  0.0307  0.0261  0.0046  0.0573  0.0138  0.2755  0.0000  0.0046
 0.0652  0.0302  0.0090  0.0281  0.0214  0.0135  0.5918  0.0112  0.0157  0.0281  0.0236  0.0079  0.0326  0.0157  0.0157  0.0191  0.0427  0.0247  0.0202  0.0045  0.0629  0.0090  0.0192  0.0000  0.0045
 0.0350  0.0376  0.0064  0.0318  0.0445  0.0254  0.0318  0.4625  0.0191  0.0382  0.0318  0.0127  0.0445  0.0159  0.0318  0.0382  0.0350  0.0223  0.0191  0.0064  0.0389  0.0477  0.0396  0.0000  0.0064
 0.0393  0.0136  0.0135  0.0147  0.0147  0.0368  0.0172  0.0074  0.3925  0.0196  0.1399  0.0307  0.0123  0.0123  0.0110  0.0147  0.0209  0.0331  0.1473  0.0049  0.0520  0.0172  0.0133  0.0000  0.0049
 0.0371  0.0123  0.0135  0.0127  0.0169  0.0455  0.0177  0.0084  0.0962  0.0211  0.4796  0.0413  0.0118  0.0118  0.0135  0.0202  0.0202  0.0278  0.0801  0.0059  0.0675  0.0186  0.0156  0.0000  0.0059
 0.0475  0.0345  0.0072  0.0345  0.0590  0.0130  0.0360  0.0173  0.0230  0.3984  0.0360  0.0130  0.0345  0.0230  0.0446  0.0892  0.0446  0.0331  0.0273  0.0043  0.0561  0.0144  0.0535  0.0000  0.0043
 0.0435  0.0167  0.0134  0.0167  0.0234  0.0402  0.0234  0.0134  0.0837  0.0301  0.1640  0.3005  0.0167  0.0134  0.0234  0.0268  0.0301  0.0335  0.0770  0.0067  0.0472  0.0201  0.0234  0.0000  0.0067
 0.0282  0.0141  0.0088  0.0141  0.0159  0.4891  0.0211  0.0141  0.0529  0.0159  0.0951  0.0211  0.0141  0.0088  0.0088  0.0159  0.0211  0.0211  0.0458  0.0141  0.0468  0.0740  0.0131  0.0000  0.0088
 0.0474  0.0229  0.0086  0.0258  0.0301  0.0108  0.0301  0.0108  0.0215  0.0345  0.0301  0.0086  0.0194  0.5780  0.0172  0.0215  0.0366  0.0301  0.0258  0.0022  0.0518  0.0108  0.0252  0.0000  0.0022
 0.0916  0.0427  0.0145  0.0407  0.0436  0.0175  0.0553  0.0160  0.0247  0.0451  0.0349  0.0131  0.0451  0.0247  0.0276  0.0334  0.3499  0.0684  0.0349  0.0044  0.0601  0.0145  0.0375  0.0000  0.0044
 0.0608  0.0335  0.0148  0.0312  0.0329  0.0197  0.0362  0.0115  0.0444  0.0378  0.0542  0.0164  0.0362  0.0230  0.0230  0.0296  0.0773  0.3721  0.0592  0.0049  0.0548  0.0148  0.0291  0.0000  0.0049
 0.0253  0.0126  0.0063  0.0126  0.0189  0.0505  0.0253  0.0126  0.0253  0.0189  0.0442  0.0126  0.0126  0.0063  0.0126  0.0189  0.0189  0.0189  0.0253  0.5770  0.0288  0.0568  0.0165  0.0000  0.0063
 0.0337  0.0168  0.0078  0.0156  0.0234  0.1090  0.0208  0.0389  0.0363  0.0260  0.0571  0.0156  0.0182  0.0130  0.0182  0.0234  0.0260  0.0234  0.0389  0.0234  0.0418  0.4315  0.0214  0.0000  0.0078
 0.0583  0.0143  0.0160  0.0149  0.0194  0.0297  0.0206  0.0069  0.1372  0.0217  0.1086  0.0263  0.0137  0.0137  0.0137  0.0183  0.0274  0.0412  0.3907  0.0046  0.0373  0.0171  0.0172  0.0000  0.0046
 0.0342  0.2965  0.0062  0.4978  0.0762  0.0124  0.0389  0.0155  0.0187  0.0373  0.0233  0.0078  0.0575  0.0187  0.0249  0.0249  0.0435  0.0295  0.0202  0.0031  0.0540  0.0093  0.0565  0.0000  0.0031
 0.0460  0.0562  0.0061  0.0752  0.4138  0.0138  0.0292  0.0215  0.0184  0.0629  0.0307  0.0107  0.0338  0.0215  0.0537  0.0414  0.0460  0.0307  0.0261  0.0046  0.0573  0.0138  0.2755  0.0000  0.0046
 0.0663  0.0496  0.0358  0.0523  0.0543  0.0502  0.0621  0.0356  0.0585  0.0566  0.0833  0.0266  0.0463  0.0435  0.0373  0.0517  0.0552  0.0492  0.0631  0.0317  0.0510  0.0404  0.0477  0.0000  0.0266
 0.0663  0.0496  0.0358  0.0523  0.0543  0.0502  0.0621  0.0356  0.0585  0.0566  0.0833  0.0266  0.0463  0.0435  0.0373  0.0517  0.0552  0.0492  0.0631  0.0317  0.0510  0.0404  0.0477  0.0000  0.0266
//
blimps-3.9/examples/000075500001460000012000000000001041505766700147775ustar00jorjastaff00000400000027blimps-3.9/examples/README000064400001460000012000000001021020716123500156320ustar00jorjastaff00000400000027For Block Searcher, see blimps/
For Block Maker,    see protomat/
blimps-3.9/examples/blimps/000075500001460000012000000000001043043273200162505ustar00jorjastaff00000400000027blimps-3.9/examples/blimps/README000064400001460000012000000036021041506443500171350ustar00jorjastaff00000400000027	Sample BLIMPS files (Block Searcher)


S. Henikoff & J.G. Henikoff, "Protein family classification based on 
searching a database of blocks." Genomics 19:97-107 (1994). 
http://blocks.fhcrc.org/blocks_search.html


Three C-shell scripts here explain how to execute BLIMPS two ways
followed by three post-processing programs:

Search a sequences vs a blocks database (Block Searcher):
1. blimps.blkprob.csh: executes blimps followed by blkprob interactively.
Just accept all the defaults. blkprob is the current post-processing
program and gives combined E-values for each hit.

2. blimps.blksort.csh: executes blimps followed by blksort,
the original post-processing program which gives rank statistics.
Just accept all the defaults.

Search a set of blocks vs a sequence database:
3. multimat.csh: This script is not interactive, just execute & examine
the output files. multimat is not easy to use as it requires precise
file names, which are explained within the script. You may find it easier
to use Tim Bailey's MAST program to search blocks vs a sequence database.
The program $BLIMPS_DIR/bin/blk2pssm will prepare the blocks for input to
mast (blk2pssm   M). MAST may be
obtained at http://www.sdsc.edu/MEME .

To test implementation, run the *.csh files, accepting all the default
answers, and compare the output files with those in distribution/ .

-------------------------------------------------------------------------

Two perl scripts here demonstrate how to run bulk searches:

batch-search.pl
       Sample script to do bulk Block Searches locally
       Argument is 

www-search.pl
       Sample script to do bulk Block Searches on the web server
       Replaces Email Block Searcher
       Arguments are  
       Requires libwww-perl         (http://www.linpro.no/lwp/)

blimps-3.9/examples/blimps/batch-search.pl000075500001460000012000000053360776373640700211700ustar00jorjastaff00000400000027#!/usr/bin/perl -w

#	Sample script to do bulk Block Searches locally
#	Extract all sequences from a file of sequences in FASTA format
#	Arguments are 
#	Output files are named seq.*

# Read in the sequences (in FASTA format), one at a time, and then
# execute block searcher locally.

$blocks = "sample.blocks";			# Blocks database
$blimps_dir = "../..";		# Or use environment var $BLIMPS_DIR
$frq = "$blimps_dir/docs/default.amino.frq";	# Amino acid frequencies
$qij = "$blimps_dir/docs/default.qij";		# Amino acid substitution freqs
$blimps = "$blimps_dir/bin/blimps";
$blkprob = "$blimps_dir/bin/blkprob";

if (@ARGV < 1)
{
   print "USAGE batch-search.pl \n";
   exit(-1);
}
open(SEQS, $ARGV[0]);
$nseq = $count = 0;
while ()
{
   if ($_ =~ m/^>/)		#	start of new sequence
   {
      if ($count > 0)		#	process previous sequence
      {
         close(SEQ);
	 &ex_blimps($nseq);
         $count = 0;
      }
      $nseq++;
      open(SEQ, ">$$.seq.$nseq");
   }  # end of new seq
   print SEQ "$_";
   $count++;
}
close(SEQS);

#	Last sequence
close(SEQ);
if ($count > 0)
{ &ex_blimps($nseq); }

exit(0);
#----------------------------------------------------------------------------
#  Write the blimps configuration file, execute blimps and blkprob
sub ex_blimps
{
   local($nseq) = @_;
	 #	Make the blimps configuration file
	 #	Change this for your site
	 open(CF, ">$$.cf");
	 #	Basic options
	 print CF "DB\t$blocks\n";		# Blocks database
	 print CF "SQ\t$$.seq.$nseq\n";		# Query sequence
	 print CF "TY\tauto\n";			# Sequence type
	 print CF "OU\t$$.raw.$nseq\n";		# Output file
	 print CF "FR\t$frq\n";			# Amino acid frquencies
	 print CF "CO\t3\n";			# PSSM type (don't change)
	 print CF "OP alts: 5.0 $qij :alts\n";	# Pseudo-count calculation
	 #	Search options
	 print CF "RE\tyes\n";			# Repeats allowed
						#  no=> only best score reported
	 #	Ignore raw scores < 945, use only for searching large dbs
#	 print CF "SV\tyes\n";			# no => consider all raw scores
	 print CF "NU\t0\n";			# Number of results to report
						#  0=> program decides
	 #	Options for translated DNA query sequences
	 print CF "ST\t2\n";			# Strands to search (DNA only)
	 print CF "GE\t0\n";			# Genetic code (DNA only)
	 #	Other output options
	 print CF "ER\t2\n";			# Error level
	 print CF "HI\tno\n";			# Score histogram

	 close(CF);
	 #	Execute blimps (raw scores) and blkprob (evalue)
 	 system("$blimps $$.cf");
	 #	-mast = mast statistics, don't change
	 #	-E = evalue cutoff
	 #	-all => all output; alternatives are -sum or -gff
 	 system("$blkprob $$.cf -mast -E 1.0 -all > $$.out.$nseq");
	 #	Remove unneeded files
#	 system("rm -f $$.cf $$.seq.$nseq $$.raw.$nseq");
}  # end of ex_blimps
blimps-3.9/examples/blimps/blimps.blkprob.csh000075500001460000012000000110660733502707300217060ustar00jorjastaff00000400000027#!/bin/csh
#    This is blimps.csh :  example of how to execute blimps & blkprob
#     Prompts for input, creates .cs file, executes blimps
#	blkprob looks for these files in the current directory:
#		blkprob.stp (documentation)
#		blksort.stn (percentiles for normalized scores)
#		blksort.bias (list of blocks with compositional bias)
#		repeats.dat (list of groups known to have repeated motifs)
#
unalias rm
limit coredumpsize 1k

#	Set this to where blimps was installed
setenv BLIMPS_DIR ../..

echo "BLIMPS Search Generator"
echo "One search will be started for each query..."
#
#     Get the search type   SE --- not needed, but used to figure
#                                  out SQ or BL vs DB
#
set search = BLOCK
echo "Search Types: BLOCK  => sequence vs Blocks Database"
echo "              MATRIX => block vs sequence database"
echo -n "Enter search type (BLOCK or MATRIX) [$search]: "
set answer = ($<)
if ($#answer != 0) then
   set search = $answer
endif
#
#     Get the query sequences  SQ or BL
#
set noglob
set all = $cwd/*.pro
echo "Enter query sequence(s) or matrices [$all]: "
set answer = ($<)
unset noglob
if ($#answer != 0) then
   set pros = ($answer)
else
   set pros = ($all)
endif
#
#   Get the database     DB
#
set noglob
if ($search == BLOCK) then
   set db = sample.blocks
else
   set db = /swiss/swiss-prot.dat
   echo "Sample database names: /genbank/gb*.seq"
endif
echo "Enter database name [$db]: "
set answer = ($<)
unset noglob
if ($#answer != 0) then
   set db = ($answer)
endif
echo $db
#
#   Get the frequency file   FR
#
set freq = $BLIMPS_DIR/docs/default.amino.frq
echo -n "Enter frequency file name [$freq]: "
set answer = ($<)
if ($#answer != 0) then
   set freq = $answer
endif
#   
#   Get the output location  OU
#
set out = $cwd
echo -n "Enter output directory [$out]: "
set answer = ($<)
if ($#answer != 0) then
   set out = $answer
endif
#
#   Get the file extension
#
set ext = bli
echo -n "Enter the output file extension [$ext]: "
set answer = ($<)
if ($#answer != 0) then
    set ext = $answer
endif
#
#	Get the number of results
#
if ($search == BLOCK) then
     set NU = "   0"
else if ($search == MATRIX) then
     set NU = " 500"
else set NU = " 350"
endif
echo -n "Enter the number of results to save (0 for default) [$NU]: "
set answer = ($<)
if ($#answer != 0) then
   set NU = $answer
endif
#
#   See if they want to change the parameters:
#             ERror_level, STrands, REpeats, NUmber_to_report
#
set ER = "   2"
set ST = "   2"
set CO = "   3"
if ($search == BLOCK) then
     echo "Keeping REpeats is turned on."
     set RE = "   1"
else 
     echo "Keeping REpeats is turned off."
     set RE = "   0"
endif
echo -n "Do you want to change the search parameters (y/n)? [n]: "
set answer = ($<)
if ($answer == "y" || $answer == "Y") then
   echo -n "Enter error message level parameter (ER) [$ER]: "
   set answer = ($<)
   if ($#answer != 0) then
      set ER = $answer
   endif
   echo -n "Enter strands parameter (ST) [$ST]: "
   set answer = ($<)
   if ($#answer != 0) then
      set ST = $answer
   endif
   echo -n "Enter repeat parameter, 1=yes, 0=none (RE) [$RE]: "
   set answer = ($<)
   if ($#answer != 0) then
      set RE = $answer
   endif
   echo -n "Enter number of results (NU) [$NU]: "
   set answer = ($<)
   if ($#answer != 0) then
      set NU = $answer
   endif
   echo -n "Enter sequence weighting option (CO) [$CO]: "
   set answer = ($<)
   if ($#answer != 0) then
      set CO = $answer
   endif
endif
#
#   Now start the searches
#
foreach pro ($pros)
   echo $pro
   set tpro = $pro:t
   set rpro = $tpro:r
   echo "Creating $rpro.cs..."
   echo "ER   $ER"           >$rpro.cs
   echo "FR   $freq"          >>$rpro.cs
   if ($search == MATRIX) then
      echo "BL   $pro"        >>$rpro.cs
   else
      echo "SQ   $pro"        >>$rpro.cs
   endif
   foreach d ($db)
      echo "DB   $d"             >>$rpro.cs
   end
   echo "OU   $out/$rpro.$ext" >>$rpro.cs
#   echo "SE   $search"         >>$rpro.cs
   echo "ST   $ST"             >>$rpro.cs
   echo "RE   $RE"             >>$rpro.cs
   echo "NU   $NU"             >>$rpro.cs
   echo "CO   $CO"             >>$rpro.cs
   echo "//"                   >>$rpro.cs
   echo "Executing blimps ..."
   date
#	Execute blimps & then blkprob if it was a BLOCK search
   echo "Executing blimps ... output in $out/$rpro.$ext"
   $BLIMPS_DIR/bin/blimps $rpro.cs  >/dev/null 
#	Other common blkprob options: Cutoff evalue: "-E 10"
   if ($search == BLOCK) then
      echo "Executing blkprob ... output in $out/$rpro.blkprob"
      $BLIMPS_DIR/bin/blkprob $rpro.cs >$out/$rpro.blkprob
   endif
#  rm $rpro.cs
end
exit(0)
blimps-3.9/examples/blimps/blimps.blksort.csh000075500001460000012000000107770733502722000217350ustar00jorjastaff00000400000027#!/bin/csh
#    This is blimps.csh :  example of how to execute blimps & blksort
#     Prompts for input, creates .cs file, executes blimps
#	blkprob looks for these files in the current directory:
#		blksort.stp (documentation)
#		blksort.stn (percentiles for normalized scores)
#		blksort.bias (list of blocks with compositional bias)
#		repeats.dat (list of groups known to have repeated motifs)
#
unalias rm
limit coredumpsize 1k

#	Set this to where blimps was installed
setenv BLIMPS_DIR ../..

echo "BLIMPS Search Generator"
echo "One search will be started for each query..."
#
#     Get the search type   SE --- not needed, but used to figure
#                                  out SQ or BL vs DB
#
set search = BLOCK
echo "Search Types: BLOCK  => sequence vs Blocks Database"
echo "              MATRIX => block vs sequence database"
echo -n "Enter search type (BLOCK or MATRIX) [$search]: "
set answer = ($<)
if ($#answer != 0) then
   set search = $answer
endif
#
#     Get the query sequences  SQ or BL
#
set noglob
set all = $cwd/*.pro
echo "Enter query sequence(s) or matrices [$all]: "
set answer = ($<)
unset noglob
if ($#answer != 0) then
   set pros = ($answer)
else
   set pros = ($all)
endif
#
#   Get the database     DB
#
set noglob
if ($search == BLOCK) then
   set db = sample.blocks
else
   set db = /swiss/swiss-prot.dat
   echo "Sample database names: /genbank/gb*.seq"
endif
echo "Enter database name [$db]: "
set answer = ($<)
unset noglob
if ($#answer != 0) then
   set db = ($answer)
endif
echo $db
#
#   Get the frequency file   FR
#
set freq = $BLIMPS_DIR/docs/default.amino.frq
echo -n "Enter frequency file name [$freq]: "
set answer = ($<)
if ($#answer != 0) then
   set freq = $answer
endif
#   
#   Get the output location  OU
#
set out = $cwd
echo -n "Enter output directory [$out]: "
set answer = ($<)
if ($#answer != 0) then
   set out = $answer
endif
#
#   Get the file extension
#
set ext = bli
echo -n "Enter the output file extension [$ext]: "
set answer = ($<)
if ($#answer != 0) then
    set ext = $answer
endif
#
#	Get the number of results
#
if ($search == BLOCK) then
     set NU = "   0"
else if ($search == MATRIX) then
     set NU = " 500"
else set NU = " 350"
endif
echo -n "Enter the number of results to save (0 for default) [$NU]: "
set answer = ($<)
if ($#answer != 0) then
   set NU = $answer
endif
#
#   See if they want to change the parameters:
#             ERror_level, STrands, REpeats, NUmber_to_report
#
set ER = "   2"
set ST = "   2"
set CO = "   3"
if ($search == BLOCK) then
     echo "Keeping REpeats is turned on."
     set RE = "   1"
else 
     echo "Keeping REpeats is turned off."
     set RE = "   0"
endif
echo -n "Do you want to change the search parameters (y/n)? [n]: "
set answer = ($<)
if ($answer == "y" || $answer == "Y") then
   echo -n "Enter error message level parameter (ER) [$ER]: "
   set answer = ($<)
   if ($#answer != 0) then
      set ER = $answer
   endif
   echo -n "Enter strands parameter (ST) [$ST]: "
   set answer = ($<)
   if ($#answer != 0) then
      set ST = $answer
   endif
   echo -n "Enter repeat parameter, 1=yes, 0=none (RE) [$RE]: "
   set answer = ($<)
   if ($#answer != 0) then
      set RE = $answer
   endif
   echo -n "Enter number of results (NU) [$NU]: "
   set answer = ($<)
   if ($#answer != 0) then
      set NU = $answer
   endif
   echo -n "Enter sequence weighting option (CO) [$CO]: "
   set answer = ($<)
   if ($#answer != 0) then
      set CO = $answer
   endif
endif
#
#   Now start the searches
#
foreach pro ($pros)
   echo $pro
   set tpro = $pro:t
   set rpro = $tpro:r
   echo "Creating $rpro.cs..."
   echo "ER   $ER"           >$rpro.cs
   echo "FR   $freq"          >>$rpro.cs
   if ($search == MATRIX) then
      echo "BL   $pro"        >>$rpro.cs
   else
      echo "SQ   $pro"        >>$rpro.cs
   endif
   foreach d ($db)
      echo "DB   $d"             >>$rpro.cs
   end
   echo "OU   $out/$rpro.$ext" >>$rpro.cs
#   echo "SE   $search"         >>$rpro.cs
   echo "ST   $ST"             >>$rpro.cs
   echo "RE   $RE"             >>$rpro.cs
   echo "NU   $NU"             >>$rpro.cs
   echo "CO   $CO"             >>$rpro.cs
   echo "//"                   >>$rpro.cs
   echo "Executing blimps ..."
   date
#	Execute blimps & then blksort if it was a BLOCK search
   echo "Executing blimps ... output in $out/$rpro.$ext"
   $BLIMPS_DIR/bin/blimps $rpro.cs  >/dev/null 
   if ($search == BLOCK) then
      echo "Executing blksort ... output in $out/$rpro.blksort"
      $BLIMPS_DIR/bin/blksort $rpro.cs >$out/$rpro.blksort
   endif
#  rm $rpro.cs
end
exit(0)
blimps-3.9/examples/blimps/blkprob.stp000064400001460000012000000066210711635307100204450ustar00jorjastaff00000400000027        ___________               ___________               ___________ 
       |\ __________\            |___________|            /__________ /|
       | |           |           |           |           |           | |
       | | **********|           |***********|           |********** | |
       | | * BLOCKS  |           |EMAIL & WWW|           |SEARCHER * | |
       | | **********|           |***********|           |********** | |
        \|___________|___________|___________|___________|___________|/
                     |\ __________\         /__________ /|
                     | |  blocks@  |       | http://   | |
                     | |   blocks. |       |  blocks.  | |
                     | |   fhcrc.  |       |  fhcrc.   | |
                     | |   org     |       |  org      | |
                      \|___________|       |___________|/


Here are your search results. The database searched was Blocks+ (10 June 00)
which includes: BLOCKS 12.0 consisting of 4071 blocks representing 998 groups
documented in InterPro 1.0/PROSITE, plus 3141 blocks from 498 groups documented 
in PRINTS 26.0 but not represented in BLOCKS, plus 2382 blocks from 569 groups 
documented in PFAM 5.3 but not represented in BLOCKS or PRINTS, plus
962 blocks from 250 groups documented in PRODOM 99.1 but not represented in
BLOCKS, PRINTS or PFAM, plus 282 blocks from 76 groups documented in DOMO 2.0
but not represented in BLOCKS, PRINTS, PFAM or PRODOM for a total of 10,838
blocks from 2391 groups.  Get more information at http://blocks.fhcrc.org.
If you found the Blocks Searcher useful, please cite:
   S Henikoff & JG Henikoff, "Protein family classification
   based on searching a database of blocks", Genomics 19:97-107 (1994).
Please report problems to:  webmaster@blocks.fhcrc.org
==============================================================================
Each hit consists of one or more blocks from a protein group found
in the query sequence. One set of the highest-scoring blocks that are in the 
correct order and separated by distances comparable to the Blocks database is 
selected for analysis. If this set includes multiple blocks the probability 
that the lower scoring blocks support the highest scoring block is reported. 
Maps of the database blocks and query sequence are shown:
AAA represents a block roughly in proportion to its width.
  : represents the minimum distance between blocks in the database.
  . represents the maximum distance between blocks in the database.
< > indicate the sequence has been truncated to fit the page.
The query map is aligned on the highest scoring block. Multiple block hits 
that are consistent with the highest scoring block are separated by colons.
Block hits that are not consistent are mapped below. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database is
shown. The distance between detected blocks is listed as (min, max): for the
database entry followed by the distance in the query. Upper case in the query
indicates at least one occurrence of the residue in that column of the block.

=============================================================================
Note: For searches using DNA queries, "Location" refers to the position
in the query in base pairs from 5' to 3' on the + strand, whereas the map and 
alignment show the translated position in amino acid residues.
============================================================================= 
blimps-3.9/examples/blimps/blksort.bias000064400001460000012000010206710711635140700206050ustar00jorjastaff00000400000027BP00240A    6      15           2           13               2    33
BP00485B   10      45           6           13               4    40
BP00659A   36     630          26            4              17    47
BP00659B   52    1326          92            6              34    65
BP00659C   45     990          92            9              31    68
BP00659D   47    1081          43            3              26    55
BP01078B    8      28           3           10               2    25
BP01081B   38     703          27            3              10    26
BP01692C   41     820          21            2              13    31
BP01901B   34     561          18            3              10    29
BP01901D   50    1225          49            4              25    50
BP01921G    5      10           3           30               2    40
BP01938B   36     630          16            2              11    30
BP02038    27     351          20            5              11    40
BP02198A   42     861          21            2              11    26
BP02198B   27     351           8            2               8    29
BP02232A   39     741          34            4              21    53
BP02232B   29     406          31            7              16    55
BP02232C   35     595          23            3              12    34
BP02232D   48    1128          42            3              24    50
BP02232E   28     378          17            4              12    42
BP02232F   31     465          26            5              14    45
BP02232G   43     903          26            2              15    34
BP02232H   55    1485          47            3              29    52
BP02232I   39     741          44            5              19    48
BP02232J   55    1485          74            4              30    54
BP02232K   40     780          32            4              18    45
BP02232L   40     780          38            4              19    47
BP02232M   34     561          39            6              21    61
BP02232N   46    1035          59            5              29    63
BP02232O   48    1128          81            7              34    70
BP02232P   41     820          43            5              24    58
BP02263A   17     136           6            4               6    35
BP02263D   42     861          29            3              17    40
BP02279C   16     120           5            4               4    25
BP02279D   34     561          19            3              13    38
BP02279E   44     946          34            3              22    50
BP02318B   18     153          13            8               9    50
BP02343    26     325           8            2               7    26
BP02413A   44     946          19            2              12    27
BP02413B   46    1035          19            1              15    32
BP02414A   27     351          12            3               7    25
BP02434B   27     351           9            2               8    29
BP02446B    8      28           6           21               4    50
BP02534B   37     666          14            2              10    27
BP02591A   12      66           6            9               3    25
BP02591B   12      66           9           13               5    41
BP02591C   42     861         141           16              29    69
BP02593B   24     276          26            9               7    29
BP02646B   15     105           7            6               4    26
BP02646C   30     435          20            4              11    36
BP02646D   39     741          60            8              17    43
BP02646E   44     946          85            8              21    47
BP02646F   27     351          20            5               9    33
BP02646G   31     465          45            9              14    45
BP02646H   41     820          99           12              24    58
BP02646I   44     946          73            7              23    52
BP02646J   36     630          23            3              15    41
BP02646K   26     325          12            3               9    34
BP02646L   36     630          29            4              17    47
BP02646M   39     741          26            3              16    41
BP02646N   35     595          19            3              13    37
BP02646O   40     780          18            2              13    32
BP02659A   17     136           7            5               6    35
BP02659C   50    1225          26            2              20    40
BP02659D   18     153           6            3               5    27
BP02659E   35     595          19            3              10    28
BP02744A   51    1275          32            2              18    35
BP02744C   40     780          14            1              11    27
BP02772C   38     703          12            1              10    26
BP02799B   55    1485          26            1              15    27
BP02799E   10      45           6           13               3    30
BP02876A    9      36           3            8               3    33
BP02876D   44     946          13            1              11    25
BP02876F   41     820          17            2              13    31
BP03068B   44     946          20            2              13    29
BP03073B   14      91           5            5               4    28
BP03073F   40     780          20            2              12    30
BP03134B   12      66           5            7               4    33
BP03191A   51    1275          71            5              33    64
BP03191B   30     435          26            5              15    50
BP03191C   30     435          28            6              16    53
BP03191D   35     595          38            6              19    54
BP03191E   33     528          23            4              17    51
BP03191F   30     435          26            5              15    50
BP03191G   31     465          39            8              16    51
BP03191H   38     703          57            8              25    65
BP03191I   39     741          49            6              24    61
BP03191J   18     153          12            7               8    44
BP03260C   35     595          15            2              11    31
BP03287B   47    1081          30            2              19    40
BP03289C   24     276           7            2               6    25
BP03317B   24     276           9            3               6    25
BP03319C   29     406          22            5              15    51
BP03319D   28     378          25            6              14    50
BP03319E   33     528          22            4              13    39
BP03319F   32     496          17            3              10    31
BP03319G   22     231          13            5               9    40
BP03319H   32     496          24            4              13    40
BP03319J   48    1128          43            3              24    50
BP03319K   38     703          19            2              12    31
BP03319L   43     903          37            4              23    53
BP03319O   29     406          16            3              12    41
BP03319P   28     378          38           10              16    57
BP03319Q   30     435          19            4              13    43
BP03319S   37     666          28            4              18    48
BP03319U   24     276           7            2               6    25
BP03360A   49    1176          26            2              16    32
BP03360C   30     435           9            2               8    26
BP03360D   46    1035          16            1              12    26
BP03360F   55    1485          21            1              15    27
BP03369A   36     630          13            2              10    27
BP03369B   45     990          31            3              13    28
BP03369C   50    1225          39            3              20    40
BP03369D   55    1485          41            2              20    36
BP03369E   55    1485          28            1              17    30
BP03394C   38     703          28            3              14    36
BP03394G   34     561          24            4              12    35
BP03484A   40     780          35            4              18    45
BP03484B   28     378          19            5              13    46
BP03484C   34     561          31            5              18    52
BP03484D   39     741          42            5              23    58
BP03484E   41     820          35            4              21    51
BP03484F   32     496          39            7              18    56
BP03484G   53    1378          87            6              35    66
BP03484H   52    1326          55            4              33    63
BP03484I   38     703          33            4              21    55
BP03501A   39     741          25            3              14    35
BP03501D   40     780          28            3              15    37
BP03538A   27     351          24            6              12    44
BP03538B   54    1431          72            5              35    64
BP03538C   32     496          17            3              12    37
BP03538D   40     780          34            4              22    55
BP03538E   39     741          55            7              20    51
BP03538F   29     406          22            5              14    48
BP03538G   31     465          37            7              17    54
BP03538H   33     528          23            4              15    45
BP03538I   24     276          15            5              10    41
BP03538J   20     190           8            4               8    40
BP03538K   51    1275          58            4              30    58
BP03538L   33     528          30            5              16    48
BP03556B   49    1176          42            3              27    55
BP03556C   40     780          22            2              16    40
BP03556E   50    1225          17            1              13    26
BP03556F   34     561          11            1               9    26
BP03580D   46    1035          23            2              14    30
BP03580E   38     703          17            2              11    28
BP03591A   38     703          51            7              22    57
BP03591C   40     780          29            3              18    45
BP03591D   39     741          25            3              17    43
BP03591E   54    1431          30            2              19    35
BP03657D   36     630          25            3              16    44
BP03657E   33     528          12            2               9    27
BP03657G   33     528          12            2              10    30
BP03657H   33     528          16            3              10    30
BP03657J   54    1431          30            2              18    33
BP03658B   25     300          10            3               7    28
BP03658C   48    1128          36            3              23    47
BP03658D   48    1128          17            1              12    25
BP03698A   50    1225          25            2              13    26
BP03698B   41     820          24            2              13    31
BP03736A   40     780          21            2              14    35
BP03736B   31     465          17            3              12    38
BP03736C   45     990          22            2              14    31
BP03736D   55    1485          50            3              21    38
BP03742A   13      78           4            5               4    30
BP03742D   34     561          24            4              13    38
BP03742F   32     496          12            2               9    28
BP03746A   36     630          30            4              17    47
BP03746B   43     903          31            3              20    46
BP03746C   29     406          24            5              14    48
BP03746D   32     496          20            4              13    40
BP03746E   26     325          14            4              10    38
BP03746F   42     861          29            3              15    35
BP03746G   50    1225          50            4              27    54
BP03749A   51    1275          36            2              18    35
BP03749C   53    1378          29            2              19    35
BP03749D   44     946          17            1              14    31
BP03764A   33     528          23            4              13    39
BP03764B   28     378          13            3               9    32
BP03764C   35     595          14            2              12    34
BP03764D   35     595          18            3              12    34
BP03764E   37     666          16            2              10    27
BP03764F   48    1128          37            3              17    35
BP03764G   27     351          20            5              14    51
BP03801A   52    1326          23            1              16    30
BP03801C   46    1035          66            6              28    60
BP03820A   40     780          41            5              24    60
BP03820B   19     171           8            4               7    36
BP03872A   16     120          11            9               5    31
BP03872D   37     666          31            4              17    45
BP03872E   52    1326          76            5              32    61
BP04013    27     351          10            2               7    25
BP04024A   55    1485          73            4              32    58
BP04024B   35     595          48            8              22    62
BP04055A   12      66           3            4               3    25
BP04060B   44     946          29            3              16    36
BP04060C   33     528          13            2               9    27
BP04060D   31     465          14            3              11    35
BP04098A   31     465          16            3               9    29
BP04137C   40     780          21            2              15    37
BP04137D   38     703          29            4              19    50
BP04137E   29     406          24            5              16    55
BP04137F   36     630          32            5              20    55
BP04137G   22     231          11            4               9    40
BP04137H   54    1431          38            2              23    42
BP04137I   47    1081          33            3              23    48
BP04137J   41     820          47            5              24    58
BP04137K   48    1128          21            1              15    31
BP04137L   55    1485          53            3              26    47
BP04141A   40     780          29            3              12    30
BP04141C   47    1081          26            2              17    36
BP04158B   21     210          10            4               7    33
BP04175C   33     528          12            2               9    27
BP04175F   20     190           5            2               5    25
BP04188D   12      66           3            4               3    25
BP04209    42     861          55            6              26    61
BP04234A   15     105           5            4               5    33
BP04236B   48    1128          46            4              26    54
BP04263A   53    1378          81            5              35    66
BP04263B   55    1485          92            6              38    69
BP04285A   34     561          15            2              12    35
BP04285C   24     276          13            4               7    29
BP04287E   31     465          11            2               9    29
BP04289B   44     946          60            6              29    65
BP04289C   50    1225          44            3              26    52
BP04289D   49    1176          19            1              14    28
BP04341A   31     465          26            5              14    45
BP04341B   42     861          35            4              21    50
BP04341C   40     780          45            5              22    55
BP04341D   55    1485          91            6              37    67
BP04341E   27     351          21            5              13    48
BP04341F   37     666          34            5              20    54
BP04341G   41     820          22            2              13    31
BP04341H   34     561          31            5              17    50
BP04352A   47    1081          59            5              29    61
BP04352B   38     703          41            5              23    60
BP04352C   28     378          15            3              12    42
BP04352D   27     351          13            3              11    40
BP04352E   29     406          21            5              12    41
BP04352G   28     378          12            3               9    32
BP04352H   28     378          10            2               8    28
BP04352I   43     903          21            2              16    37
BP04352J   10      45           3            6               3    30
BP04352K   30     435          12            2              10    33
BP04352L   16     120           6            5               5    31
BP04367A   33     528          30            5              17    51
BP04367B   40     780          42            5              25    62
BP04367C   22     231           9            3               8    36
BP04367D   32     496          26            5              16    50
BP04367E   34     561          36            6              18    52
BP04367F   55    1485          30            2              18    32
BP04369A   51    1275          23            1              15    29
BP04369B   39     741          14            1              10    25
BP04369C   47    1081          24            2              15    31
BP04369E   34     561          18            3              13    38
BP04369H   46    1035          23            2              14    30
BP04369I   36     630          14            2              11    30
BP04380B   26     325          16            4              10    38
BP04380E   38     703          18            2              12    31
BP04380F   39     741          18            2              12    30
BP04381C   19     171          12            7               7    36
BP04381D   19     171           6            3               5    26
BP04409F   35     595          14            2              10    28
BP04417A   41     820          46            5              21    51
BP04417B   46    1035          46            4              23    50
BP04417C   47    1081          55            5              23    48
BP04417D   54    1431          79            5              31    57
BP04417E   45     990         107           10              31    68
BP04417F   51    1275          87            6              33    64
BP04417G   38     703          40            5              23    60
BP04417H   15     105           6            5               5    33
BP04417I   54    1431         102            7              34    62
BP04417J   50    1225         180           14              30    60
BP04417K   34     561          23            4              17    50
BP04417L   33     528          29            5              19    57
BP04417M   28     378          29            7              12    42
BP04417N   30     435          30            6              16    53
BP04417O   30     435          52           11              20    66
BP04417P   34     561          27            4              17    50
BP04417Q   39     741          37            4              20    51
BP04417R   36     630          26            4              16    44
BP04417S   31     465          18            3              12    38
BP04417T   34     561          33            5              18    52
BP04417U   40     780          38            4              21    52
BP04417V   42     861          34            3              20    47
BP04417W   43     903          59            6              26    60
BP04417X   22     231           7            3               6    27
BP04458    40     780          63            8              24    60
BP04462A   49    1176          19            1              13    26
BP04462B   38     703          44            6              17    44
BP04462C   18     153          19           12              12    66
BP04462D   27     351           9            2               8    29
BP04498C   16     120           5            4               4    25
BP04509B   33     528          16            3               9    27
BP04558A   32     496          18            3              13    40
BP04558B   33     528          30            5              17    51
BP04558C   39     741          21            2              14    35
BP04568A   48    1128          24            2              16    33
BP04576A   44     946          40            4              22    50
BP04576B   37     666          28            4              17    45
BP04576D   49    1176          39            3              25    51
BP04602D   41     820          15            1              12    29
BP04603A   22     231          12            5               8    36
BP04636B   27     351           8            2               7    25
BP04669A   53    1378          32            2              20    37
BP04669B   53    1378          30            2              20    37
BP04669C   54    1431          36            2              21    38
BP04669D   35     595          20            3              11    31
BP04709A   24     276           7            2               6    25
BP04725B   37     666          13            1              10    27
BP04742    45     990          37            3              24    53
BP04751    48    1128          25            2              13    27
BP04753A   35     595          86           14              20    57
BP04753B   39     741          65            8              21    53
BP04757A   35     595          47            7              20    57
BP04772A   25     300           9            3               7    28
BP04772B   29     406          14            3               9    31
BP04782B   28     378          10            2               8    28
BP04782C   25     300          10            3               8    32
BP04782D   51    1275          68            5              31    60
BP04782E   41     820          15            1              11    26
BP04797A   41     820          46            5              24    58
BP04797B   50    1225          42            3              20    40
BP04805B   44     946          33            3              22    50
BP04821B   40     780          35            4              19    47
BP04821C   53    1378          24            1              15    28
BP04821D   51    1275          53            4              23    45
BP04821E   26     325          20            6              13    50
BP04821F   46    1035          15            1              12    26
BP04837A   54    1431          24            1              16    29
BP04880C   12      66           5            7               4    33
BP04887A   42     861          18            2              14    33
BP04887B   19     171          10            5               7    36
BP04900D   54    1431          45            3              26    48
BP04900E   48    1128          30            2              22    45
BP04924A   28     378           9            2               7    25
BP04960B   44     946          13            1              11    25
BP04960C   46    1035          22            2              14    30
BP04960D   15     105           4            3               4    26
BP04983C   26     325          21            6              13    50
BP04983E   47    1081          44            4              19    40
BP04994A   53    1378          34            2              16    30
BP04994C   26     325          12            3               9    34
BP04994D   44     946          14            1              11    25
BP04994E   30     435          14            3              11    36
BP04994F   44     946          23            2              14    31
BP04994G   54    1431          45            3              22    40
BP04997A   29     406          15            3              13    44
BP04997B   39     741          40            5              20    51
BP04997C   31     465          14            3              11    35
BP04997D   38     703          37            5              21    55
BP04997E   26     325          12            3               9    34
BP04997F   36     630          32            5              20    55
BP04999A   40     780          22            2              13    32
BP04999B   45     990          24            2              17    37
BP04999C   52    1326          37            2              22    42
Block    Width Total Pairs Biassed Pairs Percent Biassed
DM00031A   48    1128          33            2              17    35
DM00191A   13      78          14           17               5    38
DM00191C   16     120           5            4               4    25
DM00191D   39     741          35            4              15    38
DM00303A   50    1225          46            3              21    42
DM00315B   12      66           3            4               3    25
DM00315D   44     946          22            2              14    31
DM00315G   36     630          24            3              11    30
DM00396A    8      28           3           10               2    25
DM00522B   14      91           6            6               4    28
DM00864A   21     210          17            8               6    28
DM00893C   42     861          15            1              12    28
DM00895G   10      45           5           11               4    40
DM00984B   55    1485          48            3              18    32
DM00984C   14      91           6            6               6    42
DM01038    28     378          27            7              13    46
DM01071A   16     120          25           20              11    68
DM01071B   19     171          10            5               6    31
DM01071C   41     820          48            5              26    63
DM01071D   47    1081          40            3              26    55
DM01111A   29     406          21            5              12    41
DM01111B   37     666          42            6              19    51
DM01111C   29     406          30            7              17    58
DM01111D   46    1035          23            2              15    32
DM01111E   49    1176          28            2              18    36
DM01111G   41     820          38            4              20    48
DM01111H   42     861          50            5              24    57
DM01111I   30     435          17            3              11    36
DM01111J   34     561          11            1               9    26
DM01111K   30     435          14            3              10    33
DM01111L   28     378          13            3               9    32
DM01111M   24     276          13            4               9    37
DM01191B   47    1081          39            3              18    38
DM01253A   16     120           9            7               4    25
DM01283A   36     630          40            6              12    33
DM01283C   43     903          30            3              16    37
DM01283D   44     946          26            2              15    34
DM01354A   28     378          14            3              11    39
DM01354B   28     378           9            2               8    28
DM01354C   18     153           7            4               5    27
DM01354D   28     378          23            6              12    42
DM01354F   36     630          29            4              16    44
DM01354G   31     465          27            5              16    51
DM01354H   40     780          24            3              18    45
DM01354I   41     820          43            5              22    53
DM01354J   32     496          19            3              10    31
DM01354K   32     496          34            6              15    46
DM01354L   27     351          15            4               9    33
DM01354M   30     435          18            4              10    33
DM01354N   45     990          40            4              19    42
DM01354O   46    1035          57            5              26    56
DM01354P   34     561          34            6              19    55
DM01354Q   55    1485         135            9              39    70
DM01354R   30     435          15            3              11    36
DM01354S   21     210          12            5               8    38
DM01354T   43     903          43            4              24    55
DM01354V   47    1081          51            4              25    53
DM01354W   20     190           9            4               6    30
DM01354X   39     741          35            4              18    46
DM01354Y   40     780          31            3              18    45
DM01354Z   49    1176          61            5              31    63
DM01379A   19     171          15            8               9    47
DM01415B   48    1128          58            5              22    45
DM01443B   40     780          31            3              21    52
DM01443C   40     780          42            5              23    57
DM01443D   36     630          47            7              23    63
DM01443E   44     946          42            4              25    56
DM01443F   36     630          29            4              16    44
DM01443G   31     465          19            4              13    41
DM01537B   47    1081          19            1              14    29
DM01551A   30     435          25            5               9    30
DM01554A   10      45           5           11               4    40
DM01554C   16     120           6            5               5    31
DM01554E   17     136           6            4               5    29
DM01595A   41     820          23            2              16    39
DM01595B   28     378          12            3              10    35
DM01595D   25     300          13            4              11    44
DM01595E   33     528          26            4              14    42
DM01595F   24     276          10            3               7    29
DM01595I   18     153           8            5               7    38
DM01619A   54    1431          58            4              28    51
DM01619B   32     496          14            2              10    31
DM01619C   28     378          12            3               8    28
DM01619D   33     528          14            2               9    27
DM01688A   47    1081          41            3              23    48
DM01688B   48    1128          39            3              22    45
DM01688D   23     253          11            4               7    30
DM01688E   31     465          15            3               9    29
DM01688G   32     496          20            4              10    31
DM01688H   38     703          28            3              16    42
DM01688I   48    1128          51            4              23    47
DM01688J   37     666          18            2              13    35
DM01688K   39     741          29            3              17    43
DM01688L   10      45           4            8               3    30
DM01688M   44     946          50            5              25    56
DM01688N   28     378          30            7              15    53
DM01688O   27     351          18            5              13    48
DM01688P   45     990          71            7              25    55
DM01688Q   19     171           8            4               6    31
DM01724    20     190          15            7               9    45
DM01753B   10      45           3            6               3    30
DM01753C   39     741          22            2              15    38
DM01774    43     903          65            7              27    62
DM01782B   33     528          19            3              11    33
DM01782F   16     120          13           10               6    37
DM01857D   38     703          13            1              11    28
DM01857E   39     741          12            1              10    25
DM01857F   27     351          16            4              12    44
DM01865B   49    1176          19            1              13    26
DM01865D   38     703          14            1              12    31
DM01907    46    1035          38            3              22    47
DM01909    40     780          29            3              17    42
DM01912A   32     496          16            3              12    37
DM01912B   20     190          10            5               6    30
DM01912C   31     465          23            4              14    45
DM01922A   20     190           6            3               6    30
DM01922C   39     741          26            3              11    28
DM01945A   23     253           9            3               6    26
DM01945B   27     351          13            3              10    37
DM01945C   42     861          24            2              15    35
DM01945D   43     903          40            4              21    48
IPB000006  46    1035         162           15              23    50
IPB000007C 32     496          14            2              12    37
IPB000007E 29     406          15            3              10    34
IPB000009A 37     666          19            2              14    37
IPB000009B 55    1485          68            4              32    58
IPB000009C 47    1081          35            3              20    42
IPB000009D 42     861          34            3              20    47
IPB000009E 40     780          20            2              14    35
IPB000009F 46    1035          36            3              21    45
IPB000009G 34     561          15            2              11    32
IPB000011A 42     861          14            1              11    26
IPB000011B 28     378           8            2               7    25
IPB000011C 39     741          17            2              12    30
IPB000011F 39     741          24            3              14    35
IPB000036E 33     528          20            3              13    39
IPB000036F 53    1378          37            2              18    33
IPB000043B 46    1035          26            2              15    32
IPB000043D 54    1431          32            2              21    38
IPB000043E 40     780          21            2              14    35
IPB000053B 44     946          33            3              13    29
IPB000053C 47    1081          22            2              15    31
IPB000059A 24     276          10            3               8    33
IPB000059B 11      55           7           12               4    36
IPB000060A 33     528          12            2               9    27
IPB000060E 32     496          27            5              15    46
IPB000077  46    1035          39            3              16    34
IPB000079A 31     465          33            7              16    51
IPB000096B 36     630          31            4              15    41
IPB000096C 31     465          14            3              11    35
IPB000098A 54    1431          70            4              33    61
IPB000098B 46    1035          41            3              25    54
IPB000115D 22     231          14            6               9    40
IPB000118A 49    1176          69            5              32    65
IPB000118B 36     630          56            8              21    58
IPB000118C 32     496          35            7              18    56
IPB000118D 47    1081          57            5              29    61
IPB000118E 30     435          31            7              16    53
IPB000118F 29     406          29            7              16    55
IPB000118G 35     595          33            5              20    57
IPB000118H 37     666          49            7              20    54
IPB000118I 43     903          41            4              22    51
IPB000118J 40     780          52            6              23    57
IPB000118K 48    1128          64            5              31    64
IPB000118L 27     351          24            6              13    48
IPB000118M 29     406          23            5              10    34
IPB000118N 46    1035          65            6              26    56
IPB000120  55    1485          46            3              14    25
IPB000122D 38     703          22            3              10    26
IPB000122E 28     378          43           11              17    60
IPB000122G 46    1035          37            3              17    36
IPB000124A 30     435          11            2               8    26
IPB000126A 16     120           5            4               4    25
IPB000131E 48    1128          40            3              21    43
IPB000133A 55    1485          29            1              16    29
IPB000133B 46    1035          23            2              14    30
IPB000133C 34     561          13            2               9    26
IPB000138A 32     496          18            3              12    37
IPB000138B 27     351          14            3              11    40
IPB000138D 36     630          24            3              16    44
IPB000138E 34     561          16            2              12    35
IPB000138F 34     561          23            4              14    41
IPB000138G 35     595          47            7              18    51
IPB000146B 24     276          10            3               7    29
IPB000146E 26     325          11            3               7    26
IPB000158B 46    1035          45            4              17    36
IPB000164A 51    1275          19            1              13    25
IPB000164B 53    1378          59            4              26    49
IPB000165B 30     435          17            3              11    36
IPB000167B 15     105          12           11               6    40
IPB000171A 31     465          17            3               9    29
IPB000171E 11      55           4            7               4    36
IPB000173A 16     120          10            8               6    37
IPB000175A 52    1326          32            2              13    25
IPB000175C 52    1326          19            1              14    26
IPB000177A 41     820          25            3              16    39
IPB000177C 41     820          25            3              17    41
IPB000177D 46    1035          30            2              19    41
IPB000177E 37     666          20            3              14    37
IPB000177F 28     378          17            4              10    35
IPB000177G 29     406          16            3               9    31
IPB000177H 39     741          16            2              13    33
IPB000177I 40     780          32            4              20    50
IPB000177J 41     820          19            2              12    29
IPB000177K 33     528          22            4              13    39
IPB000177L 39     741          36            4              18    46
IPB000177M 35     595          28            4              18    51
IPB000177N 35     595          40            6              17    48
IPB000177O 29     406          14            3              10    34
IPB000178B 42     861          35            4              22    52
IPB000178C 47    1081          58            5              29    61
IPB000179B 53    1378          21            1              14    26
IPB000179C 55    1485          38            2              21    38
IPB000180A 27     351          12            3               8    29
IPB000180B 30     435          28            6              14    46
IPB000180C 36     630          20            3              15    41
IPB000180D 28     378           9            2               8    28
IPB000180E 34     561          34            6              19    55
IPB000180F 37     666          28            4              16    43
IPB000180G 29     406          21            5              12    41
IPB000180H 22     231          14            6               8    36
IPB000180I 28     378          22            5              11    39
IPB000180J 40     780          49            6              21    52
IPB000180K 42     861          51            5              23    54
IPB000180L 43     903          27            2              14    32
IPB000185A 52    1326          26            1              13    25
IPB000185B 40     780          25            3              15    37
IPB000185C 52    1326          30            2              16    30
IPB000185D 53    1378          27            1              17    32
IPB000185G 40     780          44            5              20    50
IPB000185H 47    1081          60            5              20    42
IPB000193A 32     496          19            3              14    43
IPB000193B 35     595          13            2              10    28
IPB000193C 33     528          20            3              15    45
IPB000193D 38     703          46            6              21    55
IPB000193E 44     946          20            2              16    36
IPB000193F 39     741          25            3              16    41
IPB000193G 41     820          46            5              22    53
IPB000193H 41     820          34            4              22    53
IPB000193I 31     465          20            4              14    45
IPB000193J 35     595          35            5              21    60
IPB000193K 30     435          31            7              14    46
IPB000193L 36     630          23            3              14    38
IPB000196B 42     861          23            2              11    26
IPB000196C 49    1176          32            2              14    28
IPB000214A 23     253           7            2               6    26
IPB000221  27     351          37           10               7    25
IPB000271  41     820          38            4              14    34
IPB000272  36     630          13            2               9    25
IPB000274A 43     903          21            2              15    34
IPB000274B 51    1275          32            2              19    37
IPB000274C 16     120           5            4               4    25
IPB000274D 53    1378          32            2              16    30
IPB000274E 42     861          55            6              24    57
IPB000274F 39     741          25            3              16    41
IPB000274G 54    1431          37            2              21    38
IPB000274H 34     561          14            2              11    32
IPB000274J 46    1035          35            3              17    36
IPB000274L 33     528          15            2              12    36
IPB000274M 23     253           7            2               6    26
IPB000274O 18     153           8            5               5    27
IPB000274P 38     703          23            3              17    44
IPB000278A 12      66           3            4               3    25
IPB000278B 28     378          24            6              14    50
IPB000283A 28     378          10            2               7    25
IPB000283B 33     528          15            2              13    39
IPB000289A 24     276          12            4               8    33
IPB000289B 33     528          32            6              14    42
IPB000303E 15     105          10            9               4    26
IPB000308A 27     351          18            5              11    40
IPB000308B 40     780          36            4              20    50
IPB000308C 50    1225          21            1              14    28
IPB000308D 55    1485          81            5              32    58
IPB000310A 49    1176          31            2              16    32
IPB000310B 39     741          17            2              11    28
IPB000310C 17     136           7            5               6    35
IPB000310F 20     190           7            3               6    30
IPB000310G 41     820          15            1              12    29
IPB000310I 26     325           8            2               7    26
IPB000310L 22     231          14            6               7    31
IPB000319D 22     231          11            4               6    27
IPB000319E 11      55           3            5               3    27
IPB000327A 49    1176          20            1              15    30
IPB000337B 48    1128          23            2              15    31
IPB000337C 48    1128          34            3              22    45
IPB000337D 32     496           9            1               8    25
IPB000337K 23     253          22            8               7    30
IPB000337O 51    1275          41            3              23    45
IPB000352C 47    1081          33            3              20    42
IPB000364B 31     465          21            4              12    38
IPB000364F 53    1378          51            3              20    37
IPB000364G 34     561          27            4              14    41
IPB000364H 55    1485          53            3              25    45
IPB000364J 50    1225          29            2              18    36
IPB000364K 38     703          18            2              13    34
IPB000384A 43     903          20            2              13    30
IPB000384B 35     595          13            2              10    28
IPB000389B 36     630          49            7              22    61
IPB000396A 24     276           8            2               6    25
IPB000396C 11      55           4            7               3    27
IPB000402A 55    1485          25            1              14    25
IPB000419A 31     465           9            1               9    29
IPB000420  12      66           6            9               4    33
IPB000439B 41     820          60            7              21    51
IPB000439C 53    1378          26            1              20    37
IPB000447A 49    1176          47            3              16    32
IPB000451C 44     946          21            2              16    36
IPB000453B 46    1035          21            2              12    26
IPB000453C 24     276          12            4               8    33
IPB000453E 47    1081          19            1              12    25
IPB000453F 29     406          14            3               8    27
IPB000464A 22     231          10            4               6    27
IPB000465D 40     780          28            3              10    25
IPB000476  21     210          10            4               8    38
IPB000484B 55    1485          37            2              26    47
IPB000484C 48    1128          64            5              28    58
IPB000484D 55    1485          56            3              26    47
IPB000500B 54    1431          32            2              24    44
IPB000500D 44     946          17            1              12    27
IPB000509B 55    1485          85            5              27    49
IPB000511B 14      91           4            4               4    28
IPB000530  54    1431          41            2              19    35
IPB000533B 55    1485          69            4              22    40
IPB000533C 35     595          36            6              18    51
IPB000533D 44     946          76            8              18    40
IPB000533E 45     990          52            5              22    48
IPB000541B 16     120           7            5               6    37
IPB000541C 38     703          22            3              12    31
IPB000541D 40     780          25            3              18    45
IPB000548A 43     903          34            3              17    39
IPB000548B 38     703          20            2              12    31
IPB000548C 21     210          11            5               7    33
IPB000554C 47    1081          22            2              13    27
IPB000554D 42     861          20            2              13    30
IPB000558B 46    1035          34            3              22    47
IPB000559B 31     465          25            5              13    41
IPB000559C 53    1378          73            5              29    54
IPB000559D 43     903          25            2              13    30
IPB000559E 36     630          15            2               9    25
IPB000559F 39     741          25            3              16    41
IPB000559G 20     190          10            5               6    30
IPB000559H 49    1176          47            3              23    46
IPB000559I 42     861          19            2              12    28
IPB000559K 38     703          15            2              12    31
IPB000572A 46    1035          22            2              13    28
IPB000572B 37     666          21            3              13    35
IPB000572D 55    1485          47            3              26    47
IPB000572F 28     378          16            4               9    32
IPB000572G 29     406          16            3               9    31
IPB000572H 46    1035          18            1              12    26
IPB000572K 16     120           5            4               5    31
IPB000576A 42     861          66            7              17    40
IPB000576B 55    1485          47            3              21    38
IPB000576C 55    1485          53            3              24    43
IPB000576D 43     903          31            3              14    32
IPB000576E 37     666          25            3              15    40
IPB000576F 47    1081          38            3              20    42
IPB000580A 27     351          24            6              12    44
IPB000580B 30     435          14            3               9    30
IPB000585C 49    1176          23            1              14    28
IPB000585D 32     496          16            3              12    37
IPB000590A 53    1378          36            2              23    43
IPB000590B 50    1225          38            3              22    44
IPB000590C 38     703          13            1              11    28
IPB000590D 41     820          16            1              11    26
IPB000592  55    1485          27            1              19    34
IPB000598B 53    1378          28            2              14    26
IPB000598C 36     630          13            2              10    27
IPB000614  23     253           7            2               6    26
IPB000631C 11      55           6           10               3    27
IPB000634D 13      78           9           11               4    30
IPB000643B 54    1431          37            2              20    37
IPB000643C 54    1431          27            1              19    35
IPB000647A 45     990          54            5              27    60
IPB000647B 28     378          36            9              17    60
IPB000647C 43     903          45            4              25    58
IPB000647D 27     351          19            5              12    44
IPB000647E 43     903          37            4              22    51
IPB000647F 42     861          39            4              21    50
IPB000647H 38     703          15            2              10    26
IPB000659D 30     435          13            2               8    26
IPB000663  18     153           8            5               5    27
IPB000669A 11      55           3            5               3    27
IPB000672E 37     666          17            2              11    29
IPB000678A 22     231          15            6               9    40
IPB000678B 26     325           9            2               7    26
IPB000678C 38     703          51            7              16    42
IPB000682B 44     946          26            2              12    27
IPB000685A 55    1485          58            3              29    52
IPB000685B 52    1326          45            3              26    50
IPB000685C 54    1431          47            3              26    48
IPB000685D 55    1485          68            4              30    54
IPB000685E 55    1485          77            5              33    60
IPB000689A 18     153           8            5               5    27
IPB000689C 44     946          27            2              15    34
IPB000691A 53    1378          17            1              14    26
IPB000692B 55    1485          26            1              15    27
IPB000692C 40     780          19            2              12    30
IPB000698A 48    1128          34            3              20    41
IPB000698B 48    1128          30            2              17    35
IPB000698C 49    1176          33            2              19    38
IPB000698D 55    1485          25            1              17    30
IPB000704A 47    1081          26            2              17    36
IPB000704D 36     630          11            1               9    25
IPB000705H 12      66          10           15               4    33
IPB000706D 15     105           5            4               4    26
IPB000716B 23     253          15            5               6    26
IPB000726D 44     946          25            2              14    31
IPB000741A 48    1128          21            1              15    31
IPB000741B 36     630          16            2              10    27
IPB000741D 43     903          21            2              13    30
IPB000741E 35     595          13            2              10    28
IPB000741F 36     630          20            3              14    38
IPB000749C 51    1275          35            2              22    43
IPB000749E 50    1225          28            2              17    34
IPB000753A 17     136          15           11               6    35
IPB000753B 26     325           9            2               7    26
IPB000753C 39     741          50            6              19    48
IPB000753D 42     861          37            4              20    47
IPB000753E 45     990          44            4              24    53
IPB000753F 42     861          22            2              13    30
IPB000753G 50    1225          55            4              27    54
IPB000762A 36     630          25            3              11    30
IPB000762B 45     990          35            3              16    35
IPB000766A 34     561          26            4              15    44
IPB000766B 39     741          21            2              16    41
IPB000766C 27     351          15            4              10    37
IPB000766D 36     630          15            2              11    30
IPB000766E 47    1081          29            2              18    38
IPB000766F 39     741          41            5              21    53
IPB000766G 39     741          17            2              12    30
IPB000768D 17     136          10            7               6    35
IPB000768G 37     666          14            2              11    29
IPB000771D 14      91           7            7               4    28
IPB000773A 43     903          50            5              22    51
IPB000773B 39     741          26            3              15    38
IPB000773C 53    1378          52            3              26    49
IPB000779A 42     861          43            4              16    38
IPB000779B 39     741          47            6              18    46
IPB000779C 48    1128          40            3              22    45
IPB000781B 40     780          12            1              10    25
IPB000789  41     820          26            3              17    41
IPB000791A 23     253           7            2               6    26
IPB000791B 44     946          24            2              12    27
IPB000791C 41     820          30            3              13    31
IPB000808B 42     861          15            1              11    26
IPB000811B 40     780          52            6              18    45
IPB000811E 40     780          17            2              11    27
IPB000811G 37     666          15            2              12    32
IPB000811H 53    1378          21            1              16    30
IPB000811I 35     595          12            2              10    28
IPB000811J 44     946          31            3              19    43
IPB000811K 55    1485          70            4              31    56
IPB000816B 50    1225          30            2              17    34
IPB000817A 42     861          37            4              15    35
IPB000817B 46    1035          76            7              28    60
IPB000817C 33     528          36            6              18    54
IPB000817D 29     406          18            4              11    37
IPB000818A 45     990          60            6              27    60
IPB000818B 46    1035          26            2              15    32
IPB000818C 53    1378          62            4              27    50
IPB000818D 55    1485          53            3              29    52
IPB000819A 16     120           7            5               4    25
IPB000819C 52    1326          22            1              15    28
IPB000830A 42     861          22            2              15    35
IPB000830C 49    1176          31            2              21    42
IPB000830D 43     903          36            3              23    53
IPB000830E 37     666          15            2              11    29
IPB000842B 46    1035          21            2              15    32
IPB000849C 20     190           9            4               6    30
IPB000849E 41     820          21            2              12    29
IPB000849G 41     820          28            3              12    29
IPB000867B 16     120           9            7               5    31
IPB000881  41     820          68            8              25    60
IPB000883B 43     903          24            2              13    30
IPB000883D 34     561          21            3              12    35
IPB000883F 49    1176          26            2              16    32
IPB000890B 11      55           6           10               5    45
IPB000890D 14      91           4            4               4    28
IPB000890E 41     820          29            3              12    29
IPB000892A 38     703          53            7              22    57
IPB000892B 37     666          14            2              11    29
IPB000892C 25     300          28            9              11    44
IPB000898B 47    1081          26            2              15    31
IPB000898C 34     561          14            2               9    26
IPB000898E 31     465           9            1               8    25
IPB000898F 20     190           7            3               6    30
IPB000903B 45     990          21            2              14    31
IPB000903C 34     561          32            5              18    52
IPB000903D 43     903          20            2              15    34
IPB000903F 33     528          13            2              10    30
IPB000903G 50    1225          31            2              18    36
IPB000915B 36     630          39            6              18    50
IPB000918C 52    1326          24            1              16    30
IPB000920A 46    1035          23            2              15    32
IPB000920B 35     595          19            3              14    40
IPB000920D 42     861          23            2              12    28
IPB000927A 13      78           5            6               4    30
IPB000927E 25     300          13            4               7    28
IPB000933A 45     990          53            5              22    48
IPB000933B 31     465          17            3              14    45
IPB000933C 42     861          42            4              21    50
IPB000933D 46    1035          49            4              24    52
IPB000933E 40     780          27            3              18    45
IPB000933F 17     136           9            6               6    35
IPB000933G 26     325          11            3               9    34
IPB000933H 47    1081          24            2              16    34
IPB000940A 44     946          24            2              15    34
IPB000940D 39     741          24            3              15    38
IPB000940E 38     703          12            1              10    26
IPB000941A 22     231           7            3               6    27
IPB000941B 45     990          19            1              12    26
IPB000941C 53    1378          23            1              15    28
IPB000952D 10      45           4            8               3    30
IPB000956A 34     561          14            2              11    32
IPB000956B 30     435          39            8              16    53
IPB000956C 35     595          57            9              20    57
IPB000956D 31     465          37            7              15    48
IPB000957B 32     496          16            3               9    28
IPB000957D 31     465          16            3              12    38
IPB000957F 53    1378          24            1              15    28
IPB000965E 47    1081          26            2              17    36
IPB000970C 35     595          14            2               9    25
IPB000970E 54    1431          24            1              15    27
IPB000981A 28     378          16            4               9    32
IPB000981B 20     190          13            6               7    35
IPB000981C 26     325          13            4               7    26
IPB000993C 53    1378          65            4              29    54
IPB000993D 53    1378          22            1              15    28
IPB000993F 53    1378          34            2              17    32
IPB000996A 27     351          41           11              16    59
IPB000996B 42     861          44            5              25    59
IPB000996C 35     595          45            7              21    60
IPB000996D 24     276          10            3               9    37
IPB000996E 54    1431          71            4              35    64
IPB001000D 12      66           3            4               3    25
IPB001002A 21     210          13            6               6    28
IPB001006A 39     741          23            3              16    41
IPB001006B 36     630          10            1               9    25
IPB001006C 20     190           8            4               5    25
IPB001006D 55    1485          38            2              22    40
IPB001006E 32     496          28            5              17    53
IPB001006F 36     630          14            2              11    30
IPB001006G 35     595          27            4              15    42
IPB001006H 42     861          20            2              17    40
IPB001006I 32     496          19            3              15    46
IPB001006J 40     780          33            4              20    50
IPB001023C 54    1431          49            3              27    50
IPB001043A 22     231           7            3               6    27
IPB001043C 55    1485          32            2              20    36
IPB001043J 37     666          19            2              12    32
IPB001043K 38     703          20            2              12    31
IPB001043M 36     630          16            2              11    30
IPB001045B 46    1035          33            3              20    43
IPB001047A 31     465          14            3               9    29
IPB001050  43     903          21            2              17    39
IPB001083A 46    1035          30            2              15    32
IPB001084A 12      66           5            7               3    25
IPB001084C 45     990          42            4              19    42
IPB001084D 54    1431          94            6              35    64
IPB001085A 53    1378          26            1              16    30
IPB001093D 35     595          23            3              13    37
IPB001093E 50    1225          47            3              17    34
IPB001099B 51    1275          27            2              16    31
IPB001099C 55    1485          22            1              14    25
IPB001102B 52    1326          20            1              16    30
IPB001102D 40     780          26            3              15    37
IPB001102E 43     903          14            1              11    25
IPB001102F 33     528          15            2              10    30
IPB001106A 47    1081          41            3              19    40
IPB001106B 54    1431          78            5              31    57
IPB001106C 36     630          35            5              20    55
IPB001106D 55    1485          40            2              24    43
IPB001106E 54    1431          61            4              33    61
IPB001106F 55    1485          78            5              31    56
IPB001106G 55    1485          23            1              15    27
IPB001106H 53    1378          28            2              18    33
IPB001114D 39     741          17            2              11    28
IPB001114E 41     820          21            2              12    29
IPB001117D 11      55           6           10               3    27
IPB001129A 38     703          19            2              15    39
IPB001129B 16     120           4            3               4    25
IPB001137C 44     946          14            1              11    25
IPB001141A 47    1081          48            4              23    48
IPB001141B 41     820          35            4              17    41
IPB001141C 19     171          10            5               7    36
IPB001147A 16     120           9            7               5    31
IPB001147C 55    1485          59            3              27    49
IPB001152  40     780          61            7              23    57
IPB001153A 45     990          29            2              17    37
IPB001169B 41     820          23            2              13    31
IPB001169D 52    1326          19            1              15    28
IPB001169H 23     253          20            7               8    34
IPB001169I 22     231          18            7               7    31
IPB001169J 20     190          15            7               5    25
IPB001170B 41     820          26            3              13    31
IPB001170F 33     528          15            2              11    33
IPB001171D 42     861          17            1              12    28
IPB001171E 16     120           4            3               4    25
IPB001171F 43     903          20            2              11    25
IPB001171G 53    1378          33            2              15    28
IPB001185A 42     861          40            4              17    40
IPB001185C 12      66           5            7               3    25
IPB001187B 33     528          20            3              15    45
IPB001187C 38     703          28            3              17    44
IPB001187D 45     990          51            5              27    60
IPB001187E 39     741          44            5              22    56
IPB001195  29     406          36            8              15    51
IPB001197B 40     780          19            2              12    30
IPB001197C 33     528          20            3              10    30
IPB001199B 12      66           3            4               3    25
IPB001199C 39     741          24            3              14    35
IPB001199D 42     861          34            3              19    45
IPB001199F 24     276          13            4               7    29
IPB001199G 26     325          13            4               7    26
IPB001199H 52    1326          27            2              16    30
IPB001208E 46    1035          16            1              13    28
IPB001210  36     630          13            2              11    30
IPB001211B 28     378          23            6              10    35
IPB001212A 21     210          16            7               6    28
IPB001225B 55    1485          63            4              31    56
IPB001225C 55    1485          72            4              36    65
IPB001225D 55    1485          79            5              33    60
IPB001225E 52    1326          39            2              25    48
IPB001233A 36     630          17            2              11    30
IPB001233B 14      91           8            8               5    35
IPB001233D 40     780          15            1              10    25
IPB001233E 32     496          12            2               8    25
IPB001237A 49    1176          70            5              28    57
IPB001237B 23     253           7            2               6    26
IPB001237C 34     561          26            4              14    41
IPB001237D 43     903          43            4              25    58
IPB001237E 55    1485          76            5              34    61
IPB001237F 40     780          41            5              23    57
IPB001237G 44     946          26            2              18    40
IPB001237H 34     561          23            4              14    41
IPB001237I 40     780          40            5              22    55
IPB001241I 36     630          13            2               9    25
IPB001260A 37     666          31            4              13    35
IPB001260B 27     351          10            2               8    29
IPB001260C 43     903          29            3              18    41
IPB001260E 24     276          15            5              11    45
IPB001260F 35     595          20            3              12    34
IPB001270A 33     528          18            3              12    36
IPB001270G 36     630          25            3              13    36
IPB001270H 35     595          17            2              12    34
IPB001271A 20     190          10            5               7    35
IPB001272A 37     666          16            2              10    27
IPB001272C 24     276          13            4               9    37
IPB001272D 33     528          27            5              14    42
IPB001272E 34     561          14            2              10    29
IPB001272G 52    1326          43            3              26    50
IPB001273B 41     820          21            2              14    34
IPB001273C 55    1485          28            1              18    32
IPB001273D 43     903          33            3              21    48
IPB001273E 39     741          34            4              22    56
IPB001273F 49    1176          20            1              14    28
IPB001273G 43     903          14            1              11    25
IPB001280A 52    1326          35            2              19    36
IPB001280B 33     528          20            3              12    36
IPB001280C 50    1225          55            4              25    50
IPB001280D 42     861          18            2              13    30
IPB001280E 29     406          11            2               8    27
IPB001280G 39     741          24            3              15    38
IPB001280H 30     435          19            4              13    43
IPB001280I 27     351          27            7              14    51
IPB001280K 49    1176          46            3              25    51
IPB001280L 32     496          15            3              11    34
IPB001282D 52    1326          16            1              13    25
IPB001284A 40     780          25            3              15    37
IPB001284B 15     105           8            7               5    33
IPB001285A 53    1378          50            3              27    50
IPB001285B 48    1128          55            4              29    60
IPB001285C 46    1035          35            3              19    41
IPB001285D 48    1128          45            3              25    52
IPB001285E 28     378          18            4               8    28
IPB001294D 44     946          45            4              22    50
IPB001294E 38     703          19            2              15    39
IPB001294F 38     703          21            2              13    34
IPB001294G 55    1485          44            2              25    45
IPB001294H 55    1485          43            2              26    47
IPB001294I 52    1326          47            3              25    48
IPB001294K 53    1378          32            2              22    41
IPB001295C 12      66           5            7               3    25
IPB001299B 37     666          13            1              10    27
IPB001299D 50    1225          22            1              13    26
IPB001308  52    1326          49            3              22    42
IPB001312F 15     105           8            7               5    33
IPB001319  52    1326         137           10              36    69
IPB001323A 33     528          30            5              13    39
IPB001323C 39     741          14            1              10    25
IPB001324A 19     171           7            4               5    26
IPB001325A 21     210          12            5               6    28
IPB001326B 16     120          18           15               7    43
IPB001326C 35     595          19            3              11    31
IPB001326D 38     703          22            3              15    39
IPB001343B 42     861          67            7              14    33
IPB001348B 20     190           7            3               5    25
IPB001349B 42     861          20            2              13    30
IPB001359A 26     325          10            3               8    30
IPB001359B 36     630          27            4              14    38
IPB001359C 45     990          22            2              19    42
IPB001359E 39     741          28            3              15    38
IPB001359F 49    1176          49            4              30    61
IPB001359G 54    1431          56            3              30    55
IPB001359H 18     153          24           15              10    55
IPB001363A 37     666          17            2              13    35
IPB001363B 46    1035          36            3              21    45
IPB001363C 51    1275          32            2              19    37
IPB001363D 47    1081          15            1              13    27
IPB001377B 47    1081          41            3              20    42
IPB001377C 37     666          25            3              16    43
IPB001378B 15     105           5            4               4    26
IPB001380A 28     378          20            5              11    39
IPB001380B 32     496          21            4              13    40
IPB001380C 37     666          17            2              12    32
IPB001393A 43     903          36            3              21    48
IPB001393B 52    1326          65            4              30    57
IPB001393C 52    1326          87            6              32    61
IPB001393D 49    1176          75            6              30    61
IPB001393E 49    1176          62            5              29    59
IPB001393F 46    1035          65            6              27    58
IPB001401A 35     595          21            3              12    34
IPB001401B 51    1275          58            4              24    47
IPB001401C 44     946          29            3              16    36
IPB001404A 45     990          38            3              24    53
IPB001404B 45     990          27            2              16    35
IPB001404C 44     946          19            2              12    27
IPB001404G 37     666          13            1              11    29
IPB001415A 35     595          23            3              13    37
IPB001422A 50    1225          82            6              31    62
IPB001422B 38     703          15            2              10    26
IPB001423A 46    1035          45            4              14    30
IPB001426B 35     595          15            2              13    37
IPB001426C 54    1431          37            2              23    42
IPB001426G 44     946          12            1              11    25
IPB001426H 26     325           8            2               7    26
IPB001426I 31     465           9            1               8    25
IPB001426J 39     741          26            3              16    41
IPB001426K 54    1431          53            3              30    55
IPB001426L 20     190           8            4               7    35
IPB001426M 22     231          10            4               9    40
IPB001426N 27     351          19            5              12    44
IPB001426O 33     528          25            4              17    51
IPB001426P 25     300           8            2               7    28
IPB001426Q 49    1176          56            4              25    51
IPB001429E 29     406          19            4              10    34
IPB001429H 27     351          11            3               8    29
IPB001449G 54    1431          21            1              15    27
IPB001449H 49    1176          64            5              24    48
IPB001449I 39     741          23            3              15    38
IPB001449L 22     231           7            3               6    27
IPB001450  12      66           6            9               3    25
IPB001463A 48    1128          41            3              14    29
IPB001465F 28     378          15            3              10    35
IPB001465G 31     465          10            2               9    29
IPB001465J 39     741          20            2              14    35
IPB001474C 53    1378          31            2              21    39
IPB001485D 12      66           6            9               3    25
IPB001489C 13      78          15           19               5    38
IPB001501A 21     210          12            5               7    33
IPB001501C 53    1378          42            3              20    37
IPB001501H 35     595          20            3              13    37
IPB001501I 16     120           4            3               4    25
IPB001510E 55    1485          19            1              15    27
IPB001514A 45     990          16            1              12    26
IPB001522A 10      45           7           15               4    40
IPB001522C 30     435          15            3              13    43
IPB001522D 42     861          29            3              15    35
IPB001522F 54    1431          32            2              22    40
IPB001523A 55    1485          66            4              29    52
IPB001524E 12      66           5            7               3    25
IPB001531B 38     703          18            2              12    31
IPB001553B 54    1431          62            4              27    50
IPB001553C 44     946          38            4              22    50
IPB001553D 34     561          12            2               9    26
IPB001554C 36     630          20            3              14    38
IPB001554D 45     990          29            2              14    31
IPB001559C 26     325          10            3               7    26
IPB001563B 24     276          10            3               6    25
IPB001569  41     820          21            2              11    26
IPB001572D 25     300           8            2               7    28
IPB001572G 38     703          23            3              12    31
IPB001572H 50    1225          37            3              21    42
IPB001576H 22     231          14            6               7    31
IPB001580D 45     990          21            2              13    28
IPB001582B 40     780          27            3              10    25
IPB001582C 41     820          20            2              14    34
IPB001586A 35     595          12            2               9    25
IPB001586F 46    1035          24            2              16    34
IPB001587C 34     561          12            2               9    26
IPB001589C 33     528          23            4              13    39
IPB001597A 46    1035          31            2              18    39
IPB001597B 52    1326          54            4              25    48
IPB001597H 38     703          23            3              13    34
IPB001597I 48    1128          29            2              19    39
IPB001600  28     378          15            3              10    35
IPB001608E 30     435          11            2               8    26
IPB001614A 47    1081          54            4              23    48
IPB001614B 55    1485          59            3              26    47
IPB001614D 54    1431          41            2              24    44
IPB001618A 42     861          31            3              13    30
IPB001618B 40     780          33            4              14    35
IPB001618C 54    1431          27            1              15    27
IPB001640A 11      55           8           14               3    27
IPB001649F 38     703          15            2              10    26
IPB001653G 18     153           9            5               6    33
IPB001656C 12      66           4            6               3    25
IPB001661B 25     300          10            3               8    32
IPB001672F 19     171          10            5               6    31
IPB001672H 36     630          17            2              13    36
IPB001679G 43     903          18            1              11    25
IPB001684A 29     406          14            3               8    27
IPB001684B 51    1275          25            1              13    25
IPB001692C 51    1275          30            2              13    25
IPB001692D 38     703          16            2              12    31
IPB001692E 42     861          22            2              11    26
IPB001695A 22     231          15            6               8    36
IPB001695B 39     741          51            6              24    61
IPB001695C 29     406          31            7              17    58
IPB001695D 23     253          27           10              14    60
IPB001695E 55    1485         110            7              39    70
IPB001695F 29     406          40            9              17    58
IPB001695G 26     325          16            4              12    46
IPB001695H 28     378          21            5              13    46
IPB001695I 43     903          46            5              25    58
IPB001695J 27     351          17            4              13    48
IPB001695K 36     630          33            5              21    58
IPB001695L 36     630          33            5              21    58
IPB001697E 54    1431          25            1              16    29
IPB001697F 50    1225          47            3              26    52
IPB001698A 55    1485          49            3              23    41
IPB001698D 37     666          19            2              14    37
IPB001701B 15     105           6            5               4    26
IPB001702A 21     210          11            5               9    42
IPB001702B 21     210          11            5               7    33
IPB001702C 38     703          38            5              17    44
IPB001702D 24     276          15            5              12    50
IPB001702F 29     406          11            2               8    27
IPB001702G 33     528          15            2              11    33
IPB001702H 24     276          18            6              10    41
IPB001707D 38     703          17            2              10    26
IPB001712B 52    1326          38            2              22    42
IPB001712C 49    1176          31            2              15    30
IPB001712D 30     435           9            2               8    26
IPB001717B 48    1128          28            2              18    37
IPB001717D 39     741          37            4              19    48
IPB001717E 34     561          29            5              17    50
IPB001717F 42     861          49            5              23    54
IPB001717G 34     561          27            4              16    47
IPB001717H 29     406          32            7              16    55
IPB001717I 48    1128          61            5              28    58
IPB001717J 34     561          24            4              17    50
IPB001717K 41     820          44            5              20    48
IPB001717L 34     561          21            3              13    38
IPB001717M 27     351          14            3               9    33
IPB001717N 25     300          10            3               8    32
IPB001717P 30     435          14            3               9    30
IPB001727A 38     703          26            3              16    42
IPB001727C 11      55           9           16               5    45
IPB001727D 52    1326          40            3              22    42
IPB001727E 25     300           9            3               8    32
IPB001729  33     528          93           17              22    66
IPB001741B 40     780          28            3              10    25
IPB001744A 39     741          17            2              11    28
IPB001744C 41     820          43            5              14    34
IPB001744D 32     496          19            3              10    31
IPB001744F 42     861          17            1              12    28
IPB001744G 46    1035          15            1              12    26
IPB001748B 29     406          14            3               9    31
IPB001748C 37     666          31            4              17    45
IPB001748D 10      45           7           15               4    40
IPB001752C 22     231          14            6               7    31
IPB001754B 39     741          15            2              11    28
IPB001754E 11      55           7           12               5    45
IPB001757F 24     276           8            2               6    25
IPB001759D 39     741          16            2              11    28
IPB001776A 50    1225          39            3              19    38
IPB001776B 52    1326          21            1              16    30
IPB001776C 55    1485          26            1              17    30
IPB001780B 41     820          19            2              13    31
IPB001797A 50    1225          21            1              15    30
IPB001797B 37     666          13            1              10    27
IPB001797C 32     496          14            2              10    31
IPB001797D 43     903          37            4              18    41
IPB001797E 51    1275          32            2              18    35
IPB001797F 55    1485          36            2              17    30
IPB001818C 44     946          38            4              18    40
IPB001818D 32     496          17            3              13    40
IPB001820B 12      66           4            6               3    25
IPB001824E 53    1378          48            3              24    45
IPB001824F 55    1485          41            2              22    40
IPB001824G 40     780          26            3              17    42
IPB001824H 43     903          35            3              22    51
IPB001824I 52    1326          23            1              13    25
IPB001825A 19     171          10            5               6    31
IPB001827B 20     190           6            3               5    25
IPB001827C 40     780          28            3              15    37
IPB001837A 15     105           4            3               4    26
IPB001844E 52    1326          20            1              13    25
IPB001852A 44     946          51            5              21    47
IPB001852B 36     630          24            3              15    41
IPB001852C 48    1128          50            4              24    50
IPB001852D 48    1128          61            5              25    52
IPB001863A 16     120           5            4               4    25
IPB001868B 46    1035          19            1              14    30
IPB001868C 31     465          18            3              12    38
IPB001868F 41     820          35            4              16    39
IPB001868G 43     903          32            3              18    41
IPB001868H 36     630          23            3              14    38
IPB001869F 43     903          24            2              15    34
IPB001869G 40     780          12            1              10    25
IPB001869H 27     351          11            3               8    29
IPB001869I 53    1378          34            2              20    37
IPB001874A 29     406          12            2               9    31
IPB001874C 51    1275          22            1              15    29
IPB001890B 34     561          12            2               9    26
IPB001891C 35     595          43            7              15    42
IPB001891F 10      45           8           17               4    40
IPB001894A 38     703          13            1              12    31
IPB001894B 48    1128          34            3              21    43
IPB001900D 18     153           6            3               5    27
IPB001920A 38     703          19            2              10    26
IPB001924A 49    1176          28            2              14    28
IPB001924B 42     861          47            5              19    45
IPB001924C 44     946          26            2              14    31
IPB001924D 44     946          50            5              15    34
IPB001924F 49    1176          42            3              21    42
IPB001924G 45     990          23            2              15    33
IPB001924H 22     231          12            5               8    36
IPB001924I 24     276          10            3               8    33
IPB001924K 32     496          16            3              10    31
IPB001929B 38     703          15            2              10    26
IPB001931A 40     780          25            3              16    40
IPB001937A 20     190           9            4               7    35
IPB001937B 36     630          18            2              12    33
IPB001937D 30     435          12            2              10    33
IPB001937E 38     703          16            2              10    26
IPB001937F 36     630          12            1              11    30
IPB001937G 41     820          41            5              23    56
IPB001942  11      55           4            7               3    27
IPB001944E 18     153           8            5               5    27
IPB001944F 11      55           4            7               4    36
IPB001944G 13      78           6            7               4    30
IPB001947B 10      45           4            8               3    30
IPB001949C 42     861          32            3              12    28
IPB001949D 30     435          16            3              10    33
IPB001951A 40     780          32            4              13    32
IPB001951B 31     465          21            4              14    45
IPB001951C 30     435          26            5              16    53
IPB001957B 47    1081          18            1              12    25
IPB001977A 15     105           8            7               5    33
IPB001981A 37     666          23            3              16    43
IPB001981B 51    1275          59            4              31    60
IPB001984D 50    1225          28            2              14    28
IPB001984E 40     780          25            3              16    40
IPB001984I 55    1485          30            2              16    29
IPB001985A 12      66           4            6               3    25
IPB001985B 52    1326          25            1              13    25
IPB001986A 31     465          11            2               8    25
IPB001991F 55    1485          28            1              16    29
IPB001991G 54    1431          64            4              28    51
IPB001991H 45     990          28            2              15    33
IPB001999B 55    1485          53            3              15    27
IPB001999C 48    1128          30            2              21    43
IPB001999D 43     903          28            3              16    37
IPB001999E 47    1081          31            2              19    40
IPB002000C 14      91           6            6               4    28
IPB002011C 52    1326          26            1              16    30
IPB002028A 29     406          11            2               8    27
IPB002029A 14      91           4            4               4    28
IPB002034D 46    1035          29            2              13    28
IPB002037A 21     210           9            4               6    28
IPB002038B 44     946          59            6              18    40
IPB002039C 38     703          20            2              14    36
IPB002041A 45     990          59            5              24    53
IPB002041B 41     820          37            4              19    46
IPB002041C 35     595          27            4              16    45
IPB002046A 37     666          22            3              12    32
IPB002046C 51    1275          29            2              18    35
IPB002051C 49    1176          25            2              17    34
IPB002051E 35     595          10            1               9    25
IPB002057B 16     120           5            4               4    25
IPB002057C 33     528          13            2              10    30
IPB002057E 35     595          22            3              15    42
IPB002057F 32     496          14            2              12    37
IPB002057G 21     210           8            3               6    28
IPB002072D 55    1485          32            2              16    29
IPB002076D 17     136           7            5               5    29
IPB002078C 28     378           9            2               7    25
IPB002081A 11      55           3            5               3    27
IPB002081C 50    1225          21            1              14    28
IPB002087B 33     528          11            2              10    30
IPB002088C 39     741          22            2              15    38
IPB002088D 24     276           7            2               6    25
IPB002091A 42     861          22            2              12    28
IPB002091E 26     325          10            3               7    26
IPB002101A 32     496          31            6              16    50
IPB002101B 52    1326         113            8              31    59
IPB002103B 43     903          25            2              15    34
IPB002117C 32     496          14            2              12    37
IPB002117D 32     496          17            3              13    40
IPB002117E 51    1275          27            2              18    35
IPB002117F 47    1081          53            4              24    51
IPB002133A 54    1431          47            3              28    51
IPB002133C 23     253          10            3               7    30
IPB002133E 40     780          82           10              23    57
IPB002133F 39     741          21            2              13    33
IPB002135A 28     378          13            3               7    25
IPB002135F 11      55           3            5               3    27
IPB002136D 52    1326          24            1              15    28
IPB002151C 36     630          33            5              20    55
IPB002151D 32     496          37            7              17    53
IPB002151E 36     630          31            4              18    50
IPB002151F 48    1128          67            5              31    64
IPB002151G 52    1326          49            3              25    48
IPB002151H 48    1128          36            3              22    45
IPB002157A 10      45           4            8               3    30
IPB002157B 16     120           5            4               4    25
IPB002157D 38     703          12            1              10    26
IPB002171E 18     153          11            7               7    38
IPB002172  20     190           9            4               5    25
IPB002181C 37     666          20            3              10    27
IPB002181G 30     435          12            2              10    33
IPB002202C 46    1035          21            2              16    34
IPB002202D 48    1128          34            3              17    35
IPB002202E 36     630          22            3              11    30
IPB002202F 40     780          19            2              13    32
IPB002218A 44     946          27            2              12    27
IPB002218F 29     406          14            3              10    34
IPB002218G 52    1326          71            5              30    57
IPB002218H 52    1326          46            3              25    48
IPB002226A 52    1326          19            1              16    30
IPB002226B 55    1485          35            2              20    36
IPB002358C 41     820          29            3              15    36
IPB002359B 40     780          11            1              11    27
IPB002359D 44     946          15            1              12    27
IPB002360A 34     561          30            5              13    38
IPB002364C 24     276          13            4               7    29
IPB002365C 17     136          10            7               6    35
IPB002381A 52    1326          28            2              17    32
IPB002381B 53    1378          74            5              33    62
IPB002381C 36     630          18            2              11    30
IPB002467D 38     703          16            2              10    26
IPB002468B 44     946          18            1              11    25
IPB002993A 28     378          14            3               9    32
IPB002993C 41     820          32            3              17    41
IPB002994B 24     276          10            3               8    33
IPB002994C 27     351          13            3               8    29
IPB002995D 37     666          21            3              12    32
PF00064A   26     325          15            4               8    30
PF00064B   53    1378          31            2              22    41
PF00064C   43     903          16            1              12    27
PF00064D   37     666          16            2              13    35
PF00064E   28     378          12            3               9    32
PF00064G   36     630          25            3              12    33
PF00242A   43     903          53            5              25    58
PF00242B   42     861          29            3              19    45
PF00242C   44     946          53            5              25    56
PF00242D   30     435          17            3              12    40
PF00242G   40     780          40            5              23    57
PF00242H   32     496          27            5              16    50
PF00242I   40     780          75            9              25    62
PF00242J   44     946          52            5              26    59
PF00242K   45     990          63            6              28    62
PF00242L   54    1431          62            4              29    53
PF00242M   45     990          47            4              27    60
PF00242N   50    1225          58            4              29    57
PF00242O   41     820          46            5              22    53
PF00242P   28     378          18            4              13    46
PF00242Q   46    1035          73            7              27    58
PF00421A   55    1485          21            1              16    29
PF00421D   34     561          18            3               9    26
PF00424A   28     378          48           12              13    46
PF00426A   25     300          15            5              10    40
PF00426B   29     406          24            5              14    48
PF00426C   27     351          21            5              10    37
PF00426D   37     666          23            3              14    37
PF00426H   22     231           8            3               6    27
PF00426J   41     820          40            4              23    56
PF00426K   33     528          21            3              14    42
PF00426L   42     861          45            5              24    57
PF00426M   28     378          15            3              11    39
PF00426N   38     703          45            6              22    57
PF00426O   45     990          49            4              28    62
PF00426P   34     561          31            5              18    52
PF00426Q   28     378          26            6              15    53
PF00426R   30     435          30            6              16    53
PF00426S   38     703          36            5              11    28
PF00426T   25     300          13            4              10    40
PF00426U   39     741          30            4              19    48
PF00426V   37     666          31            4              18    48
PF00426W   27     351          23            6              15    55
PF00426X   30     435          34            7              17    56
PF00434B   38     703          11            1              11    28
PF00434C   32     496          10            2               8    25
PF00434D   28     378          21            5              10    35
PF00434F   30     435          11            2              10    33
PF00434G   35     595          27            4              18    51
PF00469B   39     741          23            3              15    38
PF00469D   46    1035          19            1              12    26
PF00504A   55    1485          19            1              14    25
PF00506C   41     820          22            2              19    46
PF00506D   29     406          30            7              17    58
PF00506E   42     861          48            5              23    54
PF00506F   38     703          40            5              19    50
PF00506G   46    1035          37            3              23    50
PF00506H   31     465          11            2               9    29
PF00506I   36     630          32            5              18    50
PF00506J   41     820          34            4              19    46
PF00510E   30     435          19            4              11    36
PF00513B   35     595          14            2               9    25
PF00513D   35     595          15            2              10    28
PF00514B    6      15           3           20               2    33
PF00516A   22     231          12            5               7    31
PF00516B   44     946          24            2              18    40
PF00516D   44     946          25            2              17    38
PF00516G   27     351          13            3               9    33
PF00516J   44     946          38            4              18    40
PF00516K   53    1378          52            3              26    49
PF00516L   48    1128          26            2              17    35
PF00516M   52    1326          32            2              19    36
PF00516O   36     630          24            3              13    36
PF00519E   45     990          32            3              15    33
PF00519G   40     780          21            2              15    37
PF00521A   32     496          22            4              16    50
PF00521B   50    1225          47            3              24    48
PF00521D   26     325          17            5              11    42
PF00521E   12      66           4            6               3    25
PF00542C   40     780          18            2              11    27
PF00568B   10      45           5           11               3    30
PF00598A   43     903          41            4              20    46
PF00598B   44     946          28            2              18    40
PF00598C   32     496          16            3              11    34
PF00598D   55    1485          50            3              28    50
PF00599A   28     378          17            4              14    50
PF00599B   35     595          47            7              21    60
PF00599C   34     561          38            6              17    50
PF00600A   27     351          12            3              10    37
PF00600B   30     435          29            6              15    50
PF00600C   21     210          12            5               8    38
PF00600D   34     561          16            2              12    35
PF00600E   46    1035          52            5              29    63
PF00600F   32     496          21            4              14    43
PF00600G   34     561          22            3              13    38
PF00601A   55    1485          32            2              18    32
PF00601B   38     703          21            2              15    39
PF00602A   55    1485          53            3              17    30
PF00602B   52    1326          29            2              17    32
PF00602C   40     780          32            4              17    42
PF00602D   39     741          32            4              20    51
PF00602F   55    1485          23            1              14    25
PF00602G   48    1128          35            3              17    35
PF00602J   55    1485          24            1              18    32
PF00603A   55    1485          23            1              15    27
PF00603B   41     820          16            1              12    29
PF00603C   39     741          17            2              11    28
PF00603D   55    1485          18            1              14    25
PF00603H   55    1485          51            3              26    47
PF00603J   43     903          24            2              17    39
PF00604A   55    1485          56            3              22    40
PF00604B   55    1485          21            1              15    27
PF00604C   52    1326          35            2              21    40
PF00604D   54    1431          23            1              16    29
PF00604G   55    1485          35            2              22    40
PF00609C   39     741          25            3              16    41
PF00609D   15     105           8            7               5    33
PF00609E   24     276          16            5               9    37
PF00623C   39     741          15            2              10    25
PF00624A   41     820          55            6              25    60
PF00624B   46    1035          55            5              29    63
PF00624C   24     276          18            6              11    45
PF00624D   22     231          22            9              12    54
PF00624E   15     105           8            7               6    40
PF00624F   36     630         105           16              23    63
PF00624G   55    1485         269           18              40    72
PF00624H   32     496          57           11              19    59
PF00624I   30     435         122           28              21    70
PF00624J   55    1485         211           14              43    78
PF00624K   38     703          70            9              24    63
PF00624L   55    1485         155           10              38    69
PF00624M   51    1275         140           10              36    70
PF00624N   42     861          99           11              28    66
PF00647F   11      55           4            7               3    27
PF00692D   10      45           6           13               3    30
PF00699    50    1225          26            2              15    30
PF00714C   36     630          13            2              10    27
PF00718A   28     378          15            3              11    39
PF00718C   37     666          20            3              14    37
PF00718D   31     465          13            2               9    29
PF00718E   26     325          11            3               9    34
PF00718F   49    1176          62            5              27    55
PF00718G   42     861          34            3              18    42
PF00718H   26     325          17            5              11    42
PF00721A   36     630          16            2              10    27
PF00721C   44     946          47            4              25    56
PF00737    49    1176          44            3              23    46
PF00738C   39     741          37            4              21    53
PF00738D   53    1378          45            3              25    47
PF00738G   41     820          46            5              26    63
PF00748A   42     861          17            1              11    26
PF00748B   45     990          49            4              26    57
PF00748C   37     666          34            5              21    56
PF00748D   29     406          36            8              15    51
PF00748E   49    1176          66            5              30    61
PF00748F   49    1176         125           10              33    67
PF00748G   37     666          52            7              23    62
PF00748H   39     741          82           11              25    64
PF00748I   43     903          49            5              21    48
PF00748J   30     435          37            8              17    56
PF00748K   34     561          30            5              17    50
PF00761F   35     595          29            4              15    42
PF00761G   13      78           8           10               5    38
PF00772D   52    1326          24            1              13    25
PF00774A   46    1035          32            3              13    28
PF00774B   29     406          10            2               8    27
PF00774C   18     153           7            4               6    33
PF00774D   26     325          15            4              10    38
PF00774E   29     406          29            7              15    51
PF00774F   34     561          32            5              20    58
PF00774G   38     703          46            6              23    60
PF00774H   31     465          29            6              18    58
PF00774I   45     990          46            4              25    55
PF00774J   21     210          16            7              10    47
PF00777C   55    1485          36            2              20    36
PF00778A   32     496          17            3              12    37
PF00778B   42     861          45            5              23    54
PF00778D   32     496          34            6              15    46
PF00778E   34     561          49            8              20    58
PF00778F   24     276          13            4              10    41
PF00778G   24     276          12            4               9    37
PF00778H   32     496          28            5              14    43
PF00778I   25     300           9            3               8    32
PF00778J   28     378          13            3              10    35
PF00778K   29     406          11            2              10    34
PF00778M   36     630          30            4              12    33
PF00791A   55    1485          23            1              14    25
PF00791B   55    1485          22            1              16    29
PF00793B   52    1326          20            1              16    30
PF00793C   51    1275          29            2              18    35
PF00793E   49    1176          22            1              14    28
PF00798B   33     528          14            2               9    27
PF00798F   36     630          23            3              15    41
PF00798G   39     741          22            2              12    30
PF00798H   29     406          11            2               9    31
PF00798I   37     666          25            3              16    43
PF00802A   25     300          13            4               9    36
PF00802B   28     378          29            7              12    42
PF00802D   43     903          24            2              16    37
PF00803B   53    1378          27            1              15    28
PF00803C   37     666          12            1              10    27
PF00816A   33     528          31            5              16    48
PF00816B   30     435          17            3               8    26
PF00816C   52    1326          28            2              18    34
PF00835B   44     946          14            1              11    25
PF00843A   22     231          10            4               6    27
PF00843B   45     990          46            4              22    48
PF00843C   35     595          21            3              11    31
PF00843D   24     276          10            3               8    33
PF00843E   29     406          12            2               9    31
PF00843F   34     561          25            4              17    50
PF00843G   34     561          19            3              12    35
PF00843H   35     595          13            2              10    28
PF00843I   49    1176          42            3              26    53
PF00843J   51    1275          33            2              21    41
PF00843K   46    1035          21            2              14    30
PF00845A   43     903          15            1              13    30
PF00845B   34     561          26            4              16    47
PF00845C   34     561          19            3              14    41
PF00845D   32     496          20            4              13    40
PF00846A   47    1081          47            4              25    53
PF00846B   43     903          34            3              17    39
PF00846C   37     666          36            5              21    56
PF00846D   35     595          22            3              17    48
PF00846E   36     630          17            2              12    33
PF00846G   49    1176          50            4              27    55
PF00846H   37     666          37            5              22    59
PF00846I   44     946          40            4              23    52
PF00850B   25     300          11            3               9    36
PF00850D   25     300          12            4               8    32
PF00850E   47    1081          57            5              27    57
PF00850F   34     561          30            5              13    38
PF00850G   33     528          15            2              10    30
PF00852A    9      36           4           11               3    33
PF00852C   25     300          10            3               8    32
PF00852D   39     741          26            3              15    38
PF00852E   39     741          18            2              16    41
PF00852F   45     990          42            4              21    46
PF00869B   50    1225          24            1              16    32
PF00869C   41     820          24            2              13    31
PF00869D   47    1081          18            1              13    27
PF00869E   23     253          11            4               9    39
PF00869F   53    1378          63            4              22    41
PF00869H   54    1431          26            1              14    25
PF00869K   34     561          19            3              13    38
PF00869L   41     820          22            2              13    31
PF00869N   32     496          29            5              13    40
PF00869O   42     861          34            3              19    45
PF00869P   53    1378          39            2              24    45
PF00869Q   24     276          10            3               7    29
PF00869R   39     741          17            2              11    28
PF00869S   34     561          14            2              11    32
PF00869T   47    1081          19            1              13    27
PF00869U   52    1326          26            1              19    36
PF00869V   33     528          11            2              10    30
PF00869Y   22     231           8            3               6    27
PF00869Z   43     903          17            1              11    25
PF00878A   48    1128          48            4              24    50
PF00878B   38     703          38            5              20    52
PF00878C   38     703          40            5              20    52
PF00878D   45     990          52            5              25    55
PF00878E   32     496          22            4              17    53
PF00878F   37     666          36            5              19    51
PF00878G   38     703          32            4              18    47
PF00878H   27     351          20            5              14    51
PF00878I   43     903          44            4              25    58
PF00878J   54    1431          71            4              37    68
PF00878K   36     630          19            3              15    41
PF00878L   33     528          28            5              18    54
PF00878M   39     741          32            4              20    51
PF00878N   44     946          45            4              25    56
PF00878O   39     741          35            4              20    51
PF00878P   31     465          20            4              13    41
PF00878Q   35     595          18            3              13    37
PF00878R   55    1485          79            5              35    63
PF00878S   55    1485          59            3              29    52
PF00878T   27     351          14            3               9    33
PF00878U   41     820          33            4              23    56
PF00878V   31     465          16            3              12    38
PF00878W   41     820          42            5              20    48
PF00878X   42     861          40            4              24    57
PF00878Y   55    1485          74            4              35    63
PF00878Z   18     153          12            7               8    44
PF00901A   54    1431          40            2              21    38
PF00901B   46    1035          42            4              22    47
PF00901D   55    1485          48            3              21    38
PF00901E   55    1485          33            2              19    34
PF00901G   45     990          39            3              17    37
PF00921E   23     253          10            3               8    34
PF00921F   27     351          16            4               8    29
PF00921G   38     703          14            1              10    26
PF00922C   19     171          13            7               6    31
PF00925C   20     190           7            3               6    30
PF00925D   43     903          25            2              14    32
PF00926C   52    1326          24            1              15    28
PF00945D   53    1378          20            1              15    28
PF00945E   55    1485          29            1              18    32
PF00952C   34     561          17            3              11    32
PF00952D   46    1035          37            3              20    43
PF00960A   39     741          20            2              13    33
PF00968B   30     435          19            4              12    40
PF00968E   39     741          16            2              10    25
PF00968G   39     741          12            1              10    25
PF00969C   50    1225          18            1              13    26
PF00969D   30     435          10            2               9    30
PF00969E   35     595          16            2               9    25
PF00973C   31     465          10            2               8    25
PF00973D   53    1378          43            3              20    37
PF00997A   38     703          24            3              16    42
PF00997C   38     703          25            3              15    39
PF01007A   47    1081          21            1              13    27
PF01007B   51    1275          24            1              16    31
PF01007C   38     703          14            1              11    28
PF01007E   50    1225          25            2              16    32
PF01020    48    1128          36            3              15    31
PF01021A   30     435          14            3              10    33
PF01050C   30     435          15            3               9    30
PF01054A   54    1431          82            5              37    68
PF01054B   35     595          50            8              21    60
PF01054C   29     406          23            5              14    48
PF01054D   30     435          27            6              17    56
PF01054E   33     528          28            5              17    51
PF01054F   37     666          40            6              22    59
PF01054G   29     406          16            3              13    44
PF01062F   54    1431          30            2              16    29
PF01074E   28     378          11            2               9    32
PF01103C   43     903          20            2              12    27
PF01103E   54    1431          22            1              18    33
PF01103G   31     465          15            3               8    25
PF01103H   29     406          15            3              10    34
PF01103I   53    1378          33            2              19    35
PF01103J   39     741          35            4              16    41
PF01103K   46    1035          19            1              16    34
PF01103L   50    1225          31            2              22    44
PF01104B   49    1176          23            1              14    28
PF01112B   44     946          35            3              15    34
PF01140A   54    1431          46            3              24    44
PF01140B   35     595          28            4              12    34
PF01298E   29     406          26            6              12    41
PF01298K   21     210          16            7               7    33
PF01308A   50    1225          74            6              33    66
PF01308B   30     435          18            4              13    43
PF01308C   54    1431          71            4              32    59
PF01308D   55    1485          70            4              34    61
PF01308E   45     990          42            4              23    51
PF01308F   28     378          21            5              11    39
PF01308G   55    1485          66            4              34    61
PF01314C   44     946          23            2              15    34
PF01314E   33     528          22            4              11    33
PF01317B   17     136           8            5               5    29
PF01317C   39     741          17            2              10    25
PF01317E   30     435          19            4               9    30
PF01318A   39     741          26            3              15    38
PF01318B   31     465          15            3               8    25
PF01318C   28     378          11            2               7    25
PF01318D   28     378          24            6              12    42
PF01318E   36     630          19            3              13    36
PF01320B   41     820          16            1              12    29
PF01320C   17     136           8            5               6    35
PF01323B   16     120           8            6               6    37
PF01340A   29     406          25            6              16    55
PF01340B   22     231          15            6               9    40
PF01340C   25     300          15            5              10    40
PF01340D   23     253          21            8              10    43
PF01342A   35     595          14            2              10    28
PF01345B   33     528          30            5              17    51
PF01345C   34     561          46            8              21    61
PF01345D   34     561          32            5              20    58
PF01345E   30     435          19            4              14    46
PF01356    44     946          22            2              14    31
PF01358A   28     378          18            4              10    35
PF01358B   46    1035          61            5              26    56
PF01358C   29     406          21            5              13    44
PF01358D   33     528          19            3              12    36
PF01358E   32     496          15            3              12    37
PF01358F   29     406          15            3              11    37
PF01358G   37     666          21            3              14    37
PF01358H   41     820          32            3              21    51
PF01358I   50    1225          31            2              18    36
PF01361B   44     946          15            1              11    25
PF01364A   50    1225          15            1              13    26
PF01364C   54    1431          26            1              16    29
PF01364D   38     703          18            2              15    39
PF01364F   54    1431          30            2              18    33
PF01364G   39     741          43            5              22    56
PF01370A   11      55           6           10               3    27
PF01371A   44     946          22            2              13    29
PF01371B   37     666          12            1              10    27
PF01372    26     325          21            6              13    50
PF01374A   14      91           6            6               4    28
PF01374B   33     528          26            4              15    45
PF01374E   38     703          20            2              14    36
PF01392E   52    1326          16            1              13    25
PF01405    30     435          25            5              15    50
PF01414B   35     595          39            6              10    28
PF01429A   42     861          31            3              15    35
PF01429B   48    1128          20            1              14    29
PF01429D   38     703          20            2              12    31
PF01429E   49    1176          64            5              22    44
PF01429F   49    1176          33            2              20    40
PF01429G   29     406          10            2               8    27
PF01448A   50    1225          20            1              16    32
PF01448B   41     820          16            1              11    26
PF01448C   18     153           8            5               5    27
PF01448E   22     231           7            3               6    27
PF01448F   34     561          18            3              12    35
PF01448G   53    1378          35            2              22    41
PF01448H   47    1081          35            3              21    44
PF01454D   51    1275          32            2              22    43
PF01462A    8      28           3           10               2    25
PF01468D   52    1326          29            2              15    28
PF01468E   36     630          33            5              13    36
PF01473D   34     561          16            2               9    26
PF01474B   40     780          27            3              16    40
PF01474D   55    1485          23            1              14    25
PF01474E   50    1225          44            3              26    52
PF01481B   51    1275          18            1              14    27
PF01493C   47    1081          23            2              15    31
PF01493F   51    1275          21            1              17    33
PF01493H   46    1035          26            2              13    28
PF01493I   55    1485          56            3              24    43
PF01493J   40     780          37            4              19    47
PF01493K   36     630          24            3              14    38
PF01493L   38     703          28            3              14    36
PF01493M   32     496          27            5              15    46
PF01493N   35     595          12            2               9    25
PF01493O   45     990          31            3              18    40
PF01493P   36     630          20            3               9    25
PF01493Q   44     946          36            3              18    40
PF01496E   24     276           9            3               6    25
PF01496H   39     741          23            3              13    33
PF01498E   24     276           8            2               7    29
PF01505A   38     703          37            5              23    60
PF01505B   50    1225          41            3              20    40
PF01505C   23     253           8            3               6    26
PF01505D   42     861          25            2              14    33
PF01505E   50    1225          31            2              17    34
PF01505F   50    1225          38            3              19    38
PF01505G   39     741          30            4              17    43
PF01505H   33     528          23            4              13    39
PF01505I   29     406          15            3              11    37
PF01505J   50    1225          52            4              26    52
PF01505K   47    1081          64            5              28    59
PF01505L   38     703          42            5              23    60
PF01505M   28     378          33            8              15    53
PF01505N   51    1275          92            7              27    52
PF01505O   53    1378          53            3              28    52
PF01513B   44     946          19            2              12    27
PF01520A   14      91           8            8               5    35
PF01524A   44     946          19            2              14    31
PF01524B   42     861          22            2              12    28
PF01529B   45     990          32            3              12    26
PF01531A   37     666          28            4              17    45
PF01531B   24     276           6            2               6    25
PF01531C   33     528          27            5              15    45
PF01531D   23     253          18            7              10    43
PF01531E   30     435          25            5              14    46
PF01531F   33     528          24            4              15    45
PF01531G   24     276          17            6              11    45
PF01531H   41     820          46            5              26    63
PF01535B   11      55           4            7               3    27
PF01550A   37     666          26            3              17    45
PF01550B   25     300          10            3               8    32
PF01550E   32     496          27            5              16    50
PF01550F   43     903          38            4              19    44
PF01550H   20     190           7            3               5    25
PF01559A   39     741          37            4              18    46
PF01559B   24     276          26            9               9    37
PF01559C   32     496          46            9              19    59
PF01559D   32     496          29            5              13    40
PF01561C   52    1326          34            2              22    42
PF01561E   40     780          26            3              13    32
PF01561F   23     253           7            2               6    26
PF01561G   43     903          48            5              26    60
PF01561H   37     666          34            5              21    56
PF01561I   45     990          47            4              24    53
PF01561J   37     666          14            2              11    29
PF01561K   24     276           9            3               6    25
PF01561L   31     465          13            2               9    29
PF01561M   50    1225          39            3              25    50
PF01561N   32     496          19            3              14    43
PF01561O   38     703          39            5              21    55
PF01561P   45     990          45            4              25    55
PF01561Q   38     703          42            5              22    57
PF01561R   48    1128          36            3              23    47
PF01561S   40     780          26            3              11    27
PF01561T   33     528          24            4              15    45
PF01561U   28     378          11            2               9    32
PF01561V   48    1128          48            4              24    50
PF01561W   47    1081          37            3              21    44
PF01571F   36     630          16            2              10    27
PF01581A    7      21           2            9               2    28
PF01586    46    1035          50            4              20    43
PF01587A   14      91           5            5               4    28
PF01598A   32     496          21            4               8    25
PF01600D   34     561          17            3              11    32
PF01600F   53    1378          32            2              18    33
PF01600G   43     903          38            4              18    41
PF01600H   47    1081          53            4              27    57
PF01600I   38     703          20            2              16    42
PF01600L   48    1128          53            4              25    52
PF01607C   13      78           6            7               4    30
PF01608H   24     276          12            4               6    25
PF01608I   29     406          10            2               8    27
PF01615E   43     903          23            2              13    30
PF01615F   11      55           3            5               3    27
PF01616A    6      15           3           20               2    33
PF01616B   47    1081          36            3              16    34
PF01619F   22     231           7            3               7    31
PF01621A   34     561          12            2              10    29
PF01621E   38     703          17            2              11    28
PF01621F   53    1378          25            1              17    32
PF01621G   35     595          16            2              10    28
PF01621H   40     780          24            3              13    32
PF01623A   26     325          20            6              11    42
PF01626F   27     351           9            2               7    25
PF01635A   51    1275          22            1              14    27
PF01636D   18     153           7            4               5    27
PF01639    37     666          16            2              10    27
PF01641B   23     253          10            3               7    30
PF01644B   30     435           9            2               8    26
PF01644C   49    1176          22            1              13    26
PF01644E   47    1081          32            2              20    42
PF01644F   50    1225          17            1              13    26
PF01647A   22     231          13            5               7    31
PF01647C   42     861          37            4              17    40
PF01647F   39     741          14            1              11    28
PF01651A   51    1275          31            2              18    35
PF01651B   44     946          15            1              11    25
PF01651C   35     595          17            2              10    28
PF01658A   43     903          29            3              15    34
PF01658B   19     171           6            3               5    26
PF01658C   32     496           9            1               8    25
PF01658D   50    1225          38            3              22    44
PF01658E   46    1035          25            2              17    36
PF01658F   33     528          21            3              15    45
PF01658G   37     666          29            4              18    48
PF01658H   27     351          15            4               9    33
PF01658I   16     120           9            7               7    43
PF01658J   55    1485          40            2              25    45
PF01658K   50    1225          27            2              16    32
PF01660B   16     120           6            5               5    31
PF01660F   10      45           4            8               3    30
PF01662C   23     253           8            3               6    26
PF01670B   16     120           7            5               6    37
PF01670C   50    1225          29            2              13    26
PF01670D   47    1081          25            2              16    34
PF01671C   43     903          23            2              12    27
PF01673B   12      66           5            7               4    33
PF01692C   55    1485          68            4              31    56
PF01697B   55    1485          29            1              16    29
PF01697C   36     630          19            3              12    33
PF01698A   33     528          28            5              16    48
PF01698B   38     703          39            5              18    47
PF01698E   41     820          40            4              24    58
PF01698F   29     406          21            5              12    41
PF01698G   39     741          35            4              22    56
PF01698H   50    1225          44            3              27    54
PF01700A   48    1128          40            3              24    50
PF01700B   40     780          23            2              17    42
PF01700C   54    1431          26            1              19    35
PF01700D   50    1225          37            3              21    42
PF01700E   34     561          39            6              17    50
PF01700F   35     595          27            4              17    48
PF01700G   45     990          28            2              19    42
PF01700I   39     741          13            1              12    30
PF01700J   53    1378          22            1              15    28
PF01700K   47    1081          41            3              25    53
PF01700M   26     325          13            4               8    30
PF01700N   37     666          19            2              15    40
PF01700O   33     528          19            3              11    33
PF01700Q   55    1485          44            2              23    41
PF01701    32     496           9            1               8    25
PF01703A   38     703          35            4              17    44
PF01703B   45     990          20            2              12    26
PF01703C   32     496          25            5              13    40
PF01703D   40     780          28            3              17    42
PF01703E   52    1326          34            2              18    34
PF01703G   34     561          28            4              16    47
PF01703H   27     351           9            2               7    25
PF01713B    8      28           2            7               2    25
PF01714C   42     861          21            2              12    28
PF01714D   51    1275          31            2              16    31
PF01714E   44     946          23            2              14    31
PF01716C   47    1081          27            2              15    31
PF01716D   36     630          24            3              17    47
PF01716E   33     528          26            4              16    48
PF01716F   37     666          18            2              13    35
PF01718A   48    1128          32            2              21    43
PF01718B   12      66           4            6               3    25
PF01718C   32     496          13            2               9    28
PF01718D   20     190           6            3               6    30
PF01718E   36     630          13            2               9    25
PF01718I   34     561          21            3              13    38
PF01721A   20     190           9            4               7    35
PF01723B   51    1275          33            2              13    25
PF01725C   10      45           3            6               3    30
PF01726C   46    1035          28            2              13    28
PF01731B   53    1378          24            1              14    26
PF01731C   27     351           9            2               7    25
PF01731E   55    1485          24            1              14    25
PF01731F   43     903          20            2              13    30
PF01737A   35     595          14            2               9    25
PF01746C   42     861          18            2              11    26
PF01746D   49    1176          19            1              13    26
PF01766A   35     595          23            3              17    48
PF01766B   24     276          21            7              10    41
PF01766C   45     990          63            6              26    57
PF01766D   37     666          30            4              19    51
PF01766E   37     666          18            2              10    27
PF01766F   51    1275          70            5              33    64
PF01766G   39     741          27            3              19    48
PF01766H   42     861          49            5              25    59
PF01766J   50    1225          33            2              17    34
PF01766K   54    1431          46            3              29    53
PF01766L   39     741          23            3              15    38
PF01766M   37     666          34            5              17    45
PF01770B   55    1485          25            1              18    32
PF01770C   51    1275          41            3              21    41
PF01770D   36     630          17            2              10    27
PF01770E   50    1225          31            2              17    34
PF01772B   27     351           7            1               7    25
PF01775A   40     780          23            2              14    35
PF01775B   35     595          20            3              11    31
PF01775C   47    1081          38            3              22    46
PF01775D   21     210           7            3               6    28
PF01776A   45     990          24            2              15    33
PF01776B   50    1225          60            4              24    48
PF01779    45     990          46            4              21    46
PF01781A   29     406          16            3              10    34
PF01781B   35     595          30            5              16    45
PF01786B   40     780          31            3              17    42
PF01786C   28     378          11            2               7    25
PF01786D   46    1035          18            1              13    28
PF01788    39     741          34            4              14    35
PF01789B   38     703          29            4              17    44
PF01789C   29     406          16            3              12    41
PF01789D   29     406          10            2               9    31
PF01789E   31     465          18            3              11    35
PF01789F   34     561          28            4              16    47
PF01793C   39     741          16            2              12    30
PF01793E   43     903          30            3              17    39
PF01793F   34     561          14            2               9    26
PF01798B   46    1035          19            1              12    26
PF01800D   46    1035          29            2              17    36
PF01806C   52    1326          19            1              13    25
PF01806D   35     595          15            2              11    31
PF01806G   32     496          16            3              14    43
PF01806H   47    1081          43            3              19    40
PF01806I   34     561          22            3              14    41
PF01807A   49    1176          26            2              15    30
PF01807F   10      45           3            6               3    30
PF01808A   49    1176          41            3              22    44
PF01808C   32     496          15            3              10    31
PF01808D   20     190           7            3               5    25
PF01808H   37     666          24            3              14    37
PF01808I   49    1176          17            1              13    26
PF01811A   36     630          28            4              15    41
PF01811B   17     136           9            6               7    41
PF01811C   43     903          30            3              21    48
PF01811D   28     378          20            5              14    50
PF01811E   48    1128          63            5              31    64
PF01811F   25     300          14            4              12    48
PF01811G   51    1275          34            2              23    45
PF01837A   17     136          13            9               9    52
PF01837C   14      91           5            5               4    28
PF01840B   42     861          26            3              16    38
PF01840C   18     153           9            5               6    33
PF01845A   36     630          33            5              21    58
PF01845B   23     253          13            5              10    43
PF01845C   42     861          41            4              25    59
PF01846B   11      55           7           12               4    36
PF01851D   13      78           5            6               4    30
PF01853B   54    1431          23            1              16    29
PF01853D   37     666          17            2              11    29
PF01857G   44     946          24            2              15    34
PF01857I   39     741          21            2              13    33
PF01861B   11      55           4            7               3    27
PF01861D   42     861          48            5              21    50
PF01861E   45     990          27            2              18    40
PF01868A   37     666          16            2              12    32
PF01869C   12      66           4            6               4    33
PF01893B   36     630          17            2              11    30
PF01917A   52    1326          54            4              21    40
PF01920A   48    1128          26            2              13    27
PF01921E   34     561          17            3              13    38
PF01924A   45     990          31            3              17    37
PF01924D   49    1176          18            1              13    26
PF01924G   48    1128          31            2              14    29
PF01933A   31     465          15            3               8    25
PF01933B   26     325          16            4               8    30
PF01933E   32     496          29            5              14    43
PF01935A   34     561          13            2              11    32
PF01935F   35     595          20            3              13    37
PF01935G   44     946          27            2              15    34
PF01941A   30     435          19            4              11    36
PF01941C   27     351          10            2               7    25
PF01941D   42     861          18            2              13    30
PF01941E   25     300          14            4              10    40
PF01941F   40     780          27            3              19    47
PF01941G   34     561          35            6              19    55
PF01941H   21     210          11            5               8    38
PF01941I   35     595          23            3              14    40
PF01946D   35     595          30            5              14    40
PF01960B   16     120           4            3               4    25
PF01960F   20     190           7            3               6    30
PF01964B   48    1128          31            2              23    47
PF01964D   28     378          13            3               8    28
PF01964E   53    1378          30            2              19    35
PF01964F   37     666          31            4              18    48
PF01964G   35     595          27            4              15    42
PF01968A   13      78           4            5               4    30
PF01968F   52    1326          45            3              17    32
PF01979C   44     946          22            2              12    27
PF01979D   26     325           9            2               7    26
PF01981A   22     231           8            3               6    27
PF01981B   41     820          23            2              12    29
PR00001A   14      91           7            7               4    28
PR00001B   14      91          10           10               4    28
PR00019B   14      91           9            9               4    28
PR00021A   13      78          22           28               9    69
PR00021B   10      45           8           17               5    50
PR00021C    7      21           4           19               3    42
PR00021D    9      36           8           22               4    44
PR00029A   16     120          12           10               7    43
PR00029B   16     120          18           15               8    50
PR00029C   13      78           9           11               5    38
PR00029D   12      66          11           16               5    41
PR00049A   17     136           8            5               7    41
PR00049B   17     136          20           14               8    47
PR00049C   15     105           7            6               6    40
PR00049D   15     105          57           54              12    80
PR00055A   12      66           6            9               3    25
PR00055B    8      28           2            7               2    25
PR00058A   20     190          17            8               7    35
PR00058B   20     190           8            4               7    35
PR00058C   21     210          11            5               8    38
PR00058D   20     190           8            4               6    30
PR00058E   20     190           8            4               5    25
PR00104A   15     105           6            5               4    26
PR00117A   18     153           7            4               5    27
PR00117B   18     153          10            6               7    38
PR00117C   19     171          11            6               7    36
PR00117D   20     190          10            5               7    35
PR00117E   19     171          11            6               7    36
PR00152C   27     351          22            6              10    37
PR00152E   30     435          11            2               9    30
PR00152F   27     351          11            3               8    29
PR00158A   21     210          15            7              10    47
PR00158B   18     153          15            9               9    50
PR00158C   20     190          10            5               8    40
PR00158D   20     190          12            6               9    45
PR00158E   19     171          12            7               8    42
PR00158F   23     253          17            6              11    47
PR00167A   16     120           6            5               5    31
PR00167C   25     300          12            4               8    32
PR00167D   27     351           9            2               8    29
PR00168B   16     120           7            5               5    31
PR00168C   15     105          12           11               7    46
PR00168D   19     171           7            4               6    31
PR00168E   24     276          11            3               9    37
PR00168F   22     231          10            4               8    36
PR00169G   23     253           7            2               6    26
PR00180A   23     253          20            7               8    34
PR00180B   25     300          11            3               7    28
PR00180C   22     231           9            3               8    36
PR00184A   26     325          23            7              14    53
PR00184B   20     190          17            8               7    35
PR00184C   18     153          10            6               7    38
PR00184D   18     153           8            5               6    33
PR00184E   21     210           9            4               8    38
PR00184F   27     351          20            5              14    51
PR00184G   25     300          16            5              11    44
PR00193C   28     378          12            3               9    32
PR00193D   29     406          17            4              11    37
PR00204B   13      78           4            5               4    30
PR00204C   13      78          10           12               7    53
PR00207A   18     153           8            5               5    27
PR00208B   15     105          23           21               8    53
PR00210A   20     190          26           13              11    55
PR00210B   21     210           9            4               6    28
PR00210C   23     253          19            7              12    52
PR00210D   10      45           3            6               3    30
PR00210E   12      66           5            7               4    33
PR00210F   15     105          17           16               9    60
PR00210G   15     105          17           16               9    60
PR00210H   17     136           9            6               6    35
PR00210I   16     120           5            4               5    31
PR00221E   17     136           7            5               5    29
PR00221G   13      78           9           11               5    38
PR00221H   14      91           5            5               4    28
PR00222A   21     210          10            4               7    33
PR00222C   17     136          10            7               6    35
PR00222E   21     210          11            5               7    33
PR00230A   19     171          10            5               6    31
PR00230B   20     190           7            3               5    25
PR00231E   16     120           6            5               5    31
PR00234D   20     190           5            2               5    25
PR00235F   20     190           6            3               6    30
PR00236E   16     120           7            5               6    37
PR00240A   16     120           5            4               5    31
PR00240B   20     190          21           11              10    50
PR00240C   20     190          30           15              12    60
PR00240D   20     190           9            4               7    35
PR00240E   20     190          17            8              10    50
PR00240F   21     210          13            6               8    38
PR00241E   11      55           4            7               3    27
PR00241F   12      66           4            6               4    33
PR00241H   18     153           8            5               6    33
PR00243D   10      45           4            8               4    40
PR00243E   15     105           8            7               5    33
PR00243I   15     105           4            3               4    26
PR00244A   12      66           3            4               3    25
PR00244C   11      55           6           10               3    27
PR00244H   19     171          12            7               7    36
PR00246E   14      91           9            9               4    28
PR00247A   23     253          10            3               7    30
PR00247B   21     210          14            6              10    47
PR00247C   27     351          21            5              14    51
PR00247D   19     171           6            3               6    31
PR00247E   21     210          16            7               8    38
PR00247F   23     253          22            8              11    47
PR00247G   26     325          12            3               9    34
PR00250B   25     300           9            3               7    28
PR00250E   25     300          16            5              10    40
PR00250F   24     276          18            6              10    41
PR00250G   22     231          17            7              10    45
PR00284A   15     105           8            7               4    26
PR00299C   21     210          11            5               8    38
PR00299D   14      91           5            5               4    28
PR00299E   20     190          13            6               7    35
PR00299F   22     231           7            3               6    27
PR00299G   16     120           7            5               5    31
PR00308A   15     105          46           43              10    66
PR00308B   12      66          24           36               7    58
PR00308C   10      45          28           62               7    70
PR00329D   24     276          13            4              10    41
PR00334A   22     231          12            5               7    31
PR00334B   24     276          52           18              13    54
PR00334C   23     253          51           20              17    73
PR00337A   17     136          10            7               7    41
PR00337B   17     136          12            8               7    41
PR00337C   19     171          15            8               9    47
PR00337D   11      55           5            9               4    36
PR00337F   14      91           6            6               5    35
PR00343B    8      28           2            7               2    25
PR00349G   16     120           6            5               5    31
PR00352A   12      66           4            6               3    25
PR00357A   17     136           8            5               7    41
PR00357C   16     120           5            4               4    25
PR00358B   17     136           8            5               7    41
PR00358D   19     171           6            3               5    26
PR00361B   18     153           9            5               7    38
PR00361C   15     105           7            6               5    33
PR00361D   15     105          10            9               7    46
PR00361E   18     153           6            3               6    33
PR00361F   23     253          11            4               7    30
PR00362C   14      91           4            4               4    28
PR00362D   23     253          22            8              12    52
PR00362F   16     120           6            5               5    31
PR00362G   15     105           5            4               4    26
PR00366C   17     136           9            6               6    35
PR00366E   19     171          13            7               7    36
PR00367A   12      66           3            4               3    25
PR00373D   15     105           5            4               4    26
PR00373F   19     171           6            3               6    31
PR00373G   17     136          10            7               7    41
PR00373H   20     190          12            6               7    35
PR00375A   21     210          11            5               8    38
PR00375B   21     210          10            4               9    42
PR00375C   20     190          24           12              10    50
PR00375D   20     190          15            7              10    50
PR00375E   20     190          13            6               9    45
PR00375F   22     231          14            6              10    45
PR00384A   14      91           6            6               5    35
PR00384D   13      78           8           10               5    38
PR00391B   21     210           7            3               6    28
PR00393A   24     276          12            4               8    33
PR00393B   15     105           6            5               4    26
PR00393C   13      78          12           15               6    46
PR00393E   21     210          16            7              10    47
PR00393F   19     171          14            8               8    42
PR00394A   20     190          13            6               7    35
PR00394B   21     210          13            6               9    42
PR00394C   16     120          10            8               6    37
PR00394D   21     210          16            7              10    47
PR00394E   20     190          11            5               7    35
PR00409D   15     105           5            4               4    26
PR00409F   20     190           7            3               5    25
PR00414A   23     253          21            8              11    47
PR00414B   20     190           9            4               8    40
PR00414C   17     136          13            9               7    41
PR00414D   20     190           5            2               5    25
PR00414F   19     171           5            2               5    26
PR00414G   19     171           5            2               5    26
PR00424D   20     190           9            4               6    30
PR00425A   12      66           3            4               3    25
PR00426D   12      66           7           10               4    33
PR00426F   15     105          13           12               8    53
PR00426H   16     120           8            6               6    37
PR00427B   12      66           3            4               3    25
PR00427C   14      91           4            4               4    28
PR00427E   16     120           6            5               6    37
PR00427F   17     136           7            5               5    29
PR00427G   17     136           6            4               5    29
PR00429A   19     171           8            4               7    36
PR00429B   14      91          15           16               8    57
PR00429C   16     120          11            9               7    43
PR00429D   16     120           4            3               4    25
PR00429E   18     153          10            6               7    38
PR00429F   12      66           3            4               3    25
PR00429G   22     231          26           11              11    50
PR00430B   19     171           7            4               6    31
PR00432A   29     406          21            5               9    31
PR00432B   29     406          14            3              11    37
PR00432C   29     406          17            4              11    37
PR00432D   30     435          20            4              14    46
PR00440C   10      45           4            8               4    40
PR00440G   11      55           4            7               3    27
PR00441E   12      66           3            4               3    25
PR00442B   11      55           5            9               4    36
PR00443A   15     105           8            7               5    33
PR00443D   16     120           9            7               7    43
PR00443E   15     105           5            4               4    26
PR00447A   27     351          12            3               8    29
PR00447D   24     276           7            2               7    29
PR00447E   20     190           8            4               7    35
PR00448A   20     190          10            5               7    35
PR00448C   18     153          11            7               6    33
PR00448D   24     276          17            6              11    45
PR00448E   20     190           8            4               6    30
PR00460D   19     171          14            8               9    47
PR00460E   25     300          18            6              13    52
PR00460F   24     276          11            3               7    29
PR00460G   25     300          19            6              11    44
PR00460H   29     406          17            4              13    44
PR00460K   30     435          14            3               9    30
PR00460L   27     351          15            4               9    33
PR00462D   20     190          12            6               5    25
PR00462H   28     378          11            2               8    28
PR00462J   23     253          13            5               8    34
PR00462L   26     325           8            2               7    26
PR00466A   19     171          14            8               9    47
PR00466B   24     276          33           11              15    62
PR00466C   21     210          18            8              10    47
PR00466E   18     153          10            6               8    44
PR00466F   19     171           8            4               7    36
PR00470A   20     190           9            4               7    35
PR00470B   21     210           7            3               6    28
PR00470D   20     190           5            2               5    25
PR00492A   16     120           8            6               5    31
PR00492B   19     171           7            4               6    31
PR00492E   13      78           7            8               4    30
PR00493B   21     210          15            7               9    42
PR00493C   18     153           8            5               5    27
PR00493D   21     210           9            4               6    28
PR00493E   17     136           8            5               6    35
PR00493F   21     210          11            5               8    38
PR00493G   21     210          11            5               9    42
PR00493H   24     276           8            2               7    29
PR00494A   22     231          13            5               9    40
PR00494B   18     153           6            3               5    27
PR00494C   23     253          15            5               9    39
PR00494D   20     190          15            7               9    45
PR00494E   20     190          19           10               9    45
PR00494F   20     190           6            3               5    25
PR00494G   17     136           8            5               5    29
PR00494H   20     190          11            5               6    30
PR00494I   20     190          14            7               8    40
PR00495A   19     171           7            4               6    31
PR00495B   19     171          16            9               9    47
PR00495C   21     210          11            5               8    38
PR00495D   19     171          10            5               8    42
PR00495E   21     210          24           11               9    42
PR00495F   21     210          19            9              11    52
PR00495G   16     120          15           12               8    50
PR00496A   22     231          21            9              11    50
PR00496B   18     153          14            9               9    50
PR00496C   14      91           6            6               5    35
PR00497A   18     153          11            7               8    44
PR00497B   19     171          11            6               9    47
PR00497C   16     120           7            5               6    37
PR00497D   22     231           8            3               7    31
PR00497E   20     190          13            6               9    45
PR00497F   12      66           5            7               4    33
PR00498C   20     190          12            6               9    45
PR00498D   22     231          12            5               8    36
PR00498E   20     190           9            4               7    35
PR00498F   20     190          11            5               8    40
PR00500A   19     171          26           15              12    63
PR00500B   21     210           9            4               8    38
PR00500C   24     276           8            2               7    29
PR00500E   20     190          17            8              10    50
PR00500F   20     190          18            9              10    50
PR00500G   23     253          14            5              12    52
PR00500H   22     231           9            3               7    31
PR00500I   23     253          18            7              11    47
PR00510A   20     190           9            4               6    30
PR00510C   20     190           8            4               5    25
PR00512A   17     136          14           10               7    41
PR00512B   18     153           9            5               7    38
PR00512C   16     120           7            5               6    37
PR00512D   20     190          15            7               9    45
PR00512E   17     136           7            5               6    35
PR00512F   20     190          11            5               8    40
PR00512G   16     120          12           10               8    50
PR00513A   12      66           8           12               4    33
PR00513C   17     136          10            7               7    41
PR00513D   18     153          19           12               8    44
PR00513E   16     120          11            9               5    31
PR00515A   14      91           7            7               6    42
PR00515B   15     105           7            6               4    26
PR00515C   17     136           8            5               6    35
PR00515D   20     190           9            4               8    40
PR00515E   16     120          10            8               6    37
PR00515F   17     136          10            7               6    35
PR00515G   19     171          10            5               7    36
PR00516A   20     190          13            6               9    45
PR00516B   15     105           4            3               4    26
PR00516D   18     153          11            7               7    38
PR00516E   18     153           9            5               6    33
PR00516F   18     153          10            6               7    38
PR00517A   20     190          10            5               7    35
PR00517B   18     153           8            5               7    38
PR00517C   13      78           8           10               6    46
PR00517D   12      66          12           18               6    50
PR00517E   17     136          10            7               7    41
PR00517F   17     136           7            5               5    29
PR00517G   16     120           7            5               4    25
PR00517H   15     105           9            8               7    46
PR00518A   17     136          13            9               8    47
PR00518B   18     153           7            4               5    27
PR00518C    9      36           7           19               4    44
PR00518D   17     136           9            6               7    41
PR00520A   17     136           9            6               5    29
PR00520B   11      55           4            7               4    36
PR00520D   14      91           5            5               5    35
PR00521A   20     190          10            5               7    35
PR00521B   19     171           9            5               7    36
PR00521C   20     190          11            5               8    40
PR00521D   21     210          22           10               9    42
PR00521E   21     210          13            6               9    42
PR00521F   21     210          17            8              12    57
PR00521G   23     253          15            5               9    39
PR00521H   20     190           9            4               6    30
PR00521I   18     153           7            4               6    33
PR00522A   20     190           9            4               7    35
PR00522B   23     253          15            5              10    43
PR00522C   20     190          14            7               9    45
PR00522D   20     190          12            6               9    45
PR00522G   20     190          14            7               9    45
PR00524A   21     210          13            6               8    38
PR00524B   19     171          12            7               6    31
PR00524C   20     190          17            8               8    40
PR00524D   17     136          13            9               9    52
PR00524E   17     136          13            9               9    52
PR00524F   14      91          13           14               7    50
PR00524G   12      66           4            6               4    33
PR00525A   14      91           7            7               5    35
PR00525B   15     105          17           16               8    53
PR00525D   14      91           6            6               5    35
PR00525E   13      78           5            6               4    30
PR00525F   19     171          14            8               9    47
PR00526C   18     153           8            5               6    33
PR00526F   14      91           7            7               4    28
PR00526H   20     190          11            5               7    35
PR00527A   17     136          10            7               7    41
PR00527B   17     136          10            7               8    47
PR00527C   16     120          10            8               7    43
PR00527D   15     105           7            6               5    33
PR00527E   15     105          13           12               7    46
PR00527F   19     171          10            5               7    36
PR00527G   18     153          10            6               8    44
PR00527I   20     190          40           21              13    65
PR00528B   21     210          11            5               9    42
PR00528C   21     210          14            6               9    42
PR00528D   22     231          16            6              10    45
PR00528E   19     171          10            5               8    42
PR00528F   20     190          14            7              10    50
PR00531B   16     120          11            9               5    31
PR00531C   17     136           8            5               6    35
PR00531D   16     120           5            4               5    31
PR00531E   19     171           7            4               6    31
PR00531F   18     153          11            7               8    44
PR00531G   19     171           9            5               8    42
PR00532A   16     120           8            6               7    43
PR00532B   14      91           6            6               6    42
PR00532C   13      78          10           12               6    46
PR00532D   14      91           6            6               5    35
PR00532E   11      55           7           12               4    36
PR00532F   18     153          16           10               9    50
PR00532G   16     120           5            4               4    25
PR00533A   17     136           5            3               5    29
PR00533B   17     136           9            6               7    41
PR00533C   17     136           9            6               6    35
PR00533D   17     136           7            5               5    29
PR00533E   18     153          12            7               6    33
PR00533F   16     120           6            5               6    37
PR00533G   18     153           7            4               6    33
PR00534D   13      78           5            6               4    30
PR00534F   12      66           4            6               3    25
PR00537B   17     136           6            4               5    29
PR00537C   15     105           5            4               4    26
PR00537E   18     153           8            5               5    27
PR00537F   13      78           7            8               5    38
PR00537G   15     105           5            4               4    26
PR00538A   17     136          13            9               7    41
PR00538B   20     190          15            7               9    45
PR00538C   19     171          28           16              11    57
PR00538D   18     153          14            9               8    44
PR00538E   17     136          13            9               8    47
PR00538F   18     153          15            9               8    44
PR00539A   17     136           6            4               5    29
PR00539B   19     171          11            6               8    42
PR00539C   17     136          13            9               7    41
PR00539D   19     171           7            4               6    31
PR00539E   20     190          12            6               8    40
PR00539F   15     105           8            7               5    33
PR00539G   19     171           9            5               6    31
PR00540A   20     190          11            5               7    35
PR00540B   22     231          18            7               9    40
PR00540C   20     190          13            6               9    45
PR00540D   20     190           8            4               6    30
PR00540F   20     190          19           10              11    55
PR00540G   19     171          15            8               8    42
PR00541A   11      55           3            5               3    27
PR00541B   16     120           7            5               4    25
PR00541C   21     210          16            7               9    42
PR00541D   19     171           8            4               7    36
PR00541E   11      55           6           10               3    27
PR00542A   17     136           7            5               7    41
PR00542B   19     171          12            7               8    42
PR00542C   19     171          11            6               7    36
PR00542D   21     210           9            4               7    33
PR00542E   19     171           9            5               7    36
PR00542F   19     171           8            4               6    31
PR00542G   18     153           8            5               6    33
PR00542H   15     105           8            7               5    33
PR00543A   19     171           8            4               7    36
PR00543B   18     153           8            5               6    33
PR00543C   18     153           6            3               6    33
PR00543E   15     105           7            6               6    40
PR00543F   17     136           9            6               7    41
PR00543G   20     190           9            4               7    35
PR00543H   20     190          14            7               9    45
PR00544B   18     153           8            5               6    33
PR00544C   15     105           8            7               5    33
PR00544D   23     253          17            6              10    43
PR00544E   17     136          13            9               7    41
PR00544F   17     136           9            6               5    29
PR00544G   20     190          15            7              11    55
PR00544H   20     190          16            8              10    50
PR00545A   15     105          11           10               7    46
PR00545B   20     190          26           13              11    55
PR00545C   21     210           7            3               7    33
PR00545E   21     210          12            5              10    47
PR00545F   18     153          10            6               7    38
PR00545G   20     190          18            9              10    50
PR00545H   20     190          13            6               9    45
PR00546C   17     136          10            7               8    47
PR00546D   19     171          23           13              10    52
PR00546E   18     153          12            7               6    33
PR00546F   20     190           8            4               6    30
PR00546G   22     231          15            6              11    50
PR00546H   20     190          11            5               8    40
PR00546I   23     253          16            6               9    39
PR00551B   20     190          11            5               8    40
PR00551C   16     120           7            5               5    31
PR00551D   19     171          14            8               8    42
PR00551E   15     105           4            3               4    26
PR00551F   23     253          19            7              11    47
PR00551G   24     276          10            3               8    33
PR00551H   18     153           8            5               6    33
PR00551I   20     190           7            3               6    30
PR00552A   11      55           6           10               4    36
PR00552D   16     120           7            5               5    31
PR00554A   14      91           7            7               4    28
PR00554C   15     105           5            4               4    26
PR00554E   12      66           3            4               3    25
PR00554F   13      78           5            6               4    30
PR00554G   20     190          11            5               7    35
PR00556A   19     171           8            4               7    36
PR00556B   21     210          15            7              10    47
PR00556C   18     153           5            3               5    27
PR00556D   20     190          11            5               9    45
PR00556E   18     153          15            9               8    44
PR00556F   20     190           8            4               6    30
PR00556G   19     171           7            4               6    31
PR00557A   23     253          17            6               9    39
PR00557B   16     120           9            7               7    43
PR00557C   18     153          12            7               9    50
PR00557D   18     153           5            3               5    27
PR00557E   20     190           7            3               6    30
PR00557F   20     190           8            4               5    25
PR00559A   20     190          20           10               9    45
PR00559B   19     171           8            4               7    36
PR00559C   18     153          13            8               7    38
PR00559D   20     190          18            9              11    55
PR00559E   21     210           8            3               8    38
PR00559F   12      66           5            7               4    33
PR00560A   18     153          19           12               9    50
PR00560B   16     120          17           14               9    56
PR00560C   20     190          19           10              11    55
PR00560D   20     190          35           18              12    60
PR00560F   16     120          24           20               8    50
PR00562A   21     210           8            3               7    33
PR00562B   18     153           6            3               5    27
PR00562C   17     136          10            7               7    41
PR00562D   17     136          10            7               6    35
PR00562E   19     171          19           11              11    57
PR00562F   20     190          17            8              10    50
PR00562G   20     190           7            3               6    30
PR00564A   17     136           8            5               7    41
PR00564C   16     120          12           10               9    56
PR00564D   15     105           8            7               6    40
PR00564E   18     153           7            4               6    33
PR00564F   17     136          18           13               9    52
PR00564G   18     153          13            8               7    38
PR00564H   19     171          13            7               7    36
PR00565C   17     136           5            3               5    29
PR00565D   19     171          15            8               9    47
PR00565E   22     231           9            3               8    36
PR00565F   17     136           7            5               6    35
PR00565G   18     153           5            3               5    27
PR00566A   14      91           7            7               4    28
PR00566E   17     136           6            4               5    29
PR00567A   12      66           5            7               3    25
PR00567B   21     210           6            2               6    28
PR00567C   15     105          12           11               9    60
PR00567D   18     153           7            4               6    33
PR00569A   18     153          34           22              13    72
PR00569B   15     105          10            9               6    40
PR00569C   15     105           8            7               6    40
PR00569D   15     105          16           15               6    40
PR00569E   22     231          18            7              10    45
PR00571A   19     171          10            5               7    36
PR00571B   18     153           9            5               6    33
PR00571C   17     136           8            5               5    29
PR00571D   21     210          15            7               9    42
PR00571F   15     105           5            4               5    33
PR00571G   19     171          16            9              10    52
PR00571H   15     105           9            8               6    40
PR00574C   11      55           3            5               3    27
PR00574D   12      66           7           10               4    33
PR00575A   18     153          14            9               7    38
PR00575B   16     120           4            3               4    25
PR00575D   15     105           5            4               4    26
PR00575E   16     120          10            8               6    37
PR00576A   16     120           5            4               4    25
PR00576C   16     120           9            7               7    43
PR00576D   12      66           6            9               5    41
PR00576F   17     136          12            8               8    47
PR00577B   17     136           9            6               7    41
PR00577E   18     153           9            5               7    38
PR00577G   19     171           6            3               5    26
PR00579A   19     171           9            5               7    36
PR00579B   17     136           7            5               5    29
PR00579C   17     136           6            4               5    29
PR00579F   14      91           4            4               4    28
PR00580A   25     300          23            7              14    56
PR00580B   16     120          13           10               6    37
PR00580C   17     136          17           12               8    47
PR00580D   17     136          14           10               8    47
PR00580E   22     231          27           11              11    50
PR00580F   21     210          19            9              11    52
PR00580G   20     190          21           11              10    50
PR00581B   13      78           7            8               4    30
PR00581C   21     210          15            7               8    38
PR00581E   16     120          23           19              10    62
PR00581F   18     153          12            7               8    44
PR00581G   19     171           6            3               6    31
PR00581H   18     153          11            7               7    38
PR00582A   12      66           5            7               4    33
PR00582B   19     171          20           11              10    52
PR00582D   14      91           9            9               7    50
PR00582E   22     231          19            8              11    50
PR00584C   13      78           5            6               4    30
PR00584D   12      66          10           15               6    50
PR00584E    8      28           3           10               3    37
PR00586A   21     210          15            7               8    38
PR00586B   18     153           8            5               6    33
PR00586C   22     231           8            3               6    27
PR00586D   18     153           6            3               5    27
PR00586E   21     210          13            6               8    38
PR00586F   23     253          16            6              11    47
PR00586G   24     276          35           12              13    54
PR00586H   24     276          17            6              12    50
PR00587A   20     190          23           12              11    55
PR00587B   20     190          16            8               9    45
PR00587C   19     171           7            4               6    31
PR00587D   18     153           8            5               7    38
PR00587E   21     210          11            5               8    38
PR00587F   20     190           8            4               7    35
PR00588A   18     153           5            3               5    27
PR00588B   20     190           6            3               5    25
PR00588C   16     120           5            4               4    25
PR00588D   20     190          12            6               8    40
PR00588E   18     153          15            9               9    50
PR00588F   19     171          19           11              10    52
PR00591A   14      91           9            9               6    42
PR00591B   15     105          13           12               7    46
PR00591C   15     105          10            9               7    46
PR00591D   17     136          10            7               8    47
PR00591E   15     105           6            5               5    33
PR00592C   16     120           5            4               4    25
PR00592E   22     231          21            9              11    50
PR00592F   24     276          15            5              10    41
PR00592G   16     120          10            8               6    37
PR00592H   19     171          13            7               7    36
PR00592J   21     210           9            4               6    28
PR00592K   15     105           5            4               4    26
PR00592M   23     253          17            6              10    43
PR00594A   17     136           7            5               6    35
PR00594C   18     153           8            5               7    38
PR00594D   16     120          11            9               7    43
PR00594E   17     136           7            5               5    29
PR00594F   17     136           9            6               5    29
PR00594G   20     190          16            8               9    45
PR00597G   23     253           9            3               6    26
PR00606B   14      91           5            5               5    35
PR00609B    8      28           2            7               2    25
PR00609D    8      28           3           10               2    25
PR00628A   20     190           6            3               5    25
PR00629A   16     120          10            8               6    37
PR00629B   23     253          14            5               9    39
PR00629C   12      66           6            9               5    41
PR00629E   29     406          19            4              13    44
PR00629F   27     351          16            4              12    44
PR00632A   19     171           5            2               5    26
PR00632B   18     153           7            4               6    33
PR00632C   23     253          11            4               9    39
PR00632D   22     231          11            4               8    36
PR00636A   20     190          11            5               7    35
PR00636B   19     171           7            4               6    31
PR00636C   15     105           8            7               6    40
PR00636D   19     171           9            5               7    36
PR00636E   17     136           5            3               5    29
PR00636G   20     190          11            5               9    45
PR00636H   19     171           8            4               7    36
PR00636I   19     171          13            7               9    47
PR00637A   14      91          10           10               6    42
PR00637B   15     105           7            6               6    40
PR00637D   18     153          11            7               7    38
PR00637E   16     120           5            4               4    25
PR00639A   20     190          17            8              10    50
PR00639B   17     136           7            5               5    29
PR00639C   16     120           7            5               4    25
PR00639D   16     120           7            5               6    37
PR00639E   19     171          16            9              10    52
PR00640A   16     120           8            6               6    37
PR00640D   17     136           7            5               6    35
PR00640E   15     105          12           11               6    40
PR00642A   20     190           9            4               6    30
PR00642B   17     136           6            4               5    29
PR00642C   17     136           7            5               6    35
PR00642D   15     105           6            5               5    33
PR00642E   20     190           7            3               6    30
PR00642F   21     210          27           12              11    52
PR00642G   18     153           7            4               6    33
PR00642H   23     253          14            5              10    43
PR00642I   21     210          15            7               9    42
PR00643A   20     190           7            3               5    25
PR00643B   17     136           7            5               6    35
PR00643C   16     120           4            3               4    25
PR00643D   12      66           6            9               5    41
PR00643E   18     153          12            7               8    44
PR00643F   19     171           6            3               6    31
PR00643G   15     105          12           11               6    40
PR00643H   18     153          11            7               8    44
PR00643I   20     190           9            4               6    30
PR00644D   12      66          10           15               6    50
PR00644E   16     120           9            7               6    37
PR00644G   15     105           9            8               7    46
PR00645A   17     136           6            4               5    29
PR00645B   16     120           8            6               5    31
PR00645C   17     136           7            5               6    35
PR00645F   21     210          12            5               8    38
PR00645G   18     153          16           10               9    50
PR00645I   19     171          21           12              11    57
PR00646B   20     190          12            6               9    45
PR00646E   18     153          10            6               8    44
PR00646F   18     153           9            5               7    38
PR00646G   18     153           6            3               5    27
PR00646H   16     120          13           10               7    43
PR00646I   20     190          10            5               8    40
PR00651A   21     210           7            3               6    28
PR00651B   15     105           6            5               5    33
PR00651C   19     171          12            7               8    42
PR00651D   21     210          15            7               9    42
PR00651E   20     190           7            3               6    30
PR00651F   17     136           8            5               6    35
PR00651G   22     231           8            3               7    31
PR00651H   23     253          22            8              12    52
PR00652A   21     210          10            4               8    38
PR00652B   21     210          14            6              11    52
PR00652C   20     190          11            5               9    45
PR00652E   19     171          15            8               9    47
PR00652F   22     231          18            7              10    45
PR00652G   18     153           9            5               7    38
PR00653A   20     190           6            3               5    25
PR00653C   24     276          16            5               9    37
PR00653D   22     231           8            3               7    31
PR00653E   20     190          12            6               8    40
PR00653F   23     253          18            7               9    39
PR00655B   21     210           7            3               6    28
PR00655C   25     300          12            4              10    40
PR00655E   16     120           4            3               4    25
PR00655F   23     253           8            3               6    26
PR00655G   20     190           5            2               5    25
PR00656C   19     171           5            2               5    26
PR00663A   19     171          11            6               9    47
PR00663B   16     120           6            5               6    37
PR00663C   15     105           6            5               6    40
PR00663D   14      91           4            4               4    28
PR00663E   19     171          21           12              11    57
PR00663G   18     153          31           20               9    50
PR00663H   19     171          15            8               8    42
PR00663I   14      91           5            5               4    28
PR00664B   18     153           8            5               6    33
PR00664F   14      91           4            4               4    28
PR00670A   18     153          13            8               7    38
PR00670B   22     231          19            8              11    50
PR00670D   17     136           9            6               6    35
PR00670E   22     231          31           13              12    54
PR00675A   22     231           7            3               6    27
PR00675B   22     231          12            5               8    36
PR00675C   21     210          15            7              10    47
PR00675D   18     153           7            4               7    38
PR00675E   22     231          10            4               8    36
PR00675F   20     190          11            5               9    45
PR00675G   21     210           6            2               6    28
PR00675H   20     190          11            5               7    35
PR00676B   12      66           6            9               4    33
PR00676D   16     120           9            7               6    37
PR00676E   15     105           4            3               4    26
PR00676G   13      78           4            5               4    30
PR00676H   19     171           7            4               6    31
PR00676I   19     171           9            5               7    36
PR00677A   20     190           8            4               6    30
PR00677B   20     190          17            8              10    50
PR00677C   19     171          10            5               7    36
PR00677D   19     171          10            5               8    42
PR00677E   23     253          22            8              11    47
PR00677F   22     231          10            4               9    40
PR00677G   23     253          13            5               9    39
PR00677H   20     190          18            9               9    45
PR00681A   19     171           6            3               5    26
PR00681D   17     136           7            5               5    29
PR00681E   18     153           6            3               5    27
PR00681F   21     210           8            3               6    28
PR00681G   22     231           9            3               7    31
PR00681H   20     190          15            7               8    40
PR00681I   19     171           8            4               6    31
PR00692A   21     210          11            5               7    33
PR00692B   18     153           7            4               5    27
PR00692C   16     120          11            9               6    37
PR00692D   17     136           9            6               6    35
PR00692E   16     120           9            7               5    31
PR00695A   19     171           5            2               5    26
PR00695D   20     190          15            7               8    40
PR00695F   17     136           7            5               5    29
PR00699A   26     325          12            3               8    30
PR00699C   28     378           9            2               7    25
PR00699E   21     210           9            4               7    33
PR00701B   22     231           7            3               6    27
PR00701F   21     210          16            7               9    42
PR00701G   24     276          12            4               7    29
PR00701H   23     253           9            3               7    30
PR00701I   24     276          18            6              11    45
PR00702E   25     300          13            4              10    40
PR00703A   13      78           7            8               4    30
PR00703B   20     190           9            4               6    30
PR00703D   20     190          14            7               8    40
PR00704C   17     136           6            4               5    29
PR00704D   26     325          10            3               9    34
PR00704E   24     276          13            4               9    37
PR00704F   28     378          14            3               7    25
PR00704I   29     406          14            3              10    34
PR00708B   22     231           7            3               6    27
PR00708E   18     153           7            4               5    27
PR00717C   18     153           9            5               5    27
PR00729A   29     406          23            5              14    48
PR00729B   29     406          18            4              14    48
PR00729C   29     406          23            5              14    48
PR00731D   15     105           4            3               4    26
PR00739A   15     105           6            5               4    26
PR00739B   18     153           8            5               5    27
PR00746A   23     253          12            4               8    34
PR00746C   18     153           7            4               6    33
PR00746D   19     171           8            4               6    31
PR00746E   17     136           7            5               5    29
PR00746G   19     171           7            4               5    26
PR00748B   20     190          13            6               9    45
PR00748C   17     136           6            4               6    35
PR00748D   17     136           7            5               6    35
PR00748E   24     276          12            4               9    37
PR00748H   21     210           7            3               6    28
PR00749A   21     210           7            3               6    28
PR00749B   22     231           7            3               6    27
PR00749C   19     171          14            8               9    47
PR00749D   21     210          14            6               8    38
PR00749F   17     136          13            9               6    35
PR00749G   22     231          16            6              10    45
PR00749H   21     210          13            6              10    47
PR00751A   20     190          11            5               9    45
PR00751B   17     136          13            9               8    47
PR00751C   22     231          14            6              10    45
PR00751D   17     136           6            4               5    29
PR00751E   17     136           7            5               6    35
PR00751G   20     190          12            6               9    45
PR00751H   18     153           8            5               7    38
PR00751I   18     153           7            4               6    33
PR00751J   26     325          16            4              12    46
PR00751K   19     171          14            8               8    42
PR00752A   16     120           7            5               6    37
PR00752C   16     120           9            7               6    37
PR00752D   18     153           9            5               7    38
PR00752F   11      55           3            5               3    27
PR00755A   20     190          17            8              10    50
PR00755B   23     253          10            3               7    30
PR00755C   20     190           8            4               6    30
PR00755D   22     231          19            8              10    45
PR00755E   23     253          12            4               7    30
PR00755F   22     231          12            5               8    36
PR00758A   25     300          37           12              13    52
PR00758B   25     300          18            6              13    52
PR00758E   25     300          12            4               9    36
PR00758F   23     253          12            4              10    43
PR00758G   26     325          20            6              12    46
PR00758H   25     300          18            6              12    48
PR00761A   17     136          11            8               6    35
PR00761B   19     171           9            5               7    36
PR00761C   19     171          22           12               9    47
PR00761E   19     171          24           14               8    42
PR00761F   14      91           4            4               4    28
PR00762B   20     190           9            4               5    25
PR00762C   20     190           6            3               5    25
PR00762E   17     136          12            8               6    35
PR00763A   17     136           5            3               5    29
PR00763B   20     190          11            5               7    35
PR00763C   18     153           6            3               6    33
PR00763D   21     210          12            5               9    42
PR00763F   21     210          14            6               9    42
PR00763G   21     210          11            5               9    42
PR00763H   19     171          14            8               8    42
PR00768A   30     435          19            4              11    36
PR00768B   26     325          19            5              11    42
PR00768C   30     435          27            6              16    53
PR00768D   29     406          30            7              14    48
PR00768E   30     435          43            9              20    66
PR00769A   19     171           7            4               6    31
PR00769B   23     253          19            7              12    52
PR00769C   23     253          27           10              14    60
PR00769D   21     210           8            3               6    28
PR00769E   23     253          15            5              10    43
PR00769F   23     253          14            5              10    43
PR00769G   20     190          22           11               9    45
PR00769H   23     253          19            7              12    52
PR00769I   24     276          25            9              14    58
PR00769J   21     210           8            3               7    33
PR00770D   17     136           5            3               5    29
PR00770E   19     171          14            8               8    42
PR00770F   20     190          11            5               6    30
PR00770G   18     153          12            7               9    50
PR00771A   21     210          14            6               9    42
PR00771B   27     351          15            4              11    40
PR00771D   19     171           6            3               5    26
PR00771E   21     210          13            6               8    38
PR00771F   23     253          11            4               7    30
PR00772A   22     231          11            4               8    36
PR00772B   17     136           6            4               6    35
PR00772C   20     190           8            4               7    35
PR00772D   20     190          10            5               8    40
PR00772E   14      91           5            5               4    28
PR00776B   30     435           9            2               8    26
PR00777B   13      78           7            8               5    38
PR00777C   16     120           6            5               5    31
PR00777D   16     120           5            4               4    25
PR00779A   24     276          14            5               8    33
PR00779B   20     190           6            3               5    25
PR00779C   21     210           6            2               6    28
PR00779D   25     300          10            3               7    28
PR00779E   26     325          16            4              12    46
PR00779F   23     253          10            3               8    34
PR00779G   25     300          13            4              10    40
PR00779H   22     231          14            6               9    40
PR00779I   26     325          19            5              10    38
PR00780A   26     325          42           12              15    57
PR00780B   23     253          15            5              11    47
PR00780C   26     325          23            7              15    57
PR00780D   21     210           8            3               7    33
PR00780E   26     325          18            5              12    46
PR00786C   17     136          10            7               5    29
PR00786D   12      66           3            4               3    25
PR00787A   27     351          13            3              10    37
PR00787B   25     300          23            7              13    52
PR00787C   25     300          11            3               9    36
PR00787D   25     300          29            9              13    52
PR00787E   15     105           5            4               4    26
PR00788D   20     190           8            4               8    40
PR00788E   14      91           5            5               4    28
PR00788F   16     120           6            5               5    31
PR00795A   22     231           8            3               7    31
PR00795B   19     171          13            7               8    42
PR00795C   25     300          21            7              13    52
PR00795D   24     276          12            4               7    29
PR00795E   20     190          11            5               7    35
PR00795F   23     253          20            7               9    39
PR00795G   21     210          11            5               7    33
PR00795H   24     276          12            4               9    37
PR00796B   22     231           6            2               6    27
PR00796C   21     210           9            4               7    33
PR00796F   19     171           6            3               5    26
PR00796G   12      66           3            4               3    25
PR00796I   26     325          12            3               9    34
PR00798B   25     300          10            3               7    28
PR00798C   25     300           9            3               7    28
PR00798D   25     300          11            3               8    32
PR00798E   25     300          17            5              10    40
PR00798F   27     351          27            7              14    51
PR00801A   21     210          18            8               9    42
PR00801B   17     136          11            8               7    41
PR00801C   19     171          10            5               6    31
PR00801D   18     153           7            4               5    27
PR00801E   20     190           8            4               7    35
PR00801F   20     190           8            4               6    30
PR00801G   17     136          13            9               7    41
PR00801H   18     153           8            5               7    38
PR00803B   16     120          10            8               5    31
PR00803C   17     136           8            5               5    29
PR00803D   22     231          13            5               8    36
PR00803G   17     136           8            5               5    29
PR00804A   18     153           9            5               7    38
PR00804B   18     153          13            8               9    50
PR00804C   21     210          13            6               7    33
PR00804D   15     105           7            6               5    33
PR00804E   20     190          12            6               8    40
PR00804F   18     153          10            6               7    38
PR00804G   18     153           9            5               6    33
PR00804H   23     253          13            5               9    39
PR00804I   16     120           9            7               6    37
PR00807B   26     325          10            3               9    34
PR00807D   22     231           9            3               6    27
PR00807E   20     190           6            3               5    25
PR00807F   20     190           6            3               5    25
PR00813A   26     325          16            4               9    34
PR00816D    9      36           3            8               3    33
PR00820B   15     105          11           10               7    46
PR00820C   16     120           4            3               4    25
PR00820D   14      91           8            8               5    35
PR00820F   12      66           8           12               4    33
PR00822A   18     153           6            3               5    27
PR00822B   25     300          11            3              10    40
PR00822E   17     136          11            8               8    47
PR00822G   18     153          12            7               6    33
PR00822H   24     276          12            4               8    33
PR00823C   13      78           8           10               5    38
PR00823E   20     190           6            3               5    25
PR00824A   19     171          10            5               8    42
PR00824D   13      78           4            5               4    30
PR00824E   15     105           9            8               6    40
PR00824F   19     171           9            5               6    31
PR00824G   19     171          11            6               8    42
PR00824H   20     190          14            7               9    45
PR00824I   16     120           5            4               5    31
PR00825A   18     153           6            3               5    27
PR00825B   21     210          10            4               7    33
PR00825C   18     153           6            3               6    33
PR00825D   18     153          10            6               7    38
PR00825E   18     153           6            3               5    27
PR00825F   21     210           8            3               8    38
PR00827A   16     120           4            3               4    25
PR00827B   16     120           4            3               4    25
PR00827D   13      78           5            6               4    30
PR00828A   20     190          14            7               8    40
PR00828B   23     253          25            9              13    56
PR00828C   22     231          12            5               8    36
PR00828D   24     276          15            5              11    45
PR00828E   23     253          13            5               9    39
PR00828F   20     190          17            8              10    50
PR00828G   20     190          13            6               7    35
PR00828H   22     231          20            8              12    54
PR00828I   20     190          10            5               7    35
PR00828J   23     253          24            9              11    47
PR00829B   11      55           3            5               3    27
PR00832A   23     253          13            5               9    39
PR00832B   24     276          35           12              13    54
PR00832C   23     253          23            9              10    43
PR00832D   20     190          13            6               8    40
PR00832E   23     253          28           11              11    47
PR00832F   24     276          22            7              11    45
PR00832G   22     231          15            6              11    50
PR00832H   20     190          13            6               9    45
PR00832I   20     190          16            8               9    45
PR00835B   16     120           8            6               5    31
PR00840D   21     210          10            4               6    28
PR00841C   18     153           7            4               6    33
PR00843B   21     210           8            3               6    28
PR00843E   18     153           6            3               5    27
PR00843F   23     253          20            7               9    39
PR00844A   26     325          12            3              10    38
PR00844B   18     153           6            3               5    27
PR00844C   25     300          11            3               9    36
PR00844D   28     378          32            8              14    50
PR00844E   20     190          15            7              10    50
PR00844F   24     276          13            4              10    41
PR00844G   27     351          13            3              10    37
PR00844I   29     406          14            3               9    31
PR00845A   28     378          18            4               9    32
PR00845B   28     378          15            3              11    39
PR00845C   21     210           8            3               7    33
PR00845D   21     210          11            5               8    38
PR00845E   27     351           9            2               9    33
PR00845F   30     435          21            4              15    50
PR00845G   21     210           7            3               6    28
PR00847B   14      91           5            5               5    35
PR00847E   16     120           6            5               4    25
PR00847F   17     136           9            6               7    41
PR00847G   17     136           8            5               5    29
PR00847H   11      55           8           14               3    27
PR00848B   16     120           7            5               6    37
PR00849A   25     300           8            2               7    28
PR00849B   29     406          13            3              11    37
PR00849D   27     351          14            3              10    37
PR00849E   27     351          23            6              13    48
PR00849F   25     300          15            5               9    36
PR00849H   28     378          23            6              10    35
PR00850A   29     406          54           13              19    65
PR00850B   25     300          15            5              12    48
PR00850C   27     351          19            5              12    44
PR00850D   25     300          14            4              10    40
PR00850E   25     300          19            6              12    48
PR00850F   27     351          13            3              10    37
PR00850G   24     276          21            7              12    50
PR00850H   17     136           8            5               5    29
PR00850I   30     435          21            4              11    36
PR00851B   20     190           9            4               7    35
PR00851C   27     351          12            3               9    33
PR00851D   23     253          21            8              11    47
PR00851F   23     253           7            2               6    26
PR00851H   23     253           6            2               6    26
PR00851I   19     171           5            2               5    26
PR00851J   26     325          24            7              14    53
PR00851K   24     276          14            5               9    37
PR00851L   20     190           9            4               6    30
PR00852A   18     153          18           11               7    38
PR00852B   20     190           6            3               5    25
PR00852C   19     171           8            4               6    31
PR00852D   22     231           8            3               7    31
PR00852E   23     253          13            5               7    30
PR00852F   19     171           9            5               6    31
PR00852H   23     253          14            5              10    43
PR00854B   18     153          16           10               9    50
PR00854C   12      66           6            9               3    25
PR00854E   24     276          11            3               9    37
PR00854F   12      66           4            6               3    25
PR00854G   17     136           7            5               5    29
PR00856B   16     120           6            5               5    31
PR00856C   16     120          11            9               7    43
PR00856D   17     136           7            5               6    35
PR00856E   17     136           7            5               6    35
PR00856F   16     120           7            5               6    37
PR00856H   19     171           7            4               6    31
PR00857C   19     171          11            6               7    36
PR00857D   15     105           5            4               4    26
PR00857E   15     105           9            8               5    33
PR00859A   17     136           9            6               5    29
PR00859C   17     136          18           13               8    47
PR00863A   29     406          28            6              15    51
PR00863B   12      66           3            4               3    25
PR00863C   10      45           4            8               3    30
PR00863D   27     351           8            2               8    29
PR00863E   17     136           8            5               5    29
PR00863G   15     105           7            6               5    33
PR00865B   23     253           7            2               6    26
PR00865C   26     325          20            6               9    34
PR00865E   24     276          13            4               7    29
PR00865F   21     210           9            4               8    38
PR00865G   24     276           9            3               6    25
PR00865H   23     253           9            3               6    26
PR00865I   22     231          12            5               8    36
PR00865J   18     153           5            3               5    27
PR00865K   24     276          12            4               7    29
PR00866H   12      66           5            7               4    33
PR00872A   13      78           7            8               4    30
PR00872B   13      78           7            8               4    30
PR00872C   14      91          10           10               4    28
PR00873A   16     120          12           10               6    37
PR00873B   14      91          10           10               6    42
PR00873C   11      55           8           14               5    45
PR00873D   19     171          20           11               8    42
PR00877A    9      36           4           11               3    33
PR00877B    7      21           2            9               2    28
PR00877D    8      28           3           10               2    25
PR00878B   30     435          21            4              12    40
PR00878E    8      28           2            7               2    25
PR00879A    6      15           2           13               2    33
PR00879B    9      36           3            8               3    33
PR00879C    9      36           4           11               3    33
PR00880D    6      15           2           13               2    33
PR00880F   10      45           4            8               3    30
PR00882A   18     153           5            3               5    27
PR00882B   18     153           8            5               5    27
PR00882C   20     190           6            3               6    30
PR00882G   21     210          11            5               7    33
PR00892I   21     210           9            4               6    28
PR00893A   19     171          12            7               8    42
PR00893B   18     153           6            3               5    27
PR00893C   21     210           8            3               7    33
PR00893D   24     276          13            4               9    37
PR00893E   17     136          10            7               6    35
PR00893F   19     171           9            5               7    36
PR00893G   17     136           6            4               5    29
PR00893H   28     378          21            5              13    46
PR00893I   20     190          10            5               7    35
PR00893J   21     210          14            6              12    57
PR00893K   20     190          25           13              12    60
PR00896G    8      28           3           10               2    25
PR00896H    9      36           5           13               4    44
PR00902A   22     231          29           12              11    50
PR00902B   20     190          14            7              10    50
PR00902C   25     300          50           16              17    68
PR00902D   26     325          17            5              13    50
PR00902E   21     210          14            6              10    47
PR00902F   20     190          14            7               9    45
PR00902G   23     253          20            7               9    39
PR00902H   20     190          12            6              10    50
PR00902I   23     253          15            5              10    43
PR00902J   22     231          12            5               8    36
PR00902K   24     276          13            4              10    41
PR00903A   20     190          12            6               9    45
PR00903B   21     210          10            4               7    33
PR00903C   20     190           6            3               5    25
PR00903E   20     190           6            3               6    30
PR00903F   19     171          13            7               7    36
PR00903I   18     153          11            7               6    33
PR00904A   12      66           4            6               4    33
PR00904B   16     120           9            7               5    31
PR00904C   16     120           4            3               4    25
PR00904D   19     171          21           12              11    57
PR00904E   20     190          16            8               9    45
PR00904F   16     120          13           10               8    50
PR00904G   16     120           8            6               7    43
PR00909B   22     231          11            4               8    36
PR00910A   13      78          22           28               7    53
PR00910C   16     120           6            5               6    37
PR00910D   21     210          22           10              12    57
PR00910F   18     153          10            6               7    38
PR00910G   16     120           6            5               6    37
PR00910J   20     190           7            3               6    30
PR00910K   20     190          11            5               9    45
PR00910M   18     153           9            5               6    33
PR00910N   24     276          12            4               8    33
PR00912C   16     120           5            4               4    25
PR00912D   17     136           8            5               6    35
PR00912E   16     120          11            9               5    31
PR00912F   17     136          11            8               6    35
PR00913B   22     231           8            3               7    31
PR00913E   23     253           9            3               6    26
PR00913F   17     136           9            6               6    35
PR00914A   20     190           8            4               6    30
PR00914B   20     190           8            4               6    30
PR00914D   21     210          13            6               7    33
PR00914G   13      78           4            5               4    30
PR00915B   19     171           6            3               5    26
PR00915C   18     153           8            5               6    33
PR00917A   20     190          11            5               7    35
PR00917B   20     190          14            7              10    50
PR00917C   22     231          12            5               9    40
PR00917D   23     253           7            2               6    26
PR00917E   22     231          15            6              10    45
PR00917F   19     171           9            5               7    36
PR00917G   18     153          17           11               9    50
PR00917H   20     190           8            4               6    30
PR00917I   20     190          12            6               8    40
PR00919A   18     153           7            4               5    27
PR00919C   23     253          11            4               8    34
PR00919D   20     190           9            4               6    30
PR00919E   21     210          15            7               9    42
PR00919F   22     231           7            3               7    31
PR00919G   23     253           8            3               6    26
PR00919H   20     190           7            3               5    25
PR00920C   22     231          10            4               7    31
PR00920G   22     231          13            5               9    40
PR00921A   21     210           8            3               7    33
PR00921D   18     153           7            4               5    27
PR00921E   23     253          14            5               9    39
PR00921F   23     253           8            3               6    26
PR00921G   15     105           5            4               5    33
PR00921H   20     190           7            3               6    30
PR00922C   15     105           4            3               4    26
PR00923B   11      55           8           14               5    45
PR00923E   17     136           6            4               5    29
PR00923G   16     120           4            3               4    25
PR00933A   22     231          14            6              10    45
PR00933B   19     171           8            4               6    31
PR00933D   21     210          10            4               7    33
PR00933E   24     276          15            5               9    37
PR00934B   19     171          13            7               7    36
PR00934C   18     153           7            4               6    33
PR00934E   18     153          17           11               7    38
PR00934G   19     171           7            4               5    26
PR00934I   23     253          10            3               8    34
PR00940B   19     171          16            9               9    47
PR00940C   18     153           5            3               5    27
PR00940D   23     253          22            8              11    47
PR00940E   19     171           9            5               8    42
PR00940G   20     190           9            4               7    35
PR00940H   21     210          10            4               8    38
PR00943A   15     105           6            5               4    26
PR00943B   21     210           8            3               7    33
PR00943C   19     171           7            4               5    26
PR00943D   20     190           5            2               5    25
PR00943E   20     190          12            6               6    30
PR00943F   19     171          18           10              10    52
PR00943G   15     105          10            9               7    46
PR00943H   16     120           6            5               5    31
PR00943I   18     153          12            7               7    38
PR00943J   15     105           6            5               5    33
PR00948A   16     120          12           10               6    37
PR00948B   25     300          18            6              10    40
PR00948C   23     253           6            2               6    26
PR00948D   18     153          12            7               8    44
PR00955A   14      91           5            5               4    28
PR00957A   18     153          11            7               8    44
PR00957B   27     351          39           11              15    55
PR00957C   21     210          15            7              10    47
PR00957D   22     231          12            5               9    40
PR00957E   16     120           7            5               6    37
PR00957F   17     136           8            5               6    35
PR00957G   19     171          24           14               9    47
PR00957H   11      55           6           10               4    36
PR00962B   23     253           8            3               7    30
PR00962C   21     210          17            8               9    42
PR00962D   24     276          12            4               9    37
PR00962E   19     171          11            6               8    42
PR00962F   20     190           7            3               5    25
PR00962G   25     300          10            3               7    28
PR00962H   20     190           5            2               5    25
PR00964B   19     171          14            8               7    36
PR00964C   21     210          10            4               8    38
PR00967A   20     190           8            4               7    35
PR00967B   22     231          10            4               8    36
PR00967C   20     190          21           11              10    50
PR00967D   22     231          12            5               8    36
PR00967E   22     231          15            6              11    50
PR00967F   23     253          14            5               9    39
PR00967G   20     190          17            8               9    45
PR00967H   15     105           5            4               4    26
PR00967I   15     105           5            4               4    26
PR00967J   18     153           8            5               5    27
PR00968A   17     136           9            6               7    41
PR00968B   19     171           7            4               5    26
PR00968F   11      55           3            5               3    27
PR00968G   21     210          18            8               9    42
PR00977A   23     253          14            5              11    47
PR00977B   21     210          14            6               8    38
PR00977C   18     153           9            5               6    33
PR00977E   16     120          10            8               5    31
PR00978B   20     190          13            6               9    45
PR00978C   20     190          13            6               8    40
PR00978D   18     153          12            7               8    44
PR00978E   21     210          13            6               9    42
PR00978F   19     171           7            4               6    31
PR00978G   20     190          11            5               8    40
PR00978H   20     190          15            7               8    40
PR00978I   23     253          10            3               8    34
PR00979E   22     231           9            3               6    27
PR00980E   14      91           9            9               4    28
PR00982D   18     153           6            3               5    27
PR00983C   19     171           9            5               7    36
PR00984B   24     276          10            3               6    25
PR00984C   16     120           5            4               5    31
PR00985E   19     171           6            3               5    26
PR00989B   15     105           6            5               4    26
PR00989C   16     120           4            3               4    25
PR00995A   16     120           5            4               4    25
PR00996E   15     105           5            4               4    26
PR00998A   21     210          10            4               8    38
PR00998C   20     190          10            5               7    35
PR00998D   20     190           8            4               6    30
PR00998E   17     136           7            5               6    35
PR00998H   22     231           9            3               6    27
PR00998I   19     171           5            2               5    26
PR01008B   16     120           4            3               4    25
PR01009C   19     171           9            5               5    26
PR01010B   16     120          14           11               7    43
PR01010D   20     190           7            3               5    25
PR01010E   18     153           7            4               6    33
PR01010F   19     171           6            3               5    26
PR01013A   16     120           9            7               5    31
PR01013B   16     120           4            3               4    25
PR01013C   17     136           6            4               5    29
PR01013D   19     171          14            8              10    52
PR01013E   12      66           5            7               4    33
PR01013F   14      91          12           13               6    42
PR01013G   18     153          10            6               7    38
PR01014A   18     153           8            5               5    27
PR01014B   17     136          11            8               8    47
PR01014C   18     153           8            5               6    33
PR01014D   14      91           6            6               5    35
PR01014E   16     120           7            5               5    31
PR01014F   17     136           7            5               5    29
PR01014H   19     171          11            6               7    36
PR01014I   17     136           7            5               6    35
PR01014J   14      91           5            5               4    28
PR01014K   16     120           6            5               4    25
PR01015B   14      91           5            5               4    28
PR01015C   14      91           4            4               4    28
PR01015D   16     120           8            6               6    37
PR01015E   11      55           7           12               5    45
PR01015H   12      66           4            6               3    25
PR01015I   14      91           5            5               5    35
PR01015J   15     105           9            8               6    40
PR01016A   15     105           7            6               5    33
PR01016B   15     105           6            5               5    33
PR01016E   17     136           7            5               6    35
PR01016F   17     136          10            7               6    35
PR01016G   20     190          14            7               9    45
PR01016H   25     300          18            6              11    44
PR01016I   18     153          10            6               8    44
PR01016J   24     276          22            7              10    41
PR01016K   17     136           7            5               6    35
PR01016L   17     136          10            7               7    41
PR01018A   19     171          10            5               7    36
PR01018B   18     153          13            8               8    44
PR01018C   17     136           9            6               6    35
PR01018D   18     153          20           13              10    55
PR01018F   15     105          10            9               7    46
PR01018G   23     253          18            7              11    47
PR01018H   22     231          20            8               9    40
PR01022A   17     136           7            5               6    35
PR01022B   15     105           6            5               6    40
PR01022C   15     105           5            4               4    26
PR01022D   16     120           7            5               6    37
PR01022E   20     190          10            5               8    40
PR01022F   20     190          10            5               8    40
PR01024A   12      66           6            9               5    41
PR01024B   13      78           6            7               5    38
PR01024C   15     105           6            5               5    33
PR01024D   16     120           6            5               5    31
PR01024E   11      55           5            9               4    36
PR01024F   18     153          11            7               7    38
PR01024G   18     153          17           11              10    55
PR01024H   14      91          16           17               6    42
PR01024I   17     136          18           13               8    47
PR01025B   14      91           4            4               4    28
PR01025D   15     105           5            4               4    26
PR01025E   19     171          16            9              10    52
PR01025G   20     190          15            7              10    50
PR01025I   19     171           6            3               5    26
PR01036A   25     300          21            7              12    48
PR01036B   23     253          17            6              10    43
PR01036C   21     210          19            9              10    47
PR01036D   25     300          35           11              14    56
PR01036E   25     300          24            8              12    48
PR01036F   19     171           9            5               8    42
PR01036G   19     171           7            4               5    26
PR01036H   26     325          28            8              14    53
PR01036I   25     300          26            8              11    44
PR01036J   21     210           8            3               6    28
PR01036K   21     210          10            4               8    38
PR01036L   20     190          17            8              11    55
PR01044A   16     120          11            9               7    43
PR01044C   25     300          15            5              10    40
PR01044D   21     210           8            3               6    28
PR01047B   24     276           8            2               7    29
PR01049A   22     231          16            6              10    45
PR01049E   15     105           5            4               4    26
PR01058A   21     210          10            4               8    38
PR01058B   16     120           5            4               5    31
PR01058C   14      91           6            6               5    35
PR01058F   14      91          13           14               6    42
PR01059A   18     153           8            5               7    38
PR01059B   12      66           4            6               3    25
PR01059E   14      91           5            5               4    28
PR01059F   25     300          14            4               9    36
PR01059G   17     136          12            8               6    35
PR01059H   20     190          13            6              10    50
PR01059I   16     120           5            4               5    31
PR01059J   17     136           7            5               6    35
PR01059K   23     253          18            7              11    47
PR01060A   19     171           7            4               5    26
PR01060B   15     105           6            5               4    26
PR01060C   12      66           3            4               3    25
PR01060D   13      78           5            6               4    30
PR01060E   26     325          15            4              10    38
PR01060I   14      91           5            5               4    28
PR01060J   20     190          10            5               7    35
PR01061A   23     253          19            7              11    47
PR01061B   19     171           7            4               5    26
PR01061C   16     120           6            5               5    31
PR01061D   16     120           6            5               5    31
PR01061E   10      45           4            8               4    40
PR01062A   15     105           5            4               4    26
PR01062B   22     231          14            6               9    40
PR01062C   17     136          10            7               7    41
PR01062E   16     120          11            9               8    50
PR01063A   19     171          10            5               6    31
PR01063E   15     105           5            4               4    26
PR01070A   15     105          10            9               7    46
PR01070B   19     171          11            6               8    42
PR01070C   18     153          11            7               6    33
PR01072A   11      55           5            9               3    27
PR01072C   18     153          10            6               6    33
PR01073A   21     210           7            3               7    33
PR01073B   15     105           7            6               5    33
PR01073C   12      66          18           27               8    66
PR01074A   23     253          23            9              11    47
PR01074C   19     171          10            5               8    42
PR01074D   17     136          12            8               9    52
PR01076A   21     210          16            7               9    42
PR01076B   24     276          17            6              10    41
PR01076C   21     210           7            3               6    28
PR01076D   22     231          21            9              11    50
PR01076E   16     120           5            4               4    25
PR01076F   22     231          10            4               9    40
PR01076G   21     210          19            9              11    52
PR01079A   12      66           5            7               4    33
PR01079B   18     153           8            5               6    33
PR01079F   14      91           7            7               4    28
PR01080A   24     276          12            4              10    41
PR01080B   19     171          10            5               8    42
PR01080C   19     171          13            7               9    47
PR01080D   21     210          12            5               9    42
PR01081B    9      36           4           11               3    33
PR01081C   13      78          12           15               6    46
PR01081D   18     153           7            4               6    33
PR01081F    9      36           4           11               3    33
PR01082A   14      91           7            7               5    35
PR01082B    8      28           2            7               2    25
PR01082C   13      78           5            6               4    30
PR01082D   17     136           7            5               5    29
PR01084A   12      66           8           12               6    50
PR01084D   11      55           3            5               3    27
PR01085A   17     136          17           12               8    47
PR01085D   17     136          11            8               7    41
PR01085F   15     105           7            6               6    40
PR01085G   15     105           7            6               4    26
PR01085I   20     190           9            4               7    35
PR01085K   17     136           9            6               7    41
PR01085L   27     351          30            8              15    55
PR01086B   30     435          26            5              15    50
PR01086C   12      66           3            4               3    25
PR01086D   21     210          22           10              10    47
PR01086E   21     210          10            4               8    38
PR01086F   17     136           5            3               5    29
PR01086G   25     300          23            7              14    56
PR01086H   19     171          15            8               9    47
PR01086I   18     153          13            8               9    50
PR01087B    8      28           2            7               2    25
PR01087D   11      55           4            7               3    27
PR01087E   10      45           4            8               3    30
PR01087F    8      28           4           14               3    37
PR01087G   13      78           6            7               4    30
PR01087H   11      55           5            9               4    36
PR01087K   19     171           8            4               7    36
PR01087L   14      91           4            4               4    28
PR01087M   22     231          20            8              12    54
PR01087N   22     231          15            6              10    45
PR01087P   26     325          19            5              12    46
PR01089A   14      91           7            7               5    35
PR01089B   12      66          12           18               6    50
PR01089C   18     153          13            8               7    38
PR01089D   11      55          10           18               4    36
PR01090A   15     105           5            4               4    26
PR01090B   22     231           8            3               7    31
PR01090C   19     171           8            4               7    36
PR01090D   30     435          35            8              17    56
PR01091A   18     153          10            6               7    38
PR01091B   19     171          17            9              10    52
PR01091C   11      55          10           18               6    54
PR01091D   17     136          13            9               7    41
PR01092A   28     378          27            7              14    50
PR01092B   15     105           6            5               5    33
PR01092D   24     276          20            7              12    50
PR01092E   23     253          30           11              13    56
PR01093B    9      36           4           11               3    33
PR01093C   13      78           8           10               5    38
PR01093D   17     136           9            6               7    41
PR01093E   11      55           3            5               3    27
PR01094A    9      36           6           16               5    55
PR01094D   19     171          17            9               9    47
PR01095A   20     190          18            9              10    50
PR01095B   26     325          35           10              15    57
PR01095C   15     105           6            5               5    33
PR01095D   20     190           9            4               5    25
PR01095E   16     120           7            5               6    37
PR01095F   22     231          16            6              10    45
PR01095G   19     171           9            5               8    42
PR01095H   24     276          10            3               9    37
PR01095I   25     300          14            4              10    40
PR01095J   21     210          24           11              11    52
PR01095K   27     351          34            9              15    55
PR01097A   22     231           8            3               6    27
PR01097C   14      91          10           10               4    28
PR01105A   19     171          10            5               8    42
PR01105B   13      78           5            6               4    30
PR01105C   20     190          11            5               8    40
PR01105D   15     105           4            3               4    26
PR01105E   16     120           6            5               6    37
PR01105G   16     120           7            5               6    37
PR01105I   17     136           9            6               6    35
PR01106A   16     120          13           10               8    50
PR01106C   11      55           5            9               4    36
PR01106F   13      78           8           10               5    38
PR01106G   14      91           6            6               4    28
PR01106H   18     153          10            6               6    33
PR01107A   17     136           9            6               6    35
PR01107B   14      91           6            6               5    35
PR01110B   21     210          10            4               8    38
PR01110D    8      28           3           10               2    25
PR01110E   15     105           4            3               4    26
PR01113A   11      55           3            5               3    27
PR01113B   10      45           7           15               4    40
PR01113D    8      28           2            7               2    25
PR01113E   11      55           3            5               3    27
PR01114A   11      55           6           10               5    45
PR01114B    7      21           2            9               2    28
PR01114D   11      55           4            7               3    27
PR01115A    8      28           6           21               4    50
PR01115E    7      21           2            9               2    28
PR01116C    8      28           3           10               3    37
PR01119A    7      21           4           19               3    42
PR01119B    9      36           4           11               3    33
PR01119E    9      36           3            8               3    33
PR01120C   11      55           7           12               5    45
PR01120D    8      28           3           10               2    25
PR01120E   17     136           7            5               7    41
PR01121B   13      78           5            6               5    38
PR01121D   14      91           8            8               5    35
PR01121E   10      45           3            6               3    30
PR01121G   10      45           4            8               3    30
PR01121H   20     190           6            3               5    25
PR01121I   17     136           8            5               7    41
PR01121J   21     210          26           12              11    52
PR01122A   13      78           7            8               5    38
PR01122B    9      36           3            8               3    33
PR01122C   14      91           5            5               4    28
PR01122E   15     105           7            6               6    40
PR01122G   15     105           5            4               4    26
PR01122H   16     120           5            4               5    31
PR01122I   14      91           7            7               6    42
PR01129A   21     210          40           19               9    42
PR01129B   18     153          10            6               8    44
PR01129D   14      91           4            4               4    28
PR01129F   14      91           7            7               5    35
PR01129G   21     210          13            6               9    42
PR01129H   18     153           8            5               6    33
PR01129I   18     153           6            3               5    27
PR01129J   18     153          10            6               7    38
PR01129K   17     136           9            6               7    41
PR01130A   23     253          11            4               8    34
PR01130B   21     210          20            9              11    52
PR01130C   24     276          13            4              10    41
PR01130D   18     153          11            7               8    44
PR01130E   22     231           9            3               7    31
PR01130F   18     153          15            9               9    50
PR01130G   17     136           8            5               5    29
PR01130I   25     300          28            9              15    60
PR01132A   11      55           7           12               5    45
PR01132B   10      45           3            6               3    30
PR01132E   10      45           6           13               4    40
PR01133A   11      55           3            5               3    27
PR01133C   12      66           7           10               4    33
PR01135D   11      55           7           12               4    36
PR01136C   11      55           6           10               5    45
PR01138B   10      45           3            6               3    30
PR01138D    9      36           9           25               5    55
PR01139A    6      15           2           13               2    33
PR01139C    7      21           2            9               2    28
PR01139D   12      66           3            4               3    25
PR01140B   10      45           3            6               3    30
PR01143A   19     171          18           10               8    42
PR01143C   19     171           7            4               5    26
PR01143D   12      66           4            6               3    25
PR01143E   21     210          13            6               9    42
PR01143F   18     153           9            5               8    44
PR01143G   18     153          20           13              10    55
PR01143H   21     210           6            2               6    28
PR01143J   18     153           9            5               7    38
PR01144A   19     171          17            9               8    42
PR01144B   17     136           8            5               5    29
PR01144C   15     105          14           13               7    46
PR01144D   12      66           4            6               3    25
PR01144E   22     231          13            5               9    40
PR01144F   13      78           9           11               6    46
PR01144H   15     105           7            6               4    26
PR01144I   16     120           6            5               5    31
PR01144J   23     253          14            5              11    47
PR01145A   20     190          31           16               9    45
PR01145B   20     190          13            6               8    40
PR01145C   15     105           7            6               6    40
PR01145D   19     171          10            5               7    36
PR01145E   17     136           7            5               6    35
PR01145F   19     171           7            4               6    31
PR01145G   26     325          19            5              14    53
PR01145H   16     120          13           10               6    37
PR01145I   17     136           7            5               6    35
PR01145J   20     190           8            4               7    35
PR01145K   21     210           9            4               8    38
PR01145L   23     253          17            6              10    43
PR01145M   16     120           5            4               5    31
PR01145N   22     231           9            3               8    36
PR01145O   26     325          14            4              10    38
PR01149B   15     105           6            5               5    33
PR01149C   13      78           9           11               6    46
PR01149E   16     120           4            3               4    25
PR01149F   16     120           6            5               5    31
PR01151A   19     171          12            7               8    42
PR01151B   13      78           5            6               4    30
PR01151C   14      91           4            4               4    28
PR01151D   12      66           5            7               4    33
PR01151E   20     190          11            5               8    40
PR01151H   19     171          23           13              10    52
PR01151I   16     120           8            6               6    37
PR01151J   24     276          17            6               9    37
PR01151K   17     136           8            5               5    29
PR01151L   13      78           8           10               5    38
PR01152A   24     276          26            9              13    54
PR01152B   17     136           6            4               6    35
PR01152C   24     276          18            6              13    54
PR01152D   17     136           5            3               5    29
PR01152E   21     210          12            5               9    42
PR01152F   19     171           7            4               6    31
PR01152G   20     190          10            5               8    40
PR01152I   22     231          14            6              10    45
PR01152J   19     171          29           16               8    42
PR01153A   19     171           6            3               5    26
PR01153B   17     136           6            4               5    29
PR01153C   17     136           5            3               5    29
PR01153D   26     325          19            5              13    50
PR01153E   23     253           9            3               7    30
PR01153F   18     153           7            4               6    33
PR01153G   22     231          11            4               8    36
PR01153H   15     105           5            4               4    26
PR01153I   13      78           4            5               4    30
PR01153J   23     253          22            8              12    52
PR01153K   25     300          14            4               8    32
PR01156A   22     231           9            3               7    31
PR01156B   18     153           8            5               7    38
PR01156C   19     171           6            3               6    31
PR01156D   18     153           8            5               6    33
PR01156E   20     190          14            7               8    40
PR01156G   15     105           7            6               6    40
PR01156I   17     136           8            5               6    35
PR01156J   22     231          23            9              10    45
PR01157A   13      78           7            8               4    30
PR01168B   11      55           3            5               3    27
PR01168C   19     171           9            5               6    31
PR01170A   16     120           8            6               6    37
PR01170B   17     136           9            6               7    41
PR01170C   19     171          11            6               8    42
PR01170D   17     136           7            5               6    35
PR01170E   21     210          12            5               9    42
PR01170F   17     136           6            4               5    29
PR01171B   17     136           6            4               5    29
PR01171C   10      45           5           11               4    40
PR01171D   15     105           8            7               6    40
PR01172B   11      55           6           10               5    45
PR01172C   15     105           6            5               5    33
PR01174D   11      55           3            5               3    27
PR01174F   17     136           8            5               6    35
PR01174G   20     190           7            3               6    30
PR01177A   22     231          14            6               8    36
PR01177B   18     153           7            4               5    27
PR01177C   16     120           6            5               6    37
PR01177D   19     171          21           12               8    42
PR01177E   24     276          13            4              10    41
PR01177F   26     325          34           10              15    57
PR01177G   22     231          20            8              10    45
PR01177H   23     253          20            7              12    52
PR01177I   24     276          29           10              15    62
PR01177J   19     171          23           13              11    57
PR01184D   13      78           5            6               4    30
PR01188A   17     136          17           12               9    52
PR01188B   14      91          13           14               6    42
PR01188C   17     136          23           16              11    64
PR01188D   20     190          13            6               9    45
PR01189A   16     120           9            7               6    37
PR01189B   21     210          25           11              12    57
PR01189C   20     190          14            7               9    45
PR01189D   18     153          15            9               9    50
PR01190B   15     105           4            3               4    26
PR01191B    7      21           2            9               2    28
PR01192B    8      28           3           10               3    37
PR01192C   11      55           3            5               3    27
PR01193B   13      78           7            8               5    38
PR01193C   13      78           5            6               5    38
PR01193D   11      55           5            9               4    36
PR01194A   14      91           5            5               4    28
PR01194B    7      21           4           19               3    42
PR01194C    8      28           6           21               3    37
PR01195A   15     105           6            5               5    33
PR01195B   18     153           5            3               5    27
PR01195D   18     153           6            3               6    33
PR01197B   10      45           4            8               3    30
PR01197C   13      78           4            5               4    30
PR01198B   18     153          12            7               8    44
PR01199A   14      91           5            5               4    28
PR01199C   14      91           4            4               4    28
PR01200A   13      78           6            7               5    38
PR01201B   10      45           4            8               3    30
PR01202A   16     120          14           11               7    43
PR01202B   14      91           6            6               5    35
PR01202C   18     153           8            5               7    38
PR01203C   11      55           4            7               3    27
PR01204D   16     120           6            5               4    25
PR01207A    9      36           4           11               3    33
PR01207C   12      66           3            4               3    25
PR01208A   13      78           5            6               4    30
PR01208B   18     153          18           11               8    44
PR01208D   13      78          10           12               6    46
PR01209C   12      66           5            7               4    33
PR01209D   10      45           3            6               3    30
PR01209E   11      55           3            5               3    27
PR01209F   11      55           4            7               3    27
PR01211B   15     105           9            8               8    53
PR01211C   20     190          17            8              11    55
PR01211D   24     276          24            8              13    54
PR01211E   16     120           8            6               5    31
PR01214A   12      66           6            9               4    33
PR01214B   24     276          38           13              17    70
PR01214C   19     171          10            5               8    42
PR01214D   14      91          10           10               5    35
PR01215D   20     190           7            3               6    30
PR01215E   22     231          12            5               8    36
PR01215F   20     190           7            3               6    30
PR01220A   17     136           8            5               5    29
PR01223A   26     325          36           11              17    65
PR01223B   24     276          27            9              13    54
PR01223C   27     351          25            7              15    55
PR01223D   25     300          35           11              14    56
PR01223E   24     276          23            8              12    50
PR01223F   25     300          30           10              15    60
PR01223G   23     253          17            6              11    47
PR01226A   15     105           8            7               7    46
PR01226G   22     231          12            5               8    36
PR01226H   22     231           8            3               7    31
PR01227A   13      78           4            5               4    30
PR01227B   13      78           8           10               6    46
PR01227C   14      91           7            7               5    35
PR01227D    9      36           4           11               3    33
PR01227E   12      66          14           21               7    58
PR01227H   10      45          11           24               5    50
PR01230A   14      91           7            7               5    35
PR01230B    7      21           2            9               2    28
PR01230C    8      28           2            7               2    25
PR01232A    7      21           2            9               2    28
PR01232E   13      78           5            6               4    30
PR01232F    8      28           3           10               3    37
PR01233A   24     276          17            6              12    50
PR01233B   22     231          10            4               8    36
PR01233C   20     190          11            5               8    40
PR01233D   20     190           6            3               6    30
PR01233E   21     210          10            4               7    33
PR01233F   20     190           9            4               7    35
PR01233G   26     325          19            5              12    46
PR01233H   24     276          10            3               8    33
PR01233I   23     253          23            9              14    60
PR01233J   24     276          18            6              12    50
PR01233K   23     253          20            7              10    43
PR01235A   19     171           8            4               5    26
PR01235B   16     120           5            4               5    31
PR01235C   20     190           9            4               7    35
PR01235D   15     105           9            8               6    40
PR01235E   22     231          13            5               8    36
PR01235F   20     190           5            2               5    25
PR01237A   24     276          42           15              15    62
PR01237B   22     231          27           11              13    59
PR01237C   20     190          16            8               9    45
PR01237D   12      66           3            4               3    25
PR01237E   23     253          22            8              12    52
PR01237F   19     171          16            9              11    57
PR01237G   21     210          21           10              10    47
PR01237H   21     210           8            3               6    28
PR01238A   18     153           6            3               5    27
PR01239D   17     136           9            6               5    29
PR01240A   26     325          10            3               8    30
PR01240B   30     435          19            4              14    46
PR01240C   30     435          14            3               8    26
PR01240D   20     190          13            6               9    45
PR01240E   20     190          10            5               7    35
PR01240F   30     435          12            2              11    36
PR01240G   17     136          12            8               6    35
PR01242A   10      45           4            8               3    30
PR01242D   15     105           6            5               5    33
PR01242E   16     120           5            4               5    31
PR01242G   16     120          14           11               7    43
PR01245H   16     120           6            5               4    25
PR01252B   12      66           5            7               4    33
PR01252C   15     105           5            4               4    26
PR01252D   12      66           3            4               3    25
PR01252E   12      66           4            6               4    33
PR01252F   11      55           4            7               3    27
PR01252G   12      66           4            6               3    25
PR01253A   14      91           6            6               5    35
PR01253B    8      28           4           14               3    37
PR01253E    9      36           3            8               3    33
PR01253F   17     136          10            7               7    41
PR01253G   14      91           9            9               6    42
PR01255A   10      45           3            6               3    30
PR01256A   13      78          10           12               6    46
PR01256B   13      78          24           30               8    61
PR01257A    7      21           3           14               3    42
PR01257B   10      45           8           17               5    50
PR01258B    8      28           4           14               3    37
PR01258C    8      28           4           14               3    37
PR01258D    7      21           4           19               3    42
PR01259C   13      78           6            7               4    30
PR01259D   14      91           5            5               4    28
PR01262C   23     253           7            2               6    26
PR01263A   16     120           5            4               4    25
PR01263B   12      66           4            6               3    25
PR01263E   12      66          10           15               4    33
score cutoff >0.500. Bias-fraction cutoff >25 percent.
3922 biassed blocks found in the 10838 blocks.
77E   24     276          13            4              10    41
PR01177blimps-3.9/examples/blimps/blksort.stn000064400001460000012000000072620576113232200204700ustar00jorjastaff00000400000027 1001       0.44 
 1002       0.75 
 1003       1.17 
 1004       1.49 
 1005       2.10 
 1006       2.56 
 1007       3.00 
 1008       3.73 
 1009       4.29 
 1010       4.99 
 1011       5.51 
 1012       6.33 
 1013       7.11 
 1014       7.98 
 1015       8.73 
 1016       9.70 
 1017      10.71 
 1018      11.45 
 1019      12.58 
 1020      13.70 
 1021      14.83 
 1022      15.93 
 1023      16.96 
 1024      18.15 
 1025      19.23 
 1026      20.59 
 1027      21.78 
 1028      22.96 
 1029      24.20 
 1030      25.34 
 1031      26.53 
 1032      27.88 
 1033      29.27 
 1034      30.82 
 1035      32.42 
 1036      33.96 
 1037      35.33 
 1038      36.53 
 1039      37.73 
 1040      39.32 
 1041      40.90 
 1042      42.18 
 1043      43.63 
 1044      45.39 
 1045      46.86 
 1046      48.06 
 1047      49.41 
 1048      50.43 
 1049      51.93 
 1050      53.16 
 1051      54.20 
 1052      55.84 
 1053      57.12 
 1054      58.47 
 1055      59.89 
 1056      61.18 
 1057      62.45 
 1058      63.68 
 1059      64.99 
 1060      66.30 
 1061      67.40 
 1062      68.45 
 1063      69.42 
 1064      70.40 
 1065      71.48 
 1066      72.32 
 1067      73.25 
 1068      74.39 
 1069      75.33 
 1070      76.21 
 1071      76.96 
 1072      77.78 
 1073      78.45 
 1074      79.28 
 1075      80.11 
 1076      80.80 
 1077      81.71 
 1078      82.37 
 1079      83.02 
 1080      83.77 
 1081      84.41 
 1082      84.99 
 1083      85.55 
 1084      86.22 
 1085      86.72 
 1086      87.35 
 1087      87.88 
 1088      88.18 
 1089      88.64 
 1090      89.08 
 1091      89.45 
 1092      89.83 
 1093      90.12 
 1094      90.51 
 1095      90.85 
 1096      91.29 
 1097      91.47 
 1098      91.67 
 1099      91.93 
 1100      92.28 
 1101      92.65 
 1102      92.84 
 1103      93.06 
 1104      93.32 
 1105      93.57 
 1106      93.79 
 1107      94.06 
 1108      94.38 
 1109      94.72 
 1110      95.01 
 1111      95.13 
 1112      95.34 
 1113      95.46 
 1114      95.71 
 1115      95.80 
 1116      96.04 
 1117      96.18 
 1118      96.35 
 1119      96.44 
 1120      96.48 
 1121      96.60 
 1122      96.71 
 1123      96.83 
 1124      96.94 
 1125      97.05 
 1126      97.11 
 1127      97.29 
 1128      97.35 
 1129      97.44 
 1130      97.53 
 1131      97.64 
 1132      97.76 
 1133      97.79 
 1134      97.82 
 1135      97.96 
 1136      98.05 
 1137      98.11 
 1138      98.14 
 1139      98.25 
 1140      98.32 
 1141      98.39 
 1142      98.48 
 1143      98.54 
 1144      98.55 
 1145      98.60 
 1146      98.64 
 1147      98.69 
 1148      98.71 
 1149      98.75 
 1150      98.80 
 1151      98.81 
 1152      98.83 
 1153      98.86 
 1154      98.92 
 1155      98.95 
 1156      98.96 
 1157      98.98 
 1159      99.03 
 1160      99.07 
 1161      99.09 
 1162      99.10 
 1163      99.15 
 1165      99.18 
 1166      99.19 
 1167      99.24 
 1168      99.27 
 1169      99.28 
 1170      99.31 
 1171      99.33 
 1172      99.35 
 1173      99.36 
 1174      99.41 
 1176      99.42 
 1177      99.44 
 1178      99.45 
 1180      99.47 
 1181      99.48 
 1182      99.51 
 1188      99.53 
 1191      99.56 
 1196      99.57 
 1197      99.59 
 1200      99.60 
 1201      99.62 
 1202      99.63 
 1210      99.65 
 1211      99.66 
 1212      99.68 
 1222      99.70 
 1224      99.71 
 1225      99.73 
 1228      99.74 
 1234      99.76 
 1237      99.77 
 1241      99.79 
 1245      99.80 
 1246      99.82 
 1260      99.83 
 1261      99.85 
 1264      99.86 
 1267      99.88 
 1269      99.89 
 1273      99.91 
 1284      99.92 
 1285      99.94 
 1287      99.95 
 1337      99.97 
 1380      99.98 
 1399     100.00 
6      91.29 
 1097      91.47 
 1098      91.67 
 1099      91.93 
 1100      92.28 
 1101      92.65 
 1102      92.84 
 1103      93.06 
 1104      93.32 
 1105      93.57 
 1106      93.79 
 1107      94.06 
 1108      94.38 
 1109      94.72 
 1110      95.01 
 1111      95.13 
 1112      95.34 
 1113      95.46 
 1114      95.blimps-3.9/examples/blimps/blksort.stp000064400001460000012000000144700711635310700204730ustar00jorjastaff00000400000027        ___________               ___________               ___________ 
       |\ __________\            |___________|            /__________ /|
       | |           |           |           |           |           | |
       | | **********|           |***********|           |********** | |
       | | * BLOCKS  |           |EMAIL & WWW|           |SEARCHER * | |
       | | **********|           |***********|           |********** | |
        \|___________|___________|___________|___________|___________|/
                     |\ __________\         /__________ /|
                     | |  blocks@  |       | http://   | |
                     | |   blocks. |       |  blocks.  | |
                     | |   fhcrc.  |       |  fhcrc.   | |
                     | |   org     |       |  org      | |
                      \|___________|       |___________|/

==============================================================================
      Attention Blocks E-mail users: See new searching options at
	      http://blocks.fhcrc.org/help/email.html
==============================================================================
Here are your search results. The database searched was Blocks+ (10 June 00)
which includes: BLOCKS 12.0 consisting of 4071 blocks representing 998 groups
documented in InterPro 1.0/PROSITE, plus 3141 blocks from 498 groups documented 
in PRINTS 26.0 but not represented in BLOCKS, plus 2382 blocks from 569 groups 
documented in PFAM 5.3 but not represented in BLOCKS or PRINTS, plus
962 blocks from 250 groups documented in PRODOM 99.1 but not represented in
BLOCKS, PRINTS or PFAM, plus 282 blocks from 76 groups documented in DOMO 2.0
but not represented in BLOCKS, PRINTS, PFAM or PRODOM for a total of 10,838
blocks from 2391 groups.  Get more information at http://blocks.fhcrc.org.
If you found the Blocks Searcher useful, please cite:
   S Henikoff & JG Henikoff, "Protein family classification
   based on searching a database of blocks", Genomics 19:97-107 (1994).
Please report problems to:  webmaster@blocks.fhcrc.org
==============================================================================
Each numbered result consists of one or more blocks from a Prosite group found
in the query sequence. One set of the highest-scoring blocks that are in the 
correct order and separated by distances comparable to the Blocks database is 
selected for analysis. If this set includes multiple blocks the probability 
that the lower scoring blocks support the highest scoring block is reported. 
Maps of the database blocks and query sequence are shown:
AAA represents the first block roughly in proportion to its width.
  : represents the minimum distance between blocks in the database.
  . represents the maximum distance between blocks in the database.
< > indicate the sequence has been truncated to fit the page.
The query map is aligned on the highest scoring block. Multiple block hits 
that are consistent with the highest scoring block are separated by colons.
Block hits that are not consistent are mapped below. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database is
shown. The distance between detected blocks is listed as (min, max): for the
database entry followed by the distance in the query. Upper case in the query
indicates at least one occurrence of the residue in that column of the block.

The following nomogram is provided to aid interpretation of scores and 
probability estimates. It summarizes results from 7,082 searches using 
shuffled protein queries. "Shuffled percentiles" are calculated from scores
obtained for the top-scoring block in each search:

   1400 *-----------|-----------|-----------|-----------|100.00  
        |\                                              |        
        | \                                             |        
   1350 -  \                                            - 99.99  
        |   \                                           |        
        |    \               < 1/7000 searches          |        
   1300 -     \                                         - 99.96 S
 A      *      \                                        |       H
 N      | \     \                                       |       U
 C 1250 -  \     \                                      - 99.82 F
 H      |   \     \                                     |       F
 O      |    \     \                                    |       L
 R 1200 -     \     * \ \ \ \                           - 99.60 E
        |      \              \ *  \                    |       D
 B      |        \   < 1/1000         \                 |
 L 1150 *           *   searches        \               - 98.80 P
 O      | \           \ \                 \             |       E
 C      |    \            \ \               *           |       R
 K 1100 -       \             \ * \ \ \ \ \   \         - 92.28 C
        |           *   < 1/100 searches    *   \       |       E
 S      |              \                     \    \     |       N
 C 1050 -                 \ \ \ * \            \    \   - 53.16 T
 O      |                           \ \ \         \  \  |       I
 R      |                                 \          \\ |       L
 E 1000 |-----------|-----------|-----------|-----------|  0.00 E
        0          -1          -2          -3          -4 
                             LOG(P)

For example, a first hit with anchor block score of 1150 (98.80th percentile)
and estimated P-value of .01 (log(P) = -2) is expected to occur by chance
less than once in 1000 searches but more than once in 7000 searches
using protein queries of typical length and composition. It is not appropriate
to apply this nomogram to hits other than the first hit reported.

For interpretation of block hits, you might find it worthwhile to obtain the
full set of blocks and documentation for a group. To do this, send a blank
message to blocks@blocks.fhcrc.org with the subject heading: GET BL????? e.g.,  
'Subject: GET BL00044' (0s are zeros) for full information on this group.
=============================================================================
Note: For searches using DNA queries, "Location" refers to the position
in the query in base pairs from 5' to 3' on the + strand, whereas the map and 
alignment show the translated position in amino acid residues as before.
============================================================================= 
blimps-3.9/examples/blimps/example.pro000064400001460000012000000006150603236343700204370ustar00jorjastaff00000400000027>HAIR_DROME HAIRY PROTEIN
MVTGVTAANM TNVLGTAVVP AQLKETPLKS DRRSNKPIME KRRRARINNC LNELKTLILD
ATKKDPARHS KLEKADILEK TVKHLQELQR QQAAMQQAAD PKIVNKFKAG FADCVNEVSR
FPGIEPAQRR RLLQHLSNCI NGVKTELHQQ QRQQQQQSIH AQMLPSPPSS PEQDSQQGAA
APYLFGIQQT ASGYFLPNGM QVIPTKLPNG SIALVLPQSL PQQQQQQLLQ HQQQQQQLAV
AAAAAAAAAA QQQPMLVSMP QRTASTGSAS SHSSAGYESA PGSSSSCSYA PSSPANSSYE
PMDIKPSVIQ RVPMEQQPLS LVIKKQIKEE EQPWRPW
blimps-3.9/examples/blimps/example.pros000064400001460000012000002117470673775511600206470ustar00jorjastaff00000400000027>ACVS_EMENI|P27742 DELTA-(L-ALPHA-AMINOADIPYL)-L-CYSTEINYL-D-VALINE SYNTHET
MSPPGLLSED GPGYSGGYAD PTVPKVNWKQ SNGKSAGGNG DVDAGNGNID PSKSGVGVQV
CFAGGLEGWK AGISKITERC DLSSIATNST KYQLAVTGFS DGPDDYNEYS VPFPSEVLVA
MEEMCLARDI SMRSVIQFAV HYVLKGFGGG SHTVAASIDV GDDPNNIATS YTITPSIVCH
ESRQGQTVMQ EIQSMEKLNQ LRKQEMHPGE AGLSLIRMGL FDILVIFADA NKCEGLIAGL
PLAVMVCEGG GRLQVRIHFS GSLFRQKTLV DIAEALNVLF AKAASGGATP VRDLELLSAE
QKQQLEEWNK TDGEYPECKR LNHLIEEATQ LHEDKVAIVY KRRQLTYGEL NAQANCFAHY
LRSIGILPEQ LVALFLEKSE NLIVTILGIW KSGAAYVPID PTYPDERVRF VLEDTQAKVI
IASNHLAERL QSEVISDREL SIIRLEHCLS AIDQQPSTFP RANLRDPSLT SKQLAYVTYT
SGTTGFPKGI LKQHTNVVNS ITDLSARYGV TGDHHEAILL FSAYVFEPFV RQMLMALVNG
HLLAMVDDAE KYDAEKLIPF IREHKITYLN GTASVLQEYD FSSCPSLKRL ILVGENLTES
RYLALRRHFK NCILNEYGFT ESAFVTALNV FEPGSARNNT SLGRPVRNVK CYILNKSLKR
VPIGATGELH IGGLGISKGY LNRPDLTPQR FIPNPFQTDH EKELGLNQLM YKTGDLARWL
PNGEIEYLGR ADFQIKLRGI RIEPGEIEST LAGYPGVRTS LVVSKRLRHG EKETTNEHLV
GYYVGDNTSV SETALLQFLE LKLPRYMIPT RLVRVSQIPV TVNGKADLRA LPSVDLIQPK
VSSCELTDEV EIALGKIWAD VLGAHHLSIS RKDNFFRLGG HSITCIQLIA RIRQQLGVII
SIEDVFSSRT LERMAELLRS KESNGTPDER ARPQLKTVAG EVANANVYLA NSLQQGFVYQ
FLKNMGRSEA YVMQSVLRYD VNINPDLFKK AWKQVQHMLP TLRLRFQWGQ DVLQVIDEDQ
PLNWWFLHLA DDSALPEEQK LLELQRRDLA EPYDLAAGSL FRIYLIEHSS TRFSCLFSCH
HAILDGWSLP LLFRKTHGTY LHLLHGHSLR TLEDPYRQSQ QYLQDHREDH LRYWAGIVNQ
IEERCDMNAL LNERSRYKIQ LADYDKVEDQ QQLTLTVPDA SWLSKLRQTC SAQGITLHSI
LQFVWHAVLH AYGGGTHTVT GTTISGRNLP VSGIERSVGL YINTLPLVIN QLAYKNKTVL
EAIRDVQAIV NGMNSRGNVE LGRLQKNELK HGLFDSLFVL ENYPILDKSE EMRQKSELKY
TIEGNIEKLD YPLAVIAREV DLTGGFTFTI CYARELFDEI VISELLQMVR DTLLQVAKHL
DDPVRSLEYL SSAQMAQLDA WNATDAEFPD TTLHAMFEKE AAQKPDKVAV VYEQRSLTYR
QLNERANRMA HQLKSDISPK PNSIIALVVD KSEHMIATIL AVWKTGGAYV PIDPEYPDDR
IRYILEDTSA IAVISDACYL SRIQELAGES VRLYRSDIST QTDGNWSVSN PAPSSTSTDL
AYIIYTSGTT GKPKGVMVEH HGVVNLQISL SKTFGLRDTD DEVILSFSNY VFDHFVEQMT
DAILNGQTLV MLNDAMRSDK ERLYQYIETN RVTYLSGTPS VISMYEFSRF KDHLRRVDCV
GEAFSQPVFD QIRDTFQGLI INGYGPTEIS ITTHKRLYPF PERRTDKSIG QQIGNSTSYV
LNADMKRVPI GAVGELYLGG EGVARGYHNR PEVTAERFLR NPFQTDSERQ NGRNSRLYRT
GDLVRWIPGS NGEIEYLGRN DFQVKIRGLR IELGEIEAVM SSHPDIKQSV VIAKSGKEGD
QKFLVGYFVA SSPLSPGAIR RFMQSRLPGY MIPSSFIPIS SLPVTPSGKL DTKALPTAEE
KGAMNVLAPR NEIESILCGI SAGLLDISAQ TIGSDSDFFT LGGDSLKSTK LSFKIHEVFG
RTISVSALFR HRTIESLAHL IMNNVGDIQE ITPVDYDNRR KIAVSPAQER LLFIHELEGG
GNAYNIDAAF ELPPYIDQSR VEEALYTILS RHEALRTFLL RDQATGTFYQ KILTTDEAKC
MLIIEKSAVS TIDQIDSIVG RLSQHIFRLD SELPWLAHIV THKTGNLYLT LSFHHTCFDA
WSLKIFEREL RVFCASKQKG GNMPILPMPQ VQYKEYAEHH RRRLGKNQIQ KLSDFWLQRL
DGLEPLQLLP DYPRPAQFNY DGGDLSVILD GVVLETLRGI AKDHGVTLYA VLLAVYCLML
STYTHQVDIA VGVPISHRTH PLFQSIVGFF VNMVVVRVDV KDFAVHDLIR RVMKPLVDAQ
LHQDMPFQDV TKLLRVDNDA SRHPLVQTVF NFESDMDKEF ETTPSIQDTA TIAPYQSVQR
IKSVAKFDLN ATATESGSAL KINFNYATSL FRKETIQGFL ETYRHLLLQL SYLGSQGLKE
DTKLLLVRPE EMSGPHLPLA GLSNGAETLE AISLSRAFEF EAFRVPDRAA VVQGDKSLSY
TELNKRANQL ARYIQSVAHL RPDDKVLLIL DKSIDMIICI LAIWKTGSAY VPLDPSYPKE
RVQCISEVVQ AKILITESRY ASAWGSQTST ILAIDSPKVS NMVNNQATHN LPNIAGIKNL
AYIIFTSGTS GKPKGVLVEQ GGVLHLRDAL RKRYFGIECN EYHAVLFLSN YVFDFSIEQL
VLSIMSGHKL IIPEGEFVAD DEFYITANGQ RLSYLSGTPS LLQQIDLARL NHLQVVTAAG
EQLHAAQFNK LRSGFRGPIY NAYGITETTV YNIVSEFSAQ SQFENALREL LPGTRAYLLN
HATQPVPMNA VGELYLAGDC VARGYLNQPV LTGDRFIQNP FQTEQDIACG SYPRLYRTGD
LFRCRLDRQH QPYLEYLGRA DLQVKIRGYR IEPSEVQNVL ASCPGVRECA VVAKYENTDA
YSRIAKFLVG YYTPDTETVS DSSILAHMKS KLPAYMVPKY LCRLEGGLPV TINGKLDVRK
LPDIGNPQHQ ISYNPPRDVL EADLCRLWAS ALGTERCGID DDLFRLGGDS ITALHLAAQI
HHQIGRKVTV RDIFDHPTIR GIHDNVMVKL VPHNVPQFQA EQQTVLGDAP LLPIQIWFLS
KSLQHPSHWN HTFYLRTPDL DVTTLSTAVA ELQLYHDAFR MRLRQIDGRT VQCFADDISP
VQLRVLNVKD VDGSAAIDQQ LQKYQSDFDL EKGPICAAAY LHGYEDRSAR VWFSVHHIII
DIVSWQILAR DLQILYEGGT LGRKSSSVRQ WAEALQSYQG SASERAYWEG LLAQTAANIS
ALPPVTGTRT RLARTWSDDR TVILLNEASN QNASIQDLLL AAVGLALQQV TPGSPSMITL
EGHGREEIVD PTLDLSRTLG WFTSMYPFEI PPLNVETLSQ GIASLRECLR QVPARGIGFG
SLYGYCKHQM PQVTFNYLGQ LTSKQSITDQ WALAVGDGEM QYGLTTSPAD RDQSSFAVDI
TASCVNGALS VEMNSAWSLE KSMRFISRIE EVLNMILSGT LAQQATPVLT PQVFNEEMYT
PYFEFSKTPR RGPILFLLPP GEGGAESYFN NIVKHLPTTN MVVFNNYYLH SKSLNTFEKL
AEMYLGHIRQ IQPDGPYHFI GWSFGGTIAM EISRQLVGLG STIGLLGIID TYFNVPGATR
AIGLGDTEVL DPIHHISQPE PADFQCLPAS TDYIILFKAT RVNDKFQSEN QRRLYEYYDK
TLLNDLDWLL PGASNIHLVR LEEDTHFSWA TNPRQIAHVC STIEKFLARY
>AST5_DROME|P10083 ACHAETE-SCUTE COMPLEX PROTEIN T5 (ACHAETE) | PS00038
MALGSENHSV FNDDEESSSA FNGPSVIRRN ARERNRVKQV NNGFSQLRQH IPAAVIADLS
NGRRGIGPGA NKKLSKVSTL KMAVEYIRRL QKVLHENDQQ KQKQLHLQQQ HLHFQQQQQH
QHLYAWHQEL QLQSPTGSTS SCNSISSYCK PATSTIPGAT PPNNFHTKLE ASFEDYRNNS
CSSGTEDEDI LDYISLWQDD L
>CP4C_BLADI|P29981 CYTOCHROME P450 4C1 (EC 1.14.14.1) (CYPIVC1) | PS00086
MEFITILLST ALFIVTFLFL FRQGAKRARF VYLVNKLPGP TAYPVVGNAI EAIVPRNKLF
QVFDRRAKLY GPLYRIWAGP IAQVGLTRPE HVELILRDTK HIDKSLVYSF IRPWLGEGLL
TGTGAKWHSH RKMITPTFHF KILDIFVDVF VEKSEILVKK LQSKVGGKDF DIYPFITHCA
LDIICETAMG IQMNAQEESE SEYVKAVYEI SELTMQRSVR PWLHPKVIFD LTTMGKRYAE
CLRILHGFTN KVIQERKSLR QMTGMKPTIS NEEDELLGKK KRLAFLDLLL EASENGTKMS
DTDIREEVDT FMFEGHDTTS AGICWALFLL GSHPEIQDKV YEELDHIFQG SDRSTTMRDL
ADMKYLERVI KESLRLFPSV PFIGRVLKED TKIGDYLVPA GCMMNLQIYH VHRNQDQYPN
PEAFNPDNFL PERVAKRHPY AYVPFSAGPR NCIGQKFATL EEKTVLSSIL RNFKVRSIEK
REDLTLMNEL ILRPESGIKV ELIPRLPADA C
>CRTI_RHOCA|P17054 PHYTOENE DEHYDROGENASE (EC 1.3.-.-) (PHYTOENE DESATURASE
MSKNTEGMGR AVVIGAGLGG LAAAMRLGAK GYKVTVVDRL DRPGGRGSSI TKGGHRFDLG
PTIVTVPDRL RELWADCGRD FDKDVSLVPM EPFYTIDFPD GEKYTAYGDD AKVKAEVARI
SPGDVEGFRH FMWDAKARYE FGYENLGRKP MSKLWDLIKV LPTFGWLRAD RSVYGHAKKM
VKDDHLRFAL SFHPLFIGGD PFHVTSMYIL VSQLEKKFGV HYAIGGVQAI ADAMAKVITD
QGGEMRLNTE VDEILVSRDG KATGIRLMDG TELPAQVVVS NADAGHTYKR LLRNRDRWRW
TDEKLDKKRW SMGLFVWYFG TKGTAKMWKD VGHHTVVVGP RYKEHVQDIF IKGELAEDMS
LYVHRPSVTD PTAAPKGDDT FYVLSPVPNL GFDNGVDWSV EAEKYKAKVL KVIEERLLPG
VAEKITEEVV FTPETFRDRY LSPLGAGFSL EPRILQSAWF RPHNASEEVD GLYLVGAGTH
PGAGVPSVIG SGELVAQMIP DAPKPETPAA AAPKARTPRA KAAQ
>CYRG_MOUSE|P34902 CYTOKINE RECEPTOR COMMON GAMMA CHAIN PRECURSOR (GAMMA-C 
MLKLLLSPRS FLVLQLLLLR AGWSSKVLMS SANEDIKADL ILTSTAPEHL SAPTLPLPEV
QCFVFNIEYM NCTWNSSSEP QATNLTLHYR YKVSDNNTFQ ECSHYLFSKE ITSGCQIQKE
DIQLYQTFVV QLQDPQKPQR RAVQKLNLQN LVIPRAPENL TLSNLSESQL ELRWKSRHIK
ERCLQYLVQY RSNRDRSWTE LIVNHEPRFS LPSVDELKRY TFRVRSRYNP ICGSSQQWSK
WSQPVHWGSH TVEENPSLFA LEAVLIPVGT MGLIITLIFV YCWLERMPPI PPIKNLEDLV
TEYQGNFSAW SGVSKGLTES LQPDYSERFC HVSEIPPKGG ALGEGPGGSP CSLHSPYWPP
PCYSLKPEA
>DHA6_YEAST|P54115 ALDEHYDE DEHYDROGENASE, CYTOSOLIC (EC 1.2.1.3) | PS00070
MTKLHFDTAE PVKITLPNGL TYEQPTGLFI NNKFMKAQDG KTYPVEDPST ENTVCEVSSA
TTEDVEYAIE CADRAFHDTE WATQDPRERG RLLSKLADEL ESQIDLVSSI EALDNGKTLA
FKARGDVTIA INCLRDAAAY ADKVNGRTIN TGDGYMNFTT LEPIGVCGQI IPWNFPIMML
AWKIAPALAM GNVCILKPAA VTPLNALYFA SLCKKVGIPA GVVNIVPGPG RTVGAALTND
PRIRKLAFTG STEVGKSVAV DSSESNLKKI TLELGGKSAH LVFDDANIKK TLPNLVNGIF
KNAGQICSSG SRIYVQEGIY DELLAAFKAY LETEIKVGNP FDKANFQGAI TNRQQFDTIM
NYIDIGKKEG AKILTGGEKV GDKGYFIRPT VFYDVNEDMR IVKEEIFGPV VTVAKFKTLE
EGVEMANSSE FGLGSGIETE SLSTGLKVAK MLKAGTVWIN TYNDFDSRVP FGGVKQSGYG
REMGEEVYHA YTEVKAVRIK L
>DPOM_CLAPU|P22373 PROBABLE DNA POLYMERASE (EC 2.7.7.7) | PS00116
MLILLLQYNV SNPCLTNLLE NKTGTGVGLN FPLKPARLTL AQQRKRSELK KARLALRGMG
IGDFNRELRF YSTSAYTKTH WNNKDRINKW MQYDIFVDRD FESFLSHLFS DNRILFEYTY
ALLVKVRKGN KFYTIGDRQI GVLFVDIHDP FLLEVFDTII DRLAILFEEY PTELEYTCDA
LLLEFHPVRP EKIKISNLKD AKEKLAPKTF ATGMSVFNLI GGFDLRKVST PINLNKKRYY
STQVDRLNGF ITDNPRLLEF KQKFNEQLFM ASPKKKLKYE FCDTSVVFIL VKRGREYIVI
EDVKDGEFHK RIFNKTASLL LHLIDKSNGD GTWTRINGNF NTLYNLENEI IMSTKAIGLR
AIPKFLYNKK NEEEMSVLAN PNLGTIDLET TTGAQPKCYA IGFYTNLDSK PIKFYIDKNL
DSCQLVHTCI QEMMRYKYRN VLFYAHNLGK FDAVFLLKEL LRFNLTTEGL NNPYEFPAPL
TRNSDILKLT IKRTVDGKTR KVTIMDSFAL LPRSLRDLCK DYNIDNPKSY FPYLFSVDSH
LFYTGATPNI NYYLDIPKAE YLKLVKDDWD FKDETLEYLN LDLISLHQVL VKVNKAINFL
FDIEFTSCAT VSSLANKIFL SKFYDDKNKA IPLVKDIDLF NDIHEAYYGG RVEVFNPIIM
ADSTKSYYYY DVNSLYPFAS INDIPGLKCT FYEVVKANVN IHELFGFFYC KIKSPDNLYL
GLLPKRTETS LIFPGGAWEG WYFSEELKFA VAHGYEVEII KGYNFDRVSN VFNEFVQEVY
KVKCNPNNVT EKNIAKLILN SLIGRFGMNI NKIKTSLVPS EKHNELLTTR VVKSTTDLGS
GMFMDIYVPG IDKNICEDFN LDYIEVLNST NTDEKGTMPD NNVSITTAAA VLSYARIHMA
QIMLFILENN GTLYYTDTDS IVTDLKLPEE MVHQTEIGKL KLEHTITQGY FIADKTYAIV
NTEGEIIKRA KGVKSSKLTL EDYEKMYNKE VVEATKTSSK RNYKDGFVTI SDSTVKLNPT
SYTKRSRVIS KDKWIGTEII RLDKLNSKLS THTPKSLSGD KTK
>EUTE_ECOLI|P77445 ETHANOLAMINE UTILIZATION PROTEIN EUTE
MNQQDIEQVV KAVLLKMQSS DTPSAAVHEM GVFASLDDAV AAAKVAQQGL KSVAMRQLAI
AAIREAGEKH ARDLAELAVS ETGMGRVEDK FAKNVAQARG TPGVECLSPQ VLTGDNGLTL
IENAPWGVVA SVTPSTNPAA TVINNAISLI AAGNSVIFAP HPAAKKVSQR AITLLNQAIV
AAGGPENLLV TVANPDIETA QRLFKFPGIG LLVVTGGEAV VEAARKHTNK RLIAAGAGNP
PVVVDETADL ARAAQSIVKG ASFDNNIICA DEKVLIVVDS VADELMRLME GQHAVKLTAE
QAQQLQPVLL KNIDERGKGT VSRDWVGRDA GKIAAAIGLK VPQETRLLFV ETTAEHPFAV
TELMMPVLPV VRVANVADAI ALAVKLEGGC HHTAAMHSRN IENMNQMANA IDTSIFVKNG
PCIAGLGLGG EGWTTMTITT PTGEGVTSAR TFVRLRRCVL VDAFRIV
>EUTE_SALTY|P41793 ETHANOLAMINE UTILIZATION PROTEIN EUTE
MNQQDIEQVV KAVLLKMKDS SQPASTVHEM GVFASLDDAV AAAKRAQQGL KSVAMRQLAI
HAIREAGEKH ARELAELAVS ETGMGRVDDK FAKNVAQARG TPGVECLSPQ VLTGDNGLTL
IENAPWGVVA SVTPSTNPAA TVINNAISLI AAGNSVVFAP HPAAKKVSQR AITLLNQAVV
AAGGPENLLV TVANPDIETA QRLFKYPGIG LLVVTGGERV VDAARKHTNK RLIAAGAGNP
PVVVDETADL PRAAQSIVKG ASFDNNIICA DEKVLIVVDS VADELMRLME GQHAVKLTAA
QAEQLQPVLL KNIDERGKGT VSRDWVGRDA GKIAAAIGLN VPDQTRLLFV ETPANHPFAV
TEMMMPVLPV VRVANVEEAI ALAVQLEGGC HHTAAMHSRN IDNMNQMANA IDTSIFVKNG
PCIAGLGLGG EGWTTMTITT PTGEGVTSAR TFVRLRRCVL VDAFRIV
>GLGA_METJA|Q59001 PROBABLE GLYCOGEN SYNTHASE (EC 2.4.1.21) (STARCH [BACTER
MKIVILAPTI TPIVSYGGLG DVMRDLPKFL KKGNEVVVLT LNHYNRYFTL PYEDIKKITV
IYKGAKITFD VLRTKHPTTG VDLIVFSNES VNNLNVWDPI KYEIFADLVI TYLDEVKDID
VVSGHDWMCG LAIAKCNDIL DLPTTLTIHN EAFKGEMIEY KGEVMTFLEL GIKYADAVNT
VSPSHAEEIK NYPYIKKYLN NKPFCGILNG IDIDEYDPMK IIERMCNLSN NKLDPRNYAY
ISPYSAEDSH NIKPKIKYSW FYRGGVYEYV EDWNKIDKGI SATDVEVHGG VDGDIETPLI
GFVGRATHQK GFNTMFEAIP ELLEKHDIRF VFLTKGDRDI EERLKNLANE HDGRILALIG
YSLPLSSLVF AGSDWIIMPS YWEPCGLVQM EAMAYCTPVI ATETGGLKDT IIPLHPNPYE
HPNFDKATGV LFKVPDKVGF MWGVEHALNW TFYKLNEICM FMQYIRYKCP KHPYDENSPL
SMMMKNCYYH VFRNLSWQNS PSIRKYKGLF GGAIYNHYLQ P
>GLND_MYCTU|Q10961 PROBABLE [PROTEIN-PII] URIDYLYLTRANSFERASE (EC 2.7.7.59)
MEAESPCAAS DLAVARRELL SGNHRELDPV GLRQTWLDLH ESWLIDKADE IGIADASGFA
IVGVGGLGRR ELLPYSDLDV LLLHDGKPAD ILRPVADRLW YPLWDANIRL DHSVRTVSEA
LTIANSDLMA ALGMLEARHI AGDQQLSFAL IDGVRRQWRN GIRSRMGELV EMTYARWRRC
GRIAQRAEPD LKLGRGGLRD VQLLDALALA QLIDRHGIGH TDLPAGSLDG AYRTLLDVRT
ELHRVSGRGR DHLLAQFADE ISAALGFGDR FDLARTLSSA GRTIGYHAEA GLRTAANALP
RRGISALVRR PKRRPLDEGV VEYAGEIVLA RDAEPEHDPG LVLRVAAASA DTGLPIGAAT
LSRLAASVPD LPTPWPQEAL DDLLVVLSAG PTTVATIEAL DRTGLWGRLL PEWEPIRDLP
PRDVAHKWTV DRHVVETAVH AAPLATRVAR PDLLALGALL HDIGKGRGTD HSVLGAELVI
PVCTRLGLSP PDVRTLSKLV RHHLLLPITA TRRDLNDPKT IEAVSEALGG DPQLLEVLHA
LSEADSKATG PGVWSDWKAS LVDDLVRRCR MVMAGESLPQ AEPTAPHYLS LAADHGVHVE
ISPRDGERID AVIVAPDERG LVSKAAAVLA LNSLRVHSAS VNVHQGVAIT EFVVSPLFGS
PPAAELVRQQ FVGALNGDVD VLGMLQKRDS DAASLVSARA GDVQAGVPVT RTAAPPRILW
LDTAAPAKLI LEVRAMDRAG LLALLAGALE GAGAGIVWAK VNTFGSTAAD VFCVTVPAEL
DARAAVEQHL LEVLGASVDV VVDEPVGD
>GLO2_HUMAN|Q16775 HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6) (GLYOXALAS
MKVEVLPALT DNYMYLVIDD ETKEAAIVDP VQPQKVVDAA RKHGVKLTTV LTTHHHWDHA
GGNEKLVKLE SGLKVYGGDD RIGALTHKIT HLSTLQVGSL NVKCLATPCH TSGHICYFVS
KPGGSEPPAV FTGDTLFVAG CGKFYEGTAD EMCKALLEVL GRLPPDTRVY CGHEYTINNL
KFARHVEPGN AAIREKLAWA KEKYSIGEPT VPSTLAEEFT YNPFMRVREK TVQQHAGETD
PVTTMRAVRR EKDQFKMPRD
>GSHC_SCHMA|Q00277 GLUTATHIONE PEROXIDASE (EC 1.11.1.9) (GPX) | PS00460 | P
MSSSHKSWNS IYEFTVKDIN GVDVSLEKYR GHVCLIVNVA CKCGATDKNY RQLQEMHTRL
VGKGLRILAF PCNQFGGQEP WAEAEIKKFV TEKYGVQFDM FSKIKVNGSD ADDLYKFLKS
RQHGTLTNNI KWNFSKFLVD RQGQPVKRYS PTTAPYDIEG DIMELLEKK
>GYRB_ACICA|Q43947 DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177
SYKVSGGLHR VGVSVVNALS SKLHLMISRA GQVHEQEYQH GDPQYPLRVI GETDKSGTTV
RFWPSELTFT QTIFNVEILA RRLRELSFLN AGVRIVLRDE RINLGHVFDY EGGLSEKSAL
DIAGLPGKLA DCQEKDPALS ELYLVEGDSA GGSAKQGRNR KMQAILPLKG KILNVERARF
DKMISSQEVG TLITALGCGI GREEYNPDKL RYHKII
>GYRB_ACIJO|Q44081 DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177
SYKVSGGLHG VGVSVVNALS RKLELTIHRA GHIHQQEYKH GDPVYPLTVV GDTDTTGTTV
RFWPSAETFS QTIFNVDILA RRLRELSFLN AGVRIVWRDE RIHAEHVFDY EGGLSEKSAL
DIAGLPGKLA DCQEKDPALS ELYLVEGDSA GGSAKQGRNR KMQAILPLKG KILNVERARF
DKMISSQEVG TLITALGCGI GREEYNPDKL RYHKII
>GYRB_ACIS1|Q44272 DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177
SYKVSGGLHG VGVSVVNALS EKLELTIHRA GKIHEQEYRH GDSQYPLKVV GDTNRTGTRV
RFWPSAETFS QTIFNVDILA RRLRELSLLN AGVRIVLRDE RINAEHVFDY EGGLSEKSAL
DIAGLPGKLA DCQEKDPALS ELYLVEGDSA GGSAKQGRNR KMQAILPLKG KILNVERARF
DRMISSAEVG TLITALGCGI GREEYNPDKL RYHKII
>GYRB_ACIS6|Q44277 DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177
SYKVSGGLHG VGVSVVNALS KKLHLTIHRA GQIHEQEYAH GDPQYPLKVV GETDTSGTTV
RFWPSELTFS QTIFSVDILA RRLRELSFLN AGVRIVLRDE RVNLEHIYDY EVGLSEKSAL
DIAGLPGKLA DCQEKDPALS ELYLVEGDSA GGSAKQGRNR KMQAILPLKG KILNVERARF
DKMISSQEVG TLITALGCGI GREEYNPDKL RYHKII
>GYRB_ACIS8|Q44275 DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177
SHKVSGGLHG VGVSVVNALS SKLELTVQRA GQIHEQEYQH GVPQYPLRVV GQTERTGTKV
RFWPSAETFS QTIFNVDILA RRLRELSFLN AGVRIVLCDE RINLEHVFDY EGGLSEKSAL
DIAGLPGKLA DCQEKDPALS ELFLVEGDSA GGSAKQGRNR KMQAILPLKG KILNVERARF
DRMISSAEVG TLITALGCGI GREEYNPDKL RYHKIV
>GYRB_ACIS9|Q44276 DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177
SYKVSGGLLR VGVSVVNALS KKLHLTIHRA GQIHEQEYAH GDPQYPLKVV GETDTSGTTV
RFWPSEWTFS QTIFSVDILA RRLRELSFLN AGVRIVLRDE RVNLEHIYDY EVGLSEKSAL
DIAGLPGKLA DCQEKDPALS ELYLVEGDSA GGSAKQGRNR KMQAILPLKG KILNVERARF
DKMISSQEVG TLITALGCGI GREEYNPDKL RYHKII
>HBB1_TRICR|P10785 HEMOGLOBIN BETA-1 CHAIN (MAJOR) | PS01033
TFTNDESQHI HDVCGKIPVD QVGAEALGRL ILVNPWTRRY FKSFGDLSSA EAIQHNPKVA
SHGAKVMHSI AEAVKHLDDL KAYYADLSTI HCKKLYVDPA NFKLFGGIVS IVTGMHLGTD
YTAQKQAAFE KFLHHVEAAL ATGYH
>HOFB_HAEIN|P44622 PROTEIN TRANSPORT PROTEIN HOFB HOMOLOG | PS00662
MTSYALLHTQ RVTAKNGEVF TISPDLWERN QQQQSLLLRY FALPLKEENN RLWLGVDSLS
NLSACETIAF ITGKPVEPIL LESSQLKELL QQLTPNQMQV EEQVKFYQHQ ETHFEQEDDE
PVIRLLNQIF ESALQKNASD IHLETLADQF QVRFRIDGVL QPQPLISKIF ANRIISRLKL
LAKLDISENR LPQDGRFQFK TTFSDILDFR LSTLPTHWGE KIVLRAQQNK PVELSFSELG
MTENQQQAFQ RVLSQPQGLI LVTGPTGSGK SISLYTALQW LNTPDKHIMT AEDPIEIELD
GIIQSQINPQ IGLDFNRLLR TFLRQDPDII MLGEIRDEES AMIALRAAQT GHLVLSTLHT
NDAISAISRL QQLGIQQYEI KNSLLLVIAQ RLVRKLCSKC GGNLANSCDC HQGYRGRIGV
YQFLHWQQND YQTDFKNLRA SGLEKVSQGI TDEKEIERVL GKNL
>ITA2_BOVIN|P53710 PLATELET MEMBRANE GLYCOPROTEIN IA PRECURSOR (G (FRAGMENT
PLQLVLVFSQ GILNCCVAYN VGLPKAKIFS GPSSEQFGYA VQQFINPKGN WLLVGSPWSG
FPKNRMGDVY KCPVDLSTTT CEKLNLQTST SMSNVTEMKT NMSLGLTLTR NVGTGGFLTC
GPLWAQQCGS QYYTTGVCSD VSPDFQLRTS FAPAVQTCPS FIDVVVVCDE SNSIYPWDAV
KNFLEKFVQG LDIGPTKTQM GLIQYANNPR VVFNLNTFKS KDEMIKATSQ TFQYGGDLTN
TFKAIQYARD TAYSTAAGGR PGATKVMVVV TDGESHDGSK LKAVIDQCNK DNILRFGIAV
LGYLNRNALD TKNLIKEIKA IASIPTERHF FNVSDEADLL EKAGTIGEQI FSIEGTVQGG
DNFQMEMSQV GFSAEYSPQN NILMLGAVGA YDWSGTVVQK TPHGHLIFSK QAFEQILQDR
NHSSYLGYSV ASISTGNSVH FVAGAPRANY TGQIVLYSVN ENGNVTVIQS QRGDQIGSYF
GSVLCAVDVN KDTITDVLLV GAPMYMNDLK KEEGRVYLFT ITKGILNWHQ FLEGPNGLEN
ARFGSAIAAL SDINMDGFND VIVGSPLENQ NSGAVYIYNG HEGMIRLRYS QKILGSDRAF
SSHLQYFGRS LDGYGDLNGD SITDVSVGAF GQVVQLWSQS IADVSVDASF TPKKITLLNK
NAEIKLKLCF SAKFRPTNQN NQVAIVYNIT IDEDQFSSRV ISRGLFKENN ERCLQKTMIV
SQAQRCSEYI IHIQEPSDII SPLNLCMNIS LENPGTNPAL EAYSETVKVF SIPFHKDCGD
DGVCISDLVL NVQQLPATQQ QPFIVSNQNK RLTFSVQLKN KKESAYNTEI VVDFSENLFF
ASWSMPVDGT EVTCQIASSQ KSVTCNVGYP ALKSKQQVTF TINFDFNLQN LQNQASISFR
ALSESQEENM ADNSVNLKLS LLYDAEIHIT RSTNINFYEV SLDGNVSSVV HSFEDIGPKF
IFSIKVTTGS VPVSMASVII HIPQYTKDKN PLMYLTGVHT DQAGDISCEA EINPLKIGQT
SSSVSFKSEN FRHIKELNCR TASCSNIMCW LRDLQVKGEY FLNVSTRIWN GTFAASTFQT
VQLTAAAEID TYNPQIYVIE ENTVTIPLTI MKPHEKVEVP TGVIVGSVIA GILLLLALVA
ILWKLGFFKR KYEKMAKNPD ETDETTELNS
>ITA2_HUMAN|P17301 PLATELET MEMBRANE GLYCOPROTEIN IA PRECURSOR (GPIA) (COLL
MGPERTGAAP LPLLLVLALS QGILNCCLAY NVGLPEAKIF SGPSSEQFGY AVQQFINPKG
NWLLVGSPWS GFPENRMGDV YKCPVDLSTA TCEKLNLQTS TSIPNVTEMK TNMSLGLILT
RNMGTGGFLT CGPLWAQQCG NQYYTTGVCS DISPDFQLSA SFSPATQPCP SLIDVVVVCD
ESNSIYPWDA VKNFLEKFVQ GLDIGPTKTQ VGLIQYANNP RVVFNLNTYK TKEEMIVATS
QTSQYGGDLT NTFGAIQYAR KYAYSAASGG RRSATKVMVV VTDGESHDGS MLKAVIDQCN
HDNILRFGIA VLGYLNRNAL DTKNLIKEIK AIASIPTERY FFNVSDEAAL LEKAGTLGEQ
IFSIEGTVQG GDNFQMEMSQ VGFSADYSSQ NDILMLGAVG AFGWSGTIVQ KTSHGHLIFP
KQAFDQILQD RNHSSYLGYS VAAISTGEST HFVAGAPRAN YTGQIVLYSV NENGNITVIQ
AHRGDQIGSY FGSVLCSVDV DKDTITDVLL VGAPMYMSDL KKEEGRVYLF TIKKGILGQH
QFLEGPEGIE NTRFGSAIAA LSDINMDGFN DVIVGSPLEN QNSGAVYIYN GHQGTIRTKY
SQKILGSDGA FRSHLQYFGR SLDGYGDLNG DSITDVSIGA FGQVVQLWSQ SIADVAIEAS
FTPEKITLVN KNAQIILKLC FSAKFRPTKQ NNQVAIVYNI TLDADGFSSR VTSRGLFKEN
NERCLQKNMV VNQAQSCPEH IIYIQEPSDV VNSLDLRVDI SLENPGTSPA LEAYSETAKV
FSIPFHKDCG EDGLCISDLV LDVRQIPAAQ EQPFIVSNQN KRLTFSVTLK NKRESAYNTG
IVVDFSENLF FASFSLPVDG TEVTCQVAAS QKSVACDVGY PALKREQQVT FTINFDFNLQ
NLQNQASLSF QALSESQEEN KADNLVNLKI PLLYDAEIHL TRSTNINFYE ISSDGNVPSI
VHSFEDVGPK FIFSLKVTTG SVPVSMATVI IHIPQYTKEK NPLMYLTGVQ TDKAGDISCN
ADINPLKIGQ TSSSVSFKSE NFRHTKELNC RTASCSNVTC WLKDVHMKGE YFVNVTTRIW
NGTFASSTFQ TVQLTAAAEI NTYNPEIYVI EDNTVTIPLM IMKPDEKAEV PTGVIIGSII
AGILLLLALV AILWKLGFFK RKYEKMTKNP DEIDETTELS S
>KINN_HUMAN|Q12840 NEURONAL KINESIN HEAVY CHAIN (NKHC) | PS00411 | PS50067
MAETNNECSI KVLCRFRPLN QAEILRGDKF IPIFQGDDSV VIGGKPYVFD RVFPPNTTQE
QVYHACAMQI VKDVLAGYNG TIFAYGQTSS GKTHTMEGKL HDPQLMGIIP RIARDIFNHI
YSMDENLEFH IKVSYFEIYL DKIRDLLDVT KTNLSVHEDK NRVPFVKGCT ERFVSSPEEI
LDVIDEGKSN RHVAVTNMNE HSSRSHSIFL INIKQENMET EQKLSGKLYL VDLAGSEKVS
KTGAEGAVLD EAKNINKSLS ALGNVISALA EGTKSYVPYR DSKMTRILQD SLGGNCRTTM
FICCSPSSYN DAETKSTLMF GQRAKTIKNT ASVNLELTAE QWKKKYEKEK EKTKAQKETI
AKLEAELSRW RNGENVPETE RLAGEEAALG AELCEETPVN DNSSIVVRIA PEERQKYEEE
IRRLYKQLDD KDDEINQQSQ LIEKLKQQML DQEELLVSTR GDNEKVQREL SHLQSENDAA
KDEVKEVLQA LEELAVNYDQ KSQEVEEKSQ QNQLLVDELS QKVATMLSLE SELQRLQEVS
GHQRKRIAEV LNGLMKDLSE FSVIVGNGEI KLPVEISGAI EEEFTVARLY ISKIKSEVKS
VVKRCRQLEN LQVECHRKME VTGRELSSCQ LLISQHEAKI RSLTEYMQSV ELKKRHLEES
YDSLSDELAK LQAQETVHEV ALKDKEPDTQ DADEVKKALE LQMESHREAH HRQLARLRDE
INEKQKTIDE LKDLNQKLQL ELEKLQADYE KLKSEEHEKS TKLQELTFLY ERHEQSKQDL
KGLEETVARE LQTLHNLRKL FVQDVTTRVK KSAEMEPEDS GGIHSQKQKI SFLENNLEQL
TKVHKQLVRD NADLRCELPK LEKRLRATAE RVKALEGALK EAKEGAMKDK RRYQQEVDRI
KEAVRYKSSG KRAHSAQIAK PVRPGHYPAS SPTNPYGTRS PECISYTNSL FQNYQNLYLQ
ATPSSTSDMY FANSCTSSGA TSSGGPLASY QKANMDNGNA TDINDNRSDL PCGYEAEDQA
KLFPLHQETA AS
>KINN_MOUSE|P28738 NEURONAL KINESIN HEAVY CHAIN (NKHC) | PS00411 | PS50067
MADPAECSIK VMCRFRPLNE AEILRGDKFI PKFKGEETVV IGQGKPYVFD RVLPPNTTQE
QVYNACAKQI VKDVLEGYNG TIFAYGQTSS GKTHTMEGKL HDPQLMGIIP RIAHDIFDHI
YSMDENLEFH IKVSYFEIYL DKIRDLLDVS KTNLAVHEDK NRVPYVKGCT ERFVSSPEEV
MDVIDEGKAN RHVAVTNMNE HSSRSHSIFL INIKQENVET EKKLSGKLYL VDLAGSEKVS
KTGAEGAVLD EAKNINKSLS ALGNVISALA EGTKTHVPYR DSKMTRILQD SLGGNCRSRM
FICCSPSSYN DAETKSTLMF GQRAKTIKNT ASVNLELTAE QWKKKYEKEK EKTKAQKETI
AKLEAELSRW RNGENVPETE RLAGEDSALG AELCEETPVN DNSSIVVRIA PEERQKYEEE
IRRLYKQLDD KDDEINQQSQ LIEKLKQQML DQEELLVSTR GDNEKVQREL SHLQSENDAA
KDEVKEVLQA LEELAVNYHQ KSQEVEEKSQ QNQLLVDELS QKVATMLSLE SELQRLQEVS
GHQRKRIAEV LNGLMRDLSE FSVIVGNGEI KLPVEISGAI EEEFTVARLY ISKIKSEVKS
VVKRCRQLEN LQVECHRKME VTGRELSSCQ LLISQHEAKI RSLTEYMQTV ELKKRHLEES
YDSLSDELAR LQAHETVHEV ALKDKEPDTQ DAEEVKKALE LQMENHREAH HRQLARLRDE
INEKQKTIDE LKDLNQKLQL ELEKLQADYE RLKNEENEKS AKLQELTFLY ERHEQSKQDL
KGLEETVARE LQTLHNLRKL FVQDVTTRVK KSAEMEPEDS GGIHSQKQKI SFLENNLEQL
TKVHKQLVRD NADLRCELPK LEKRLRATAE RVKALEGALK EAKEGAMKDK RRYQQEVDRI
KEAVRYKSSG KRGHSAQIAK PVRPGHYPAS SPTNPYGTRS PECISYTNNL FQNYQNLHLQ
AAPSSTSDMY FASSGRTSVA PLASYQKANM DNGNATDIND NRSDLPCGYE AEDQAKLFPL
HQETAAS
>LEF4_NPVAC|P41477 LATE EXPRESSION FACTOR 4
MDYGDFVIEK EISYSINFSQ DLLYKILNSY IVPNYSLAQQ YFDLYDENGF RTRIPIQSAC
NNIISSVKKT NSKHKKFVYW PKDTNALVPL VWRESKEIKL PYKTLSHNLS KIIKVYVYQH
DKIEIKFEHV YFSKSDIDLF DSTMANKISK LLTLLENGDA SETLQNSQVG SDEILARIRL
EYEFDDDAPD DAQLNVMCNI IADMEALTDA QNISPFVPLT TLIDKMAPRK FEREQKIVYG
DDAFDNASVK KWALKLDGMR GRGLFMRNFC IIQTDDMQFY KTKMANLFAL NNIVAFQCEV
MDKQKIYITD LLQVFKYKYN NRTQYECGVN ASYAIDPVTA IECINYMNNN VQSVTLTDTC
PAIELRFQQF FDPPLQQSNY MTVSVDGYVV LDTELRYVKY KWMPTTELEY DAVNKSFNTL
NGPLNGLMIL TDLPELLHEN IYECVITDTT INVLKHRRDR IVPN
>MA2X_HUMAN|P49641 ALPHA-MANNOSIDASE IIX (EC 3.2.1.114) (MANNOSYL-OLIGOSACC
MKLKKQVTVC GAAIFCVAVF SLYLMLDRVQ HDPTRHQNGG NFPRSQISVL QNRIEQLEQL
LEENHEIISH IKDSVLELTA NAEGPPAMLP YYTVNGSWVV PPEPRPSFFS ISPQDCQFAL
GGRGQKPELQ MLTVSEELPF DNVDGGVWRQ GFDISYDPHD WDAEDLQVFV VPHSHNDPGW
IKTFDKYYTE QTQHILNSMV SKLQEDPRRR FLWAEVSFFA KWWDNINVQK RAAVRRLVGN
GQLEIATGGW VMPDEANSHY FALIDQLIEG HQWLERNLGA TPRSGWAVDP FGYSSTMPYL
LRRANLTSML IQRVHYAIKK HFAATHSLEF MWRQTWDSDS STDIFCHMMP FYSYDVPHTC
GPDPKICCQF DFKRLPGGRI NCPWKVPPRA ITEANVAERA ALLLDQYRKK SQLFRSNVLL
VPLGDDFRYD KPQEWDAQFF NYQRLFDFFN SRPNLHVQAQ FGTLSDYFDA LYKRTGVEPG
ARPPGFPVLS GDFFSYADRE DHYWTGYYTS RPFYKSLDRV LEAHLRGAEV LYSLAAAHAR
RSGLAGRYPL SDFTLLTEAR RTLGLFQHHD AITGTAKEAV VVDYGVRLLR SLVNLKQVII
HAAHYLVLGD KETYHFDPEA PFLQVDDTRL SHDALPERTV IQLDSSPRFV VLFNPLEQER
FSMVSLLVNS PRVRVLSEEG QPLAVQISAH WSSATEAVPD VYQVSVPVRL PALGLGVLQL
QLGLDGHRTL PSSVRIYLHG RQLSVSRHEA FPLRVIDSGT SDFALSNRYM QVWFSGLTGL
LKSIRRVDEE HEQQVDMQVL VYGTRTSKDK SGAYLFLPDG EASPTSPRSP PCCVSLKALS
SQRWLRTMST FTRRSGFTIC QGWRGCLWTY HPWWTSGTTS TRSWPCTSIQ TSTARVQPRR
YLKKLPLQAN FYPMPVMAYI QDAQKRLTLH TAQALGVSSL KDGQLEVILD RRLMQDDNRG
LGQGLKDNKR TCNRFRLLLE RRTVGSEVQD SHSTSYPSLL SHLTSMYLNA PALALPVARM
QLPGPGLRSF HPLASSLPCD FHLLNLRTLQ AEEDTLPSAE TALILHRKGF DCGLEAKNLG
FNCTTSQGKV ALGSLFHGLD VVFLQPTSLT LLYPLASPSN STDVYLEPME IATFRLRLG
>MAOC_FLAPR|P36444 MALATE OXIDOREDUCTASE, CHLOROPLAST PRECURSOR (EC 1.1.1.4
MMSLNSSSVV KSSISGVSWT QSQSVRLSVR RPMVVAMVNS NGRPERSVGV SVDGAVKDVN
APVAVEVADS ESKKPTAVVG GGVEDVYGED SATEDHFITP WSVSVASGYS LLRDPHHNKG
LAFTEKERDA HYLRGLLPPV VVNHDLQVKK MMHNIRQYEV PLQRYQAMMD LQERNERLFY
KLLIENIEEL LPIVYTPTVG EACQKYGTIF KNPQGLYISL KDKGKVLEIL KNWPQKKIQV
IVVTDGERIL GLGDLGCQGM GIPVGKLSLY TALGGIRPSA CLPITIDVGT NNEKMLNDEF
YIGLRQRRAS GKEYAELMNE FMSAVKQNYG EKVLIQFEDF ANHNAFDLLE KYRTTHLVFN
DDIQGTASVV LAGLISALKL VGGSLADHKF LFLGAGEAGT GIAELIALEI SKQTNAPLEE
TRKKIWLVDS KGLIVRSRLD SLQHFKKPWA HDHEPVNKFL DAVKAIKPTV LIGSSGAGQT
FTKEVVEAMS SFNEKPIILA LSNPTSQSEC TAEQAYTWSE GRTIFASGSP FAPVEYNGKV
YVSGQSNNAY IFPGFGLGLI ISGAIRVHDE MLLAASEALA EQVTQEHFDN GLIYPPFTNI
RKISAHIAAK VAAKAYELGL ASRLPQPENL VAYAESCMYS PKYRNYR
>MAOC_LYCES|P37222 MALATE OXIDOREDUCTASE, CHLOROPLAST (EC 1.1.1.4 (FRAGMENT
IRHESTVTGG VQDVYGEDSA TEDQSITPWT LSVASGFSLL RNPHYNKGLA FSERERDTHY
LRGLLPPVVI SHDLQVKKMM NSIRKYDVPL QRYMAMMDLQ EMNERLFYKL LIDNVEELLP
IVYTPTVGEA CQKYGWIFKR PQGLFFSLKE KGKIHEVLKN WPEKKIQVIV VTDGERILGL
GDLGCQGMGI PVGKLSLYSA LGGIRPSACL PVTIDVGQTM KFVDDEFYIG LRQRRATGQE
YSELLDEFMY AVKQNYGEKV LIQFEDFANH NAFNLLAKYG TSHLVFNDDI QGTASVVLAG
LMAALNLVGG SLSEHTFLFL GAGEAGTGIA ELIALEMSKQ TGIPLEETRK KIWMVDSKGL
IVKSRMEMLQ HFKRPWAHDH EPVQELVNAV KSIKPTVLIG SSGAGRTFTK EVVQAMATFN
EKPIIFALSN PTSQSECTAE EAYSWSEGRA IFASGSPFAP VEYNGKVYAS GQANNAYIFP
GFGLGLIISG AIRVHDDMLL VASEALADEV SQENFEKGTH IPPFSNIRKI SAHIAKVAAK
AYELGLATRL PQPKDLVAYA ESCMYSPAYR SYR
>MAOM_AMAHP|P37224 MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 65 KD ISOFORM
MLVLCSRSRL TSSLIRRLKD QIANVSNHRS FATSEGHRLA IVNKRSLDIL QDPWFNKGTA
FSMTERDRLD LRGLLPPNVM TTEQQIERFT ADLRVLELTT KDGPSDTYDL AKWRILNRLH
DRNETMFFKV LIENIEEYAP IVSTPTVGLV CQKFSGLYRR PRGMYFSSDD RGEMMSMVYN
WPAEQVDMIV VTDGSRILGL GDLGVHGIGV AIGKLDLYVA AAGINPQRVL PVMIDVGTNN
EDLLKNPLYL GLQKKRLDGE EYLAVMDEFM EAVFTRWPNV IVQFEDIQNK WALTLLQRYR
HKYRTFNVDV QGTSGVAIAG LLGAVRAQGR PMIDFPKQKI VVAGAGSSGV GVLNAARKTM
ARMLGNDESA FDRARSQFWV VDDKGLITEK RANLDPEVQP FAWKENEISL QGLNEGAKLV
EVVRQVKPDV LLGLSAYGGL FSKEVLEALK DSTSTRPAIF AMSNPTKNAE CTPEEAFSIV
GDHVVYASGS PFKDVDLGNG KIGHVNQGNN MYLFPGIGLG VLLSGSRIIS DSMFQAAAER
LAGYMTDEEV INGVIYPSIS RIRDITKEVA AAVIKEAVEE DLAEGYRDMD ARELQKLNEE
QILEYIEKNM WNPEYPTLVY KKR
>MAOM_SOLTU|P37221 MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 62 KD ISOFORM
MAIFSNQMRL SSTLLKRLHQ RVAAAVNSSS SRNFTTTEGH RPTIVHKRSL DILHDPWFNK
GTAFSFTERD RLHIRGLLPP NVMSFEQQIA RFMADLKRLE VQARDGPSDP YVLAKWRILN
RLHDRNETLY YKVLMENIEE YAPIVYTPTV GLVCQKYSGL FRRPRGMYFS AEDRGEMMSM
VYNWPADQVD MIVVTDGSRI LGLGDLGIQG IGIAIGKLDL YVAAAGINPQ RVLPVMIDVG
TDNENLLKDP LYLGLQDHRL DGEEYIEVID EFMEAVFTRW PHVIVQFEDF QSKWAFKLLQ
RYRNNYRMFN DDIQGTAGVA IAGLLGAVRA QGRPMIDFPK MKIVVAGAGS AGIGVLNAAR
KTMARMLGNT EIAFESARSQ FWVVDAKGLI TEARENVDPD ARPFARKIKE IERQGLSEGA
TLAEVVREVK PDVLLGLSAC GGLFSKEVLE ALKHSTSTRP AIFPMSNPTR NAECTPEEAF
SILGENIIFA SGSPFKDVDL GNGHVGHCNQ ANNMFLFPGI GLGTLLSGSR IVSDGMLQAA
AECLAAYITE EEVLKGIIYP SISRIRDITK EVAAAVVKEA IEEDLAEGYR EMDSRELRKL
DEAQISEFVE NNMWSPDYPT LVYKKD
>MAON_SOLTU|P37225 MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 59 KD ISOFORM
MWRVARSAAS TFRRTRRLST AISAPCIVHK RGADILHDPW FNKDTGFPMT ERDRLGLRGL
LPPRVISFEQ QYDRFMESFR SLEKNTEGQP DSVVSLAKWR ILNRLHDRNE TLYYRVLIDN
IKDFAPIIYT PTVGLVCQNY SGLFRRPRGM YFSAKDKGEM MSMIFNWPST QVDMIVLTDG
SRILGLGDLG VQGIGIPIGK LDMYVAAAGI NPQRVLPVML DVGTNNQKLL EDPLYLGLRQ
PRLEGEEYLS IVDEFVEAVH ARWPKAVVQF EDFQAKWAFE TLDRYRKKFC MFNDDIQGTA
GVALAGLLGT VRAQGRPLTD FANQKIVVVG AGSAGLGVLK MALQAVSRMT GPSADPHFFL
LDKNGLITKD RKDIDPAALP FAKAHHEIEG LGLQEGAGLA EVVKKVKPHV LLGLSGVGGI
FHEEVLRAMK ESDSVRPAIF AMSNPTNNAE CCPVDAFKLA GEDIVFASGS PFANVDLGNG
KIGHVNQANN MYLFPGIGLG ALLSGARNIS DTMLEAAAEC LASYMSDDEI NRGILYPSID
DIRDITAEVG AAVLRAAVAE DLAEGHGDVG VKELQHMSKE ETIEHVRQNM WYPVYGPLVH
E
>MAOX_MESCR|P37223 MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME) 
MGGSNALNEM TNGSDGITGG VADVYGEEFA TQDQLVTPWS FSVACGHSLL RDPQHNKGLA
FTEKERDAHF LRGLLPPVVL SQELQEKKFL TTLRQYQVPL QKYMAMMDLQ ERNEKLFYKL
LVDHVEELLP LVYTPTVGEG CQKYGSIFRR PQGLFISLKD KGRILELLRN WPEKKIQVIV
VTDGERILGL GDLGCQGMGI PVGKLSLYSA LGGVCPSACL PITLDVGTNN QKLLDDEFYI
GLKQKRATGE EYAEFVQEFM SAVKQNYGEK ILVQFEDFAN HNAFELLEKY RTTHLVFNDD
IQGTASVVLA GLIASLKLLG GTLADHKFLF LGAGEAGTGI AELIALEMSK KTKAPVEQMR
KKIWLVDSKG LVVSSRKETL QQFKLPWAHE HEPITTLIDA VQAIKPTVLI GTSGKGKQFT
KEVVEAMANI NAKPLILALS NPTSQSECTA EEAYTWSQGH AIFASGSPFD PVEYEGRTFV
PGQANNAYIF PGFGLGLIMC GAIRVHDDML LAASEALASQ VTGEHFIKGL IYPPFKDIRK
ISAHIAAGVA AKAYELGLAS RLPQPADLVK FAESCMYNPT YRSFR
>MAOX_PHAVU|P12628 MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME) 
MSSISLKENG GEVSVKKDYS NGGGVRDLYG EDSATEDHLI TPWTFSVASG CSLLRDPRYN
KGLAFTEGER DAHYLRGLLP PSVFNQELQE KRLMHNLRQY EVPLHRYMAL MDLQERNERL
FYKLLIDNVA ELLPVVYTPT VGEACQKYGS IFRRPQGLYI SLKEKGKILE VLKNWPEKSI
QVIVVTDGER ILGLGDLGCQ GMGIPVGKLS LYTALGGVRP SSCLPVTIDV GTNNEKLLND
EFYIGLRQRR ATGQEYATFL DEFMRAVKQN YGEKVLVQFE DFANHNAFDL LEKYSSSHLV
FNDDIQGTAS VVLAGLLASL KLVGGTLADH TFLFLGAGEA GTGIAELIAV EVSKQTKAPV
EETRKKIWLV DSKGLIVSSR LESLQQFKKP WAHEHEPVKG LLEAVKAIKP TVLIGSSGAG
KTFTKEVVET MASLNEKPLI LALSNPTSQS ECTAEEAYTW SKGRAIFASG SPFDPVEYEG
KLFVPGQANN AYIFPGFGLG LIMSGAIRVR DEMLLAASEA LAAQVSEENY DKGLIYPPFT
NIRKISANIA AKVAAKAYDL GLASHLKRPK DLVKYAESCM YSPGYRSYR
>MAOX_POPTR|P34105 MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME) 
MESTLKEMRD GASVLDMDPK STVGGGVEDV YGEDRATEDQ LVTPWTISVA SGYTLLRDPH
HNKGLAFTEK ERDAHYLRGL LPPTTISQQL QEKKLMNTIR QYQLPLQKYT AMMELEERNE
RLFYKLLIDN VEELLPVVYT PTVGEACQKY GSIFKRPQGL YISLKEKGKV LDVLKNWPQK
SIQVIVVTDG ERILGLGDLG CQGIGIPVGK LSLYTALGGV RPSACLPVTI DVGTNNEQLL
KDEFYIGLRQ RRATGQEYSE LLHEFMTAVK QNYGEKVLIQ FEDFANHNAF DLLAKYGTTH
LVFNDDIQGT AAVVLAGLIS ALKLLGGSLA DHTFLFLGAG EAGTGIAELI ALEMSRRSKT
PLEETRKKIW LTDSKGLIVS SRKESLQHFK KPWAHEHEPV KGLLEVVKAI KPIVLIGTSG
VGKTFTKEVI EAMASFNEKP LILALSNPTS QSECTAQEAY TWTKGKAIFA SGSPFDPVEY
EGKVFVPGQS NNAYIFPGLG LGLVISGAIR VHDDMLLAAA EALAGQIKEE YLAKGLIYPP
LSNIRKISVQ IAANVAAKAY ELGLATRLPR PENLVKHAES CMYSPAYRYY R
>MAOX_VITVI|P51615 MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME) 
MESTLKDIRD GASVLDLDPK ATVGGGVEDL YGEDFATEDQ LVTPWTVSVA SGYSLLRDPR
HNKGLAFNDK ERDAHYLCGL LPPVVSTQEL QERKLMNSIR QYQVPLQKYM AMMDLQERNE
RLFYKLLIDN VEELLPVVYT PTVGEACQKY GSIFRRPQGL YISLKEKGKI LEVLKNWPER
RIQVIVVTDG ERILGLGDLG CQGMGIPVGK LSLYTALGGV RPSACLPITI DVGTNNEKLL
ANEFYIGLKQ RRATGKEYSE FLQEFMSPVK QNYGEKVLIQ FEDFANHNAF DLLAKYGTTH
LAFNDDIQGT ASVVLAGIVS ALRLLGGTLA DHKFLFLGAG EAGTGIAELI ALEMSKQTKC
PIEETRKKIW LVDSKGLIVG SRKDSLQQFK KPWAHEHEPV KDLLDAVKVI KPTVLIGSSG
VGKAFTKEVI EAMASCNEKP LILALSNPTS QSECTAEEAY TWTQGRAIFA SGSPFDPVEY
NGKTFVPGQA NNAYIFPGLG MGLVISGAIR VHDEMLLAAS EALARQVTQE NFDKGLIYPP
FSNIRKISAH IAANVAAKAY ELGLATRLPQ PENLVKYAES CMYSPVYRSY R
>MSH5_YEAST|Q12175 MUTS PROTEIN HOMOLOG 5 | PS00486
MSHEWLISAS ETMRSIGNGE GLRDKGAVVA NNDGEFNEGD TNREEDSSTI FSFDFDEEIV
MCIDFSGGKL GCSILDYHTK TLKAFDQDYV VNKTTISSHD LIDDADMSSN DISLLLGLLI
MEANPTVCLV PARLEDWIFD YIKTKCDEIN CRLELQPIKR FKKWDLLQSL QLRGHDNQTI
LNDILSNSKF TTTVTLGTVG CILANHEQLG EYNDSTASSN MVTGRLVQNA FEDVIHGIRY
IDIRDRMVLD ENTISALHIF PTAHKLGHDK MMRNGFFSVF ELFNQVSSDY ARRILKSWLI
NPLTNKKRIE TRYSIIRTLL DKQNAIIFSD LSQSIKRCPD AFGFINQLRS GKSTLGTWSK
VASFLEKGIA IFQLVSSLKL GSDEANILHD IKNKVDISAL KECLRKVETV IDFDTSRDTK
TLTINTGVDN RLDECRNIYN HLEGILLDVA RETQIFLLNT MPQEDCKTTK SLEKLVNAVY
IPQLGYLVTI SVLMEPLLDG IPNLQWEEIF RSSENIYFKN GRVLELDETY GDIYGAISDF
EIEILFSLQE QILRRKTQLT AYNILLSELE ILLSFAQVSA ERNYAEPQLV EDECILEIIN
GRHALYETFL DNYIPNSTMI DGGLFSELSW CEQNKGRIIV VTGANASGKS VYLTQNGLIV
YLAQIGCFVP AERARIGIAD KILTRIRTQE TVYKTQSSFL LDSQQMAKSL SLATEKSLIL
IDEYGKGTDI LDGPSLFGSI MLNMSKSEKC PRIIACTHFH ELFNENVLTE NIKGIKHYCT
DILISQKYNL LETAHVGEDH ESEGITFLFK VKEGISKQSF GIYCAKVCGL SRDIVERAEE
LSRMINRGDD VVQQCGNLTE KEMREFQKNQ EIVKKFLSWD LDLETTTTSE NLRLKLKNFL
R
>NIFK_AZOVI|P07329 NITROGENASE MOLYBDENUM-IRON PROTEIN BETA CHAIN (EC 1.18.
SQQVDKIKAS YPLFLDQDYK DMLAKKRDGF EEKYPQDKID EVFQWTTTKE YQELNFQREA
LTVNPAKACQ PLGAVLCALG FEKTMPYVHG SQGCVAYFRS YFNRHFREPV SCVSDSMTED
AAVFGGQQNM KDGLQNCKAT YKPDMIAVST TCMAEVIGDD LNAFINNSKK EGFIPDEFPV
PFAHTPSFVG SHVTGWDNMF EGIARYFTLK SMDDKVVGSN KKINIVPGFE TYLGNFRVIK
RMLSEMGVGY SLLSDPEEVL DTPADGQFRM YAGGTTQEEM KDAPNALNTV LLQPWHLEKT
KKFVEGTWKH EVPKLNIPMG LDWTDEFLMK VSEISGQPIP ASLTKERGRL VDMMTDSHTW
LHGKRFALWG DPDFVMGLVK FLLELGCEPV HILCHNGNKR WKKAVDAILA ASPYGKNATV
YIGKDLWHLR SLVFTDKPDF MIGNSYGKFI QRDTLHKGKE FEVPLIRIGF PIFDRHHLHR
STTLGYEGAM QILTTLVNSI LERLDEETRG MQATDYNHDL VR
>NOD1_RHIGA|P50331 NODULATION PROTEIN D I | PS00044
MRFRGLDLNL LVALDALMTE RQLTAAARRI NLSQPAMSAA IARLRNYFHD DLFVMQGREL
ILTPRAEALA PAVRDTLLHI QLSVIAWDPI KPAESDRRFR IILSDFMTLI FMEKVIKRIA
REAPRVTFEL LPLDDDPDEL LRRGDVDFLI LPDLLMPNIH PKAKLFDETL VCVGCPMNKQ
LEDRLSMEKF MSMGHVAAKF GRLMKPSVEQ WLLLEHGFRR RIELVVPGFT LIPPLLVGTD
RIATLPMRLV KHFEQTIPLK IVEHPLPPLH FPLAVQWPAL HNTDPGNIWM REIMFDEASR
MEASSETSAV
>NRAM_INBBE|P27907 NEURAMINIDASE (EC 3.2.1.18)
MLPSTIQTLT LFLTSGGVLL SLYVSASLSY LLYSDILLKF SSKITAPTMT LDCANASNVQ
AVNRSATKEM TFLLPEPEWT YPRLSCQGST FQKALLISPH RFGEARGNSA PLIIREPFIA
CGPKECKHFA LTHYAAQPGG YYNGTREDRN KLRHLISVKL GKIPTVENSI FHMAAWSGSA
CHDGREWTYI GVDGPDSNAL IKIKYGEAYT DTYHSYANNI LRTQESACNC IGGDCYLMIT
DGSASGISKC RFLKIREGRI IKEIFPTGRV EHTEECTCGF ASNKTIECAC RDNSYTAKRP
FVKLNVETDT AEIRLMCTET YLDTPRPDDG SITGPCESNG DKGRGGIKGG FVHQRMASKI
GRWYSRTMSK TERMGMELYV RYDGDPWTDS DALAHSGVMV SMKEPGWYSF GFEIKDKKCD
VPCIGIEMVH DGGKKTWHSA ATAIYCLMGS GQLLWDTVTG VDMAL
>NRAM_INBHK|P16191 NEURAMINIDASE (EC 3.2.1.18)
MLPSTIQTLT LFLTSGGVLL SLYVSASLSY LLYSDILLKF SSTKRTAPTM SLDCANVSNV
QAVNRSATKE MTFLLPEPEW TYPRLSCQGS TFQKALLISP HRFGETRGNS APLIIREPFV
ACGPKECRHF ALTHYAAQPG GYYNGTRKDR NKLRHLISVK LGKIPTVENS IFHMAAWSGS
ACHDGREWTY VGVDGPDSNA LIKIKYGEAY TDTYHSYANN ILRTQESACN CIGGDCYLMI
TDGSASGISK CRFLKIREGR IIKEIFPTGR VEHTEECTCG FASNKTIECA CRDNSYTAKR
PFVKLNVETD TAEIRLMCTE TYLDTPRPDD GSITGPCESN GDKGLGGIKG GFVHQRMASK
IGRWYSRTMS KTERMGMELY VKYDGDPWTD SDALAPSGVM VSMKEPGWYS FGFEIKDKKC
DVPCIGIEMV HDGGKETWHS AATAIYCLMG SGQLLWDTVT GVDMAL
>NRAM_INBLN|P16193 NEURAMINIDASE (EC 3.2.1.18)
MLPSTIQTLT LFLTSGGVLL SLYVSASLSY LLYSDILLKF SPKITAPTMT LDCANASNVQ
AVNRSATKEM TFLLPEPEWT YPRLSCQGST FQKALLISPH RFGEARGNSA PLIIREPFIA
CGPKECKHFA LTHYAAQPGG YYNGTREDRN KLRHLISVKL GKIPTVENSI FHMAAWSGSA
CHDGREWTYI GVDGPDSNAL IKIKYGEAYT DTYHSYANNI LRTQESACNC IGGDCYLMIT
DGSASGISEC RFLKIREGRI IKEIFPTGRV EHTEECTCGF ASNKTIECAC RDNNYTAKRP
FVKLNVETDT AEIRLMCTET YLDTPRPDDG SITGPCESNG DKGRGGIKGG FVHQRMASKI
GRWYSRTMSK TERMGMELYV KYDGDPWTDS DALAPSGVMV SIKEPGWYSF GFEIKDKKCD
VPCIGIEMVH DGGKKTWHSA ATAIYCLMGS GQLLWDTVTG VDMAL
>NRAM_INBMF|P16199 NEURAMINIDASE (EC 3.2.1.18)
MLPSTIQTLT LFLTSGGVLL SLYVSASLSY LLYSDILLRF SSKITAPTMT LDCANASNVQ
AVNRSATKEM TFLLPEPEWT YPRLSCQGST FQKALLISPH RFGEARGNSA PLIIREPFIA
CGPKECKHFA LTHYAAQPGG YYNGTREDRN KLRHLISVKL GKIPTVENSI FHMAAWSGSA
CHDGREWTYI GVDGPDSNAL IKIKYGEAYT DTYHSYANNI LRTQESACNC IGGDCYLMIT
DGSASGISEC RFLKIREGRI IKEIFPTGRV EHTEECTCGF ASNKTIECAC RDNSYTAKRP
FVKLNVETDT AEIRLMCTET YLDTPRPDDG SITGPCESDG DKGRGGIKGG FVHQRMASKI
GRWYSRTMSK TERMGMELYV KYDGDPWTDS DALAPSGVMV SMKEPGWYSF GFEIKDKKCD
VPCIGIEMVH DGGKKTWHSA ATAIYCLMGS GQLLWDTVTG VDMAL
>NRAM_INBOR|P16201 NEURAMINIDASE (EC 3.2.1.18)
MLPSTIQTLT LFLTSGGVLL SLYVSASLSY LLYSDILLKF STTKITAPTM SLDCANISNV
QAVNRSATKE MTFLLPEPEW TYPRLSCQGS TFQKALLISP HRFGEARGNS APLIIREPFI
ACGPKECKHF ALTHYAAQPG GYYNGTRKDR NKLRHLISVK LGKIPTVENS IFHMAAWSGS
ACHDGREWTY IGVDGPDSNA LIKIKYGEAY TDTYHSYANN ILRTQESACN CIGGDCYLMI
TDGSASGISK CRFLKIREGR IIKEIFPTGR VEHTEECTCG FASNKTIECA CRDNSYTAKR
PFVKLNVETD TAEIRLMCTE TYLDTPRPDD GSITGPCESN GDKGLGGIKG GFVHQRMASK
IGRWYSRTMS KTERMGMELY VKYDGDPWTD SDALAPSGVM VSMKEPGWYS FGFEIKDKKC
DVPCIGIEMV HDGGKETWHS AATAIYCLMG SGQLLWDTVT GVDMAL
>NRAM_INBSI|P16203 NEURAMINIDASE (EC 3.2.1.18)
MLPSTIQTLT LFLTSGGVLL SLYVSASLSY LLYSDILLKF SPTKRTAPTM SLDCANVSNV
QAVNRSATKE MTFLLPEPEW TYPRLSCQGS TFQKALLISP HRFGEARGNS APLIIREPFI
ACGPKECKHF ALTHYAAQPG GYYNGTRKDR NKLRHLISVK LGKIPTVENS IFHMAAWSGS
ACHDGREWTY IGVDGPDSNA LIKIKYGEAY TDTYHSYANN ILRTQESACN CIGGDCYLMI
TDGSASGISK CRFLKIREGR IIKEIFPTGR VEHTEECTCG FASNKTIECA CRDNSYTAKR
PFVKLNVETD TAEIRLMCTE TYLDTPRPDD GSITGPCESN GDKGLGGIKG GFVHQRMASK
IGRWYSRTMS KTERMGMELY VKYDGDPWTD SEALAPSGVM VSMKEPGWYS FGFEIKDKKC
DVPCIGIEMV HDGGKETWHS AATAIYCLMG SGQLLWDTVT GVDMAL
>NRAM_INBUS|P16205 NEURAMINIDASE (EC 3.2.1.18)
MLPSTIQTLT LFLTSGGVLL SLYVSASLSY LLYSDILLKF SPTKRTAQTM SLDCANASNV
QAVNHSATKE MTFLLPEPEW TYPRLSCQGS TFQKALLISP HRFGEARGNS APLIIREPFI
ACGPKECKHF ALTHYAAQPG GYYNGTREDR NKLRHLISVK LGKIPTVENS IFHMAAWSGS
ACHDGREWTY IGVDGPDSNA LIKIKYGEAY TDTYHSYANN ILRTQESACN CIGGDCYLMI
TDGSASGISK CRFLKIREGR IIKEIFPTGR VEHTEECTCG FASNKTIECA CRDNSYTAKR
PFVKLNVETD TAEIRLMCTE TYLDTPRPDD GSITGPCESN GDKGRGGIKG GFVHQRMASK
IGRWYSRTMS KTERMGMELY VKYDGDPWTD SDALAPSGVM VSMKEPGWYS FGFEIKDKKC
DVPCIGIEMV HDGGKKTWHS AATAIYCLMG SGQLLWDTVT GVDMAL
>NRAM_INBVI|P16207 NEURAMINIDASE (EC 3.2.1.18)
MLPSTIQTLT LFLTSGGVLL SLYVSASLSY LLYSDILLKF SPKITAPTMT LDCTNASNVQ
AVNRSATKEM TFLLPEPEWT YPRLSCQGST FQKALLISPH RFGEARGNSA PLIIREPFIA
CGPKECKHFA LTHYAAQPGG YYNGTREDRN KLRHLISVKL GKIPTVENSI FHMAAWSGSA
CHDGREWTYI GVDGPDSNAL IKIKYGEAYT DTYHSYANNI LRTQESACNC IGGDCYLMIT
DGSASGISKC RFLKIREGRI IKEIFPTGRV EHTEECTCGF ASNKTIECAC RDNNYTAKRP
FVKLNVETDT AEIRLMCTET YLDTPRPDDG SITGPCESNG DKGRGGIKGG FVHQRMASKI
GRWYSRTMSK TERMGMELYV KYDGDPWTDS DALDPSGVMV SIKEPGWYSF GFEIKDKKCD
VPCIGIEMVH DGGKKTWHSA ATAIYCLMGS GQLLWDTVTG VDMAL
>NRAM_INBYB|Q90021 NEURAMINIDASE (EC 3.2.1.18)
MLPSTIQTLT LFLTSGGVLL SLYVSASLSY LLYSDILLKF SPTEITAPKV PLDCANASNV
QAVNRSATKG MTLLLSEPEW TYPRLSCQGS TFQKALLISP HRFGESRGNS APLIIREPFI
ACGPKECKHF ALTHYAAQPG GYYNGTREDR NKLRHLISVK LGKIPTVENS IFHMAAWSGS
ACHDGREWTY IGVDGPDSNA LIKIKYGEAY TDTYHSYANN ILRTQESACN CIGGDCYLMI
TDGSASGISK CRFLKIREGR IIKEIFPTGR VEHTEECTCG FASNKTIECA CRDNSYTAKR
PFVKLNVETD TAEIRLMCTE TYLDTPRPDD GSITGPCESN GDKGRGGIKG GFVHQRMASK
IGRWYSRTMS KTERMGMELY VKYDGDPWTD SDALAPSGVM VSMKEPGWYS FGFEIKDKKC
DVPCIGIEMV HDGGKKTWHS AATAIYCLMG SGQLLWDTVT GVDMAL
>NUCL_HUMAN|P19338 NUCLEOLIN (PROTEIN C23) | PS00030
VKLAKAGKNQ GDPKKMAPPP KEVEEDSEDE EMSEDEEDDS SGEEVVIPQK KGKKAAATSA
KKVVVSPTKK VAVATPAKKA AVTPGKKAAA TPAKKTVTPA KAVTTPGKKG ATPGKALVAT
PGKKGAAIPA KGAKNGKNAK KEDSDEEEDD DSEEDEEDDE DEDEDEDEIE PAAMKAAAAA
PASEDEDDED DEDDEDDDDD EEDDSEEEAM ETTPAKGKKA AKVVPVKAKN VAEDEDEEED
DEDEDDDDDE DDEDDDDEDD EEEEEEEEEE PVKEAPGKRK KEMAKQKAAP EAKKQKVEGT
EPTTAFNLFV GNLNFNKSAP ELKTGISDVF AKNDLAVVDV RIGMTRKFGY VDFESAEDLE
KALELTGLKV FGNEIKLEKP KGKDSKKERD ARTLLAKNLP YKVTQDELKE VFEDAAEIRL
VSKDGKSKGI AYIEFKTEAD AEKTFEEKQG TEIDGRSISL YYTGEKGQNQ DYRGGKNSTW
SGESKTLVLS NLSYSATEET LQEVFEKATF IKVPQNQNGK SKGYAFIEFA SFEDAKEALN
SCNKREIEGR AIRLELQGPR GSPNARSQPS KTLFVKGLSE DTTEETLKES FDGSVRARIV
TDRETGSSKG FGFVDFNSEE DAKEAMEDGE IDGNKVTLDW AKPKGEGGFG GRGGGRGGFG
GRGGGRGGRG GFGGRGRGGF GGRGGFRGGR GGGGDHKPQG KKTKFE
>NUCL_MOUSE|P09405 NUCLEOLIN (PROTEIN C23) | PS00030
VKLAKAGKTH GEAKKMAPPP KEVEEDSEDE EMSEDEDDSS GEEEVVIPQK KGKKATTTPA
KKVVVSQTKK AAVPTPAKKA AVTPGKKAVA TPAKKNITPA KVIPTPGKKG AAQAKALVPT
PGKKGAATPA KGAKNGKNAK KEDSDEDEDE EDEDDSDEDE DDEEEDEFEP PIVKGVKPAK
AAPAAPASED EEDDEDEDDE EDDDEEEEDD SEEEVMEITT AKGKKTPAKV VPMKAKSVAE
EEDDEEEDED DEDEDDEEED DEDDDEEEEE EEPVKAAPGK RKKEMTKQKE APEAKKQKVE
GSEPTTPFNL FIGNLNPNKS VNELKFAISE LFAKNDLAVV DVRTGTNRKF GYVDFESAED
LEKALELTGL KVFGNEIKLE KPKGRDSKKV RAARTLLAKN LSFNITEDEL KEVFEDAMEI
RLVSQDGKSK GIAYIEFKSE ADAEKNLEEK QGAEIDGRSV SLYYTGEKGQ RQERTGKTST
WSGESKTLVL SNLSYSATKE TLEEVFEKAT FIKVPQNPHG KPKGYAFIEF ASFEDAKEAL
NSCNKMEIEG RTIRLELQGS NSRSQPSKTL FVKGLSEDTT EETLKESFEG SVRARIVTDR
ETGSSKGFGF VDFNSEEDAK AAKEAMEDGE IDGNKVTLDW AKPKGEGGFG GRGGGRGGFG
GRGGGRGGRG GFGGRGRGGF GGRGGFRGGR GGGGDFKPQG KKTKFE
>OE66_NPVAC|Q00704 OCCLUSION-DERIVED VIRUS ENVELOPE PROTEIN E66 (ODV-E66)
MSIVLIIVIV VIFLICFLYL SNSNNKNDAN KNNAFIDLNP LPLNATTATT TTAVATTTTN
NNNSIVAFRQ NNIQELQNFE RWFKNNLSYS FSQKAEKVVN PNRNWNDNTV FDNLSPWTSV
PDFGTVCHTL IGYCVRYNNT SDTLYQNPEL AYNLINGLRI ICSKLPDPPP HQQAPWGPVA
DWYHFTITMP EVFMNITIVL NETQHYDEAA SLTRYWLGLY LPTAVNSMGW HRTAGNSMRM
GVPYTYSQIL RGYSLAQIRQ EQGIQEILNT IAFPYVTQGN GLHVDSIYID HIDVRAYGYL
INSYFTFAYY TYYFGDEVIN TVGLTRAIEN VGSPEGVVVP GVMSRNGTLY SNVIGNFITY
PLAVHSADYS KVLTKLSKTY YGSVVGVTNR LAYYESDPTN NIQAPLWTMA RRIWNRRGRI
INYNANTVSF ESGIILQSLN GIMRIPSGTT STQSFRPTIG QTAIAKTDTA GAILVYAKFA
EMNNLQFKSC TLFYDHGMFQ LYYNIGVEPN SLNNTNGRVI VLSRDTSVNT NDLSFEAQRI
NNNNSSEGTT FNGVVCHRVP ITNINVPSLT VRSPNSSVEL VEQIISFQTM YTATASACYK
LNVEGHSDSL RAFRVNSDEN IYVNVGNGVK ALFNYPWVMV KENNKVSFMS ANEDTTIPFS
VIMNSFTSIG EPALQYSPSN CFVYGNGFKL NNSTFDLQFI FEIV
>OE66_NPVOP|O10305 OCCLUSION-DERIVED VIRUS ENVELOPE PROTEIN E66 (ODV-E66)
MGLITLILAL IVVLFVCVFA SNSSKPANNA SFADNGAQRT AREFGPAARG GELLEFERWF
KDTLATVFAQ KAEKVANPTR AWNAETVFDN LSPWTSAADF GTVCHTLIGY CVRYNSPGDA
LHHSPDLANN LISGLRAICA RLPDPPPHQQ APWGPVADWY HFTITMPEVF MTVTIVLDNT
PHYDEAAALT RHWLALYLPT AVTSMGWHRT AGNAMRMGVP YAYGQLLRGY SAQQIAQEPG
VQETLKTVAF PYVAAGNGLH PDSIYIDHLD VRAYGYLINS FFTFAYYTRL FGADVVNTEG
LTRAIENVGS PEGVVVPGVM SRNGTLYSNV IGNFVDYPIA VHSADLSKVL TKLSDSYYGA
VVGATTRLAY YEADPTNNTQ APLWTMTRRI WNRRARVINY NANTVMFESG IILQSLNGVL
RVPSTTTSTQ SFRPAVGKTA LAKTRTAGAI LVHARFAEMN NLQFKSCTLF YDHGMFQLYY
NIGVEPNSLN NVNGRVVVLS RDTSVNTNDL SFEAQRLNNN NSSDGSAFNG VVCQRVPITN
FNVPSLTVRS PSASVELVEQ IISFQNMYTA SAVACYKLNV EGHSDALRAY RINMDEVVYV
TTGEGVKALF AYPWLMLKED AAVVFMSANE DLVVPMSVIN NAFSAIDEPG LQYAPVNCFL
YGNGFRLNDS LANLQFQFEI IN
>PARF_PARTE|P47244 PARAFUSIN | PS00710
MVLFLLPLRL GHNLWRIEAP RVQVTQPYAG QKPGTSGLRK KVSEATQPNY LENFVQSIFN
TLRKDELKNV LFVGGDGRYF NRQAIFSIIR LAYANDISEV HVGQAGLMST PASSHYIRKV
NEEVGNCIGG IILTASHNPG GKEHGDFGIK FNVRTGAPAP EDFTDQIYTH TTKIKEYLTV
DYEFEKHINL DQIGVYKFEG TRLEKSHFEV KVVDTVQDYT QLMQKLFDFD LLKGLFSNKD
FSFRFDGMHG VAGPYAKHIF GTLLGCSKES LLNCDPSEDF GGGHPDPNLT YAHDLVELLD
IHKKKDVGTV PQFGAACDGD ADRNMILGRQ FFVTPSDSLA VIAANANLIF KNGLLGAARS
MPTSGALDKV AAKNGIKLFE TPTGWKFFGN LMDAGLINLC GEESFGTGSN HIREKDGIWA
VLAWLTILAH KNKNTDHFVT VEEIVTQYWQ QFGRNYYSRY DYEQVDSAGA NKMMEHLKTK
FQYFEQLKQG NKADIYDYVD PVDQSVSKNQ GVRFVFGDGS RIIFRLSGTG SVGATIRIYF
EQFEQQQIQH ETATALANII KLGLEISDIA QFTGRNEPTV IT
>PH81_YEAST|P17442 PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO81 (CDK 
MKFGKYLEAR QLELAEYNSH FIDYKALKKL IKQLAIPTLK ASSDLDLHLT LDDIDEKIIH
QRLQENKAAF FFKLERELEK VNGYYLARES DLRIKFNILH SKYKDYKING KLNSNQATSF
KNLYAAFKKF QKDLRNLEQY VELNKTGFSK ALKKWDKRSQ SHDKDFYLAT VVSIQPIFTR
DGPLKLNDET LHILLELNDI DNNNRRADIQ SSTFTNDDDD DNNTSNNNKH NNNNNNNNNN
NNNNNNNNIL HNNYELTTSK ISENQLEHLF QASSSSLDME MEIENWYKEI LNIATVKDVQ
RKHALLRNFR ETKIFTYLLQ NSSESFHKNV FSLLKECLTT LFLLLVASPL DDNSLHIFYK
SNQDHIDLSY CDEDDQVFSR KNVFHEAASC PEKSRLFILD EALTTSKLSK ETVQKLLNAQ
DIHSRVPLHY AAELGKLEFV HSLLITNLLE DVDPIDSDSK TPLVLAITNN HIDVVRDLLT
IGGANASPIE KPILDYSKNV ISSTKVQFDP LNVACKFNNH DAAKLLLEIR SKQNADNAKN
KSSQHLCQPL FKKNSTGLCT LHIVAKIGGD PQLIQLLIRY GADPNEIDGF NKWTPIFYAV
RSGHSEVITE LLKHNARLDI EDDNGHSPLF YALWESHVDV LNALLQRPLN LPSAPLNEIN
SQSSTQRLNT IDLTPNDDKF DLDIQDSIPD FALPPPIIPL RKYGHNFLEK KIFIKLKLRP
GLESIKLTQD NGIIMSSSPG RITLSSNLPE IIPRNVILPV RSGEINNFCK DISETNDEED
DDEISEDHDD GEIIFQVDSI DDFSMDFEIF PSFGTRIIAK TTAMPFLFKK VAINSIATMN
LPLFDTRLNN IGSLTLDYQI IFPYPGNPLK IINYEPYWKS TGSDLMTSSK DGNFVTSSSL
NGSFISVLVC ALNDETIVAA PKPYVEFKGT KILLNDLTKE QLEKVVDYDF GKIDGSFDEV
TLKQYLSSRV VPLRSLLEVI PGSAQLVIRV YFPTDKEIDT IPIKISPFIN INQFIDKLLL
IIFEHERFLR HSGSGSMRQI VFSSCNWEAC SILNWKQPNF PVLLQMKNLL RDSTTGKFVG
DTPNCLKELA VNPQKMSYLN TELINIHTMV QFAMNNNLLG VTLPYEVLKI CPSLARIIKQ
NGLLLIASVG ENDQIPADGG YSGIYYACEL LFENNIDM
>PPS2_BACSU|P39846 PEPTIDE SYNTHETASE 2 | PS00012 | PS00455 | PS50075
MAQSAQIQDI YPLSHMQEGM LFHSLMDFSS KAYIEQTSFT ITGNLCVDSF QKSLNLLVSR
YDIFRTIFIK EVPDLTGPQQ VVLSNRELTV YREDISRLAD QEQQTLIDAF MTKDREKGFD
LQKDPLMRLA LFDRGDSQYT CVWTHHHIIM DGWCLGIILK EFFSMYDSLK NNSPVQLGST
VPYSRYIEWL GEQDQEETAA YWSEYLKEYG NTASIPRIKR RTADGNYKAD QVSFSLAPDM
VEKLTEAAQN WGVTLNTLFM SIWGVLLHRY NAADDAVFGS VISGRPSAID GIESMVGLFI
NTVPVRIRSA EGITFSSLVK AVQEDILSSE QHGYYPLYEI QNHSPLKQGL IDHIFVFENY
PVQLHQALSV ESENDEGALK LSDISMSEQT NYDFNIVIVP GESFYIKFSY NADVYEREEM
LRIQGHLKQA LDCILTNPDV AVSDINIVPP EEQQVIQLFN ETERPYVNKT IPQLFEEQAH
KTPEAAALKM GNECWTYRQL QVRANQIAHA LIEKGVGSGD IVAVMMGRSM EMPAALLGIW
KAGGAYMPLD PHFPAERLSF LLKDSQAAQL LIEEDLISLI PPSYEGNTIT IEHTESYQTE
APNMPPGDLA YLIYTSGTTG RPKGVLVDHH GIANTLQWRR EEYSMTEQDI SLHLFSYVFD
GCVTSLFTPL LSGACVLLTT DDEAKDVLAL KRKIARYKVS HMIIVPSLYR VLLEVMTADD
AKSLRIVTFA GEAVTPDLLE LNQIICPSAE LANEYGPTEN SVATTILRHL NKKERITIGH
PIRNTKVFVL HGNQMQPIGA AGELCISGAG LARGYYKQQE LTQKAFSDHP FLEGERLYRT
GDAGRFLPDG TIEYIGRFDD QVKIRGYRIE LREIETVLRQ APGVKEAAVL ARDVSAEEKE
LVAYIVPEKG NSLPDLYQHL AGTLPSYMIP ASIINISQMP LTSSGKLDRF ALPEPENNTS
VTYMAPRTLI EADLAHIWED VLNKQHIGIR DDFFQLGGQS LKAAALVSRI HKKLNVELPL
SEVFSYPTVE SMAVKLMSLK EHAFTQIEPA DQRDVYPLSF SQKRLYALHQ LADDSTGYNM
PAVLELRGNL NRQRLRSVLT ELVNRHEALR TVFVLDRDEP VQIIYPEMAF DLKELEMESE
QMLESAIETF IKPFYLSSGP LFRACVITMG NNRGFLLLDM HHIIADGVSM STLVQEFTDL
YCGKELPALN LHYKDFAVWQ QEKHPKELYK KQEAYWLGQL GGSLPTLELP LDKTRPRLPD
FRGGTIEVNI DKDMADELHR LMAETGTTLY MILLAVYSIL LSKLSGQEDI VVGSPAAGRP
HADLERVIGM FVNTLAMRSK PEGHKTFSSY LHDIRHLALT AYEHQDYPFE ELADKLDTNR
EVNRNPLFDA MLVLQSSEDF RFEVPGLSIS SVTPKHDISK FDLTLHAEEH LSGIRCRFEY
STALFEEETI TQWASYFIEL VKGVTADTEM RISNMQLLPA AERRLLLEKM GQYAAYPRNE
NIVSLFEKQV AQYPEHIAVV CGHSQLTYRD LNEKAERAAA MLIKQGVRTG DIVGLMLDRS
PDMIIGVLSI LKAGGAYLPI DPEYPKERIS FMLNDSGAKL LLTERGLNKP ADYTGHILYI
DECENNSIPA DVNIEEIVTD QPAYVIYTSG TTGQPKGVIV EHRNVISLLK HQNLPFEFNH
EDVWTLFHSY CFDFSVWEMF GALLNGSTLV VVSKETARDP QAFRLLLKKE RVTVLNQTPT
AFYGLMLEDQ NHTDHLNIRY VIFGGEALQP GLLQSWNEKY PHTDLINMYG ITETTVHVTF
KKLSAADIAK NKSNIGRPLS TLQAHVMDAH MNLQPTGVPG ELYIGGEGVA RGYLNRDELT
ADRFVSNPYL PGDRLYRTGD LAKRLSNGEL EYLGRIDEQV KVRGHRIELG EIQAALLQYP
MIKEAAVITR ADEQGQTAIY AYMVIKDQQA ANISDIRTYL KNALPDFMLP ARMIQIDSIP
VTVNGKLDQK ALPEPEKQAY TADDISPRNE IETVMAEIWE ELLNVDELGV SANFFKLGGD
SIKALQVCAR LKQRGFETTV REMFEHQTLG ELSARVRKDV RAIDQGPVEG EITWTPIQQW
FFSQSLESHH FNQSVMIYRA ERFDEAALRK VLKSLVTHHD ALRIVCRHED GRQVQINRGI
DLSDEELYAL ELFDVKDSLT EARNTIEEAA SRMQEHIRLE TGPLLHAGLF RTENGDHLFL
TIHHLVVDAV SWRILFEDFS TAYKQAVSGE SIKLPQKTDS YLTYSQRIAD YSISRQVQRE
AAYWDECENR HIQPIPKDND AASNTFKDTE VIDFELSRHH TELLLTAAHK AYSTEMNDIL
LTALGLALQK WTGNNQFKIS MEGHGRESYL EDIDISRTVG WFTSIYPVWL DMRDSDHKDK
EERLGHLIKQ TKDMLHRIPH KGAGYGVLKY ISKRWGSQKN SPEISFNYLG QFDQDIQSNA
FEVSDIKPGN EISPNWERPY ALDISGAVSS GCLNMHIIYN RFQFEEKTIQ TFSRHFKQTL
ENIIEHCTGK ENQEWSASDF TDEDLTLDEL SEIMGAVNKL
>PSRC_WOLSU|P31077 POLYSULFIDE REDUCTASE CHAIN C (SULPHUR REDUCTASE CHAIN C
MNQMWGSIEQ YNTVVWHWPI AVYLFLAGLS AGAIISAIII KWMKGNESSP WDGIIKAGAL
IAPLTIGAGL LLLIFDLTRP LHFWKLLIFY NFSSVMTLGV LALFAYFPVV LIFLLGVFKK
ELCDEGPFGF LAPLANIAYS MARPLEIVTF VLAIGVGAYT GFLLSAMYSY PLLNTPILPL
LFLASGISAG ISGNLLIGLL FFGKSTKGEN VGYLHGLDFK VILFEAFLLF ILFVGMYYQG
GSTAEVAKAA LTTGGLASLF WLGVAGMGLA LPVVLNVALP HGIKHSSGFV MLNALIVLAG
VMALRFYILY AGQTFVG
>PTP1_DROME|P35992 PROTEIN-TYROSINE PHOSPHATASE 10D PRECURSOR (EC 3.1.3.48)
MLYQLSKATT RIRLKRQKAV PQHRWLWSLA FLAAFTLKDV RCADLAISIP NNPGLDDGAS
YRLDYSPPFG YPEPNTTIAS REIGDEIQFS RALPGTKYNF WLYYTNFTHH DWLTWTVTIT
TAPDPPSNLS VQVRSGKNAI ILWSPPTQGS YTAFKIKVLG LSEASSSYNR TFQVNDNTFQ
HSVKELTPGA TYQVQAYTIY DGKESVAYTS RNFTTKPNTP GKFIVWFRNE TTLLVLWQPP
YPAGIYTHYK VSIEPPDAND SVLYVEKEGE PPGPAQAAFK GLVPGRAYNI SVQTMSEDEI
SLPTTAQYRT VPLRPLNVTF DRDFITSNSF RVLWEAPKGI SEFDKYQVSV ATTRRQSTVP
RSNEPVAFSD FRDIAEPGKT FNVIVKTVSG KVTSWPATGD VTLRPLPVRN LRSINDDKTN
TMIITWEADP ASTQDEYRIV YHELETFNGD TSTLTTDRTR FTLESLLPGR NYSLSVQAVS
KKMESNETSI FVVTRPSSPI IEDLKSIRMG LNISWKSDVN SKQEQYEVLY SRNGTSDLRT
QKTKESRLVI KNLQPGAAYE LKVFAVSHDL RSEPHAYFQA VYPNPPRNMT IETVRSNSVL
VHWSPPESGE FTEYSIRYRT DSEQQWVRLP SVRSTEADIT DMTKGEKYTI QVNTVSFGVE
SPVPQEVNTT VPPNPVSNII QLVDSRNITL EWPKPEGRVE SYILKWWPSD NPGRVQTKNV
SENKSADDLS TVRVLIGELM PGVQYKFDIQ TTSYGILSGI TSLYPRTMPL IQSDVVVANG
EKEDERDTIT LSYTPTPQSS SKFDIYRFSS GDAEIRDKEK LANDTDRKVT FTGLVPGRLY
NITVWTVSGG VASLPIQRQD RLYPEPITQL HATNITDTEI SLRWDLPKGE YNDFDIAYLT
ADNLLAQNMT TRNEITISDL RPHRNYTFTV VVRSGTESSV LRSSSPLSAS FTTNEAVPGR
VERFHPTDVQ PSEINFEWSL PSSEANGVIR QFSIAYTNIN NLTDAGMQDF ESEEAFGVIK
NLKPGETYVF KIQAKTAIGF GPEREYRQTM PILAPPRPAT QVVPTEVYRS SSTIQIRFRK
NYFSDQNGQV RMYTIIVAED DAKNASGLEM PSWLDVQSYS VWLPYAIDPY YPFENRSVED
FTIGTENCDN HKIGYCNGPL KSGTTIGVKV RRFTGADKFT DTAYSFPIQT DQDNTSLIVA
ITVPLTIILV LLVTLIFYKR RRNNCRKTTK DSRANDNMSL PDSVIEQNRP ILIKNFAEHY
RLMSADSDFR FSEEFEELKH VGRDQPCTFA DLPCNRPKNR FTNILPYDHS RFKLQPVDDD
EGSDYINANY VPGHNSPREF IVTQGPLHST RDDFWRMCWE SNSRAIVMLT RCFEKGREKC
DQYWPNDTVP VFYGDIKVQI LNDSHYADWV MTEFMLCRGS EQRILRHFHF TTWPDFGVPN
PPQTLVRFVR AFRDRICAEQ RPIVVHCSAG VGRSGTFITL DRILQQINTS DYVDIFGIVY
AMRKERVWMV QTEQQYICIH QCLLAVLEGK ENIVGPAREM HDNEGYEGQQ VQLDENGDVV
ATIEGHLSHH DLQQAEAEAI DDENAAILHD DQQPLTSSFT GHHTHMPPTT SMSSFGGGGG
GHTNVDAPDR
>RFAB_ECOLI|P27127 LIPOPOLYSACCHARIDE 1,6-GALACTOSYLTRANSFERASE (EC 2.4.1.-
MSFTQLMRVS MKIAFIGEAV SGFGGMETVI RDVITTFRQQ HIQSEMFFFC RNDKMDKGWL
EGIKYSCSFS NIRLGFLRRA KHIHALSKWL QEYQPDIVIC IDVISCLFAA KARKKSGIDM
PVFSWPHFSL DHKKHAEYIT CADYHLAISS GIKQQMINRG VAESTINVIF NPVETKDSVI
PAPEEGETAT FIYVGRMKFE GQKRVKDLLD GLSQAKGNWK LHVLGDGSDF EKCQAYGREL
NIDDRIVWYG WQQYPWELVQ QDIEKVSALL LTSSFEGFPM TLLEALSWGI PCISADCVSG
PADIIQPDVN GHLYQPGDIA GFVTLLNKYI AGEIHIEHEK IPASIDEFYQ SKYYDRLHKV
IISAISRRK
>RL17_SCHPO|O59794 60S RIBOSOMAL PROTEIN L17 | PS00464
MVRYSAAPAL ETKCAKARGA YLRTHFKNSR EVAFTINGMN LKKAFIFLDN VKEHKQAVPF
RRFNGGVGRT AQGKEFGVTQ ARWPVKSVNF FYDLLKNAEA NAEAKGLDMD KLIIKHVQVN
AAPKQRRRTY RAHGRVTAYL SSPSHIEIIV AEEEEAVPKA NDTVSRVSLK QGAKARNLAA
RKAITSA
>RPOC_TREPA|O83270 DNA-DIRECTED RNA POLYMERASE BETA' CHAIN (EC 2.7.7.6) (TR
MKDIRDFDSL QIKLASPDTI RAWSYGEVKK PETINYRTLR PEREGLFCER IFGTTKEWEC
FCGKFKSIRY RGVICDRCGV EVTHFKVRRE RMGHIELATP VSHIWYYRCV PSRMGLLLDL
QVIALRSVLY YEKYIVIEPG DTDLKKNQLL TETEYNDAQE RYGGGFTAGM GAEAIRTLLQ
NLDLDALVAQ LREKMMEKGA KSDKRLLRRI EIVENFRVSG NKPEWMILSV IPVIPPDLRP
MVQLDGGRFA TSDLNDLYRR VIHRNSRLIR LMELKAPDII IRNEKRMLQE AVDALFDNSK
RKPAIKGASN RPLKSISDML KGKQGRFRQN LLGKRVDYSG RSVIVVGPEL KLWQCGLPTK
MALELFKPFI MKKLVEKEIV SNIKKAKMLV EQESPKVFSV LDEVVKEHPV MLNRAPTLHR
LGIQAFEPVL VEGKAIRLHP LVCKPFNADF DGDQMAVHVP LTQAAQMECW TLMLSNRNLL
DPANGRTIVY PSQDMVLGLY YLTKERSLPE GARPRRFSSV EEVMMAAEKG VIGWQDQIQV
RYHKCDGQLV VTTAGRLVLN EEVPAEIPFV NETLDDKRIR KLIERVFKRQ DSWLAVQMLD
ALKTIGYTYA TFFGATLSMD DIIVPEQKVQ MLEKANKEVL AIASQYRGGH ITQEERYNRV
VEVWSKTSEE LTSLMMETLE RDKDGFNTIY MMATSGARGS RNQIRQLAGM RGLMAKPSGD
IIELPIRSNF KEGLNVIEFF ISTNGARKGL ADTALKTADA GYLTRRLVDI AQDVVVNEED
CGTINGIEYR AVKSGDEIIE SLAERIVGKY TLERVEHPIT HELLLDVNEY IDDERAEKVE
EAGVESVKLR TVLTCESKRG VCVCCYGRNL ARNKIVEIGE AVGIVAAQSI GQPGTQLTMR
TFHVGGTASS TTEENRITFK YPILVKSIEG VHVKMEDGSQ LFTRRGTLFF HKTLAEYQLQ
EGDSVQVRDR ARVLKDEVLY HTTDGQTVYA SVSGFARIID RTVYLVGPEQ KTEIRNGSNV
VIKADEYVPP GKTVATFDPF TEPILAEQDG FVRYEDIILG STLIEEVNTE TGMVERRITT
LKTGIQLQPR VFISDESGNA LGSYYLPEEA RLMVEEGAQV KAGTVIVKLA KAIQKTSDIT
GGLPRVSELF EARRPKNAAV LAQISGVVSF KGLFKGKRIV VVRDHYGKEY KHLVSMSRQL
LVRDGDTVEA GERLCDGCFD PHDILAILGE NALQNYLMNE IRDVYRVQGV SINDQHIGLV
VRQMLRKTEV VSVGDTRFIY GQQVDKYRFH EENRRVEAEG GQPAVARPMF QGITKAALNI
DSFISAASFQ ETNKVLTNAA IAGSVDDLCG LKENVIIGHL IPAGTGMRRY RQVKLFDKNK
RDLDVQMEEV IRRRKLEEEA LAQAVAGMEG EPEGEA
>RPOD_ORYSA|P12093 DNA-DIRECTED RNA POLYMERASE BETA" CHAIN (EC 2.7.7.6)
MAERANLVFQ NKEIDGTAMK RLISRLIDHF GMGYTSHILD QIKTLGFHQA TTTSISLGIE
DLLTIPSKGW LVQDAEQQSF LLEKHYYYGA VHAVEKLRQS VEIWYATSEY LKHEMNSNFR
ITDPSNPVYL MSFSGARGNA SQVHQLVGMR GLMADPQGQM IDLPIQSNLR EGLSLTEYII
SCYGARKGVV DTAVRTADAG YLTRRLVEVV QHIIVRRRDC GTIQAISVSP QNGMTEKLFV
QTLIGRVLAN DIYIGSRCIA TRNQDIGIGL VNRFITTFRA QPFRAQPIYI RTPFTCRSTS
WICQLCYGRS STHGDLVELG EAVGVIAGQS IGEPGTQLTL RTFHTGGVFT GGTADLVRSP
SNGKIQFNGD LVHPTRTRHG QPAFLCYIDL HITIQSQDIL HSVTIPSKSL ILVQNDQYVE
SEQVIAEIRA GTSALHFKEK VQKHIYSESD GEMHWSTDVY HAPEYQYGNL RRLPKTSHLW
ILSVSMCRSS IASFSLHKDQ DQMNTYSFSV DGRYIFGLSM ADDEVRHRLL DTFGKKDREI
LDYSTPDRIM SNGHWNFVYP SILQNNFDLL AKKRRNRFAI PLQYHQEQEK EPISCFGISI
EIPFMGVLRR NTIVAYFDDP RYKKDKKGSG IVKFRYRTLE DEYRTREKDS ENEYGSPENE
YRTREEECKT LEDEYRTREE EYETLEDEYG IPENEYETLE DEYGILEDEY RTREEESEDE
YGSPENKYRP REDKYGTLEE DSEDEHGTLE EDSEEDSEDE YGNPEEDSVL KKGVLIEHRG
TKEFSLKYQK EVDRFFFILQ ELHILPRSSS LKVLDNSIIG VDTQLTKNTR SRLGGLVRVK
RKKSHTELKI FSGDIHFPEE ADKILGGSLI PLEREKKDSK ESKKRENWVY VQWKKILKSK
EKYFVLVRPA VAYEMNEGRN LATLFPQDLF EEEGNLQLRL VNFISHENSK LTQRIYHTNS
QFVRTCLVLN WEQEEKEEAR ASLVEIRANG LIRDFLRIGL IKSTISYTRK RYDSRSAGLI
LHNRLDRTNT NSFYSKAKIQ SLSQHQEAIG TLLNRNKEYQ SLMVLSASNC SRIGFFKNSK
NPNGVKESNP RIPIPKFWGL FRNFSGLLGT IAPSISNFSS SYYLLTYNQI LLKKHLLLDN
LKQNFKVLQG LKHSLINENQ RTSNFDSNIM LDPFQLNWHF LPHDSWEETS AKIHLGQFIC
ENVCLFKSHI KKSGQIFIVN IDSFVIRAAK PYLATTGATV HGHYGEILYK GDRLVTFIYE
KARSSDITQG LPKVEQIFEA RSIDSLSPNL ERRIEDWNER IPRILGGPWG FLIGAELTIA
QSRISLVNKI QKVYRSQGVQ IHNRHIEIII RQVTSKVRVS EDGMSNVFSP GELIGLLRAE
RAGRALDESI YYRAILLGIT RVSLNTQSFI SEASFQETAR VLAKAALRGR IDWLKGLKEN
VVLGGIIPVG TGFQKFVHRY PQNKNLYFEI QKKKLFASEM RDILFLHTEL VSSDSDVTNN
FYETSESPFT PFI
>SIN3_YEAST|P22579 PAIRED AMPHIPATHIC HELIX PROTEIN
MSQVWHNSNS QSNDVATSND ATGSNERNEK EPSLQGNKPG FVQQQQRITL PSLSALSTKE
EDRRDSNGQQ ALTSHAAHIL GYPPPHSNAM PSIATDSALK QPHEYHPRPK SSSSSPSINA
SLMNAGPAPL PTVGAASFSL SRFDNPLPIK APVHTEEPKS YNGLQEEEKA TQRPQDCKEV
PAGVQPADAP DPSSNHADAN DDNNNNENSH DEDADYRPLN VKDALSYLEQ VKFQFSSRPD
IYNLFLDIMK DFKSQAIDTP GVIERVSTLF RGYPILIQGF NTFLPQGYRI ECSSNPDDPI
RVTTPMGTTT VNNNISPSGR GTTDAQELGS FPESDGNGVQ QPSNVPMVPS SVYQSEQNQD
QQQSLPLLAT SSGLPSIQQP EMPAHRQIPQ SQSLVPQEDA KKNVDVEFSQ AISYVNKIKT
RFADQPDIYK HFLEILQTYQ REQKPINEVY AQVTHLFQNA PDLLEDFKKF LPDSSASANQ
QVQHAQQHAQ QQHEAQMHAQ AQAQAQAQAQ VEQQKQQQQF LYPASGYYGH PSNRGIPQQN
LPPIGSFSPP TNGSTVHEAY QDQQHMQPPH FMPLPSIVQH GPNMVHQGIA NENPPLSDLR
TSLTEQYAPS SIQHQQQHPQ SISPIANTQY GDIPVRPEID LDPSIVPVVP EPTEPIENNI
SLNEEVTFFE KAKRYIGNKH LYTEFLKILN LYSQDILDLD DLVEKVDFYL GSNKELFTWF
KNFVGYQEKT KCIENIVHEK HRLDLDLCEA FGPSYKRLPK SDTFMPCSGR DDMCWEVLND
EWVGHPVWAS EDSGFIAHRK NQYEETLFKI EEERHEYDFY IESNLRTIQC LETIVNKIEN
MTENEKANFK LPPGLGHTSM TIYKKVIRKV YDKERGFEII DALHEHPAVT APVVLKRLKQ
KDEEWRRAQR EWNKVWRELE QKVFFKSLDH LGLTFKQADK KLLTTKQLIS EISSIKVDQT
NKKIHWLTPK PKSQLDFDFP DKNIFYDILC LADTFITHTT AYSNPDKERL KDLLKYFISL
FFSISFEKIE ESLYSHKQNV SESSGSDDGS SIASRKRPYQ QEMSLLDILH RSRYQKLKRS
NDEDGKVPQL SEPPEEEPNT IEEEELIDEE AKNPWLTGNL VEEANSQGII QNRSIFNLFA
NTNIYIFFRH WTTIYERLLE IKQMNERVTK EINTRSTVTF AKDLDLLSSQ LSEMGLDFVG
EDAYKQVLRL SRRLINGDLE HQWFEESLRQ AYNNKAFKLY TIDKVTQSLV KHAHTLMTDA
KTAEIMALFV KDRNASTTSA KDQIIYRLQV RSHMSNTENM FRIEFDKRTL HVSIQYIALD
DLTLKEPKAD EDKWKYYVTS YALPHPTEGI PHEKLKIPFL ERLIEFGQDI DGTEVDEEFS
PEGISVSTLK IKIQPITYQL HIENGSYDVF TRKATNKYPT IANDNTQKGM VSQKKELISK
FLDCAVGLRN NLDEAQKLSM QKKWENLKDS IAKTSAGNQG IESETEKGKI TKQEQSDNLD
SSTASVLPAS ITTVPQDDNI ETTGNTESSD KGAKIQ
>SN2L_CAEEL|P41877 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L
MEVDDEPESS DAADSFKRFE RLLQKTENFS HLATGAPVDT KKRGRPSKKN GIDGDHRHRK
TEQEEDEEMV ADAIKSDDLV IFDKSPFYIE NGEMRDYQVR GLNWLASLQH NKINGILADE
MGLGKTLQTI SMIGYMKHYK NKASPHLVIV PKSTLQNWAN EFKKWCPSIN AVVLIGDEAA
RNQVLRDVIL PQKFDVCCTT YEMMLKVKTQ LKKLNWRYII IDEAHRIKNE KSKLSETVRE
LNSENRLLIT GTPLQNNLHE LWALLNFLLP DIFTSSDDFD SWFSNDAMSG NTDLVQRLHK
VLQPFLLRRI KSDVEKSLLP KKEVKVYVGL SKMQREWYTK VLMKDIDIIN GAGKVEKARL
MNILMHLRKC VNHPYLFDGA EPGPPFTTDQ HLVDNSGKMV VLDKLLMKFK EQGSRVLIFS
QFSRMLDLLE DFCWWRHYEY CRLDGSTPHE DRSNAIEAYN APDSKKFIFM LTTRAGGLGI
NLATADVVII YDSDWNPQSD LQAMDRAHRI GQKKQVRVFR LITENTVDER IIEKAEAKLR
LDNIVIQQGR MSEAQKTLGK GDMISMIRHG AEQVFAAKDS TISDDDIDTI LEKAEVKTAE
LNEKMGKIDE NNLRNMTFED NAKFTVYQFE GENYKAKQAD GMGHFWIEPP KRERKANYQV
DLYYKEAMRA GNPTEKQSKA PRPKLPQVFD FQFYPRRLFE LLDKEIYHYR KTIGYVAERP
KDVPPKEAEK RQAEEQKLIN NARPLTDKEQ EEKAELLTQS VTDWTKREFQ QFVRGNEKYG
REDLESIAKE MERPLEEIQS YAKVFWERIE ELQDSEKVLS QIEKGEARIQ RKYAVKKALD
AKIAKYKAPF QQLRISYGTN KGKTYTEEED RFLVCETHRL GHDKENVFEE LRQSVRMAPQ
FRFDWFLKSR TAMELQRRCN TLITLIEREM GEVVESKPVI VTAADKKKSV AKDLSKSSGT
PTAKKVKATP K
>SPCB_DROME|Q00963 SPECTRIN BETA CHAIN | PS00019 | PS00020 | PS50003
MTTDISIVRW DPSQGPGNEY IDEYEYDGGN SSSRLFERSR IKALAEERES VQKKTFTKWV
NSHLCRVNCR IADLYVDMRD GKHLIKLLEV LSGERLPKPT KGKMRIHCLE NVDKALQFLR
EQRVHLENIG SHDIVDGNAS LNLGLIWTII LRFQIQDITI EEVDNKETKS AKDALLLWCQ
MKTAGYHNVN VRNFTTSWRD GLAFNAIIHK HRPDLVQFEK LSKTNAIHNL NNAFDVAEDK
LGLAKLLDAE DVFVEHPDEK SIITYVVTYY HYFSKLKQET VQGKRIGKVV GIAMENDKMV
HDYENFTSDL LKWIETTIQS LGEREFENSL AGVQGQLAQF SNYRTIEKPP KFVEKGNLEV
LLFTLQSKMR ANNQKPYTPK EGKMISDINK AWERLEKAEH ERELALREEL IRQEKLEQLA
ARFDRKASMR ETWLSENQRL VSQDNFGFDL AAVEAAAKKH EAIETDIFAY EERVQAVVAV
CDELESERYH DVKRILLRKD NVMRLWTYLL ELLRARRMRL EISLQLQQNF QEMLYILDNM
EEIKQLLMTD DYGKHLMGVE DLLQKHSLVE ADINILGERV KVVVQNSQKF LSDDPESYKP
CDPEIIVSRV QQLEDAYAEL VRLAVERRSR LEESRKLWQF YWDTADEENW IKEKEQIVST
DEVGHDLTTV NLMLSKHKAL ESEITSHDPQ LQNVAKVGSE LITEGHFGAD RIKDRLKEIL
NKWDHLLDLT KYRRQRLENA VEYFQLFADA DDVDNWMLDT LRIVSSEDVG RDEANVQSLL
KKHKDVADEL KNYAEVIDAL HKQAESLKLN EAEKANVDKR LEAIDNRYKE LTELAKLRKQ
RLLDALSLYK LMSEADGVEQ WIKEKTKMLD TMTPGKDIED VEIMKHRFEG FDKEMNANAS
RVAVVNQLAR QLLHVEHPNS DEILERQNHL NQEWSTLREK AEAKMDDLKS AHGVQTFYIE
CRETISWIED KKRILTETDS LEMDLTGVMT LQRRLSGMDR DLAAIQAKLS SLEREANSIE
DEHPEEAKII RERIAQIELI WEQLTQMLKE RDSKLEEAGD LHRFLRDLDH FQTWLTKTQT
DVASEDTPTS LPEAEKLLNQ HQSIREEIDN YTEDYKNMME YGERLTSEGS TSDDPQYMFL
RERLNALKDG WEELHQMWEN RQVLLSQSLD QQLFNRDARQ TEVLLSQQEH FLSKDDTPVN
LEQAENQLKR HEAFLTTMEA NDDKINTLLQ VADTLVEKDH FDADKIGKRA ENITGRRDDN
RQRALDQHEK LKNQVKLHEF LQDLEELAEW VQEKYATSQD ESYRSAKTIH SKWTRHQAFE
AEIAANKERL FEAEKSAQEL SKEKPEFKDV IEPKLKELAK QFDDLEVHTK EKGAMLFDAN
REVLVQQTCD DIDSYITDLE KQIVSGDTAN DLTSVNILMQ KQQVIQTQMA VKARQVEEID
KQTEYLQKTV PEEKIEPIVV KKTAVLERFE KIKAPLLERQ KALEKKKEAF QFCRDVEDEK
LWIDEKLPVA NSPDYGNSLF NVHVLKKKNQ SLATEIDNHE PRINAICNNG RKLIDEGHED
AKKFEALISD LTQKWQELKD AIENRRKHLL ESEKVQQYFF DAQEAESWMS EQELYMMVED
RGKDEISAQN LMKKHENLEQ SVEDYANTIR QLGEVARQFS GDDISSGDAV AVKQSQLDKL
YAGLKDLAGE RRARLNEALQ LFMLSREVDD LEQWITDREV VAGSQELGQD FDHVTLLSER
FNEFARDTEA VGGERVAKVN GIADNLIQAG HSDSATIAEW KDNLNESWQD LLELIETRTQ
MLAASRELHK FFHDCKDVLG RILEKQHGVS DELGRDAGSV STLQRKHYNF LQDLITLYSQ
VQQIQEESAK LQDAYAGDKA KEITNREQEV LHAWDNLQAM CDARKQKLAD TGDLFRFFNM
VRILMIWMED LVRQMNTSEK PRDVSGVELL MNNHQSLKAE IDTREDNFGA CISLGKELLT
RNHYASADIK DRLMTLSNSR NALLRRWEER WENLQLILEV YQFARDAAVA EAWLIAQEPY
LLSSELGHTI DEVENLIKKH EAFEKSAAAQ EERFSALERL TTFELKEMKR RQELAEEAER
QRIKEEQEAK AASEAAEQAK REAERRDDVD VGASHDDSER GGTPGAGEGH EGYVTRKHEW
DSTTKKASNR SWDKVYMAAK AGRISFYKDQ KGYKSNPELT FRGEPSYDLQ NAAIEIASDY
TKKKHVLRVK LANGALFLLQ AHDDTEMSQW VTSLKAQSDS TAVAASRSQT LPATSQKYEP
KRRSFFTLKK K
>TC1A_CAEBR|P35072 TRANSPOSABLE ELEMENT TCB1 TRANSPOSASE (TRANSPOSABLE ELEM
MDRNILRACR EDPRRTSTDI QLSVTSPNEP VPSRRTIRRR LQVAGLHGRR PVKKPLVSLK
NRKARVEWAK QHLSWGPREW ANHIWSDESK FNMFGTDGIQ WIRRPIGSRY APQYQCPTVK
HGGGSVMVWG CFSDTSMGPL KRIVGTMDRY VYEDILENTM RPWARANLGR SWVFQQDNDP
KHTSGHVANW FRRRRVNLLE WPSQSPDLNP IEHMWEELER RLKGVRASNA NQKFAQLEAA
WKSIPMTVVQ TLLESMPRRC KAVIDAKGYP TKY
>TC1A_CAEEL|P03934 TRANSPOSABLE ELEMENT TC1 TRANSPOSASE
MDRNILRSAR EDPHRTATDI QMIISSPNEP VPSKRTVRRR LQQAGLHGRK PVKKPFISKK
NRMARVAWAK AHLRWGRQEW AKHIWSDESK FNLFGSDGNS WVRRPVGSRY SPKYQCPTVK
HGGGSVMVWG CFTSTSMGPL RRIQSIMDRF QYENIFETTM RPWALQNVGR GFVFQQDNDP
KHTSLHVRSW FQRRHVHLLD WPSQSPDLNP IEHLWEELER RLGGIRASNA DAKFNQLENA
WKAIPMSVIH KLIDSMPRRC QAVIDANGYA TKY
>TC2A_CAEBR|Q04202 TRANSPOSABLE ELEMENT TCB2 TRANSPOSASE
MDRNIVRVSR EDPQRSSTDI QMVVKTPNEV TPSLRTVRRR LQDAGLHGRR PAKKPSISKK
NRIARVAWAR AHLHWGRQDW ANHVFSDESK FNLFGTDGIK WIRRPVGCRF DPSYQLQTVK
HGGGSVMVWG CFSGTSMDPL RRIDSIMDRF VYEDILENTM RPWARSTVGR AFVFQQDNDP
KHTSKHIKEW FRRRHVDLLD WPSQSPDLNP IEHLWEHVER HVRGVRASNA NQKFDQLQDV
WQAIPMSVID TILDSMPRRC QTVIDAKGFP TKY
>TC3A_CAEEL|P34257 TRANSPOSABLE ELEMENT TC3 TRANSPOSASE
MPRGSALSDT ERAQLDVMKL LNVSLHEMSR KISRSRHCIR EYLKDPVSYG TSKRAPRRKA
LSVRDERNVI RAASNSCKTA RDIRNELQLS ASKRTILNVI KRSGVIVRQK LRPAPLLSAD
HKLKRLEFAK NNMGTNWSKV VFSDEKKFNL DGPDGCRYYW RDLRKEPMVF SRRNFGGGTV
MVWGAFTEKK KLEIQFVSSK MNSTDYQNVL ELELSKYLRH YSRKDFRFQQ DNATIHVSNS
TRDYFKLKKI NLLDWPARSP DLNPIENLWG ILVRIVYAQN KTYPTVASLK QGILDAWKSI
PDNQLKSLVR SMEDRLIEII RTQGNPINY
>THIS_ECOLI|O32583 THIS PROTEIN
MQILFNDQAM QCAAGQTVHE LLEQLDQRQA GAALAINQQI VPREQWAQHI VQDGDQILLF
QVIAGG
>TRA0_ECOLI|P15025 TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS21
MLSREDFYMI KQMRQQGAYI VDIATQIGCS ERTVRRYLKY PEPPARKTRH KMVKLKPFMD
YIDMRLAENV WNSEVIFAEI KAMGYTGGRS MLRYYIQPKR KMRPSKRTVR FETQPRYQLQ
HDWGEVEVEV AGQRCKVNFA VNTLGFSRRF HVFAAPKQDA EHTYESLVRA FRYFGGCVKT
VLVDNQKAAV LKNNNGKVVF NSGFLLLADH YNFLPRACRP RRARTKGKVE RMVKYLKENF
FVRYRRFDSF THVNQQLEQW IADVADKREL RQFKETPEQR FAREQEHLQP LPDTDFDTSY
FDIRHVSWDS YIEVGGNRYS VPEALCGQPV SIRISLDDEL RIYSNEKLVA SHRLCSASSG
WQTVPEHHAP LWQQVSQVEH RPLSAYEELL
>TRA0_SHISO|P16944 TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS640
MLSREDFYMI KQMRHEGAYI VDIATQIGCS ERTVRRYLKY PEPPARKTRH KMVKLKPFMD
YIDMRLAENV WNSEVIFAEI KAMGYTGGRS MLRYYIQPKR KMRPSKRTVR FETQPGYQLQ
HDWGEVEVEV AGQRCKVNFA VNTLGFSRSF HVFAAPKHDA EHTYESLVRA FRYFGGCVKT
VLVDNQKAAV LKNNNGKVVF NSGFLLLADH YNFLPRACRP RRARTKGKVE RMVKYLKENF
FVRYRRFDSF THVNQQLEQW IADVADKREL RQFKETPEQR SRWSRNICSV TGYRLRYQLL
RYPPCVLGQL YRGWW
>TRFE_RABIT|P19134 SEROTRANSFERRIN PRECURSOR (SIDEROPHILIN) (BETA-1-METAL B
MRLAAGLLAC AALGLCLAVT EKTVRWCAVN DHEASKCANF RDSMKKVLPE DGPRIICVKK
ASYLDCIKAI AAHEADAVTL DAGLVHEAGL TPNNLKPVVA EFYGSKENPK TFYYAVALVK
KGSNFQLNEL QGKKSCHTGL GRSAGWNIPI GLLYCDLPEP RKPLEKAVAS FFSGSCVPCA
DGADFPQLCQ LCPGCGCSSV QPYFGYSGAF KCLKDGLGDV AFVKQETIFE NLPSKDERDQ
YELLCLDNTR KPVDEYEQCH LARVPSHAVV ARSVDGKEDL IWELLNQAQE HFGKDKSGDF
QLFSSPHGKN LLFKDSAYGF FKVPPRMDAN LYLGYEYVTA VRNLREGICP DPLQDECKAV
KWCALSHHER LKCDEWSVTS GGLIECESAE TPEDCIAKIM NGEADAMSLD GGYVYIAGQC
GLVPVLAENY ESTDCKKAPE EGYLSVAVVK KSNPDINWNN LEGKKSCHTA VDRTAGWNIP
MGLLYNRINH CRFDEFFRQG CAPGSQKNSS LCELCIGPSV CAPNNREGYY GYTGAFRCLV
EKGDVAFVKS QTVLQNTGGR NSEPWAKDLK EEDFELLCLD GTRKPVSEAH NCHLAKAPNH
AVVSRKDKAA CVKQKLLDLQ VEYGNTVADC SSKFCMFHSK TKDLLFRDDT KCLVDLRGKN
TYEKYLGADY IKAVSNLRKC STSRLLEACT FHKH
>TYRA_HAEIN|P43902 CHORISMATE MUTASE (EC 5.4.99.5) (CM) / PREPHENATE DEHYDR
MSFMEALKDL RSEIDSLDRE LIQLFAKRLE LVSQVGKVKH QHGLPIYAPE REIAMLQARR
LEAEKAGISA DLIEDVLRRF MRESYANENQ FGFKTINSDI HKIVIVGGYG KLGGLFARYL
RASGYPISIL DREDWAVAES ILANADVVIV SVPINLTLET IERLKPYLTE NMLLADLTSV
KREPLAKMLE VHTGAVLGLH PMFGADIASM AKQVVVRCDG RFPERYEWLL EQIQIWGAKI
YQTNATEHDH NMTYIQALRH FSTFANGLHL SKQPINLANL LALSSPIYRL ELAMIGRLFA
QDAELYADII MDKSENLAVI ETLKQTYDEA LTFFENNDRQ GFIDAFHKVR DWFGDYSEQF
LKESRQLLQQ ANDLKQG
>VIL1_MOUSE|Q62468 VILLIN
TKLNAQVKGS LNITTPGIQI WRIEAMQMVP VPSSTFGSFF DGDCYVVLAI HKTSSTLSYD
IHYWIGQDSS QDEQGAAAIY TTQMDDYLKG RAVQHREVQG NESETFRSYF KQGLVIRKGG
VASGMKHVET NSCDVQRLLH VKGKRNVLAG EVEMSWKSFN RGDVFLLDLG KLIIQWNGPE
SNRMERLRGM PLAKEIRDQE RGGRTYVGVV DGEKEGDSPQ LMAIMNHVLG PRKELKAAIS
DSVVEPAAKA ALKLYHVSDS EGKLVVREVA TRPLTQDLLK HEDCYILDQG GLKIFVWKGK
NANAQERSGA MSQALNFIKA KQYPPSTQVE VQNDGAESPI FQQLFQKWTV PNRTSGLGKT
HTVGSVAKVE QVKFDALTMH VQPQVAAQQK MVDDGSGEVQ VWRIEDLELV PVESKWLGHF
YGGDCYLLLY TYLIGEKQHY LLYIWQGSQA SQDEIAASAY QAVLLDQKYN DEPVQIRVTM
GKEPPHLMSI FKGRMVVYQG GTSRKNNLEP VPSTRLFQVR GTNADNTKAF EVTARATSLN
SNDVFILKTP SCCYLWCGKG CSGDEREMAK MVADTISRTE KQVVVEGQEP ANFWMALGGK
APYANTKRLQ EENQVITPRL FECSNQTGRF LATEIFDFNQ DDLEEEDVFL LDVWDQVFFW
IGKHANEEEK KAAATTVQEY LKTHPGNRDL ETPIIVVKQG HEPPTFTGWF LAWDPFKWSN
TKSYDDLKAE LGNSGDWSQI ADEVMSPKVD VFTANTSLSS GPLPTFPLEQ LVNKSVEDLP
EGVDPSRKEE HLSTEDFTRA LGMTPAAFSA LPRWKQQNIK KEKGLF
>Y08F_MYCTU|Q11052 PROBABLE REGULATORY PROTEIN CY50.15 | PS50006
MAGSATVEKR LDFGLLGPLQ MTIDGTPVPS GTPKQRAVLA MLVINRNRPV GVDALITALW
EEWPPSGARA SIHSYVSNLR KLLGGAGIDP RVVLAAAPPG YRLSIPDNTC DLGRFVAEKT
AGVHAAAAGR FEQASRHLSA ALREWRGPVL DDLRDFQFVE PFATALVEDK VLAHTAKAEA
EIACGRASAV IAELEALTFE HPYREPLWTQ LITAYYLSDR QSDALGAYRR VKTTLADDLG
IDPGPTLRAL NERILRQQPL DAKKSAKTTA AGTVTVLDQR TMASGQQAVA YLHDIASGRG
YPLQAAATRI GRLHDNDIVL DSANVSRHHA VIVDTGTNYV INDLRSSNGV HVQHERIRSA
VTLNDGDHIR ICDHEFTFQI SAGTHGGT
>YBDM_ECOLI|P77174 HYPOTHETICAL 23.9 KD PROTEIN IN CSTA-DSBG INTERGENIC REG
MGDTMQQRLT QDLTQFLASL PEDDRIKAIN EIRMAIHQVS PFREEPVDCV LWVKNSQLMP
NDYNPNNVAP PEKKLLQKSI EIDGFTQPIV VTHTDKNAME IVDGFHRHEI GKGSSSLKLR
LKGYLPVTCL EGTRNQRIAA TIRHNRARGR HQITAMSEIV RELSQLGWDD NKIGKELGMD
SDEVLRLKQI NGLQELFADR QYSRAWTVK
>YCF2_MARPO|P09975 HYPOTHETICAL 259 KD PROTEIN (ORF 2136)
MKQKLPKKKS LYKNLDLDEI QKIQNLGNPY TKWSLIRLLI AIFSNKRNFS TLLDFQILTS
LFFRDLYNSK KKKKFLLNIL VFLTLPFFVY ILIDKSIVEQ QNFDFLKIQK QNFIEKNNKS
ILKNNFYFLN TKFDIFLHNF FSLKKKKWYK NSLLNLIDFR SILKKKEILN LHWWKFLVLE
QIQSNWKISE ESLSELKIVL EQKNIDELKH FFEFYINQKI YPNNNWEYYF YSIFINQLKI
DIKNSKYNKN SIGFEVFLAF CEKLLFEVEF LSKPNNNNLQ MKLNCLENFS FLDIFCILNK
KLPWVNKKIF KNLQNFNESD KKLIESFFLL KIKGNLYFKN YIEFVTWQSY KKDCLDFNKF
NELNNSEIYI KIEELFSDYI YKFSKYILYE GKKSKTIIKQ SFNNNIYYKK LNSIFNFNTI
FYFDSNNLLF DWLKKNYYIN NKPFLKSFLI YSSISNQFIL FFKQKNSKSF NKNLVKKNSK
DVITNVFSKE NKIEINNFSK SIYYAFFEIL SINEIDNKFV INKISLKNIN KKKQKRFYLN
KIKSSDNFRF INLWKIKNYS SQQFVSNNSF LLNPAFEILQ QNYYLKKKNI LFFKKLNEVF
SNFFYFQYYK CKKLNIFLKF ASLEKILKKR NKKFTISIKL FKKFYKNKLN ENGEYKIESQ
ILQNEKELNK KRKKNFQFNP NIKILSFYNS SKKNIYLQNK YFFNKNLINN KLITWKKISN
KLVISNSEYN KIIWNKKNMK FFSFSKNSVL DTFFFNKKSF NIITVIFDKL KKIQLNFQEI
QKILNCFSLF FNSKNIKKTK IFKNSYFINE NLTTTFSFND KEFNIFFLEL FISEINNDFL
MRFFKKYLYY RIYKDKEILF NPIENRQLLQ NFFEKTKILT FIDFLQDPEL NYNNRFIFHL
EKKTIKNNNL LYLRLLKIFL KDKRNFLLIN EIKSFIEKKN NLFIKSQLSN VLLVKNSYKF
FDNIFNFHFL KQKEKNIEII LNNQNYFEKS LLKKTYLKNL NLNNSYSKFS YKIFIFQLLN
ILNKNNYKTF QWISELIFYS KNLNYKIQNK IEKNNYCYNK NISYKKKKIK TVNFFEKNNL
FQTNNSWFFT LEWWEYNTYI LLQIIQETFF QITDVLEYFK KKKIIEKNLK FFLKSKKISL
KTLSFHNFKL KWNLRFFNEI NYKKNYLLNF LWSDFNLINN CNNLYWVIFS LVIFIFLYYQ
KIFSIIIGSD CFHLWKNFEI IQYLTDRSRS LYFTKLTRRN KTALNKTENL LSYFFQNLTH
YITNIKFYLL TKKNLKKWLI NNKTLDLSRR KRKLLVQSLI THNKIQNYGF ELNSNKQFFT
SYFGYQITNQ QGLLYFQYLA QFFQKNLINN SLDLANKWIV FSFWHKIFSS QKLRQTNNIE
LGFQNIPVPL QFGLSYSKGI LLIGPIETGR SYLIKNLAAE SYVPLFKISI NKLLYNKPDV
ITESWMNILI ESLRRLNLTL DFAKKMSPCI IWIQNIHQLN VNRLTQNVES DPTFLLGILL
KYFQTDFSKT KKNNIIVIGS THLPKKVDPA LISPNRLDKI INVRLFNISQ RKKQFPLLLK
KKNFQLKENL FFLNEFGSRT MGYNLRDLSA LTNEVLLISI TKNRSFIDTD TLKLAFHRQI
FGLTYTNNKL NFDRIFKIVI YKVGKTIIQN ILIKSSSMNL LNIGNFLWKK NFYYLSKWYL
EPSIDESIIK ELTILTHILA CLAGTAARDS WFLLEKKAES LLPIDKLVEN DFTLAFSILE
SFFSEFPWLE ICQTNVVNSK KNKIIEFSTK NSMNIMQNGI FAIANKKFIY TQNHLQYKSS
LSQQISFNKK KNYEFKNTSW SPRFWRLSFF RSNLFDWIKR PNDFEFSYKF GFTKKKEYLF
SANLQKKNNY GQFIEKKKKE QLLYERILPR IRRRNVQELE SQFEEILLEE QFEILGFFRL
SEQYPMEYQL YNKPRLFIGK RILWDPIGLF FQIRHFVFSR REFFVDEEML RRLYVTYGAR
RERERSRSSQ KIKQFFLCRG YNKDLISKLS IRWWSQLPIN EKKNIDTLKR IEHISIQLKR
PQIFTPVYLY QRWLIENSPE KFFRFELLTH RKKWLKINSL LLNDSFIYTT LLEIYEYLLH
FFIANKKLLN QMTKILLKKG WLFENEIETI INETRQ
>YDF7_SCHPO|Q10479 PUTATIVE GLUCOSYLTRANSFERASE C17C9.07 (EC 2.4.1.-)
MGKLSMLYNA AIASTFVKVF LFPSYRSTDF EVHRNWLAIT HSLPISEWYK SSISEWTLDY
PPFFAYMECV LSWIAYFFGF DKAMLDPYNL NYVSPSTVVF QRGSVIVLEL VLLFALREYV
LSSNVKDQRN ALLTAIDIFL SPGLLIIDHI HFQYNGFLFG LLLWSIVLAK PEKNMLLSAA
IFSALICFKH IFLYVAPAYF VYLLRVYCFT PNFRPQFLNI LKLGSTVISI FLLAFGPWIY
MKQIPQLLSR LFPFSRGLCH AYWAPNFWAL YSFVDRVAFA VLPRFGYALN QGTSINAPTR
GLVGESSFAV LPNIPPALTF YICLGLQITV LIKLFIKPTW RVFVGAVTLC GWISFLFGWH
VHEKAILMVI LPFSILSLID RRYLEAFRPL AVSGYLSLLP LLFTLNEAPI KYLFTGAWIA
MLLTFDKCAP VPVKRVFLLN RVNIAYISGF VPLFIYNCFI HKLVMGDKFE FLPLMLLSTY
AAWGIFWSFV SLLWLYFTDL K
>YDIL_ECOLI|P76196 HYPOTHETICAL 15.0 KD PROTEIN IN LPP-AROD INTERGENIC REGI
MFISCSHYTM NAYELQALRH IFAMTIDECA TWIAQTGDSE SWRQWENGKC AIPDRVVEQL
LAMRQQRKKH LHAIIEKINN RIGNNTMRFF PDLTAFQRVY PDGNFIDWKI YQSVAAELYA
HDLERLC
>YENR_YEREN|P54295 YENR REGULATORY PROTEIN | PS00622
MIIDYFDNES INEDIKNYIQ RRIKTYGDLC YSYLVMNKKT PLHPTIISNY PLDWVKKYKK
NSYHLIDPVI LTAKDKVAPF AWDDNSVINK KSTDSAVFKL AREYNIVNGY TFVLHDNSNN
MATLNISNGS DDSISFDERI EINKEKIQML LIITHEKMLG LYQSNSDKNE NRNTQIERDI
FSPRENEILY WASVGKTYAE ISIILGIKRS TVKFHIGNVV RKLGVLNAKH AIRLGIELKL
IKPI
>YFEH_ECOLI|P39836 HYPOTHETICAL 36.4 KD PROTEIN IN XAPB-LIG INTERGENIC REGI
MKLFRILDPF TLTLITVVLL ASFFPARGDF VPFFENLTTA AIALLFFMHG AKLSREAIIA
GGGHWRLHLW VMCSTFVLFP ILGVLFAWWK PVNVDPMLYS GFLYLCILPA TVQSAIAFTS
MAGGNVAAAV CSASASSLLG IFLSPLLVGL VMNVHGAGGS LEQVGKIMLQ LLLPFVLGHL
SRPWIGDWVS RNKKWIAKTD QTSILLVVYT AFSEAVVNGI WHKVGWGSLL FIVVVSCVLL
AIVIVVNVFM ARRLSFNKAD EITIVFCGSK KSLANGIPMA NILFPTSVIG MMVLPLMIFH
QIQLMVCAVL ARRYKRQTEQ LQAQQESSAD KA
>YFJJ_ECOLI|P52125 HYPOTHETICAL 24.6 KD PROTEIN IN ALPA-GABD INTERGENIC REG
MTYDSEFGSH VSLYRDRIKQ VIDDSLNEHL NSMILRVDLH DPIDTENMDN PFFQPRVDSG
AISRFTSALK AKLKHDKHIK TQRKDWPDSR HSTLRYAWVR EYTKNRKRHY HLILCFNQDA
YYHLGDYDLN RNTLRTMITT AWYSALGIPI DSSGKLVNYP PNGKYLLNRK RDNFEQTYSD
LMNRVDYMTK VRTKIVGDGD RNFGCSRG
>YM8I_YEAST|Q03529 HYPOTHETICAL 44.9 KD PROTEIN IN URA10-NRC1 INTERGENIC RE
MSTNTSKTLE LFSKKTVQEH NTANDCWVTY QNRKIYDVTR FLSEHPGGDE SILDYAGKDI
TEIMKDSDVH EHSDSAYEIL EDEYLIGYLA TDEEAARLLT NKNHKVEVQL SADGTEFDST
TFVKELPAEE KLSIATDYSN DYKKHKFLDL NRPLLMQILR SDFKKDFYVD QIHRPRHYGK
GSAPLFGNFL EPLTKTAWWV VPVAWLPVVV YHMGVALKNM NQLFACFLFC VGVFVWTLIE
YGLHRFLFHF DDWLPESNIA FATHFLLHGC HHYLPMDKYR LVMPPTLFVI LCAPFYKLVF
ALLPLYWAYA GFAGGLFGYV CYDECHFFLH HSKLPPFMRK LKKYHLEHHY KNYQLGFGVT
SWFWDEVFGT YLGPDAPLSK MKYE
>YNC4_YEAST|P53970 HYPOTHETICAL 27.7 KD PROTEIN IN UME3-HDA1 INTERGENIC REG
MESIFGGFGD LVVPRPKEHL GQTDLSFGGK LLPALKICED GGESGCGGKV WIAGELLCEY
ILEKSVDHLL SKTVNGTKQF KKVLELGSGT GLVGLCVGLL EKNTFHDGTK VYVTDIDKLI
PLLKRNIELD EVQYEVLARE LWWGEPLSAD FSPQEGAMQA NNVDLVLAAD CVYLEEAFPL
LEKTLLDLTH CINPPVILMA YKKRRKADKH FFNKIKRNFD VLEITDFSKF EHYLKERTHL
FQLIRK
>YO96_CAEEL|P41846 HYPOTHETICAL 93.9 KD PROTEIN T20B12.6 IN CHROMOSOME III
MEGFQRITSS LEAEVRKKQP EKPKKPFCYF AVPDDDTTHQ KIEGSIVEGM YWKRKMEGVC
AQYKRWRIRS KHNLVTDKGG MVATCSSTSV SSMTGELKRK RKHTVPKETI ESKLRSYEPP
VKLQRSQTPK HTISDEFAWD FDDLDNVFTD DFLNSLSEPY MFPDPRDVYS GNNADIMQPG
LLPLQPTIED IMMSLGDDMP DSPPFHNDRD TMRTPTNDQP SISAQQIPQM RRSASSSASL
HQMQVAQAQA QSISQISQPS QQLQHQIQIQ QPVAARPHEF MASSIMMDYR LMPTRQSSAI
TSQMLMLSQS ASTLSSQPQY ATSTHYSTNN SFLPIRNTMT NQHHLGHTSQ HSPWNKQQQS
NFLVSLPHQS HVERILNNQP PLVPPPSRSN LLPTQNDPYL PQFLQSTQPT PQPQSHDPMM
APSRSWWLDS PLTASVQSPL SVATPLPLAN QTGPQTPLGQ LIGSADNGFL FGGNNTPGGF
KMSGTTSGVP TLSQRLEQPP ISRTSTIFGN VENKPERIFT SLTSQNTPTP SPLDISSLSR
LRTSSLNESW KMSHIVEGSP TYQAFAASVT TKPSILESPS TSGDISGPAS VPVQASQHPP
KIITPPSASS KRKEQEAAMA PLVNRQQSCD VNLLNGKMAV KVEEKSGRHY LPTTPTELKE
VTKEEPLLMS APSSVKSMRR QAPDSTLHPE ERKRILHLHA EQNRRSALKD GFDQLMDIIP
DLYSGGVKPT NAVVLAKSAD HIRRLQAEKW DKTQKIDEAK AKIEKLNQKI TSLQSNLPQS
SAPSSSSQVD SKTSLETFFD RYVKEGAKKN WRFWVVSLAT NSSILAEPDT LPDYVMQQLK
NPF
>YOUG_BACLI|Q45292 HYPOTHETICAL 17.3 KD PROTEIN IN GNTR 5'REGION
MLADAEWNEK KVLDRRTSRD HVLKGVSGGF AQLCHGKEAP LKRMNPDDWI IYYSPKQNLK
DDAPYQKFTA VGEVSDNRVY KVHAGEGFSP YRRKINFLKC RETPIHPFIP NLSFIKNKRH
WGYSFRFGHI EISEHDFKLI VKQMVKI
>YP22_YEAST|Q08968 HYPOTHETICAL 78.3 KD PROTEIN IN SSM1-GRE1 INTERGENIC REG
MGEKRTIIKA LKNSAASHFI KKLTADTSLS SIQEAINVVQ QYNATDPVRL KLFHTPRMVS
QGAHFAFCLP TKKPHYKPLL LSQNALDEFN LVQDQDLEKI LSGEKVYYSD SIFPYSTVYS
GFQFGSFAAQ LGDGRVVNLF DLKDKCSGQW QTFQLKGAGM TPFSRFADGK AVLRSSIREF
IMSEALHSIG IPSTRAMQLT LLPGTKAQRR NQEPCAVVCR FAPSWIRLGN FNLFRWRHDL
KGLIQLSDYC IEELFAGGTQ FEGKPDFNIF KRDFFPDTET KIDEQVEKDE TEVSTMTGDN
ISTLSKYDEF FRHVVSLNAN TVAHWQAYGF ANGVLNTDNT SIMGLTIDYG PFAFLDKFEP
SFTPNHDDTA KRYSFANQPS IIWWNLQQFA KDLACLLGPE ARDLELLLKG ELNSVDDALE
KTMIERVQKL VELSANEYKY VFTTRYAQIM SQRLGVDLDL EKCMSSTNLK DIEHAAEKAK
EFCDVIVEPL LDILQATKVD YNNFFIHLQN YKGPFFIKDK SDTATLFGAF DEEYLGMFFN
SKQLQQMAET EEAFAAGEKV FDANGELRLL NEKLQEIRNW TQDYLTLVPP TETAARASLA
KKANPLFVPR SWVLEEVVDD LMYSQRDGLQ DPSSELDTSA LKKLYLMSVN PYDRTKWDVT
LRPELETKWA DLSHQDDAKF MMQASCSS
>YPB4_CAEEL|Q11107 HYPOTHETICAL ZINC FINGER PROTEIN B03B8.4 IN CHROMOSOME I
MDEFELFQQL NQTAPLVKTE EPEVPDEQAN NNQSAPLRTG LSDLSHEIAA AKQREEEEAQ
RLADFMQKDM KEPAVKRKRG SEEYKKSPFR SAPLFVGPHI FLASEILLNR KLRYPHLDTL
PDPVDQQTVD KLCIVGANNE DHDEILLKSI RHVYNAMPPT FRRDWEYAAR KDVFDSRLFV
QNMPMPLSEI SVTDPRHPPS PIARGTTVRP NCCENQPLFL NMCETIEHYL GHHDVVHLFG
CDICYRVYPS RYELTKHDCK EFAEYLRQLT FKQQTLHLEA AYMYLCCSQC GLWLSVKPSG
EGKKGWTYFA TALMNHSCQP LVPVVAYFPK PLKDEGKGIR IQFQVMSELN IGLPLSCSEC
NIEEFHSVVE IEEHFKEKHE ANHTCIKCGK TFGTEFMLKH HAQSHTTQTA QFANYLQMSA
TYQPPPSSGR LPYVGFGSSI PAIGGLTSGE VQALEASENK KSEFVEPDEY TIRKKLLRWK
HAKTKKENRN ITDSNEKEFS YEPGESSGEE DFQKSLLEQD NQSSSSSDSD SDSDDFTSSK
QKKKRNIKIR GDLGYEHINR NKFFERPESE KEARKRIEKV YKKHVLLSRE RLLDPEEALR
ILEESRMDLL LVNKIFYFCT KCNYIFSKDP VVHCLSCEVT EDDLIEVYHA ASGPHAGVRC
IDPECKAHLC SVISLKTHLS DVHSKQATLE LVSGELDNFS ENRFDRSLML MAKHFTQLQF
DERTYLARFT DIECFMPFSG LLEAKDQPRP MPIRQQPQQI KPAYSLVRPD IIAPNELMRP
YTLTPAIRPG QRIKPYKVPR TSRWYSCSWC DREYESLNQF VDHLTRFHTH PCPSCGKAFS
SQNTRRTHVC SRLFAEIKGR GATLCGQCPS CPEIHQVERI FVHMLNRHFS TIEYVLATGE
LLPPARDVGI RYNHGENGGY GRSYESLRAI EQSVVDPRSP DYRLKQVKIS ALPIHGVELN
RLPARDPPMG SFTVCPPKDK NIDPRLMCYM CELTFDSYDE LTHHMDDHPE KWANCPFCAA
NTPTHFDLQK HLIQEHVVQI SGQACCAFCQ EHHRFMSSHI LFRCKRVSRC TICGVKSNDP
LANRVHIQRS HALTLRRFQC AYCIKVFVSV GEYYEHECAS GGGRVYSCTC SPNKFFNSPI
EFCDHFDSVH ILRNKCQLCS YDAPSQDGMV KHRKTHMRSG CPKEQTKKLF ILMKCLFPKH
NSGYMRFIEG GPVPASYQDV DRSQMNYLMC NMGTVSPSCH KSYAQAPRTL LEALEGVASD
SRSGGLQKVV NVTTRMNEPS SSDVIMLSDD EDDDCVVFEK AVPNGVAQGS STSTPNPESS
INCEATRQLF SKILIEKRFR PVRVETSQAG YGGAQQPGYV DEDDTDLEVA QGGKSPYGEP
VVKEVVDENG DDELAVVAEV ENSTGTLPSS ISAGREKKFK CQKCSLAFYT NGSLESHMRD
HRQDAGAQLC TETYGIPVVT KASWLCRNCC VVFENQPKYQ KHMAIHGDTC LTCIHCSGIA
FNHTAIQNHM KSHEEKKVRY SCGTCLCTFA SDLALFDHLS VAHGVSLYYF CKVCGFGSTS
ADSVFQHISI HNGHNYSLVQ RFGACPAQLL NYDPTDELEF RSQILNKTIQ LVSPSDCSHR
SMLLQCETVV SCKTCHCTQA WFNYMAFNNH SEETGFPQFK NVDLANDYRR DFPLSRHLNE
RNALSMSQFG NAKHGSANHS HGQAQPNKRT FRHEVPYRTA APRSSLQTNG SSMGSVTTNG
GRVVRPSPPN SMNVTLRRAP PQQAPPRRIV IANSAPNNTN VLRNHVAVTT KCQFKDCDKV
LHSEFDRQLH SMHSSNSSWF CRQCGHSPKS EIDLFLHYIQ VHLKPAYDKH QSNSFKSNVF
HLKCPIRSCT SPEFQSPKAF EKHMRTAHAA ELPFEASCCD ARFASKALCV KHDQEHASFL
DSNGTDASCC PICGSLSMWS LPKDPHTDCL QSHIIRHGLD YRSSCRQCLK QFPADVNQDQ
VIAHILDTHG MSMHGNTFHC NLCTTGTKTV EEFAEHCRKA HVFHILVKSS HSTRGELVVT
TGQEYENYVG LKSVTRASLN SISSQRASNA GETAQPSVLC AGSGNAALLT IAAAIGEPET
SNNTAEVLTL D
>YQHN_BACSU|P54512 HYPOTHETICAL 16.7 KD PROTEIN IN GCVT-SPOIIIAA INTERGENIC
MTTPSMEDYI EQIYMLIEEK GYARVSDIAE ALAVHPSSVT KMVQKLDKDE YLIYEKYRGL
VLTSKGKKIG KRLVYRHELL DQFLRIIGVD EEKIYNDVEG IEHHLSWNSI DRIGDLVQYF
EEDDARKKDL KSIQKKTEHH NQ
VL DSANVSRHHA VIVDTGTNYV blimps-3.9/examples/blimps/exampleA.blk000064400001460000012000000013020613277404100205000ustar00jorjastaff00000400000027ID   EXAMPLE; BLOCK
AC   exampleA; distance from previous block=(52,155)
DE   EXAMPLE
BL   WDF motif=[8,0,17] motomat=[1,80,-10] width=46 seqs=8
TC1A_CAEBR (  53) KKPLVSLKNRKARVEWAKQHLSWGPREWANHIWSDESKFNMFGTDG  45

TC3A_CAEEL ( 110) KLRPAPLLSADHKLKRLEFAKNNMGTNWSKVVFSDEKKFNLDGPDG 100

       HB1 (  98) KVPLPSPRHIKARLSLAKTYLNWPVSKWRNILWTDGSKIMLFGGTG  72

       Uhu (  82) KKPFISTKNKGTRMTFAKTHLDKDLEFWNTIIFEDESKFIIFGSDG  61

    Bari-1 ( 120) KTIEITPTNKTKRLRFALEYVKKPLDFWFNILWTDESAFQYQGSYS  80

     Minos ( 156) EKPLLTLRQKKKRLQWARERMSWTQRQWDTIIFSDEAKFDVSVGDT  78

TC1A_CAEEL (  53) KKPFISKKNRMARVAWAKAHLRWGRQEWAKHIWSDESKFNLFGSDG  42
TC2A_CAEBR (  53) KKPSISKKNRIARVAWARAHLHWGRQDWANHVFSDESKFNLFGTDG  45
//
blimps-3.9/examples/blimps/exampleA.cs000064400001460000012000000012020673775403600203510ustar00jorjastaff00000400000027ERror_level		2			-- only WARNINGs and higher
BLock  			exampleA.blk		-- the query block
DBase			/bird/swiss/swiss37.uni
OUtput_file		exampleA.bli		-- the output file
STrands_to_search	2			-- if DNA, search both strands
REpeats_allowed		NO 			-- save only best alignment
NUmber_to_report	0			-- have blimps decide
COnversion_method       3                       -- the conversion method
//
------------------------------------------------------------------------
BLIMPS (BLocks IMProved Searcher)
(C) Copyright 1993, Fred Hutchinson Cancer Research Center

exampleA.cs -- A sample configuration file to search a Block vs
		a sequence database
blimps-3.9/examples/blimps/exampleB.blk000064400001460000012000000006450613277410000205060ustar00jorjastaff00000400000027ID   EXAMPLE; BLOCK
AC   exampleB; distance from previous block=(20,24)
DE   EXAMPLE
BL   GMW motif=[8,0,17] motomat=[1,80,-10] width=11 seqs=8
       HB1 ( 168) GGPKIMVWACF  79

     Minos ( 224) FPASTMVWGCM 100

TC1A_CAEBR ( 122) GGGSVMVWGCF  36
TC1A_CAEEL ( 122) GGGSVMVWGCF  36
TC2A_CAEBR ( 122) GGGSVMVWGCF  36
TC3A_CAEEL ( 176) GGGTVMVWGAF  59
       Uhu ( 150) HGGSVMVWACI  64
    Bari-1 ( 187) GGGTVMFWGCL  68
//
blimps-3.9/examples/blimps/exampleC.blk000064400001460000012000000006450613277413200205140ustar00jorjastaff00000400000027ID   EXAMPLE; BLOCK
AC   exampleC; distance from previous block=(39,40)
DE   EXAMPLE
BL   QDN motif=[8,0,17] motomat=[1,80,-10] width=11 seqs=8
TC3A_CAEEL ( 226) FRFQQDNATIH  77

     Minos ( 275) FTFQQDGASSH 100

TC1A_CAEBR ( 172) WVFQQDNDPKH  54
TC1A_CAEEL ( 172) FVFQQDNDPKH  50
TC2A_CAEBR ( 172) FVFQQDNDPKH  50
       HB1 ( 218) WTFQQDNDQKR  82
       Uhu ( 200) FRFYQDNDQKH  79
    Bari-1 ( 238) WILQQDNAPCH 100
//
blimps-3.9/examples/blimps/exampleD.blk000064400001460000012000000007060613277415600205210ustar00jorjastaff00000400000027ID   EXAMPLE; BLOCK
AC   exampleD; distance from previous block=(18,18)
DE   EXAMPLE
BL   SIW motif=[8,0,17] motomat=[1,80,-10] width=15 seqs=8
       HB1 ( 247) WQAPPSHLNPIENLY 100

       Uhu ( 229) XPAQSPDVNVIXNLW  78

     Minos ( 304) WPSNSPDLSPIENIW  56

TC1A_CAEBR ( 201) WPSQSPDLNPIEHMW  39
TC1A_CAEEL ( 201) WPSQSPDLNPIEHLW  34
TC2A_CAEBR ( 201) WPSQSPDLNPIEHLW  34
TC3A_CAEEL ( 255) WPARSPDLNPIENLW  38
    Bari-1 ( 267) WPPQSPDLNIIENVW  53
//
blimps-3.9/examples/blimps/exampleE.blk000064400001460000012000000011730613277420300205120ustar00jorjastaff00000400000027ID   EXAMPLE; BLOCK
AC   exampleE; distance from previous block=(17,23)
DE   EXAMPLE
BL   WSR motif=[8,0,17] motomat=[1,80,-10] width=37 seqs=8
TC1A_CAEBR ( 237) LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY  56

TC1A_CAEEL ( 237) LENAWKAIPMSVIHKLIDSMPRRCQAVIDANGYATKY  65

TC2A_CAEBR ( 237) LQDVWQAIPMSVIDTILDSMPRRCQTVIDAKGFPTKY  66

TC3A_CAEEL ( 293) ILDAWKSIPDNQLKSLVRSMEDRLIEIIRTQGNPINY 100

       HB1 ( 283) VQDTWAKIPPKPCXDLVDFMPRGCKAVLANKGYPAKY  94

       Uhu ( 261) LLDEWSKISPETTRKLVSSMNNRLMEDIKAKGYHTKY  80

    Bari-1 ( 303) IAEIWSKLTLEFAQTLVRSIPKRLQAVIDAKGGVTKY  84

     Minos ( 340) LQEMWDSISQEHCKNLLSSMPKRVKCVMQAKGDVTQF  92

//
blimps-3.9/examples/blimps/lipo.pros000064400001460000012000000023420776372740700201460ustar00jorjastaff00000400000027>BBP_PIEBR BILIN-BINDING PROTEIN (BBP) 
NVYHDGACPE VKPVDNFDWS NYHGKWWEVA KYPNSVEKYG KCGWAEYTPE GKSVKVSNYH
VIHGKEYFIE GTAYPVGDSK IGKIYHKLTY GGVTKENVFN VLSTDNKNYI IGYYCKYDED
KKGHQDFVWV LSRSKVLTGE AKTAVENYLI GSPVVDSQKL VYSDFSEAAC KVN

>ICYA_MANSE INSECTICYANIN A FORM (BLUE BILIPROTEIN) 
GDIFYPGYCP DVKPVNDFDL SAFAGAWHEI AKLPLENENQ GKCTIAEYKY DGKKASVYNS
FVSNGVKEYM EGDLEIAPDA KYTKQGKYVM TFKFGQRVVN LVPWVLATDY KNYAINYNCD
YHPDKKAHSI HAWILSKSKV LEGNTKEVVD NVLKTFSHLI DASKFISNDF SEAACQYSTT
YSLTGPDRH

>LACB_BOVIN BETA-LACTOGLOBULIN PRECURSOR (BETA-LG) 
MKCLLLALAL TCGAQALIVT QTMKGLDIQK VAGTWYSLAM AASDISLLDA QSAPLRVYVE
ELKPTPEGDL EILLQKWENG ECAQKKIIAE KTKIPAVFKI DALNENKVLV LDTDYKKYLL
FCMENSAEPE QSLACQCLVR TPEVDDEALE KFDKALKALP MHIRLSFNPT QLEEQCHI

>MUP2_MOUSE MAJOR URINARY PROTEIN 2 PRECURSOR (MUP 2) 
MKMLLLLCLG LTLVCVHAEE ASSTGRNFNV EKINGEWHTI ILASDKREKI EDNGNFRLFL
EQIHVLEKSL VLKFHTVRDE ECSELSMVAD KTEKAGEYSV TYDGFNTFTI PKTDYDNFLM
AHLINEKDGE TFQLMGLYGR EPDLSSDIKE RFAKLCEEHG ILRENIIDLS NANRCLQARE

>RETB_BOVIN PLASMA RETINOL-BINDING PROTEIN (PRBP) 
ERDCRVSSFR VKENFDKARF AGTWYAMAKK DPEGLFLQDN IVAEFSVDEN GHMSATAKGR
VRLLNNWDVC ADMVGTFTDT EDPAKFKMKY WGVASFLQKG NDDHWIIDTD YETFAVQYSC
RLLNLDGTCA DSYSFVFARD PSGFSPEVQK IVRQRQEELC LARQYRLIPH NGYCDGKSER
NIL
blimps-3.9/examples/blimps/multimat.csh000075500001460000012000000026400712175416500206220ustar00jorjastaff00000400000027#!/bin/csh 
#    This is multimat.csh
#	Combine independent blimps search results for blocks
#	from the same family vs a sequence database
#
unalias rm
setenv BLIMPS_DIR ../..
#	Block family name; 1st 7 characters of each AC
#	 must be the same for each query block
set name = example
#	Blocks database for alignments;
#	  concatenate all of the query blocks into this file
set dat = $name.blocks
rm $dat $name?.blk.bli

#	Target database of sequences to search
set db = example.pros

#	Search each block vs sequence database with blimps
#	Blimps results are in $name*.bli files
set blks = ($name?.blk)
foreach blk ($blks)
	echo "BLock  			$blk" > $name.cs
	echo "DBase			$db" >> $name.cs
	echo "OUtput_file		$blk.bli" >> $name.cs
	echo "REpeats_allowed		NO" >> $name.cs
	echo "NUmber_to_report	0" >> $name.cs
	echo "//" >> $name.cs

	$BLIMPS_DIR/bin/blimps $name.cs

	cat $blk >> $dat
end

#	Post-process blimps results with multimat
#	Number of hits to report
set hits = 1000
#     The sequences in this list are considered "true positives"
#	and will not be reported by multimat (optional)
set list = none
#      Output file - frequency distribution of scores
set out = multimat.out
#
#	Execute multimat excluding known true positive hits
#$BLIMPS_DIR/bin/multimat $hits $dat $list $name?.blk.bli >$out
#	Use none instead of $list to include known true positive hits
$BLIMPS_DIR/bin/multimat $hits $dat none $name?.blk.bli >$out
exit(0)
blimps-3.9/examples/blimps/repeats.dat000064400001460000012000000220200711424137200204040ustar00jorjastaff00000400000027BL00012      4
BL00018      7
BL00019      1
BL00020      1
BL00021     37
BL00022     35
BL00023      2
BL00024      1
BL00025      5
BL00026      3
BL00027      2
BL00028     36
BL00030      3
BL00037      2
BL00061      1
BL00079      2
BL00092      1
BL00101      3
BL00107      1
BL00108      1
BL00112      2
BL00115     51
BL00129      1
BL00141      1
BL00142      1
BL00189      2
BL00190     15
BL00194      2
BL00198      5
BL00202      1
BL00205      3
BL00206      1
BL00207      1
BL00211      1
BL00212      6
BL00215      2
BL00223      7
BL00225      3
BL00229      3
BL00230     11
BL00232     33
BL00235      4
BL00241      1
BL00243      3
BL00259      3
BL00260      2
BL00267      1
BL00270     11
BL00280      2
BL00281      1
BL00282      6
BL00287      2
BL00290      2
BL00299     11
BL00309      1
BL00310      1
BL00313      7
BL00314     56
BL00317      1
BL00328      9
BL00330      4
BL00334      2
BL00344      1
BL00347      1
BL00351      1
BL00352      8
BL00354      2
BL00369      1
BL00378      1
BL00383      1
BL00420      3
BL00429      7
BL00433      1
BL00448      1
BL00452      1
BL00453      1
BL00454      1
BL00455      3
BL00478      3
BL00479      1
BL00484      9
BL00495      3
BL00498      6
BL00499      1
BL00515     12
BL00524      1
BL00562      3
BL00572      3
BL00589      1
BL00598      1
BL00606      1
BL00615      7
BL00626      6
BL00633      1
BL00652      3
BL00653      3
BL00664      2
BL00674      1
BL00678      7
BL00681      1
BL00693      1
BL00707      1
BL00740      5
BL00762      5
BL00776      1
BL00777      1
BL00782      1
BL00799      6
BL00805      2
BL00823      1
BL00832      1
BL00833      1
BL00845      1
BL00866      1
BL00867      1
BL00881      1
BL00888      1
BL00889      1
BL00904      4
BL00929      9
BL00934      1
BL00935      1
BL00983      2
BL01031      1
BL01033      8
BL01047      5
BL01052      4
BL01072      3
BL01096      1
BL01098      2
BL01139      1
BL01159      3
BL01160      3
BL01177      2
BL01178      2
BL01179      1
BL01180      4
BL01186     46
BL01187     42
BL01208      2
BL01209     35
BL01241      3
BL01248     20
BL01253     11
BL01282      2
BL01285      1
BL01286      1
BL50001      1
BL50002      3
BL50003      1
BL50004      3
BL50006      1
BL50011      1
BL50013      1
BL50014      1
BL50020      3
BL50023      3
BL50041      7
BL50042      1
BL50050      3
BL50053     11
BL50054      1
BL50055      1
BL50056      1
BL50059      1
BL50060      5
BL50064      1
BL50068     35
BL50070     37
BL50071      2
BL50075      4
BP00049 2
BP00094 3
BP00103 2
BP00113 10
BP00144 1
BP00146 1
BP00170 2
BP00171 1
BP00174 1
BP00200 1
BP00217 1
BP00224 2
BP00227 1
BP00235 1
BP00236 10
BP00239 1
BP00240 4
BP00241 4
BP00251 1
BP00254 1
BP00272 1
BP00273 1
BP00274 3
BP00277 1
BP00284 10
BP00287 2
BP00290 7
BP00302 1
BP00312 1
BP00325 2
BP00344 1
BP00368 1
BP00371 1
BP00373 1
BP00385 2
BP00393 1
BP00398 1
BP00404 1
BP00411 2
BP00413 1
BP00420 3
BP00422 1
BP00430 1
BP00435 1
BP00439 4
BP00440 1
BP00456 2
BP00458 1
BP00464 1
BP00468 1
BP00471 2
BP00479 3
BP00480 2
BP00485 2
BP00488 1
BP00495 4
BP00501 1
BP00511 1
BP00514 2
BP00519 1
BP00530 1
BP00533 5
BP00539 1
BP00540 4
BP00541 1
BP00542 1
BP00546 3
BP00547 1
BP00556 1
BP00572 1
BP00573 1
BP00581 1
BP00588 3
BP00616 1
BP00617 1
BP00624 1
BP00629 1
BP00640 2
BP00652 1
BP00659 2
BP00670 1
BP00676 1
BP00677 1
BP00687 1
BP00698 1
BP00701 3
BP00709 1
BP00714 1
BP00715 2
BP00725 1
BP00734 4
BP00750 1
BP00753 1
BP00760 1
BP00761 1
BP00780 1
BP00781 1
BP00807 2
BP00810 1
BP00813 1
BP00822 1
BP00826 1
BP00836 1
BP00854 6
BP00863 1
BP00864 2
BP00875 1
BP00892 1
BP00903 1
BP00905 1
BP00924 10
BP00928 3
BP00937 10
BP00938 1
BP00940 1
BP00942 1
BP00961 1
BP00971 1
BP00982 1
BP01002 1
BP01004 2
BP01026 1
BP01028 1
BP01029 1
BP01043 1
BP01053 2
BP01065 4
BP01067 1
BP01091 1
BP01094 1
BP01104 2
BP01113 2
BP01119 1
BP01120 1
BP01131 1
BP01138 1
BP01140 2
BP01152 1
BP01165 1
BP01171 1
BP01178 2
BP01179 1
BP01189 1
BP01195 2
BP01210 3
BP01216 1
BP01227 2
BP01233 1
BP01243 1
BP01246 1
BP01275 1
BP01286 1
BP01297 2
BP01323 1
BP01330 2
BP01335 1
BP01354 1
BP01402 1
BP01406 1
BP01417 1
BP01418 1
BP01424 1
BP01427 1
BP01436 1
BP01437 1
BP01439 1
BP01451 1
BP01463 4
BP01482 1
BP01514 1
BP01517 1
BP01524 1
BP01540 1
BP01569 1
BP01600 1
BP01606 1
BP01644 1
BP01650 1
BP01665 1
BP01672 1
BP01675 2
BP01681 1
BP01682 1
BP01692 1
BP01696 1
BP01708 1
BP01714 1
BP01732 3
BP01765 1
BP01776 1
BP01782 1
BP01795 21
BP01818 1
BP01820 1
BP01821 2
BP01828 1
BP01829 1
BP01830 1
BP01841 2
BP01847 1
BP01848 1
BP01856 1
BP01858 5
BP01862 1
BP01893 1
BP01914 1
BP01917 1
BP01927 2
BP01931 3
BP01938 1
BP01947 2
BP01948 1
BP01976 1
BP01994 1
BP01995 1
BP02002 1
BP02006 1
BP02011 2
BP02018 1
BP02028 2
BP02032 2
BP02038 4
BP02055 2
BP02078 1
BP02080 1
BP02091 1
BP02108 1
BP02117 2
BP02156 1
BP02174 1
BP02189 1
BP02194 1
BP02200 1
BP02203 1
BP02225 1
BP02232 1
BP02253 1
BP02258 1
BP02277 1
BP02284 1
BP02345 1
BP02353 1
BP02358 1
BP02386 1
BP02387 1
BP02409 1
BP02420 1
BP02425 1
BP02427 1
BP02431 2
BP02442 1
BP02468 1
BP02469 1
BP02471 1
BP02484 1
BP02506 16
BP02518 1
BP02519 1
BP02537 2
BP02546 1
BP02551 1
BP02558 1
BP02569 1
BP02574 1
BP02576 1
BP02581 1
BP02588 1
BP02591 1
BP02593 1
BP02596 3
BP02601 5
BP02624 1
BP02645 2
BP02646 3
BP02664 1
BP02674 1
BP02678 1
BP02706 2
BP02719 1
BP02724 1
BP02740 1
BP02742 1
BP02744 1
BP02769 1
BP02802 1
BP02860 1
BP02876 1
BP02879 1
BP02887 1
BP02907 1
BP02910 1
BP02928 1
BP02931 1
BP02934 1
BP02940 1
BP02948 11
BP02974 1
BP02976 2
BP02996 3
BP03043 1
BP03050 1
BP03064 1
BP03075 1
BP03085 1
BP03096 1
BP03125 12
BP03142 1
BP03145 1
BP03151 1
BP03161 1
BP03170 1
BP03188 2
BP03215 1
BP03220 1
BP03229 1
BP03230 1
BP03242 1
BP03249 3
BP03257 1
BP03277 1
BP03279 1
BP03280 1
BP03291 2
BP03302 1
BP03311 2
BP03325 1
BP03331 1
BP03333 1
BP03387 1
BP03399 1
BP03439 1
BP03443 1
BP03454 6
BP03503 1
BP03510 1
BP03512 1
BP03569 1
BP03570 1
BP03582 1
BP03583 5
BP03585 1
BP03591 3
BP03594 3
BP03644 4
BP03650 1
BP03691 1
BP03704 1
BP03711 1
BP03714 1
BP03722 1
BP03744 1
BP03754 1
BP03772 9
BP03796 1
BP03801 1
BP03802 1
BP03804 1
BP03807 1
BP03819 1
BP03830 1
BP03837 1
BP03858 1
BP03880 1
BP03888 1
BP03897 10
BP03907 1
BP03925 2
BP03932 1
BP03934 1
BP03952 1
BP03976 1
BP03984 1
BP03987 1
BP03992 2
BP04034 1
BP04036 3
BP04068 1
BP04079 2
BP04086 1
BP04093 6
BP04111 1
BP04118 1
BP04122 1
BP04133 1
BP04168 1
BP04175 1
BP04188 1
BP04189 1
BP04234 2
BP04257 5
BP04283 3
BP04292 1
BP04301 2
BP04309 1
BP04315 1
BP04342 1
BP04354 1
BP04355 1
BP04381 1
BP04393 2
BP04415 1
BP04442 1
BP04462 2
BP04537 1
BP04556 1
BP04575 1
BP04636 1
BP04659 1
BP04674 1
BP04712 1
BP04715 1
BP04722 1
BP04768 2
BP04803 1
BP04848 1
BP04850 1
BP04854 1
BP04880 1
BP04884 1
BP04934 1
BP04939 1
BP04963 2
BP04969 1
BP04987 2
BP04988 1
BP04999 1
DM00044 1
DM00046 1
DM00060 2
DM00099 5
DM00179 1
DM00191 3
DM00215 3
DM00234 2
DM00250 7
DM00270 1
DM00303 2
DM00315 2
DM00372 3
DM00396 1
DM00406 1
DM00471 1
DM00516 1
DM00517 2
DM00522 5
DM00588 1
DM00604 2
DM00611 4
DM00758 2
DM00864 1
DM01038 3
DM01098 1
DM01111 1
DM01389 1
DM01551 2
DM01552 1
DM01554 1
DM01595 1
DM01724 1
DM01753 2
DM01813 1
DM01831 1
IPB000001 30
IPB000020 12
IPB000083 20
IPB000102 18
IPB000118 6
IPB000130 9
IPB000152 949
IPB000169 205
IPB000177 13
IPB000209 284
IPB000249 1
IPB000255 9
IPB000264 48
IPB000279 200
IPB000283 15
IPB000287 26
IPB000325 3
IPB000345 52
IPB000387 46
IPB000420 15
IPB000421 16
IPB000453 18
IPB000495 44
IPB000508 12
IPB000532 41
IPB000538 36
IPB000557 13
IPB000561 1379
IPB000562 27
IPB000626 188
IPB000633 2
IPB000679 14
IPB000684 8
IPB000712 18
IPB000716 29
IPB000812 2
IPB000814 25
IPB000822 3536
IPB000873 3
IPB000950 6
IPB001002 20
IPB001007 10
IPB001023 297
IPB001054 7
IPB001064 204
IPB001084 69
IPB001117 11
IPB001156 45
IPB001169 88
IPB001202 13
IPB001239 13
IPB001343 69
IPB001368 12
IPB001370 4
IPB001395 18
IPB001412 1
IPB001443 12
IPB001450 209
IPB001464 146
IPB001484 12
IPB001487 1
IPB001526 2
IPB001580 119
IPB001589 8
IPB001651 5
IPB001680 7
IPB001687 251
IPB001781 161
IPB001792 2
IPB001881 919
IPB001928 13
IPB001934 34
IPB001969 150
IPB001993 112
IPB002003 6
IPB002040 6
IPB002048 394
IPB002049 169
IPB002052 1
IPB002078 60
IPB002088 20
IPB002098 14
IPB002105 23
IPB002126 645
IPB002151 20
IPB002155 51
IPB002162 34
IPB002172 319
IPB002194 92
IPB002202 42
IPB002219 50
IPB002221 54
IPB002223 61
IPB002290 18
IPB002364 1
IPB002464 2
IPB002465 19
IPB003015 1
IPB003016 16
PF00011 1
PF00024 1
PF00050 5
PF00052 1
PF00056 1
PF00058 2
PF00137 1
PF00144 1
PF00148 1
PF00176 1
PF00364 2
PF00431 3
PF00481 1
PF00520 1
PF00526 24
PF00567 4
PF00570 2
PF00571 1
PF00608 2
PF00612 3
PF00621 1
PF00630 3
PF00634 1
PF00664 1
PF00681 1
PF00683 1
PF00698 1
PF00704 1
PF00781 1
PF00807 2
PF00839 2
PF00892 1
PF00904 5
PF00917 1
PF00931 1
PF00963 8
PF00989 1
PF01011 8
PF01347 1
PF01352 1
PF01378 3
PF01391 2
PF01392 1
PF01394 1
PF01403 1
PF01410 1
PF01422 1
PF01436 2
PF01463 1
PF01469 6
PF01508 3
PF01579 1
PF01590 1
PF01604 1
PF01627 4
PF01629 1
PF01681 16
PF01683 7
PF01705 2
PF01744 2
PF01748 1
PF01754 1
PF01757 1
PF01760 1
PF01769 1
PF01796 1
PF01827 1
PF01833 1
PF01838 1
PF01846 2
PF01859 1
PF01869 1
PF01995 1
PF02012 2
PF02013 2
0215      2
BL00223      7
BL00225      3
BL00229      3
BL00230     11
BL00232     33
BL00235      4
BL00241      1
BL00243      3
BL00259      3
BL00260      2
BL00267      1
BL00270     11
BL00280      2
BL00281      1
BL00282      6
BL00287      2
BL00290      2
BL00299     11
BL00309      1
BL00310      1
BL00313      7
BL00314     56
BL00317      1
BL00328      9
BL00330      4
BL00334      2
BL00344      1
BL00347      1
BL00351      1
BL00352      8
BL00354      2
BL00369      1
BL00blimps-3.9/examples/blimps/sample.blocks000064400001460000012000007610130776372702600207620ustar00jorjastaff00000400000027ID   Chromo; BLOCK
AC   IPB000953; distance from previous block=(-15,1945)
DE   Chromo domain
BL   GWG;  width=38; seqs=284; 99.5%=1882; strength=1126
CBX2_MOUSE|P30658  (  12) FAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPEENI   6

CEC1_CAEEL|P34618  (   8) YTVESILEHRKKKGKSEFYIKWLGYDHTHNSWEPKENI  12

HP1_DROVI|P29227   (  24) YAVEKILDRRVRKGKVEYYLKWKGYAETENTWEPEGNL   7

PC_DROME|P26017    (  26) YAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNI  11

SWI6_SCHPO|P40381  (  83) VEKVLKHRMARKGGGYEYLLKWEGYDDPSDNTWSSEAD  25

CBX1_HUMAN|P23197  (  21) YVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENL   5
CBX3_HUMAN|Q13185  (  30) FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENL   7
CBX3_MOUSE|P23198  (  30) FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENL   7
CBX5_HUMAN|P45973  (  20) YVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNL   6
CBX5_MOUSE|Q61686  (  20) YVVEKVLDRRMVKGQVEYLLKWKGFSEEHNTWEPEKNL   8

CBX4_HUMAN|O00257  (  11) FAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENI   5
CBX4_MOUSE|O55187  (  11) FAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENI   5
CBX6_HUMAN|O95503  (  11) FAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEPEENI   7
CBX6_MOUSE|Q9DBY5  (  11) FAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEPEENI   7
CBX7_HUMAN|O95931  (  11) FAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHI   5
CBX8_HUMAN|Q9HC52  (  11) FAAEALLKRRIRKGRMEYLVKWKGWSQKYSTWEPEENI   8
CBX8_MOUSE|Q9QXV1  (  11) FAAEALLKRRIRKGRMEYLVKWKGWSQKYSTWEPEENI   8

CDY1_HUMAN|Q9Y6F8  (   7) EVEAIVDKRQDKNGNTQYLVRWKGYDKQDDTWEPEQHL   9
CDY2_HUMAN|Q9Y6F7  (   7) EVEAIVDKRQDKNGNTQYLVRWKGYDKQDDTWEPEQHL   9

AL13_SCHPO|O13953  (  19) LYEAKIVDTEMKGDVTTYLIHYKGWKNSWDEWVEQDRI  19
CHD1_HUMAN|O14646  ( 301) GDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETL  11
CHD1_MOUSE|P40201  ( 299) GDPNAGFERNKEPGDIQYLIKWKGWSHIHNTWETEETL  11
CHD1_YEAST|P32657  ( 196) VLEKTVPDLNNCKENYEFLIKWTDESHLHNTWETYESI  28
CHD2_HUMAN|O14647  ( 290) GDPSGDFDTEKDEGEIQYLIKWKGWSYIHSTWESEESL  12
CHD3_CAEEL|Q22516  ( 502) QIHRIINHLSYAKSQQDYLVKWKELSYEHATWERDDTD  15
CHD3_DROME|O16102  ( 180) LVQRVINHSEEPNGGTMYLVKWRELSYNDSSWERESDS  28
CHD3_HUMAN|Q12873  ( 632) TVHRIINHSVDKKGNYHYLVKWRDLPYDQSTWEEDEMN  13
CHD4_HUMAN|Q14839  ( 623) MIHRILNHSVDKKGHVHYLIKWRDLPYDQASWESEDVE  11
CHD5_HUMAN|Q8TD26  ( 379) LEVAHTKDAETGEEVTHYLVKWCSLPYEESTWELEEDV  10
CHDA_HUMAN|Q9P2D1  ( 125) IMDFARSTDDRGEPVTHYLVKWCSLPYEDSTWERRQDI  19
CHDB_HUMAN|Q9HCK8  ( 153) LDESHSIDKDNGEPVIYYLVKWCSLPYEDSTWELKEDV  16
CHDM_DROME|O97159  ( 613) IVQRVINHRTARDGSTMYLVKWRELPYDKSTWEEEGDD  17
CHP1_SCHPO|Q10103  (  23) EVEDILADRVNKNGINEYYIKWAGYDWYDNTWEPEQNL  24
CLR4_SCHPO|O60016  (  10) VERIVDEKLDRNGAVKLYRIRWLNYSSRSDTWEPPENL  19
EAF3_YEAST|Q12432  (  60) KLGEDESIPEEIINGKCFFIHYQGWKSSWDEWVGYDRI  26
ELF1_SCHPO|O14134  ( 820) RRVEALIGRQKLKKSFQYEIKWFGKPHKYNTWVSREIL  22
ESA1_YEAST|Q08649  (  35) ERLAEILSINTRKAPPKFYVHYVNYNKRLDEWITTDRI  19
HP1_DROME|P05205   (  24) YAVEKIIDRRVRKGKVEYYLKWKGYPETENTWEPENNL   6
HRP1_SCHPO|Q9US25  ( 305) IVERIVASETNEEGKTEYFVKWRQLPYDNCTWEDADVI  16
HRP3_SCHPO|O14139  ( 289) QVDRIVAKHLNSDGSVEYLVKWKQLLYDFCTWEASSII  26
MG15_HUMAN|Q9UBU8  (  25) LYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWVPESRV  14
MOF_DROME|O02193   ( 395) GQVLQSRTTENAAAPDEYYVHYVGLNRRLDGWVGRHRI  35
MR15_DROME|Q9Y0I1  (  36) IYEAKVLKTKPDATPVEYYIHYAGWSKNWDEWVPENRV  18
MSL3_DROME|P50536  ( 232) VPIVTIMENFVKQQAVELAISIKQDSSRARNTQSRNAR  45
RBB1_HUMAN|P29374  ( 591) IYEASIKSTEIDDGEVLYLVHYYGWNVSYDEWVKADRI  14
SU91_HUMAN|O43463  (  43) FEVEYLCDYKKIREQEYYLVKWRGYPDSESTWEPRQNL   9
SU91_MOUSE|O54864  (  43) FEVEYLCDYKKIREQEYYLVKWRGYPDSENTWEPRQNL   9
SU92_HUMAN|Q9H5I1  (  47) YEVEYLCDYKVVKDMEYYLVKWKGWPDSTNTWEPLQNL  14
SU92_MOUSE|Q9EQQ0  ( 118) YEVEYLCDYKVAKGVEYYLVKWKGWPDSTNTWEPLRNL  11
SUV9_DROME|P45975  ( 219) YVVERIECVEMDQYQPVFFVKWLGYHDSENTWESLANV  22
TI60_HUMAN|Q92993  (  26) WPLAEILSVKDISGRKLFYVHYIDFNKRLDEWVTHERL  11
YNZ8_CAEEL|P45968  (  24) FEVEKILAHKVTDNLLVLQVRWLGYGADEDTWEPEEDL  17
Q9HFY7             (1131) EVERIIDHSDAFGEELHFLVKWLGYGHEDNTWEPQSNL  17
Q8X0A0             (  27) EAKILDVQPTESGDGWSYKIHYKGWKSSWDDWVPQDRI  34
O42765             ( 934) RAIEALVGRQKLKKSFQYEVKWKYWLPKYNSWVPKEVL  17
Q08972             ( 942) RAIEAIVGRQKLKKSFQYEVKWKYWKPKYNSWVPKDVL  14
Q9Y8H1             ( 982) YEVKSILDSRLHRGKLQYLVHWKGYGYEENSWVEESDI  10
Q9C435             (1322) WEVERVISSRVLRGVLQYQVQWRGWDPDPEFYDAEGFK  64
O42934             ( 178) VEMILDSRMKKDGSGFQYYLKWEGYDDPSDNTWNDEED  28
Q9UVC1             (1162) AENEFEVEKILDKKGQRYLVKWKGYDESENTWEPRINL  23
Q9UVD8             (1195) DIVAEEVRRRGRGRKLYYEVKWKGFHQTTLEPAELLKD  23
Q9C1J9             ( 818) RIIDELVARKKLKQSYEYEVSFKGMSSAENIWISRDEL  30
Q8WZR8             (  44) EVEDILLEELDDDGKQVYLVKWERYPLEQCTWEPEDNL  19
O94446             (  35) YRKAEILMIQKRTRGVVYYVHYNDYNKRLDEWITIDNI  19
Q96E12             ( 184) NLEEEEWVRPVMKRDKQVLLHWGYYPDSYDTWIPASEI  15
Q8TDI0             ( 593) MIHRILNHSFDKKGDVHYLIKWKDLPYDQCTWEIDDID  14
Q8N8U2             (   8) EVERIVDKRKNKKGKWEYLIRWKGYGSTEDTWEPEHHL   9
Q92922             ( 212) SQDDEEWLRPVMRKEKQVLVHWGFYPDSYDTWVHSNDV  19
Q9NXA0             (   0) XMDFARSTDDRGEPVTHYLVKWCSLPYEGSTWERRQDI  22
Q9H7Z6             (  72) SAEVIQSRVNDQEGREEFYVHYVGFNRRLDEWVDKNRL   9
Q8N5Y2             (  35) IVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHV  22
Q96IP5             ( 290) GDPSGDFDTEKDEGEIQYLIKWKGWSYIHSTWESEESL  12
Q9HBP6             (  25) LYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWVPESRV  14
Q9BTB1             (  12) FAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPEENI   6
Q9Y5Z8             (  35) IVVVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHV  21
Q9BTP1             (  62) FEVEKILDMKTEGGKVLYKVRWKGYTSDDDTWEPEIHL   9
Q8WYB4             (  45) SAEVIQSRVNDQEGREEFYVHYVGFNRRLDEWVDKNRL   9
Q9H5A0             (  59) MYEASIKDSDVEGGEVLYLVHYCGWNVRYDEWIKADKI  11
Q9UFR9             (  27) MIHRILNHSFDKKGDVHYLIKWKDLPYDQCTWEIDDID  14
Q9Y4I0             ( 632) TVHRIINHSVDKKGNYHYLVKWRDLPYDQSTWEEDEMN  13
Q92923             ( 184) NLEEEEWVRPVMKRDKQVLLHWGYYPDSYDTWIPASEI  15
Q8TAQ2             ( 184) NLEEEEWVRPVMKRDKQVLLHWGYYPDSYDTWIPASEI  15
Q9Y6E1             (  41) MYEASIKDSDVEGGEVLYLVHYCGWNVRYDEWIKADKI  11
Q9P2W4             ( 268) MYEASIKDSDVEGGEVLYLVHYCGWNVRYDEWIKADKI  11
Q9BWK7             (  26) WPLAEILSVKDISGRKLFYVHYIDFNKRLDEWVTHERL  11
Q9Y654             ( -11) XXXXXXXXXXXXKDKVEYLLKWKGFSDEDNTWEPEENL   4
Q8N677             ( 290) GDPSGDFDTEKDEGEIQYLIKWKGWSYIHSTWESEESL  12
Q9HAC5             (  72) SAEVIQSRVNDQEGREEFYVHYVGFNRRLDEWVDKNRL   9
O95624             (  26) WPLAEXLSVKDISGRKLFYVHYIDFNKRLDEWVTHERL  11
Q9Y232             (  62) QVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHL   7
Q8IZR2             (  47) LEVAHTKDAETGEEVTHYLVKWCSLPYEESTWELEEDV  10
Q8IY59             (  72) SAEVIQSRVNDQEGREEFYVHYVGFNRRLDEWVDKNRL   9
Q8IXZ5             ( 620) MIHRILNHSVDKKGHVHYLIKWRDLPYDQASWESEDVE  11
Q8IWH2             ( 212) SQDDEEWLRPVMRKEKQVLVHWGFYPDSYDTWVHSNDV  19
Q25732             (   8) FEIGDILEIKKKKNGFIYLVKWKGYSDDENTWEPESNL  11
Q960X4             (  39) WPLAEIVSIKELDGRRQFYVHYVDFNKRLDEWVNEEDL  12
Q9N6U3             ( 148) VEKILAQEFNQATRQLMFLVKWKGYAVQQSTWEPLEHL  14
Q95XW8             ( 117) EKIVAHRYPNDRLNQPLYLVMWRGFPDPVSNTEMWGEE  33
O18243             ( 310) YRIEKILATRTVRGKKQHLVRWDGYGAEFDSWIDASGV  24
Q9N6T9             ( 139) FIIEKILDFKFQEGKEYFHIKWKGWPDSENTWEPIENL  11
Q19815             ( 490) QIHRIINHQSYAKSQQDYLVKWKELSYDQATWERDDSN  16
Q95SE0             (   4) FSVERVEDKRTVNGRTEYYLKWKGYPRSENTWEPVENL   8
O17916             (  20) MVEKVLDKRTGKAGRDEFLIQWQGFPESDSSWEPRENL   9
Q9VS18             ( 232) VPIVTIMENFVKQQAVELAISIKQDSSRARNTQSRNAR  45
Q9N6U0             ( 151) VEKILAQEFDVSTKQFMFLVKWKGYSMVHNTWEPLEHL  24
O77159             (   5) YEVENIIGHRKKGSQIEYHIQWKGYSLKQATYEPAKNI  25
O44139             ( 301) TKSWETLGGHIKNGFRLSFVCSNGLTIIENVVELNKNL 100
Q21370             (  37) FVVEKVLNKRLTRGGSEYYIKWQGFPESECSWEPIENL  11
Q8SWP7             ( 215) FVKVDRILHEDYDGEKVFLVKWRGQAYELSTFETAESV  25
Q9XWW0             ( 340) YDAVITDIKPDKDGKECYCIHFKGWNNRYDEQIPIGEE  32
Q9U3C6             (  20) MVEKVLDKRTGKAGRDEFLIQWQGFPESDSSWEPRENL   9
Q8T1E4             ( 246) CDIIEKRESELKNGTYDYYVHYHEFNRRLDEWVHESRM  26
Q9NHC4             (  19) VEKIIKTKYDDQLRTNLYLVKWKGYADHLNTWEPEWNL  22
Q9U3C3             (  72) NNYKSIENHEQGAKELMYYVHYEELDRRNDEWITLDKI  25
Q22430             (  34) FSPASVEYDKRRHSKYAYLVHWRGYDWKERTWEPEENL  30
O15725             ( 976) ASYEVESILNHDKVKKMYLVKFKGYPEPEWIREVDTDC  44
Q9VCU6             (   9) VVERIMDKRITSEGKVEYYIKWRGYTSADNTWEPEENC  18
O44553             (  46) WIVEKIQKMRYNGKLKRVEFLVLWEADKSKSWEPIENF  46
Q8MTK2             (  12) FAAEKILKKRYKKGRAEYLVKWQGYSSKFNTWEPVENI   9
Q9VX35             ( 233) WEVEKILDHVATKEGDMFKIRWKKYGPKDDSWEPSKNL  23
Q9TYU5             (  47) RWAEVISRCRAANGSIKFYVHYIDCNRRLDEWVQSDRL  23
Q9N4L7             (  49) WVVEKVQEMRYNGKLKRVEFLVLWQADKSTSWEPIENF  41
O61845             (1105) IVDRVVDLITEDDGQEFVLIKWKSLGYEEVTWEPIEMI  21
Q9XWW2             (  22) YDAKITDIKTNSDGKELYCVHFKGWNNRYDEKIPVGEE  23
Q8SR51             (  24) VFKAEILGKRAGKSGLEFYVHYVELNRRLDEWIDGSMI  19
Q8T9D1             ( 223) VEKIVAKRFNPRRKTHEYLVKWVDRSHHENTWEVMANL  20
Q19973             ( 117) VEKIIAHRFSGKKNKPLFLVMWRGYPNPVSHSEMWENE  35
Q9W396             (   4) FSVERVEDKRTVNGRTEYYLKWKGYPRSENTWEPVENL   8
Q9VPL9             (1946) LDMSVHTDETSGETTKHYLVKWKSLPYEDCTWELEEDV  17
O17585             (  45) YEVQDIVRSRIEGREIQYTVKWTNWNGGDTEEAERRLV  43
Q9NBL2             ( 285) TPIVTILENFVKQRAVELAIGIKQDSSRARNTLSRNAR  55
Q9VNQ0             ( 196) VEKIVAKRFNPRRKTHEYLVKWVDRSHHENTWEVMANL  20
Q9N6U2             ( 148) VEKILAQEFNQATRQLMFLVKWKGYAVQQSTWEPLEHL  14
Q9VR09             (  24) LEPLRILGACNWSGKLTFLMQWKGCDEAGLVPAEVLNV  37
Q94996             (  51) VEKILDSRFNPKTKQKEYLVKWENWPIEDSTWEPYEHL  12
Q9V856             (  22) YIVEKFLGKRYLRGRPQYLTKWEGYPIEQCTWEPLENL  28
Q8SSD0             (   7) YTVDRIVGDRKKKGVKQYLVKWEGYPDSENTWEDEKNI   8
Q9N6T8             ( 139) FIIEKILDFKFQEGKEYFHIKWKGWPDSENTWEPIENL  11
Q18313             (  78) EERFKRTKKPQLISNYFFLVKWLGYGNKEMTWEPESNI  27
Q9V855             (  24) YVVEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENV  10
O17918             (  20) MVEKVLDKRTGKAGRDEFLIQWQGFPESDSSWEPRENL   9
Q9N6U1             ( 219) YVVERIECVEVDQYQPVFFVKWLGYKDSANTWESLANV  20
Q9NAL0             ( 353) YKIEEVLKRRTRKGIKEIFVKWYGYPDKFNSWIPDIXX  20
Q9VK43             ( 302) NGIERILGKETKAGKVEFLLRYENQGGLFWQSEEFIKR  29
Q19972             (  87) YAVERVLAHRKVKGSPLYLVQWKGYPHPVWNSEMWEED  20
Q9VWP3             (  96) TYEAKVIEISVQRGVPMYLVHYTGWNNRYDEWVPRERI  10
Q24376             ( 351) HAGFDEKQTPDAETEAQFLIKWKGWSYIHNTWESEATL  22
O97425             (   7) WPLAEIVSIKELDGRRQFYVHYVDFNKRLDEWVNEEDL  12
Q9VHG0             (  27) YIVERILDRRHYMGQLQYLVKWLDYSDEDNTWESAADL  17
O17909             ( 222) DKGDPNDQIPGDKTEQQFFVKWTGWSHLHNTWESENSL  31
Q8IJG6             (1205) AERIVMHKISDITNEQVFLVKWTSCAYDQCTEETKQTL  29
Q8IHV8             (  58) NCKRKKNRKDENLDDFEFYIKWKNYDSDENTWEPFENL  21
Q8I5K4             (   8) FEIGDILEIKKKKNGFIYLVKWKGYSDDENTWEPESNL  11
Q95KT5             (   7) EVETIVDQRQDKNGNTVYLVRWKGYDKQDDTWEPEHHL  18
Q9SQW9             (1568) PEKLLDIRQSNTNSGPEVLVQWSGLSTLESTWEPLLTL  18
Q8LI34             (  83) VIERRKSSTSSSPADYEYYVHYTEFNRRLDEWVKLEQL  13
O49141             ( 345) LGIMFGDPQGTGEKTLQLMVRWKGYNSSYDTWEPYSGL  11
Q9XE85             (1438) KILETAERVTRSRVIRMCKVQWNRHSEAEATWEREDDL  27
Q8LPU5             ( 449) KLIGIRYDGTGRKKGVYFKVQWEGYGPEEDTWEPIDNL  12
Q94F87             ( 792) VDICFGDPDKTGKNGLKFKVHWKGYRSDEDTWELAEEL  16
Q94GK0             (1256) KVLEEAERHTRRKAMKFYKVQWSNHSEDEATWEREDLL  13
Q9S775             ( 190) TTVDRILACREEDGELEYLVKYKELSYDECYWESESDI  17
Q94HR8             ( 107) YEIEDIRRRRLRKGKLQYLVKWRGWPESANTWEPLENL   6
Q942K3             (1457) EILDCRMVKKGNAAIVQVRVRWGSLPDNMATWEDYDVI  25
Q9C9L8             ( 388) VGISFGVPKKLLKRGLYLKVRWLNYDDSHDTWEPIEGL  10
O50037             ( 329) VGIVFGDPKGTGEKTLHLKVRWKGYSPKYDTWEPYSGL  10
Q948W3             (   7) FKVEEVLDLRWHQNKLEYLVHWHRYDISKCTXXXXXXX  28
Q8W2R6             ( 321) LQPASVSQSRLARGVREVLVQWKDRPAAEASWVGLDDF  16
Q38940             ( 263) LGIMFGDPQGTGEKTLQLMVRWKGYNSSYDTWEPYSGL  11
Q8W513             (  77) VIERRKGSACSSPADYEYYVHYTEFNRRLDEWVKLDQL  16
Q8LSQ2             ( 322) VAEAVVNKREAAEGEGKWEYLVKWVDIEEATWEPAENV  61
O80378             (  67) KVIERRRVPSGGPNDYEYYVHYTEFNRRLDEWVKLEQL  13
Q8S6Z7             ( 189) RVLEKAERQTRRKTIKFYKVQWSNHSEDEATWEREDHL  10
Q8RUU3             (1252) PVPRQVLRARLARGVRQLLVQWEGLPASATSWEDLDDF  16
Q9FWC5             ( 852) AILERRLVKRGNAAHVQVLLKWSLLPADHATWEDYHVV  24
Q94HV4             (1377) PEPERVTRSRLARGVRQVLVHWKGESAASATWEDLDTF  13
Q947Y6             (1363) CEPERVIKARLARGVRQVLVQWKGTSAASATWEDREPF  23
O49139             ( 345) LGIMFGDPQGTGEKTLQLMVRWKGYNSSYDTWEPYSGL  11
O23159             (  50) DIPLQVQKVELRKKEWKYFVHYLGWNKNWDEWVSADRL  17
Q8L818             (  77) VIERRKGSACSSPADYEYYVHYTEFNRRLDEWVKLEQL  16
O22265             ( 270) AEVDEIVEKRGKGKDVEYLVRWKDGGDCEWVKGVHVAE  23
O50073             ( 345) LGIMFGDPQGTGEKTLQLMVRWKGYNSSYDTWEPYSGL  11
Q8S793             ( 194) GALVVAEDVGSTEGETGDKKKTEGCPNRVHITKIIKPV  86
Q94FN4             ( 388) VGISFGVPKKLLKRGLYLKVRWLNYDDSHDTWEPIEGL  10
Q8S7F8             ( 344) EILDRRLVKKGNATHVQVLIKWSSLPAHQATWEDYEVL  14
Q9ARI6             ( 449) KLIGIRYDGTGRKKGVYFKVQWEEYGPEEDTWEPIDNL  12
Q9XIG5             (1145) FPEKIVDISFTDKGNKEFLVKWQDRGVSENSWMPYKEF  24
Q9SAU3             ( 273) AEVDEIVEKRGKGKDVEYLVRWKDGGDCEWVKGVHVAE  23
O49137             ( 345) LGIMFGDPQGTGEKTLQLMVRWKGYNSSYDTWEPYSGL  11
Q8LK11             (  66) FEIEAIRRRRLRKGQLQYLVKWRGWPESANTWEPLENL   6
Q9ZS84             (1472) ILDHRVLGTSKKNTKTEFLVHWKGKSAADAVWEKAKDL  21
Q9SMT0             (   5) CPVSEIIKTRKVQGRECFEVSWNDLEGLESSIVPADLV  33
Q8SBB4             ( 419) KLAGICYGGSGREDGLYFKVQWKGYGREEDTWEPIENL  13
Q9AXT8             ( 445) KLVGICYGGSDRENGIYFKVQWEGYGPEEDTWEPIDNL  13
Q9ZVK3             ( 891) AVLEVRWRSQDKKRVADLLVQWEGLHIEDATWEEYDQL  17
Q8LHZ4             ( 475) GKIQETELKEHDGTTYEFLVKWVGKSNIHNSWISESEL  20
Q946J8             ( 108) YEIEAIRRKRVRKGKVQYLIKWRGWPETANTWEPLENL   6
Q9FU10             (1291) PEPERAVKTRLARGVRQLLIQWKGESPASATWEDADAF  13
Q9LWX1             ( 561) KVLEETERQTRRKTIKFYKVQWSNHSEDEATWEREDLL  10
Q944N1             (  93) YEIETVRRRRTVKGKVYYLIKWRGWPESANTWEPETNL  10
Q9LXD7             (  79) KVIERRRIHNGGQNDYEYYVHYTEFNRRLDEWTQLDQL  15
Q9LHM4             (1453) KVVERKMVNRQGKAVTKVLVKWSNEPLEEATWEFLFDL  30
Q8LCD4             (  79) KVIERRRIHNGGQNDYEYYVHYTEFNRRLDEWTQLDQL  15
Q8LJJ7             ( 448) CDVLATFQDNQDFDGYEFLVKWKGLDYCEATWEPCCTD  36
Q94GF6             ( 315) AILDRHMVKKGNAAVFQVLVQWGTLPAALATWEDFDVV  26
Q9LP90             (1333) VPEAVLETRYNEDGLLEALVHWQGLPVHEDTWEIAKDL  27
Q94F88             ( 388) VGISFGVPKKLLKRGLYLKVRWLNYDDSHDTWEPIEGL  10
O48579             ( 588) QPQRIVALRVSKEGNQEAYVKWTGLAYDECTWESLEEP  30
Q8W331             (1405) KVLEEAERQTRRKTIKFYKIQWSNHSEDEATWEREDLL  10
O65791             (  55) FEIEHIRRKRVKKGEVQYLVKWRGWPESANTWEPVEHL   7
O50057             ( 345) LGIMFGDPQGTGEKTLQLMVRWKGYNSSYDTWEPYSGL  11
Q9FN82             ( 108) YEIEAIRRKRVRKGKVQYLIKWRGWPETANTWEPLENL   6
Q9AYK7             ( 716) KVLEEAERQTRRKTIKFYKVQWSNHSEDEATWEQEDLL  10
Q9SZ57             ( 142) KTVDRIIACREGDDGEEYLVKYKELSYRNSYWESESDI  19
Q8SA93             (1791) PAPLKVLRAQQRRGTWHILVQWQGLSPEEATWEPLDDF  18
Q941W4             ( 968) KVLEEAERQTRRKTIKFYKVQWSNHSEDEATWEREDLL   9
O49415             ( 792) VDICFGDHDKTGKNGLKFKVHWKGYRSDEDTWELAEEL  16
Q9SI41             ( 538) IIADRISKDGLGDVVPEYLVKWQGLSYAEATWEKDVDI  12
O49144             ( 345) LGIMFGDPQGTGEKTLQLMVRWKGYNSSYDTWEPYSGL  11
Q8S680             (1521) RILDEAKKKTRTKVWRMYKVQWSNHTEDEATWESEEFL  15
Q8S6V9             ( 938) RILDEAKKRTRSKVWRMYKVQWSNHTEDEATWESEEFL  15
Q94DL2             (1526) KVLEEVERQTRRKTIKFYKVQWSNHSEDEATWEREDLL   9
Q940I7             ( 270) AEVDEIVEKRGKGKDVEYLVRWKDGGDCEWVKGVHVAE  23
Q8H854             ( 564) LEICYGDPSNTGKNGLWFKVRWKGYDPSYDTWEPIDGL  17
Q8H4N1             (1526) KVLEEAERQTRRKTIKFYKVQWSNHSEDEATWEREDLL   9
Q8H421             ( 160) RILDEAEKRTRNKVWRMYKVQWSNHTEDEATWESKEFL  15
Q8H3V5             ( 418) TVISFTSDVDQSWDDVEFYIKWKGQSFLHCQWKTLSEL  36
Q8H0H2             ( 298) LEICYGDPKEKNKPGLYFKVRWKGYGQEEDTWEPIEGL  13
Q8GZ97             (  79) KVIERRRIHNGGQNDYEYYVHYTEFNRRLDEWTQLDQL  15
Q8GVT8             (1301) KVLEEAERQTRRKTIKFYKVQWSNHSEDEATWEREDLL   9
Q9D5D8             (   8) EVERIVDKRKNKKGKWEYLIRWKGYGSTEDTWEPEHHL   9
P97496             ( 209) SQEDEEWLRPVMRRDKQVLVHWGFYPDSYDTWVHSNDV  19
Q9D1P2             (  72) SAEVIQSRVNDQEGREEFYVHYVGFNRRLDEWVDKNRL   9
Q9JIX5             ( 651) RVVKKELPSGQYTEAEEFFVKYKNYSYLHCEWATISQL  18
Q9JJB4             (  44) FEVERILDMKCEGGKNLYKVRWKGYTSEDDTWEPEVHL  13
Q9CYJ8             (  21) YVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENL   5
Q8R1E4             (  15) MYEASIKDSDVEGGEALYLVHYCGWNVRYDEWIKADKI  12
Q8VDS3             (  11) FAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHI   5
Q9CU16             (  59) FEVERILDMKCEGGKNLYKVRWKGYTSEDDTWEPEVHL  13
Q9DCC5             (  30) FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENL   7
Q8VIH0             (  26) WPLAEILSVKDISGRKLFYVHYIDFNKRLDEWVTHERL  11
Q9WTK2             (  57) QVESIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHL   7
Q8CIA0             (  12) FAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPEENI   6
Q8CI73             (  72) SAEVIQSRVNDQEGREEFYVHYVGFNRRLDEWVDKNRL   9
Q8CGZ3             (  26) WPLAEILSVKDISGRKLFYVHYIDFNKRLDEWVTHERL  11
Q8C9F3             ( 299) GDPNAGFERNKEPGDIQYLIKWKEWSHIHNTWETEETL  11
Q8C7Q2             ( 299) GDPNAGFERNKEPGDIQYLIKWKGWSHIHNTWETEETL  11
Q8C2L3             (  43) FEVEYLCDYKKIREQEYYLVKWRGYPDSENTWEPRQNL   9
Q8BZH5             (  11) FAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEPEENI   7
Q8BYH8             ( 778) LEVSFCEDKDTGESVIYYLVKWCSLPYEDSTWELKEDV  10
Q8BUB9             (  70) LEVSFCEDKDTGESVIYYLVKWCSLPYEDSTWELKEDV  10
Q8BR71             ( 643) TVHRIINHSMDKKGNYHYLVKWKDLPYDQSTWEEDEMN  19
Q8BNK2             ( 118) YEVEYLCDYKVAKGVEYYLVKWKGWPDSTNTWEPLRNL  11
Q8BM83             ( 368) MIHRILNHSVDKKGHVHYLIKWRDLPYDQASWESEDVE  11
Q8BJ76             (  72) SAEVIQSRVNDQEGREEFYVHYVGFNRRLDEWVDKNRL   9
Q8BJ75             (  47) LEVAHTKDAETGEEVTHYLVKWCSLPYEESTWELEEDV  10
Q8BJ69             (  72) SAEVIQSRVNDQEGREEFYVHYVGFNRRLDEWVDKNRL   9
Q8BIM5             (  70) LEVSFCEDKDTGESVIYYLVKWCSLPYEDSTWELKEDV  10
Q8BIE8             ( 380) LEVAHTKDAETGEEVTHYLVKWCSLPYEESTWELEEDV  10
O41148             ( 687) KILDKILGRRKLKKSYEYEVQWKNDETTQWMSRERLEE  30
Q66093             ( 905) KILDKILGRRKLKKSYEYEVQWKNDETTQWMSRERLEE  30
Q92021             (  37) DAEIVKVRYNKQAGREEYYAHYVGLNRRQNEWVDKSRL  23
O42156             (  17) FVVEKVMDRRVVNGKVEYYLKWKGFTDSDNTWEPEENL   7
Q9DF19             (  26) WPLAEILSVKDISGRRLFYVHYIDFNKRLDEWVTPERL  12
O93481             (  20) FVVEKVLDRRVVNGKVEYYLKWKGFTDADNTWEPEENL   6
Q9DGQ3             (  14) ERIIAHSNQKSAAGYPDYYCKWQGLPYSECSWEDGALI  18
Q98SI6             (  11) FAVEGIEKKRLRKGRMEYLVKWRGWSPKYNTWEPEENI   8
Q9DGQ0             (  14) ERIIAHSNQKSAAGYPDHYCKWQGLPYSECSWEDGALI  24
Q9DGQ2             ( -14) XXXXXXXXXXXXXXXIQYLIKWKGWSHIHNTWESEETL   4
O93482             (  11) FAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENI   5
Q9DGQ4             (  14) ERIIAHSNQKSAAGYPDYYCKWQGLPYSECSWEDGALI  18
O93284             (1125) WSVNKLLAVRRRGRGFQYLVDWVGYGPEDQSWVPPSYL  40
Q9W6X6             (  39) LEPERIIGATDSSGELMFLMKWKDSDEADLVPAREANT  25
Q8JIQ9             (  12) FDAECILNKRTRKGKLEYLVKWRGWSSKHNSWEPQENL   8
O42142             ( 298) GDPNAGFEKSKELGEIQYLIKWKGWSHIHNTWETEETL  12
Q9YHC4             (  12) FAAECILSKRLRKGTAEYLVKWRGWSSKHNSWEPEENI   8
Q98SV9             ( 642) YRVRRILDVRRRGREFQFLIEWEGYGPMRRSWAPRLFI  39
O42155             (  71) LEPEKIIGATDSCGELMFLMKWKDSDEADLVLAKEANL  34
O93480             (  21) YVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENL   5
Q98TL9             (  52) LDPERIIGATDSSGELMFLMKWKDSDEADLVPAREANT  25
Q91431             (  37) DADIVKTRYNKQAGREEYYVHYVGLNRRQNEWVDKSRL  12
Q9DGQ1             (  14) ERIIAHSNQKSEAGYPDYYCKWQGLPYSECSWEDGALI  18
Q91647             (  11) FAVESIEKKRIRKGRVEYLVKWRGWSSKYNTWEPEENI   5
Q8AWE2             (  11) FAAESIIKRRIRRGRMEYLVKWKGWSQKYSTWEPEENI   8
//
ID   HLH_basic; BLOCK
AC   IPB001092A; distance from previous block=(-2,3229)
DE   Basic helix-loop-helix dimerization domain bHLH
BL   ERF;  width=12; seqs=1865; 99.5%=863; strength=960
DEI_DROME|P41894   ( 103) ERTRMREINTAF   4

ESC1_SCHPO|Q04635  ( 343) ERKRRKEIKELF   3

HFR1_ARATH|Q9FE22  (  29) ERARSDEDRLIN  15

INO4_YEAST|P13902  (  54) EKKRRELERAIF   7

NUC1_NEUCR|P20824  ( 676) EQGRRNRINSAL   7

PHO4_YEAST|P07270  (  70) DSLALDDLDRAF  11

RTG1_YEAST|P32607  (  20) DRKRRDKINDRI   4

TCL5_HUMAN|Q9UL49  ( 361) ERDRRRRIRICC  12

TYE7_YEAST|P33122  (  84) EESALFPTDQFF  20

WS14_CAEEL|P41846  ( 812) EQNRRSALKDGF   5

YAWC_SCHPO|Q10186  (  97) ERRRREAISEGI   3

YNP2_CAEEL|P34555  (  12) ERTRVHTVNQAF   6

YRY3_CAEEL|Q10007  ( 182) ERCRVRNVNDGY   7

Q58467             (  77) NRLDMLKSSIVF  14

Q10466             (3230) EQLLSTGFKCKF  19

Q03082             (  65) VRRRLAALEAQF  10

Q60761             ( 144) LRRTSARLELVF  11

ARLC_MAIZE|P13526  ( 421) ERKRREKLNEMF   3
ARRS_MAIZE|P13027  ( 423) ERKRREKLNEMF   3
TT8_ARATH|Q9FT81   ( 368) ERRRREKLNEKF   2

ARN2_HUMAN|Q9HBZ2  (  61) ERRRRNKMTQYI   4
ARN2_MOUSE|Q61324  (  72) ERRRRNKMTQYI   4
ARNT_DROME|O15945  (  22) ERRRRNKMTAYI   4

ARNT_HUMAN|P27540  (  38) QRAIKRRPGLDF  12
ARNT_MOUSE|P53762  (  38) QRAIKRRSGLDF  14
ARNT_RABIT|O02748  (  38) QRAVKRRPGLDF  12
ARNT_RAT|P41739    (  38) QRAIKRRSGLDF  14

ASH1_HUMAN|P50553  ( 127) ERNRVKLVNLGF   4
ASH1_MOUSE|Q02067  ( 122) ERNRVKLVNLGF   4
ASH1_RAT|P19359    ( 124) ERNRVKLVNLGF   4
ASH1_XENLA|Q06234  (  90) ERNRVKLVNLGF   4
ASH2_HUMAN|Q99929  (  59) ERNRVKLVNLGF   4
ASH2_MOUSE|O35885  ( 127) ERNRVKLVNLGF   4
ASH2_RAT|P19360    ( 127) ERNRVKLVNLGF   4
AST3_DROME|P09774  (  92) ERNRVKQVNNGF   4
AST4_DROME|P10084  ( 108) ERNRVKQVNNSF   3
AST5_DROME|P10083  (  33) ERNRVKQVNNGF   4
AST8_DROME|P09775  ( 168) ERNRVKQVNNGF   4
O77028             ( 168) ERNRVKQVNNGF   4
O77026             (  33) ERNRVKQVNNGF   4
Q24639             (  33) ERNRVKQVNNGF   4
O77029             (  96) ERNRVKQVNNSF   3
O77031             ( 108) ERNRVKQVNNSF   3
P91703             ( 115) ERNRVKQVNNSF   3
O77030             (  91) ERNRVKQVNNGF   4
O77032             (  92) ERNRVKQVNNGF   4

ASH3_HUMAN|Q9NQ33  ( 101) ERQRVKCVNEGY   9
ASH3_MOUSE|Q9JJR7  ( 101) ERQRVKCVNEGY   9

ATH1_HUMAN|Q92858  ( 168) ERRRMHGLNHAF   4
ATH1_MOUSE|P48985  ( 165) ERRRMHGLNHAF   4
ATO_DROME|P48987   ( 264) ERRRMQNLNQAF   3
BET3_MESAU|O09029  ( 237) ERRRMHDLNDAL   3
HAN1_CHICK|Q90691  (  92) ERRRTESINSAF   3
HAN1_HUMAN|O96004  ( 103) ERRRTESINSAF   3
HAN1_MOUSE|Q64279  ( 103) ERRRTESINSAF   3
HAN1_RAT|P97832    ( 103) ERRRTESINSAF   3
HAN1_SHEEP|Q28555  ( 109) ERRRTESINSAF   3
HAN1_XENLA|O73615  (  89) ERRRTESINSAF   3
HAN2_BRARE|P57102  (  99) ERRRTQSINSAF   3
HAN2_CHICK|Q90690  ( 107) ERRRTQSINSAF   3
HAN2_HUMAN|O95300  ( 108) ERRRTQSINSAF   3
HAN2_MOUSE|Q61039  ( 108) ERRRTQSINSAF   3
HAN2_XENLA|P57101  ( 101) ERRRTISINSAF   4
LI32_CAEEL|Q10574  (  10) ERRRMNTLNVAY   6
LYL1_HUMAN|P12980  ( 146) ERWRQQNVNGAF   7
LYL1_MOUSE|P27792  ( 158) ERWRQQHVNGAF   8
NDF2_HUMAN|Q15784  ( 130) ERNRMHDLNAAL   3
NDF2_MOUSE|Q62414  ( 131) ERNRMHDLNAAL   3
NDF2_RAT|Q63689    ( 130) ERNRMHDLNAAL   3
NDF4_HUMAN|Q9HD90  (  96) ERTRMHGLNDAL   4
NDF4_MOUSE|O09105  (  96) ERTRMHGLNDAL   4
NDF4_XENLA|P79920  (  87) ERSRMHGLNDAL   3
NDF6_HUMAN|Q96NK8  ( 103) ERNRMHGLNDAL   3
NDF6_MOUSE|P48986  ( 103) ERNRMHGLNDAL   3
NDFM_CHICK|P79766  (  96) ERTRMHGLNDAL   4
NGN1_BRARE|O42606  (  79) ERNRMHNLNDAL   3
NGN1_HUMAN|Q92886  ( 101) ERNRMHNLNAAL   3
NGN1_MOUSE|P70660  ( 102) ERNRMHNLNAAL   3
NGN1_RAT|P70595    ( 102) ERNRMHNLNAAL   3
NGN2_HUMAN|Q9H2A3  (  99) ERNRMHNLNAAL   3
NGN2_MOUSE|P70447  ( 121) ERNRMHNLNAAL   3
NGN3_HUMAN|Q9Y4Z2  (  92) ERNRMHDLNSAL   3
NGN3_MOUSE|P70661  (  92) ERNRMHNLNSAL   3
OLG1_HUMAN|Q8TAK6  ( 114) ERKRMQDLNLAM   3
OLG1_MOUSE|Q9JKN5  ( 103) ERKRMQDLNLAM   3
OLG1_RAT|Q9WUQ3    ( 104) ERKRMQDLNLAM   3
OLG2_CHICK|Q90XB3  ( 115) ERKRMHDLNIAM   5
OLG2_HUMAN|Q13516  ( 117) ERKRMHDLNIAM   5
OLG2_MOUSE|Q9EQW6  ( 117) ERKRMHDLNIAM   5
ROI_DROME|Q9Y0A7   ( 147) ERRRMNSLNDAF   2
SCL_CHICK|P24899   ( 188) ERWRQQNVNGAF   7
SCX_CHICK|P59101   (  76) ERDRTNSVNTAF   6
SCX_MOUSE|Q64124   (  87) ERDRTNSVNTAF   6
TAL2_HUMAN|Q16559  (  11) ERWRQQNVNSAF   6
TAL2_MOUSE|Q62282  (  11) ERWRQQSVNNAF   6
TAL_HUMAN|P17542   ( 196) ERWRQQNVNGAF   7
TAL_MOUSE|P22091   ( 196) ERWRQQNVNGAF   7
TAP4_HUMAN|Q01664  (  57) ERRRMQSINAGF   3
TF15_CHICK|P79782  (  70) ERDRTQSVNTAF   6
TF15_HUMAN|Q12870  (  81) ERDRTQSVNTAF   6
TF15_MESAU|Q60539  (  79) ERDRTQSVNTAF   6
TF15_MOUSE|Q60756  (  79) ERDRTQSVNTAF   6
TWST_CAEEL|Q11094  (  29) ERQRTKELNDAF   3
TWST_DROME|P10627  ( 371) ERQRTQSLNDAF   3
TWST_HUMAN|Q15672  ( 117) ERQRTQSLNEAF   3
TWST_MOUSE|P26687  ( 121) ERQRTQSLNEAF   3
TWST_XENLA|P13903  (  81) ERQRTQSLNEAF   3
YLB7_CAEEL|P46581  (  28) ERARMHGLNNAL   4
YMH7_CAEEL|P34474  (  70) ERRRMQSINAGF   3
O96642             ( 104) ERQRTQSLNEAF   3

BHB3_MOUSE|Q99PV5  (  53) EKKRRDRINECI   3
BHB3_RAT|O35779    (  53) EKKRRDRINECI   3
DPN_DROME|Q26263   (  49) EKRRRARINHCL   5
ESM3_DROME|Q01068  (  20) ERKRRARINKCL   4
ESM5_DROME|P13096  (  27) ERQRRARMNKCL   4
ESM7_DROME|P13097  (  22) ERKRRARINKCL   4
ESM8_DROHY|Q07291  (  19) ERQRRARINKCL   4
ESMB_DROME|Q01069  (  22) ERKRRARINKCL   4
ESMC_DROME|Q01070  (  24) ERKRRARINKCL   4
ESMD_DROME|Q01071  (  24) ERKRRARMNLYL   3
HAIR_DROVI|P29303  (  46) EKRRRARINNCL   3
HES1_CHICK|O57337  (  44) EKRRRARINESL   2
HES1_HUMAN|Q14469  (  43) EKRRRARINESL   2
HES1_MOUSE|P35428  (  43) EKRRRARINESL   2
HES1_RAT|Q04666    (  43) EKRRRARINESL   2
HES3_MOUSE|Q61657  (   2) EKKRRARINVSL   4
HES3_RAT|Q04667    (   2) EKKRRARINLSL   2
HES5_MOUSE|P70120  (  25) EKMRRDRINSSI   5
HES5_RAT|Q03062    (  25) EKMRRDRINSSI   5
HEY1_CANFA|Q9TSZ2  (  58) EKRRRDRINNSL   2
HEY1_HUMAN|Q9Y5J3  (  58) EKRRRDRINNSL   2
HEY1_MOUSE|Q9WV93  (  58) EKRRRDRINNSL   2

CBF1_KLULA|P49379  ( 257) ERRRRQNINTAI   3
CBF1_YEAST|P17106  ( 231) ERRRRENINTAI   3
MITF_HUMAN|O75030  ( 320) ERRRRFNINDRI   3
MITF_MOUSE|Q08874  ( 320) ERRRRFNINDRI   3
MITF_RAT|O88368    (  29) ERRRRFNINDRI   3
TFE3_HUMAN|P19532  ( 355) ERRRRFNINDRI   3
TFE3_MOUSE|Q64092  ( 228) ERRRRFNINDRI   3
TFEB_HUMAN|P19484  ( 244) ERRRRFNINDRI   3
TFEB_MOUSE|Q9R210  ( 243) ERRRRFNINDRI   3

HTF4_MESAU|Q60420  ( 341) ERLRVRDINEAF   3
HTF4_PAPHA|Q28772  (  64) ERLRVRDINEAF   3
HTF4_XENLA|Q91605  (  56) ERLRVRDINEAF   3
ITF2_CHICK|Q90683  (  16) ERLRVRDINEAF   3
ITF2_RAT|Q62655    ( 334) ERLRVRDINEAF   3
MF25_XENLA|P16076  ( 105) ERRRLSKVNDAF   2
MYF5_BOVIN|P17667  (  92) ERRRLKKVNQAF   3
MYF5_CHICK|Q08856  (  94) ERRRLKKVNQAF   3
MYF5_COTJA|P34061  (  82) ERRRLKKVNQAF   3
MYF5_HUMAN|P13349  (  92) ERRRLKKVNQAF   3
MYF5_MOUSE|P24699  (  92) ERRRLKKVNQAF   3
MYF5_NOTVI|Q91154  (  92) ERRRLKKVNSAF   2
MYF5_XENLA|P24700  (  92) ERRRLKKVNQAF   3
MYF6_CHICK|Q01795  ( 102) ERRRLKKINEAF   2
MYF6_HUMAN|P23409  ( 102) ERRRLKKINEAF   2
MYF6_MOUSE|P15375  ( 102) ERRRLKKINEAF   2
MYF6_RAT|P19335    ( 102) ERRRLKKINEAF   2
MYF6_XENLA|Q92020  ( 100) ERRRLKKINEAF   2
MYO1_ONCMY|Q91205  (  93) ERRRLSKVNDAF   2
MYO2_ONCMY|Q91206  (  93) ERRRLGKVNDAF   4
MYOD_BRARE|Q90477  (  93) ERRRLSKVNDAF   2
MYOD_CAEBR|Q17295  ( 169) ERRRLRKVNEAF   2
MYOD_CHICK|P16075  ( 109) ERRRLSKVNEAF   2
MYOD_COTJA|P21572  ( 110) ERRRLSKVNEAF   2
MYOD_DROME|P22816  ( 170) ERRRLRKVNEAF   2
MYOD_HUMAN|P15172  ( 118) ERRRLSKVNEAF   2
MYOD_MOUSE|P10085  ( 118) ERRRLSKVNEAF   2
MYOD_PIG|P49811    ( 118) ERRRLSKVNEAF   2
MYOD_RAT|Q02346    ( 118) ERRRLSKVNEAF   2
MYOD_SHEEP|P29331  ( 118) ERRRLSKVNEAF   2
MYOD_XENLA|P13904  ( 104) ERRRLSKVNEAF   2
MYOG_CHICK|P17920  (  91) EKRRLKKVNEAF   2
MYOG_COTJA|P34060  (  91) EKRRLKKVNEAF   2
MYOG_HUMAN|P15173  (  90) EKRRLKKVNEAF   2
MYOG_MOUSE|P12979  (  90) EKRRLKKVNEAF   2
MYOG_PIG|P49812    (  90) EKRRLKKVNEAF   2
MYOG_RAT|P20428    (  90) EKRRLKKVNEAF   2
SUM1_LYTVA|Q00492  ( 121) ERRRLRKVNEAF   2
TFE2_MOUSE|P15806  ( 185) ERVRVRDINEAF   3

HEN1_HUMAN|Q02575  (  84) ERIRVEAFNLAF   6
HEN1_MOUSE|Q02576  (  84) ERIRVEAFNLAF   6
HEN2_HUMAN|Q02577  (  86) ERIRVEAFNLAF   6
HEN2_MOUSE|Q64221  (  86) ERIRVEAFNLAF   6

HIFA_HUMAN|Q16665  (  26) ARSRRSKESEVF   4
HIFA_MOUSE|Q61221  (  26) ARSRRSKESEVF   4
PAS1_MOUSE|P97481  (  23) ARCRRSKETEVF   7
SIMA_DROME|Q24167  (  81) ARCRRSKETEIF   9

ID3_HUMAN|Q02535   (  19) ERSLAIARGRGK  13
ID3_MOUSE|P41133   (  19) ERSLAIARGRGK  13
ID3_RAT|P41138     (  19) ERSLAIARGRGK  13

ID4_HUMAN|P47928   (  73) SRLRRLVPTIPP  14
ID4_MOUSE|P41139   (  73) SRLRRLVPTIPP  14

MAX_BRARE|P52161   (  32) ERKRRDHIKDSF   3
MAX_CHICK|P52162   (  32) ERKRRDHIKDSF   3
MAX_HUMAN|P25912   (  32) ERKRRDHIKDSF   3
MAX_MOUSE|P28574   (  32) ERKRRDHIKDSF   3
MAX_RAT|P52164     (  32) ERKRRDHIKDSF   3
MAX_XENLA|Q07016   (  32) ERKRRDHIKDSF   3

MLX_HUMAN|Q9UH92   ( 138) EQKRRDAIKRGY   5
MLX_MOUSE|O08609   ( 138) EQKRRDAIKRGY   5

MNT_HUMAN|Q99583   ( 229) EKNRRAHLKECF   5
MNT_MOUSE|O08789   ( 231) EKNRRAHLKECF   5

MUSC_HUMAN|O60682  ( 116) ERARMRVLSKAF   6
MUSC_MOUSE|O88940  ( 111) ERARMRVLSKAF   6
TF21_HUMAN|O43680  (  88) ERARMRVLSKAF   6
TF21_MOUSE|O35437  (  88) ERARMRVLSKAF   6

MXI1_RAT|O09015    (  23) ERECEHGYASSF  18

MYC1_XENLA|P06171  ( 344) ERQRRNELKLSF   2
MYC2_CYPCA|Q90342  ( 326) ERQRRNELKLSF   2
MYC2_MARMO|P20389  ( 380) ERQRRNDLRSSF   3
MYC2_SPEBE|Q64210  ( 380) ERQRRNDLRSSF   3
MYC2_XENLA|P15171  ( 345) ERQRRNELKLSF   2
MYCL_HUMAN|P12524  ( 290) ERKRRNDLRSRF   3
MYCL_MOUSE|P10166  ( 294) ERKRRNDLRSRF   3
MYCL_XENLA|Q05404  ( 270) ERKRRNDLRSRF   3
MYCM_HUMAN|P12525  ( 283) ERKRRNDQRSRF  10
MYCM_XENLA|P35805  ( 270) ERKRRNDLRSRF   3
MYCN_CHICK|P18444  ( 367) ERQRRNDLRSSF   3
MYCN_HUMAN|P04198  ( 390) ERQRRNDLRSSF   3
MYCN_MARMO|Q61976  ( 386) ERQRRNDLRSSF   3
MYCN_MOUSE|P03966  ( 388) ERQRRNDLRSSF   3
MYCN_RAT|Q63379    ( 388) ERQRRNDLRSSF   3
MYCN_SERCA|P26014  ( 352) ERQRANDLRSSF   4
MYCN_XENLA|P24793  ( 363) ERQRRNDLRSSF   3
MYCS_MOUSE|Q9Z304  ( 357) ERQRRDIMRSSF   6
MYCS_RAT|P23999    ( 355) ERQRRDIMRSSF   6
MYC_ASTVU|Q17103   ( 330) ERQRREDLRTSF   3
MYC_AVIME|P06647   ( 347) ERQRRNELKLSF   2
MYC_BRARE|P52160   ( 331) ERQRRNELKLSF   2
MYC_CALJA|P49032   ( 362) ERQRRNELKRSF   2
MYC_CANFA|Q28350   ( 363) ERQRRNELKRSF   2
MYC_CARAU|P49709   ( 324) ERQRRNELKLSF   2
MYC_CHICK|P01109   ( 340) ERQRRNELKLSF   2
MYC_FELCA|P06877   ( 363) ERQRRNELKRSF   2
MYC_FLVTT|P21438   ( 363) ERQRRNELKRSF   2
MYC_HUMAN|P01106   ( 363) ERQRRNELKRSF   2
MYC_HYLLA|P49033   ( 363) ERQRRNELKRSF   2
MYC_MARMO|P22555   ( 363) ERQRRNELKRSF   2
MYC_MOUSE|P01108   ( 363) ERQRRNELKRSF   2
MYC_ONCMY|P06646   ( 333) ERQRRNELKLSF   2
MYC_PANTR|P23583   ( 363) ERQRRNELKRSF   2
MYC_PIG|Q29031     ( 363) ERQRRNELKRSF   2
MYC_RAT|P09416     ( 363) ERQRRNELKRSF   2
MYC_SHEEP|Q28566   ( 363) ERQRRNELKRSF   2
Q91446             ( 115) ERQRRNELKLSF   2

NPA1_HUMAN|Q99742  (  54) ARSRRGKENLEF   6
NPA1_MOUSE|P97459  (  54) ARWRRGKENLEF   7
SIM1_HUMAN|P81133  (   9) ARTRREKENSEF   5
SIM1_MOUSE|Q61045  (   9) ARTRREKENSEF   5
SIM_DROME|P05709   (   9) ARTRREKENTEF   6
TRH_DROME|Q24119   (  95) ARSRRGKENYEF   9

PIF3_ARATH|O80536  ( 352) ERRRRDRINEKM   3
PIF4_ARATH|Q8W2F3  ( 266) ERRRRDRINERM   2

USF1_HUMAN|P22415  ( 208) ERRRRDKINNWI   5
USF1_MOUSE|Q61069  ( 208) ERRRRDKINNWI   5
USF1_RABIT|O02818  ( 208) ERRRRDKINNWI   5
USF1_XENBO|Q07957  ( 205) ERRRRDKINNWI   5
USF2_HUMAN|Q15853  ( 244) ERRRRDKINNWI   5
USF2_MOUSE|Q64705  ( 244) ERRRRDKINNWI   5
USF2_RAT|Q63665    ( 189) ERRRRDKINNWI   5
USF_STRPU|Q07956   ( 199) ERRRRDKINNWI   5

WS14_HUMAN|Q9NP71  ( 658) EQKRRFNIKLGF   5
WS14_MOUSE|Q99MZ3  ( 670) EQKRRFNIKLGF   5

AHR_MOUSE|P30561   (  35) SKRHRDRLNTEL   7
AHR_RABIT|O02747   (  36) SKRHRDRLNTEL   7
AHR_RAT|P41738     (  35) SKRHRDRLNTEL   7
BHB2_HUMAN|O14503  (  61) EKKRRDRINECI   3
BHB2_MOUSE|O35185  (  61) EKKRRDRINECI   3
BHB2_RAT|O35780    (  61) EKKRRDRINECI   3
BHB3_HUMAN|Q9C0J9  (  53) EKKRRDRINECI   3
BMAL_HUMAN|O00327  (  38) EKRRRDKMNSFI   4
CLOC_DROME|O61735  (  20) EKKRRDQFNSLV  10
COE1_HUMAN|Q9UH73  ( 237) RRARRLDPSEGT  12
COE1_MOUSE|Q07802  ( 242) RRARRLDPSEGT  12
COE1_RAT|Q63398    ( 242) RRARRLDPSEAA  12
COE2_BRARE|O93375  ( 240) RRSRRMDPNETV  33
COE2_MOUSE|O08792  ( 241) RRARRLDPSEAT  12
COE2_XENLA|O73741  ( 242) RRARRLDPSEAT  12
COE3_HUMAN|Q9H4W6  ( 242) RRARRLDPSEGT  12
COE3_MOUSE|O08791  ( 242) RRARRLDPSEGT  12
COE3_XENLA|O73742  ( 242) RRARRLDPSEGT  12
COE4_HUMAN|Q9BQW3  ( 343) RRARRLDPSEAA  12
COLL_DROME|P56721  ( 113) SESDATKTNNGI  15
CYCL_DROME|O61734  (  39) EKRRRDKMNTYI   4
DA_DROME|P11420    ( 563) ERIRIRDINEAL  10
ESM8_DROME|P13098  (  19) ERQRRARMNKCL   4
HAIR_DROME|P14003  (  40) EKRRRARINNCL   3
HAN1_RABIT|P57100  ( 103) ERRRTESINSAF   3
HES2_HUMAN|Q9Y543  (  22) EKRRRARINQSL   3
HES2_MOUSE|O54792  (  22) EKRRRARINESL   2
HES2_RAT|P35429    (  22) EKRRRARINESL   2
HTF4_CHICK|P30985  ( 561) ERLRVRDINEAF   3
HTF4_HUMAN|Q99081  ( 586) ERLRVRDINEAF   3
HTF4_MOUSE|Q61286  ( 610) ERLRVRDINEAF   3
HTF4_RAT|P51514    ( 611) ERLRVRDINEAF   3
INO2_YEAST|P26798  ( 245) EKIRRINTKEAF   8
ITF2_CANFA|P15881  ( 548) ERLRVRDINEAF   3
ITF2_HUMAN|P15884  ( 573) ERLRVRDINEAF   3
ITF2_MOUSE|Q60722  ( 576) ERLRVRDINEAF   3
MAD4_MOUSE|Q60948  (  62) EKHRRAKLRLYL  11
MAD_HUMAN|Q05195   (  65) EKNRRAHLRLCL   5
MAD_MOUSE|P50538   (  64) EKNRRAHLRLCL   5
MXI1_BRARE|P50541  (  85) EKNRRAHLRLCL   5
MXI1_HUMAN|P50539  (  23) ERECEHGYASSF  18
MXI1_MOUSE|P50540  (  23) ERECEHGYASSF  18
MYC1_CYPCA|Q90341  ( 319) ERQRRNELKLSF   2
MYC_AVIM2|P10395   ( 345) ERQRRNELKLSF   2
MYC_AVIMC|P01110   ( 346) ERQRRNELKLRF   2
MYC_AVIMD|P06295   ( 346) ERQRRNELKLRF   2
MYC_AVIOK|P12523   ( 340) ERQRRNELKLSF   2
MYOD_CAEEL|P22980  ( 164) ERRRLRKVNEAF   2
NCO2_MOUSE|Q61026  (  35) EKRNREQENKYI  11
NCO2_RAT|Q9WUI9    (  35) EKRNREQENKYI  11
NCO3_HUMAN|Q9Y6Q9  (  34) EKRRREQESKYI   5
NCO3_MOUSE|O09000  (  35) EKWRREQESKYI   7
NCO3_XENLA|O57539  (  36) EKRRREQESKYI   5
NDF1_CHICK|P79765  ( 113) ERNRMHGLNAAL   4
NDF1_HUMAN|Q13562  ( 110) ERNRMHGLNAAL   4
NDF1_MESAU|Q60430  ( 109) ERNRMHGLNAAL   4
NDF1_MOUSE|Q60867  ( 110) ERNRMHGLNAAL   4
NDF1_RAT|Q64289    ( 110) ERNRMHGLNAAL   4
NDF1_XENLA|Q91616  ( 111) ERNRMHGLNDAL   3
NPA2_HUMAN|Q99743  (  18) EKKRRDQFNVLI   6
NPA2_MOUSE|P97460  (  18) EKKRRDQFNVLI   6
PAS1_HUMAN|Q99814  (  23) ARCRRSKETEVF   7
PHT1_HUMAN|Q9UMS5  ( 159) NRRRRKLRKTVN  12
PHT1_MOUSE|Q9QZ09  ( 159) NRRRRKLRKTVN  12
PHTF_DROME|Q9V9A8  (  27) EQRILDGFNSVN  11
RTG3_YEAST|P38165  ( 294) ERRRRELIKQKI   4
SIM2_HUMAN|Q14190  (   9) AKTRREKENGEF   6
SIM2_MOUSE|Q61079  (   9) AKTRREKENGEF   6
SRE1_MOUSE|Q9WTN3  ( 326) EKRYRSSINDKI   6
SRE1_PIG|O97676    ( 105) EKRYRSSINDKI   6
SRE1_RAT|P56720    ( 302) EKRYRSSINDKI   6
SRE2_CRIGR|Q60429  ( 337) EKRYRSSINDKI   6
SRE2_HUMAN|Q12772  ( 339) EKRYRSSINDKI   6
TAP_DROME|O16867   ( 163) ERNRMHNLNDAL   3
TFE2_HUMAN|P15923  ( 558) ERLRVRDINEAF   3
TFE2_MESAU|P98180  ( 553) ERLRVRDINEAF   3
TFE2_RAT|P21677    ( 553) ERLRVRDINEAF   3
TFE2_XENLA|Q01978  ( 564) ERLRVKDINEAF   3
UNC3_CAEEL|Q93705  ( 131) VRLIDSSTKQAI  21
O29330             ( 329) ERLREIARKYGI  12
O29978             ( 254) NRAKLEDFREIF  15
O28341             (  29) EQAVKAAKEIGF  16
O57993             (  15) LEVAVRKTKEFI  14
O58295             ( 360) FKVRVSVMNEGN  23
O58924             (  20) ARKRRKKRVHIY  16
Q9YFX5             (   8) NRGRRTTVAYPL  18
Q9Y9X8             ( 111) SRLDRRILDSYL  13
Q9HN79             (  47) SRNAVSAVGLVA  11
Q9HJN2             (  96) EGSRSIELSAFL  23
Q9HHR8             ( 251) ASQVARSFNESL  10
Q97YW9             ( 258) ERNSVLDFVRKF  26
Q97C62             ( 329) ERFRRATWEEAL  37
Q97AQ0             (  49) AKKLRITKNIIL  15
Q971A8             (  36) MQARRISDDGLY  32
Q96ZZ9             ( 308) ESEIVDNPANLM  12
Q8ZW62             ( 145) AQRVVITLNGSG  18
O26447             ( 198) QRIVMREFGVKF  13
O27082             ( 399) TRKRMSTINQLE  28
Q9YC30             (  46) ERKAAARVQRRI  14
Q8U4C2             (  21) EKAIRFAKALPI  14
Q8U2J9             (  67) VNSRKSEIKNFF  15
Q8TK07             (  36) DQDGMLFVRNDF  51
Q8TH72             (  21) SRARKLMLRHRI  31
Q8TH19             (  30) GRRRVGKTRLVL  13
Q97Z77             (   5) KGLRRDLRKMSF  33
Q8PZ68             (   2) VHSRLDTMTRAF  21
Q8PVU4             (  32) ERKTFGIEDAGL  47
Q8PVS1             ( 147) ERQVPTLIRNGL  24
Q8PU16             ( 433) ERKMMTTLNASE  28
Q8PT78             ( 262) VQLRMLKSYSAF  32
Q92242             ( 188) EKRYRININTKI   8
Q96V45             (   6) DEQLAAGDNNGF  15
Q9UVN5             ( 782) DRKRLRGMASLF   7
Q9UTA7             (  19) SRKTRPCDNCRL  44
Q9C229             (  59) NRMRTNATNTSV  17
Q9C0Y5             ( 194) IRRICEIIRDAF  48
Q9P7B3             ( 149) ERQNAINKTRAF  17
Q9P8P8             ( 353) DEERKNALNSMI  11
Q12398             ( 275) EKKYRSNINDKI   6
Q06859             ( 259) EQARRNRLAVAL   6
Q9HEN9             ( 133) ERKRRESINTGI   3
O59677             ( 386) SQPRVSTPSLDI  21
Q92280             (  27) VRKALLCIVSAF  19
Q9C1R9             ( 288) ERRRRETINLAI   3
Q07896             ( 400) ERNQSEILKIVF  15
Q8TFJ8             ( 171) ERKRRSEMKDCF   4
O59704             ( 636) ERCRVVERGSKI  14
O60034             ( 917) ERKILNGVNGYP   9
Q06860             ( 259) EQARRNRLAVAL   6
Q8X074             ( 519) EKERVRQVEALK   9
Q9UUD1             ( 269) EKRYRTNLNDRI   7
Q9HEX7             ( 103) ERRRRETINESI   3
Q9HDP4             (  68) ERRRRENINTAI   3
O43019             ( 435) EKRYRSNLNDKI   6
Q8J1X7             ( 377) EKQYRNRLNAQF   8
Q8J0E0             (  24) ERRRREAINEGI   3
O14948             ( 148) ERRRRYNINYRI  10
Q9NY94             ( 198) ERWRQQNVNGAF   7
Q8N100             (  49) ERRRMQGLNTAF   3
Q9HAP2             ( 728) EQKRRFNIKMCF  10
Q9NYQ5             (  65) EKRRRDKMNNLI   3
Q96CY8             (  32) ERKRRDHIKDSF   3
Q96QX4             ( 210) EKLRRERIKYCC  12
Q9UEC8             ( 110) ERNRMHGLNAAL   4
Q9NX45             ( 210) ENLRRERIKYCC  19
Q8WYA3             ( 102) EKRRRDKMNNLI   3
Q9NTF6             (  11) QRKTRDGFEEHF  12
Q8TAP5             (  23) ARSRRSQETEVL   5
Q96K34             (  23) ARSRRSQETEVL   5
O43392             (  98) ERRRRNKMTAYI   4
Q8WYA1             (  68) EKRRRDKMNNLI   3
Q8WZ51             ( 832) EQLLSTGFKCKF  19
Q9UPB1             (  26) ARSRRSKESEVF   4
Q9UPG2             (  14) ERRRDAVIALGI  16
Q9NYQ4             (  52) EKRRRDKMNNLI   3
Q9ULI6             (  45) SKRHRDRLNAEL   7
Q8N6J9             ( 119) ERRRRYNINYRI  10
O43792             (  32) EKRRREQENKYL   4
Q8NAM2             (  58) EKRRRDRINNSL   2
O94945             ( 335) EQKRRFNIKMCF  10
O43372             ( 284) ERKRRNDQRSRF  10
Q9Y2N7             (  21) ARSRRSQETEVL   5
O43793             (  32) EKRRREQENKYL   4
Q8TAX8             (  23) ERKRRDHIKDSF   3
Q9HCC6             (  43) EKRRRARINESL   2
Q9NS70             (  31) EKRRRDKMNNLI   3
Q8N416             ( 121) ERNRMHNLNAAL   3
Q9Y4L8             (   3) ARSRREKENFEF  10
Q96SQ7             ( 239) ERTRVHTISAAF   6
O00146             ( 486) VRERRFRCGDCG  50
Q9Y4E9             (  17) ERRRRGEMRDLF   5
Q9Y6L9             ( 472) DTNREQRVTLQK  23
Q9UMQ5             ( 127) ERQRRNDLRSSF   3
Q9Y5R3             (  41) ERMHVLVLSSWR  27
Q8WYA5             ( 335) EQKRRFNIKMCF  10
Q8WVJ9             (  75) ERQRTQSLNEAF   3
Q16509             ( 196) ERWRQQNVNGAF   7
Q96R32             (  16) VNFLSEKKNISF  29
Q9NVW3             ( 282) EKLRQHISRNAQ  20
Q96PR6             (  58) EKRRRDRINNSL   2
Q8WYA2             (  79) EKRRRDKMNNLI   3
Q8N8Q0             (  92) ERKRMHDLNLAM   3
Q8WX40             (  82) ERERRKRMSLSC   9
Q96T93             (  34) EKKRRARINESL   2
Q9BQ98             ( 117) VRRALTHIDHSL  12
Q9BY81             (  30) ARSRRGKENFEF  12
Q9C0G2             ( 317) EIRRQIRIREVN  36
Q96CP9             ( 486) VRERRFRCGDCG  50
Q9P2S3             (  34) EKKRRARINESL   2
Q9UPH7             (  14) ARSRRSQETEVL   5
Q8NFJ8             ( 251) ERRRMHDLNDAL   3
Q9UQC6             ( 130) ERNRMHDLNAAL   3
Q9HC25             (   5) ERRRMQSINDAF   3
Q8N4N5             ( 201) ETLQKAGFSEKF  22
Q9BRJ9             (  91) EKLRMRTLARAL   6
Q96FL2             (  84) EQKRRDAIKRGY   5
Q14959             (  96) LERQRNDLRSSF  13
Q8NDC7             ( 163) ERRRRNKMTAYI   4
Q96SB7             ( 869) EQEALFKRHSAL  18
Q96QM8             (  82) ETLQKAGFSEKF  22
Q9HCA4             (  90) EKRRLKKVNEAF   2
O95262             (  17) ARSRRSQETEVL   5
Q96J63             (  31) EKRRRDKMNNLI   3
Q8WWL7             ( 869) EQEALFKRHSAL  18
Q8WU82             (  85) DRNSVIQKSCAF  35
Q96HZ4             (  34) EKKRRARINESL   2
Q9H2M4             (  82) EKRRRDKMNNLI   3
Q8NEE3             (  86) ERERRKRMSLSC   9
Q96PT9             (  26) ARSRRSKESEVF   4
Q8NDY6             ( 109) ERRRMHDLNDAL   3
Q8N2J2             (  34) EKKRRARINESL   2
Q9H8R3             ( 602) ERRRRGEMRDLF   5
Q9NQ87             (  52) EKRRRDRINSSL   2
Q9BYE0             (  21) EKRRRDRINRSL   2
O75321             ( 118) ERRRLSKVNEAF   2
Q8NGY2             (  86) LSERSISFNGCL  14
Q96HE1             ( 101) ERNRMHNLNAAL   3
Q8TBI7             ( 130) ERNRMHDLNAAL   3
Q8WXA1             (  23) ARSRRSQETEVL   5
Q9HAZ3             (  33) SKRHRDRLNAEL   7
Q8TAT1             (  53) EKKRRDRINECI   3
O15074             (  73) QRTLMEALVASY  15
Q96BZ0             ( 116) VRRALTHIDHSL  12
Q8WYA4             ( 116) EKRRRDKMNNLI   3
Q14803             (  32) ERKRRDHIKDSF   3
Q9NX04             (  71) ERLRRKQLVAGD  33
Q9H323             (  30) ARSRRGKENFEF  12
Q96RJ6             ( 110) ERKRMFNLNEAF   3
Q9BY83             (  54) ARSRRGKENLEF   6
Q9UBP5             (  57) EKRRRDRINNSL   2
O00150             (  32) EKRRREQENKYL   4
Q13804             (  32) SKRHRDRLNTEL   7
Q8IYR9             ( 103) ERNRMHGLNDAL   3
Q8IYQ8             (  82) EKNRRAHLRLCL   5
Q8IYC6             (  32) ERKRRDHIKDSF   3
Q8IYC2             (  72) ERRRRNKMTQYI   4
Q8IXV0             (  40) EKRRRARINESL   2
Q8IXF2             (  30) ARSRRGKENFEF  12
Q8IXF0             (  60) ARSRRGKENFEF  12
Q8IW56             (  20) ERTRMHGLNDAL   4
Q8IUT4             (  76) EKRRRDKMNSFI   4
Q23579             (  98) ERNRVQQLSKMF   6
Q95NH3             (  40) EKRRRARINNCL   3
Q18711             (  56) ERRRRDHIKDHF   6
Q95ZK5             ( 247) ERRRRYNINDRI   7
Q8MNK7             (1340) ERSLLKNLGGWL   9
O77278             ( 117) ERIRVEAFNVSF   8
Q9VJ16             (  59) EKRRRARINQSL   3
Q8TA56             (   0) XKRRRDKMNTYI   4
Q9TVM0             ( 124) ARDRRSKESDIF   8
Q9GRC7             (  76) ERNRVKQVNNGF   4
Q21663             ( 104) EKTRRANLRGCL   6
Q9GS19             ( 244) EKRRREAENGYI   5
P91664             (  48) ERRRRDHIKESF   3
Q9W4X2             ( 174) ERWRQQNVSGAF   7
Q8SYH4             (  98) ERTRMRDMNRAF   5
Q9VGZ5             (  71) EKRRRDRMNSCL   3
Q9VAS8             ( 199) ERFLVKISKDGF  19
Q9VG64             ( 153) DKTRIDKETRNL  22
Q24146             ( 292) ERRYRTSINDKI   7
Q9GRC6             (  70) ERNRVKQVNNGF   4
Q9VJC1             ( 137) ERRRMHDLNDAL   3
Q23388             ( 685) ERYLVHGSKIIF  21
Q9XZC7             ( 112) ERKRMNGLNAAF   3
Q9VE36             ( 112) QSALRLNVLLDF  19
Q8MRS4             ( 253) ERNVLITSALPY  14
Q9VWX7             (  30) ERKRRSRINRCL   4
Q9TZ70             (  56) ERQRREAINSGY   4
Q9N6Q1             (1247) ERERTSVEGKCA  12
Q18053             (  23) EKQRRDDTNDLL   5
O02219             (  53) ERRRRNKMTHYI   5
Q8MNH9             (  15) ERFKADETKDIY  24
Q9NHD9             ( 210) ERNRVKQVNNGF   4
Q9V8N9             ( 253) ERNVLITSALPY  14
Q8WQQ7             ( 183) ERNRVKQVNNGF   4
Q17326             ( 311) ERVRVRDINSAF   4
Q9VZP3             (  66) ERRRMLQLLKLA  16
O00947             (  39) EEDITDKTTNDL  14
Q9VN30             ( 313) KRRLRSEVNLVF  11
Q961H7             ( 103) ERTRMREINTAF   4
O77089             (1401) DRNRMDFDDSSP  30
Q8MQV4             (  81) ARCRRSKETEIF   9
Q9VGC6             ( 130) NRSLVANLGAAS  21
Q25124             ( 251) ERRRLKRVNEAY   3
Q9NFW8             (  68) EKRRRARINNSL   2
O44712             (  27) SKRHRERLNGEL   7
Q18590             (  41) ERIRVESFNMAF  10
Q19918             (  51) ERKRRDEINELL   3
Q09961             ( 102) ERKRVHQVNHGF   5
O17237             ( 777) GKKARKSLRKAF  11
Q9N4M4             ( 368) YRRRADRHRIVF  84
Q9NCL3             (1487) ERKELAKVNSAF   8
Q95X77             ( 230) VRKIQKNIFMSL  24
O76836             (  12) QRMVAAQQNNGK  21
Q9BKE5             ( 863) EQKRRYNIKNGF   9
Q9VID2             ( 165) ERMRMHSLNDAF   6
Q22060             (  19) ASDVAGPLTDDF  21
Q8T3U8             (  46) EHRRMDLPEGIL  22
O15984             (  80) ARSRRGKENYEF   9
Q9VA43             (   8) DRSMLVEYSAAF  25
Q9GSP7             (   9) ERQRTQSLNDAY   4
Q9BLX3             (  98) ERNRVRLVNLGF   4
O18374             (  40) ERMRMRVLSSAY   8
Q9VY43             (1487) ERKELAKVNSAF   8
Q8WSV7             ( 208) ERKRRYNINDRI   7
Q9GNV2             (  60) ERQRTQALNQSF   4
Q18056             (  79) ERKRRNITNELI   8
Q9XVQ0             ( 249) QQQQLNNDTIQF  22
Q9W4I4             ( 117) ERIRVEAFNVSF   8
Q8WQQ9             (  92) ERQRTESLNDAF   3
O96903             ( 634) ERQRRIGLKNLF   5
Q9GYH2             ( 220) QQLRKSNEERKL  11
Q9U911             (  33) ERNRVKQVNNGF   4
Q18612             (  32) EHRRAQCINSAF  22
Q8T1Q1             (  28) DSATSKMTKLGF  36
Q9VB47             (  80) EQKRRDAIKKGY   6
Q18054             (  71) ERKRRNITNELI   8
Q9NCW7             (1319) ERKELAKVNSAF   8
Q9VXW7             (  16) EKNRRDKLNGSI   3
O44538             ( 153) LRDEMDELGIEY  16
Q9W4Q7             ( 270) EKERRAQLKECY   5
Q9VHG3             ( 188) ERTRMRDMNRAF   5
Q9VGJ5             (  95) ERRRMFNLNEAF   3
Q9XZI1             (  83) ERRRLRKVNEAF   2
Q95NU9             (  40) EKRRRARINNCL   3
Q8MWP6             ( 309) ERRRLRKVNEAF   2
Q962X1             ( 284) RQQIRSEYKIAF  12
Q24354             ( 194) ERWRHENVSGAF  19
Q9V881             (  40) ERMRMRVLSSAY   8
Q963J8             (  20) ARDRRSKESDIF   8
Q26372             (   5) ERQRTQSLNEAF   3
Q95U62             (  66) ERRRMLQLLKLA  16
Q19917             (  28) ERKRRDEINELL   3
Q8SYL0             ( 113) QSALRLNVLLDF  19
Q9NHD8             (  24) ERNRVKQVNNGF   4
Q9U910             (  91) ERNRVKQVNNGF   4
Q24159             (  71) ERRRMLQLLKLA  16
Q9VW37             ( 292) ERRYRTSINDKI   7
Q25179             (  73) ERNRVKQVNDGF   3
Q9NK61             ( 105) ERRRMQSINAGF   3
Q9GPN7             ( 251) DKTIMKRTNNKF  11
Q9V406             ( 105) ERRRMQSINAGF   3
Q24353             (  93) ERRRRRRATLKY   7
O16380             ( 142) DCKDLTRLRKFF  91
Q26594             ( 290) ASRTMGVVGLVM  13
Q8N0R5             ( 150) EKRRRDKMNTFI   5
Q9W4J8             ( 263) ERRRRDKINSWI   5
Q9GQP6             (  80) EQKRRDAIKKGY   6
Q9VBH3             ( 125) SKMRRDLINAEI   9
P90982             (  38) ERRRRDNIKDMY   5
Q9N6W6             (  24) ERKRRARINKCL   4
Q8WQK4             (  89) ERRRLVKVNEAF   7
O16853             (  30) EKKRRARINKSL   3
Q9V758             ( 113) SESDATKTNNGI  15
Q8SXE2             (  48) ERRRRDHIKESF   3
Q94790             (   6) ERRRMNSLNDAF   2
P90977             (  35) ERKRVDQVNQGF   3
Q9N6W8             (  22) ERKRRARINKCL   4
Q9BLX4             (  68) ERNRVRQVNLGF   3
O46042             ( 270) EKERRAQLKECY   5
Q95VY6             ( 110) ERNRVKQVNNGF   4
Q17358             ( 311) ERVRVRDINSAF   4
Q23056             ( 101) VRASTTIYNEFF  28
Q9N6W7             (  24) ERKRRARMNLYL   3
Q26649             ( 358) ERRRREDLRTSF   3
Q22805             (  64) ERVRRFEGNSPP  15
O44875             ( 515) IREIVQSVNSSF  12
Q9BLJ2             ( 260) ERNRNACLNVPG  88
Q9XV13             (  44) INQRRDKETLLF  17
Q8SVU5             ( 172) HRGVTDKEKKRF  23
Q9W4S7             ( 634) ERQRRIGLKNLF   5
O45320             (  49) ERRRMHELNDEF   3
Q25427             ( 199) ERRRRDKINNWI   5
Q25428             ( 223) ERRRRDKINNWI   5
Q95Q51             ( 105) ERAAAANSSSSN  13
O02191             ( 402) ERRRLKRVNQAY   4
Q8SXF5             (  90) ERRRMQSINEAF   2
Q8SSZ1             (   0) XKRRRDKTNTYI   6
Q8SY46             ( 256) EKERRAQLKECY   5
Q9VEV9             (  11) KRRRRNGKSLKP  18
O76880             ( 174) ERWRQQNVSGAF   7
P91527             ( 246) ERRRRYNINDRI   7
Q94187             (  65) NKVTRFVMGVGF  14
Q9U450             (  71) EKRRRDRMNSCL   3
Q18277             (  22) ERQRVSEMNGMF   5
P90681             ( 140) TRSRKTALRTVF  19
Q9NB27             ( 132) ERNRMHNLNGAL   4
O44118             (  45) EKQRRDKLNASI   2
Q95WT6             ( 103) KRNTTSDLLEVI  22
Q8MQI7             (  33) ARTRREKENTEF   6
Q9VL05             (  67) ERRRTQSINNAF   3
O61543             (  11) KRRRRNGKSLKP  18
Q9V7M2             ( 112) ERKRMNGLNAAF   3
Q9GR87             ( 150) EKRRRDKMNTFI   5
Q95XG7             (  71) ERRRMNSLNDAL   2
Q8WQQ8             (   2) ERQRTESLNDAF   3
Q8WQQ6             ( 102) ERNRVKQVNNGF   4
Q9GNL5             (  91) ERNRVKQVNNGF   4
Q9VI67             (  92) ERRRMQSINEAF   2
Q9VID4             ( 920) EQKRRYNIKNGF   9
Q8MRA5             (  92) ERNRVKQVNNGF   4
Q9VYW2             (  45) EKQRRDKLNASI   2
O96520             (   9) ARTRREKENTEF   6
Q9TX44             ( 395) ERQRTQSLNDAF   3
Q8MUL7             (   9) ERQRTQSLNDAF   3
Q9VSP0             ( 169) ERSREALQTKNL  24
Q8MUL8             (   9) ERQRTQSLNDAF   3
Q8T8A9             (  22) EKKRRERINRCL   3
Q8T0M7             (  60) DRIAVDVYNYAF  15
Q8MT07             ( 370) ERQRTQSLNDAF   3
O76488             (  83) ERNRVKQVNDGF   3
Q8MQD2             ( 224) ERSDHFNLNHQY  26
Q95VQ5             ( 222) ERQRTQSLNDAF   3
Q22717             (  68) ERKRVDQVNQGF   3
Q94816             ( 243) ERRRLRKVNEAF   2
Q9VBG4             ( 242) SRQRRLAVTYFN  13
O02190             ( 402) ERRRLKRVNQAY   4
Q8T804             ( 144) ERRKQNKANNIN  18
Q9VEY3             ( 154) VRERKRIQRSAP  21
Q8T8Y9             ( 370) ERQRTQSLNDAF   3
Q94791             (   6) ERRRMNGLNEAF   2
O44711             (  53) ERRRRNKMTHYI   5
Q17588             ( 311) ERVRVRDINSAF   4
Q20561             (  50) ERKRMCSINVAF  21
Q9NHE3             ( 102) ERNRVKQVNNSF   3
Q8WQQ5             (  70) EGNRVKQVNNSF  19
Q18076             ( 198) ERSDHFNLNHQY  26
Q8T306             (  43) EKRRRARINNSL   2
Q95UA9             (  40) EKRRRARINNCL   3
Q9VPI8             ( 282) ERTRVHTISAAY   7
Q962A3             ( 135) ERWRQQNVNGAF   7
Q960W6             (  56) ERLEELKKNSVF  17
Q9N410             (  28) EKRRREEMNEVI   3
O01591             ( 126) LRDEMDELGIEY  16
Q9V7R8             (  11) ERLEELKKNSVF  17
O46319             ( 349) IRGRVAGLRSLL  15
O45486             ( 124) ARDRRSKESDIF   8
Q9VBW1             ( 155) EQQQRITIEGPY  18
O45489             (  55) ERCRMHDLNEAL   6
P90953             (  17) AQQRRQMENYEF  31
O61528             (1670) ERAAAANSSSSN  13
Q9U3E1             ( 121) ERRRMQSINAGF   3
Q8T0T6             ( 180) ETSIRGSLGTLF  18
Q9BKE4             ( 637) EQKRRYNIKNGF   9
Q9U9U4             ( 109) EKKRRDRINSSL   2
Q8IU24             (  87) ERRRLVKVNEAF   7
Q8IU23             (  89) ERRRLVKVNEAF   7
Q8IRS3             ( 263) ERRRRDKINSWI   5
Q8INT7             ( 871) EQKRRYNIKNGF   9
Q8INT6             ( 726) EQKRRYNIKNGF   9
Q8INP5             (  98) ERTRMRDMNRAF   5
Q8I812             (  17) ARSRRGKENYEF   9
Q8I7T7             (  76) ERNRVKQVNDGF   3
Q8I7T6             (  58) QRDRMREAYENL  41
Q8I7T5             (  33) ERLRVQEIRLAY   4
Q8I7I9             ( 812) EQNRRSALKDGF   5
Q8I710             ( 177) ERQRTQSLNEAF   3
Q8I1G0             ( 371) ERQRTQSLNDAF   3
Q8I066             (  20) ARDRRSKESDIF   8
Q9BE97             (  98) ERRRRNKMTAYI   4
Q8MJ65             (  70) ERQRRNELKRSF   2
Q95MD1             ( 127) ERRRRFNINDRI   3
Q8MJ69             (  84) ERQRRNELKRSF   2
Q8MJ74             (  88) ERQRRNELKRSF   2
Q9MYY5             (  93) EKRYRSSINDKI   6
Q8MJ72             (  84) ERQRRNELKRSF   2
Q8MJ66             (  86) ERQRRNELKRSF   2
Q9XTA4             (  23) ARCRRSKETEVF   7
Q95L20             (  59) ERRRLKKVNQAF   3
Q8SQA5             (   7) SKRHRDRLNTEL   7
Q8MJ70             (  84) ERQRRNELKRSF   2
Q9MZT9             ( 363) ERQRRNELKRSF   2
Q9MYY7             (  89) EKRYRSSINDKI   6
Q9XTA5             (  26) ARSRRSKESEVF   4
Q9MYT3             (  37) ERRRTQSINSAF   3
Q8MIH1             ( 118) GRQRTQSLNEAF   9
Q8MIH8             ( 122) ERQRTQSLNEAF   3
Q8MJ67             (  87) ERQRRNELKRSF   2
O77790             (  52) EKRRLKKVNEAF   2
Q8MJ64             (  83) ERQRRNELKRSF   2
O02811             (  14) ERRRDAVIALGI  16
Q95L69             (  92) ERRRLKKVNQAF   3
Q8MJ68             (  84) ERQRRNELKRSF   2
Q8MIE7             ( 119) ERQRTQSLNEAF   3
Q9MZT7             ( 363) ERQRRNELKRSF   2
Q9MYY6             (  80) ERRTRHNIIEKR  53
Q28925             ( 761) EKRLREDISVMI   7
Q8MIB5             ( 118) ERQRTQSLNEAF   3
Q8MJ71             (  81) ERQRRNELKRSF   2
Q8MIF3             ( 113) ERQRTQSLNEAF   3
Q8MI03             ( 118) ERQRTQSLNEAF   3
Q9MZT8             ( 364) ERQRRNELKRSF   2
Q8MIB9             ( 118) ERQRTQSLNEAF   3
Q8MID5             ( 114) ERQRTQSLNEAF   3
Q8MHZ4             ( 116) ERQRTQSLNEAF   3
Q9MZT6             ( 362) ERQRRNELKRSF   2
Q95L21             (  69) EKRRLKKVNEAF   2
Q9MZU0             ( 363) ERQRRNELKRSF   2
Q8MI06             ( 118) ERQRTQSLNEPF   5
Q8MJ63             (  62) ERQRRNELKRSF   2
Q8MJ73             (  86) ERQRRNELKRSF   2
Q28239             (  32) ERQRRNELKRSF   2
Q95KC9             ( 201) ETLQKAGFSEKF  22
Q9BE11             ( 294) EIRRQIRIREVN  36
Q95K45             ( 201) ETLQKAGFSEKF  22
Q8HY55             ( 175) ERRRRDKINNWI   5
Q30830             (   5) EGRCVEWLRRYL  95
Q9MJ75             (  34) GRYIRNRLPREI  45
Q9T654             (  69) SKSCMSCIDSRL  20
Q8WEV1             (  19) IRLNLRVPGSKL  21
Q9LGL7             (  73) ERRRRERINAHL   5
Q9LQH2             ( 417) HRRRRHDREERV  26
Q9AW08             ( 579) QRKSLLREKYYF  23
Q93VJ4             ( 156) ERARREKISKKM   5
Q8RV16             ( 171) ERERRTRISKRL   5
Q8L994             (  37) ARAVSDAVRTSL   8
Q9SFY5             ( 182) ARKRREKINERL   2
Q9XIN0             ( 287) SSKRSLGSDDLF  14
Q8LRU0             ( 231) ENSCSFAEELKF  22
Q9M041             (  52) ARDRRHRISDRF   5
Q94JL3             ( 105) QTILQEDLNSSF  19
Q9M8K6             (   7) ERNRRRQMNEHL   5
Q94JE7             ( 332) ERQRREKLNQRF   2
Q9LRJ4             (  26) QRPRFHKYNTLK  56
Q8S3D6             ( 153) ERLRRERIAERM   4
Q9LUK7             ( 348) ERMRREKLNHRF   6
O22418             ( 411) EKKRREKLNERF   2
Q8LHY9             ( 324) NQARSFRWNLTA  47
Q9LXA9             ( 156) ERRRRKRLNDRL   2
Q94HA7             ( 158) PRVRRERLGERI  21
Q9FHA2             ( 102) EKKRRSKINEKM   3
Q8LQW4             (  51) RRHRRHGFARFV  23
Q9LT67             ( 153) AKVRKERLGERI   6
O64908             ( 443) ERRRREKINERF   2
Q9FIP9             ( 420) ERQRREKLNQRF   2
Q8LC47             (  54) EQRRRSKINERF   3
Q9SIR1             (1206) EKQRVQSPNLNA  17
Q9M128             ( 121) ERNRRRQMNEHL   5
O82396             ( 131) ERKRREKLTQRF   3
Q8LQZ5             (  88) ERRRWEKLNEMF  37
Q8S3D9             ( 187) ERVRREKISERM   4
Q93Z71             (  60) ERNRRQKLNQRL   3
O80482             (  14) ESSRRKKPRISE  19
Q9LGU4             ( 182) EKQRRLRLTEKY   5
Q94LR3             (  10) NHKRRDRINQKM  19
Q9LN89             (  83) ERQRRQENTSLF  20
Q9LND0             ( 221) ERERRVHFKDRF  10
Q9M1K0             (  85) ERDRRRKINSLF   5
Q9ZW81             ( 246) ERERRTRISGKL   6
Q9LRN3             ( 203) ERNRRKQMNEHL   5
Q8S0N2             ( 290) ARLRRERVSDRL   3
Q948Y2             ( 383) ERRRREKLNEMF   3
Q9LET0             (  53) ERKRRARINSHL   5
Q9SS60             ( 291) ESVRMFLENLDQ  19
O64788             (  71) SRRRRKVEVVGI  14
Q40615             (   3) ERRRREKLNEMF   3
Q9FKQ6             ( 108) ERNRRKQMNHFL   6
O23696             (  51) DQRLKWRRDSAL  79
Q41780             ( 390) ERKRREKLNEMF   3
Q9FLZ1             ( 273) EQLCYNHIEIDI  34
Q9AYK0             ( 518) ERQRREKLNQRF   2
Q9ZUV1             (  49) LSRRLEGVETVR  24
Q9SA82             ( 143) ARKRRRRITEKT   8
Q8VXB1             ( 154) ENSLAAKIKRWL  15
Q9FWE1             ( 201) ERRRRKRLNDRL   2
Q8S3F2             ( 124) ERKRREKLSEKF   2
Q8S3E3             ( 161) ERLRRERIAERI   3
Q8L9U3             ( 161) ERLRRERIAERI   3
O82397             ( 124) ERKRREKLSEKF   2
Q9SW10             ( 470) ERYMVKKEGSAK  29
Q9STJ6             (  51) ERQRRQEMATLF   5
Q9FK20             ( 108) ERNRRKQMNEHL   5
Q8LSP3             ( 292) ERKRREKLQQQF  13
Q39903             (   1) AKTILLILATIF  14
Q9SYA1             ( 182) ESLKRAKDNESA  19
Q8LPT0             ( 400) ERQRREKLNQRF   2
Q9LPJ8             ( 457) ERQRREKLNQRF   2
Q8S822             (  23) CRRRAIAPNRKP  43
Q9SKX1             ( 107) EEAAERLRNLVP  15
Q9ZPY8             ( 400) ERQRREKLNQRF   2
Q9LV21             (  37) ARAVSDAVRTSL   8
Q8S3F5             ( 438) ERQRREKLNQRF   2
Q8S0C6             ( 271) ERKRREKLNDSF   2
Q8LB18             (  94) ERNRRRQMNQHL   6
Q9FUA5             (  22) EQSKRPESRGDF  32
Q9ZUG9             ( 153) ERLRRERIAERM   4
Q9C988             (  69) ERLRRMRLHASY  20
Q41101             ( 467) ERQRREKLNQRF   2
Q94D62             ( 255) ERKRREKLNDSF   2
Q9FIQ6             (  94) ERNRRRQMNQHL   6
Q9CAD0             ( 410) EKKRREKLNERF   2
Q8S470             ( 385) ERKRREKLNEMF   3
Q9ASJ3             ( 213) AKVRRERISERL   4
Q9LYM0             (   5) EHKRGSSLREKF  25
Q9FFU7             (  65) EYSRIVAYRSFF  99
Q9SRT2             ( 273) ERVRREKISERM   4
Q9ASL3             ( 395) ERRRESDRREAA  11
Q8LQF2             ( 292) ERVRREKISQRM   4
Q8LM97             (  23) CRRRAIAPNRKP  43
Q8LIB9             (  44) SRSRKLDGKVAV  21
Q9FRI0             (  75) KKKRRERIRRQL  14
Q9LV17             ( 168) ERARREKISEKM   4
Q9ZV87             (  91) ARWVLAAEDICF  12
Q9FYJ6             ( 132) LSRPLTDINPSF 100
Q9LU04             (  10) NRSRKDQLDYGL  12
Q9LSE2             ( 312) ERRRRKKLNDRL   2
Q40614             (   3) ERRRREKLNEMF   3
Q8L7J0             ( 106) ESQISAGIKTIL  11
Q8S3E7             ( 318) ERVRREKISERM   4
Q40834             (   7) ERKRREKLNEMF   3
Q9ARY0             ( 657) ERRRRDRINEKM   3
Q38736             ( 448) ERKRREKINERF   2
Q9ZPW3             ( 200) ERARREKISKKM   5
Q8LQN1             (  97) LQDDMAASTRPF  18
Q40599             (   3) ERRRREKLNEMF   3
Q8LG13             ( 153) AKVRKERLGERI   6
Q9ZSQ9             ( 123) ERKRREKMTQRF   3
Q8SB96             ( 214) ERCIVSGRSSSP  13
Q8S3D3             ( 281) ARKRRERINERL   2
Q94I55             (  33) QSLRSRSPSGVI  12
Q8S3D8             ( 183) ERARREKISKKM   5
Q9ZRX1             (  19) DNKRKDDIRHAN  19
Q9LQ08             (  82) ERQRRQEVSSLF   3
Q94ED0             ( 392) ARQRRERISERL   3
Q9SP39             ( 150) ERVRREKISERM   4
Q8S3D4             ( 316) ERVRREKIGERM   4
Q8W2F4             ( 457) ERQRREKLNQRF   2
Q8W2F5             ( 420) ERQRREKLNQRF   2
Q8VY82             (  36) SKERKDKVGERI   7
Q9FLI0             (  35) ERQRRQEMAILF   5
Q9SJX4             ( 241) ERERRVHFNDRF  10
Q9C7T4             ( 131) ERNRRKQMNEYL   4
Q93W88             ( 151) ERVRREKISERM   4
Q9LH76             ( 254) RERRVIDVANDI  13
Q8LJ97             ( 253) DRTRSQATFLRL  21
O81900             (  37) ERRRREKLHCRL  21
Q9LS08             ( 140) ERRRRERINTHL   5
Q8VZA6             (  14) EKLRREKLNEHF   4
Q9XII8             ( 269) ERKRRERINQAM   3
Q8S3D5             ( 145) ERLRRERIAERM   4
Q9XIJ2             (  23) EKDRRMRMKHLF  14
Q9LIG3             ( 313) ARQRRERISEKI   3
Q9LU71             (  60) ERNRRQKLNQRL   3
Q9LQ51             ( 145) ERARREKISERM   3
Q9LPQ6             (1054) ERVRRGKINERL   4
Q8LCW3             ( 151) ERARREKISERM   3
Q8S3E8             ( 142) EKLRREKLNDKF   3
Q9SM95             (  85) RKRRRDRINEKL   5
Q8LRT9             ( 189) ENSCSFAEELKF  22
Q9XIJ1             (  23) EKERRMRMKHLF  13
Q9SVP7             (  29) EKRIDSVENRGI  18
Q9XEF0             (  71) EKRRRDRINSHL   5
Q9FXG5             ( 140) EQEVSSSYQEDP  24
Q9M2R7             ( 219) ERARREKINARM   4
Q8LAF0             (  26) SKERKDKVGERI   7
Q8LCD1             (  59) ERNRRQKLNQRL   3
Q9FHA7             ( 137) ARHRRERISERI  10
Q9SND4             ( 134) ARHRRERISERI  10
Q8L9T3             ( 121) ERNRRKQMNEYL   4
Q9LYT0             ( 265) ERRRRDRINERM   2
Q9FSQ4             (   2) SSSRRSRSRRAG  18
Q9LK48             ( 206) ERARREKISERM   3
Q9FT09             ( 245) LKVRKEKLGGRI   9
Q9LTS4             ( 294) ERKRREKLNESF   2
Q9SGY8             ( 167) ERKRRERINQAM   3
Q40752             (   7) ERRRREKLNEMF   3
Q9LPG6             ( 276) ESSIQFVENRPF  14
Q9FXA3             (  78) ERERRKKMRDMF   5
Q8L851             ( 187) ERVRREKISERM   4
Q8L8P6             ( 119) ERVRREKINERL   3
Q9M270             ( 184) ERNRRRQMNEHI   6
Q8LBK8             (   9) SRLRIHSFGSSC  18
Q40616             (   3) ERRRREKLNEMF   3
Q9FMB6             (  42) EQRRRSKINERF   3
O65531             (1010) QRCTRLNLPEGI  34
Q9FLK6             (  87) ERRRRDRINQRM   3
Q94D54             ( 293) ERKRREKLNDSF   2
Q40602             (   3) ERRRREKLNEMF   3
Q8S483             ( 396) ERKRREKLNEMF   3
Q8VZ22             (  86) EEERYNQINSFL  24
Q8W0Q8             ( 192) EKQRVREAEGKM   9
Q8LDA7             ( 298) ERERRTRISGKL   6
Q9FJ00             ( 148) AKNRRERISERL   3
Q39204             ( 457) ERQRREKLNQRF   2
Q8S7J7             ( 117) ERNRRRQMNEYL   4
Q8S235             (  49) ARERRHRISDRF   4
Q9M0R0             ( 199) ERVRRTRISDRI   5
Q9SLT6             ( 151) ERARREKISERM   3
Q9AYI8             ( 197) ERKRREKMHQQF  15
Q9SA66             ( 154) ERLRRERIAERI   3
Q9SJW8             ( 520) ESSRPRPRDRQL  36
O81756             ( 278) ARKRRERINERL   2
Q8LFU9             ( 102) EKKRRSKINEKM   3
Q8S3E4             ( 156) ERARREKISKKM   5
Q9SJX5             ( 219) ERERRCHLNERY  22
Q9C8Z9             (  46) ARWRSEKQQRIY  25
Q9LRW0             ( 185) EREIGELIARAM  16
O82599             ( 121) ERNRRRQMNEHL   5
Q8VZJ4             ( 470) ERYMVKKEGSAK  29
Q9SYM5             ( 274) EANIKFVDNRPF  35
Q9SA36             (  21) EKTRLEALTFDK  16
Q41285             (   7) ERKRREKINEMF   3
O23192             ( 206) EKRRRSRINEKM   3
Q8RYL7             ( 229) ERRRRKKLNDRL   2
O48644             ( 457) ERQRREKLNQRF   2
Q40644             (   3) ERRRREKLNEMF   3
Q93Y53             (  51) ERLESKSIKLAM  10
O65678             ( 187) ERVRREKISERM   4
Q9SVU6             ( 286) ERRRRQKINEMM   4
Q40643             ( 404) ERRRREKLNEMF   3
Q9FLI1             (  10) ERQRRQEMASLY   5
Q9FE77             ( 160) EESDEDDVKSTG  33
Q9LSQ3             ( 114) ERLRRERIAERM   4
Q9M4A8             ( 423) ERKRREKLNEMF   3
Q94D59             ( 223) ERKRREKLNDSF   2
Q8LG61             ( 176) YEYLRDAIGDSM  29
Q9SN74             (  36) ERLKREHLNELF  10
O48535             ( 315) ERVRRTRISERM   5
Q40835             (   7) ERKRREKLNEMF   3
Q9FRI2             (  62) ERVRREKINERL   3
Q93ZM7             ( 185) EREIGELIARAM  16
Q8LEG1             ( 182) ARKRREKINERL   2
Q8S3F1             ( 137) ERKRRQKLNERL   2
Q8L5W8             ( 238) ERKRRDEFNKKM   5
Q8S3F3             ( 131) ERKRREKLTQRF   3
Q93ZB9             (  34) EKILRVAPNVKK  17
Q9LPF4             (  59) NRRLRTLLESNL  19
Q9LI31             ( 413) ERQRREKLNQRF   2
O80727             (  43) AKIRRPKNNGSF  39
Q8W5G3             ( 225) ARRRRERINGRL   3
Q9SL63             ( 293) ERKRRDRINERM   3
Q8L5W7             ( 197) ERNQRNDINKKM  10
Q9T072             ( 133) ERKRREKLTQRF   3
Q9FIX5             (  94) ERTRREKQKQSY  12
Q9LEZ3             ( 285) EQRRRSKINDRF   3
Q9ZPN6             ( 529) ERQRREKLNQRF   2
Q9XGZ1             (  33) NRSLVRQNFSRF  35
Q942Q3             ( 385) ARQRRERISERL   3
Q41102             ( 439) ERQRREKLNQRF   2
Q40603             (   3) ERRRREKLNEMF   3
Q9ZUV8             ( 136) ERRRRGRMKDKL   4
Q8LJC5             ( 224) ERAAGAPSISGF  56
Q9LTC7             ( 171) EKLRREKLNDKF   3
O24438             ( 617) ERKHRHIVEVGL  12
Q8S3E6             ( 143) ARKRRRRITEKT   8
Q8S3D7             ( 265) ERRRRDRINERM   2
Q9LSL1             ( 183) ERRRRKRLNDRL   2
Q9SZR4             (  59) ERNRRQKLNQRL   3
Q9FJL4             ( 316) ERVRREKIGERM   4
Q9C707             ( 210) AKNRRERISERL   3
Q8L8Y1             ( 184) ERNRRRQMNEHI   6
Q8W0P3             (  40) ERRRRQDMKGLC  10
Q8S490             (  84) ERVRRTRISERI   5
Q9FN69             ( 446) EKKRREKLNERF   2
Q8S3E2             ( 219) ERARREKINARM   4
Q9LPE2             (  11) SQCDSNLPNRLF  15
Q8S3E0             ( 267) ERVRREKISERM   4
O81313             ( 127) ARRRRERISEKI   3
Q9LXD8             ( 134) ARHRRERISERI  10
O64746             ( 147) ARGRRRRIAEKT  12
Q93Y00             ( 159) ERLRRERIAERI   3
Q9LJD1             ( 558) EQLRRFKIAKSD  28
O80668             (  50) AVDRDDDIDEPF  33
Q9LY78             (  57) EVALSALLSLAF  19
Q9LNJ5             ( 438) ERQRREKLNQRF   2
Q9S7Y1             ( 182) ERRRRERINNHL   5
O81348             ( 177) ERKRREKLSQRF   3
Q9FMQ9             ( 122) ERRLADQKSKQF  13
O81901             (  86) EEERYNQINSFL  24
Q8LJF6             ( 345) ERLRRERLSQGY   4
Q8LD53             (  80) EKQRRDRLNDKF   2
Q41875             ( 473) ERRRREKLNEGF   2
Q8LEZ5             ( 183) ERRRRKRLNDRL   2
O81306             ( 152) YDKRRDKINQRM  30
Q8LF81             ( 140) ERARREKISKKM   5
Q948Y3             ( 404) ERRRREKLNEMF   3
O65643             (  53) EKLRRDKLKEQF   5
Q9SFZ3             ( 158) EKLLLKSMSSGF   5
O65552             ( 202) ERLRRERIAERM   4
Q8S9Z4             (  34) KRTIKSKREQSK  21
Q40902             ( 192) VRSRMMLPGYDL  20
Q9FP06             ( 407) ERVRREKISERM   4
Q8S3E1             ( 156) ERRRRKRLNDRL   2
Q8S3E5             ( 147) ARGRRRRIAEKT  12
Q9FUA4             ( 206) EKRRRSRINEKM   3
Q9M0X8             ( 170) FKVRKEKLGDRI  19
Q9SZK7             (1326) ERRRRLRINSQF   6
Q9LT23             (  67) EKLRREKLNEHF   4
Q9C690             ( 319) ERVRRTKISERM   5
Q9SQ79             ( 483) ERVRRTRISERM   5
Q9ASX9             ( 106) EQEVSSSYQEDP  24
Q8W2F2             (  53) EKLRRDKLKEQF   5
O81072             ( 489) WQMRMRRINRRY  30
Q9SUP3             (  87) ERRLALTPEQIN  16
Q40836             (   7) ERKRREKLNEMF   3
Q9C9S9             ( 151) ERVRRGKINERL   4
Q8S9M5             (  67) ERRRRERINSHL   4
Q9C8P8             ( 196) ERVRRTRISDRI   5
Q9FTF3             (  38) HRCSKHGPEIRF  38
Q9T079             ( 440) EKERKHKINFQY  15
Q8L8X9             (  46) ARWRSEKQQRIY  25
Q8S3D2             ( 284) ARQRRERISEKI   3
Q8S3F4             ( 222) ERKRRDKINQRM   3
O23226             ( 152) ERARREKISKKM   5
Q9M1K1             (  80) ERDRRKKINTLF   5
Q41514             (   7) ERKRREKLNEMF   3
Q40833             (   7) ERKRREKLNEMF   3
Q8LBH9             (  51) ERLESKSIKLAM  10
Q9ZVX2             ( 215) ERRRRKKLNDRL   2
O49687             ( 421) ERQRREKLNQRF   2
Q9ZQS4             ( 427) ERKRREKISERF   2
Q9SQK8             ( 177) ERQRREKLNQRF   2
Q941Z7             (  77) ERDRRKQLNELY   6
Q8W2F6             ( 421) ERQRREKLNQRF   2
Q41854             ( 427) ERKRREKLNEMF   3
Q9LN95             (  83) ERQRRQENTSLF  20
O81037             ( 199) ERNRRRQMNVHL   7
Q8L467             ( 139) ERLRREKLNERF   2
Q8S3E9             ( 136) ERRRRGRMKDKL   4
Q41286             (   7) ERKRREKLNEMF   3
Q948F6             (  41) EKRRRSRINEKM   3
Q8LQ30             (  34) ERARRQTMSRLY   7
O82398             ( 137) ERKRRQKLNERL   2
Q8S3F0             ( 133) ERKRREKLTQRF   3
Q9ZVB5             (  70) ERERRKKINTMF   5
Q8LE61             ( 105) QTILQEDLNSSF  19
Q9FTJ0             (  12) RRRRVLRRRRLL  10
Q9FTQ1             (  86) ERRRRERINAHL   5
Q9AWY1             ( 263) ERRRREKLNEMF   3
Q9CAL3             (  31) ARARAVKVTCSP  22
O80674             (  75) ERRRRERINSHL   4
Q9LND7             ( 177) LKEVMRETKESF  10
Q9SJM1             ( 176) YEYLRDAIGDSM  29
Q8LIB8             ( 110) EKDVAAAVDLAV  16
O23090             ( 254) EKQRREKLNHRF   3
Q9LPW3             ( 272) ERRRRKKLNDRL   2
Q9C682             (  75) EKQRRDRLNDKF   2
Q9FYE6             (  74) ERDRRRKLNALY   6
Q9M5P3             (  51) ERLESKSIKLAM  10
Q944L0             (  10) NRSRKDQLDYGL  12
Q9FH37             (  80) EKQRRDRLNDKF   2
O23487             ( 325) ERQRREKLNQRF   2
Q940I6             ( 156) ERARREKISKKM   5
Q8LID5             ( 100) AVARHGRLDVVF  35
Q8RX65             (  35) EKLRRDKLKEQF   5
Q9CAA9             ( 318) ERVRREKISERM   4
Q9CAA4             (  54) EQRRRSKINERF   3
Q9C670             ( 238) ERVRREKISERM   4
Q9LXG5             (   5) RRSRQASSSSRI  11
Q9SEY5             (  97) LRLASALTNLGI  11
O22768             ( 161) ERLRRERIAERI   3
Q9STJ7             (  10) EKRRRQEMASLY   5
Q8LIC5             (  84) EAQVAAAVDLAV  34
Q8VWV9             ( 635) AKSARKALGLGY   7
Q9ATD7             ( 441) ERKRREKINERL   2
Q9FEA1             ( 480) ERRRREKLNERF   2
O23297             ( 133) ERLRREKLNERF   2
Q9ATD8             ( 429) ERRRREKINERL   2
O50002             ( 113) EEFRRQRLGAAQ  23
Q8L5G8             (  24) ERRRRKRDADLL   9
Q9SLX2             ( 427) ERKRREKISERF   2
Q8H8H9             ( 123) ERNRRRLMNDHL   6
Q8H8E4             ( 187) ERRRRKRLNDRL   2
Q8H7N8             ( 117) ERNRRRQMNEYL   4
Q8H6X2             ( 123) ERKRRGRMKEKL   4
Q8H102             ( 298) ERERRTRISGKL   6
Q8GZV6             ( 643) ERFRREKINERM  12
Q8GZM7             ( 293) ERKRRDRINERM   3
Q8GZ38             ( 222) ERKRRDKINQRM   3
Q8GZ13             ( 160) ERVRRGKINERL   4
Q8GYC3             (  59) ERNRRQKLNQRL   3
Q8GY61             ( 187) ERVRREKISERM   4
Q8GX46             ( 219) ERERRCHLNERY  22
Q8GWZ9             ( 133) ERNRRRQMNEHI   6
Q8GWK7             ( 162) ERVRRGKINERL   4
Q8GVF0             ( 219) ERERRCHLNERY  22
Q8GRJ1             ( 237) ERRRRDRINEKL   2
Q8VSD2             ( 396) ERLAVRKARSVQ  17
Q9AMU0             (  24) GRRLTNRFALGV  18
Q934L1             (   2) NRTVMMALVIIF  26
Q8KWC2             ( 248) ARSAEAKQREQL  18
Q99QK1             ( 213) ERLAVRKARSVQ  17
Q93SJ3             (  31) ARSALFDLNDDK  10
Q52181             ( 181) QEGIQGNLSRVF  16
Q93QG8             (  47) ERMLAEPMCIDL  85
Q93LQ4             (  15) HERRVQVIRLRK  23
Q8VSI6             ( 396) ERLAVRKARSVQ  17
O07845             ( 384) EKNLSRVFEPFF  34
Q9RMV6             (  52) TRGVSDLMNTVF  22
Q45828             (  31) LEAVRDAKKNGI  16
Q06074             (  80) YRILKHRLELVL  20
Q93HE5             ( 323) DRDRPLVVGSAK  29
Q54812             (  23) VRKLAQDGTRVF  15
Q9AE31             (  27) DRTRLALLAIAL   9
Q9FA97             (   6) DREREAKLARKT  13
Q9AIT7             ( 120) DRQTVKAPSADK  14
Q93EX7             ( 204) ERLRRGVFRTSS  21
Q9FDK7             (  39) EREKELHDNYGI  22
Q8KWW8             (  76) ARALRLEMDGVP  11
Q9S488             ( 156) ERLLSANLYLPF  30
O07469             ( 173) ESNREMVEALGF  18
O06468             (   1) MRRWRFSPRSSF  89
Q55221             (  24) RRKLALDGTRVF  16
Q937Y1             ( 206) SRTAILALAAFF  16
Q93QX7             (   8) ERRKKSGSTRLM  15
Q54206             ( 111) NKAAAFDISAGC  16
Q8VSD7             ( 396) ERLAVRKARSVQ  17
Q93NY1             ( 326) ARVCAERITEVL  13
Q9EZI2             (  47) LRGMMKARKGRI  24
O51656             ( 145) LKKALNADNFDF  20
P72627             ( 320) AQVLRRRFRRPL  10
O07744             (  75) WRWRVAFYALSA  51
Q9PDI9             (  40) EEKTLLIISVAL  14
Q9KN09             ( 341) EREKLGNLKSVL  11
Q9KEL2             (  47) AVSLQYGLNIGI  26
Q9KC74             (  29) EKQASHRYDLAF  10
Q9K9K1             ( 246) NRGIRHLSRINI  25
Q9K718             (  23) QSGRSAGLSGAI  14
Q9K0Z5             ( 167) EEKKAAKEKVAP  16
Q9JYW1             (   7) QIIRRFGLGRIF  37
Q9JXR1             (  70) IESLIADIEKAF  21
Q9JSY4             ( 192) EKARSAAAKEVQ  17
Q9I2R3             (  57) ERVRHSVLDKAS  34
Q9I201             ( 116) EQLLVARTLMGF  19
Q9I1Q7             ( 150) ERSRGAVLMDCG  44
Q9HYP7             (  80) GRRGLQDLTNSF  32
Q9HVI8             ( 843) SQQRRAERELRM   9
Q9HUF4             ( 108) RRLRRFRTRQQL  12
Q9AB09             (  31) LRIRAILERLGF  11
Q9AA40             ( 238) QKLEMAKYGKWK  20
Q9A7Z6             (  78) ARIKEREPKLDI  16
Q9A0C0             ( 300) PRQLMRLAERAF  26
Q99YD6             ( 106) ERVLKINLTGAF   8
Q99SP1             (  99) ERALEDLYNYGK  16
Q98ND6             (  37) AQQITLLYDGAF  13
Q98HM4             (  40) ERAAKVAADIGG  25
Q98H05             ( 281) LERGRAGLAIFL  34
Q98FG7             ( 213) DRERLAEFGSAI   8
Q98DE7             ( 195) VRSALAGLRIEE  21
Q98D51             (  90) MQGRMGAIAEVF  27
Q98BY8             ( 276) ERARLLQDAARL  11
Q986S8             (  45) LRKIMDDFEAAN  13
Q9FBC3             ( 106) EKVLKVNLTGAF  12
Q97PK5             (  19) ERRHRNHGGADR  29
Q97MM6             (  62) NKLLRQKPTEIK  12
Q97L06             (  89) GRLYMRDLEEAI  13
Q97KQ0             (  60) NSKVSHDFKDIF  14
Q97DR7             (  74) AKLIKRGIGIVP  12
Q97DA6             ( 102) LRMKEEDFDSVI  19
Q930R6             (  96) ERQVVLSLSRMN  11
Q92UI5             ( 354) ARLRGAFLGLSL  29
Q92JC5             ( 112) NRIDPKNPELRF  30
Q92JA3             (  74) EEAAVIRFGRFV  18
Q92FV1             (  18) TRAISARTTIPI  24
Q92DA6             (  36) ERANRNAELTQL  21
Q8ZN33             ( 198) NRPALRAVKFAL  24
Q8ZLD6             ( 258) FRLDKTGRNKMF  26
Q8ZAZ2             (  32) REITMFKPKADF  17
Q8Z269             ( 258) FRLDKTGRNKMF  26
Q8YDB5             (  50) EQTRSTHENLAK  11
Q8YAW1             (  18) TRAISARTTIPI  24
Q8Y8J1             (  36) ERANRNAELTQL  21
Q8XJS0             (  89) VERISADLNEFK  14
Q8XG63             ( 118) SRNAMIIGTAGF  18
Q8XDS3             ( 198) DKKALTSVKFAL  14
Q8XBY1             (   3) EWIIRRSVANRF  87
Q8XBW4             ( 336) QRSQLRRIMLCI  35
Q8X731             (   1) MRRLRFSPRSSF  23
Q935B7             (  42) KSRTMSLEDEYF  19
Q8UK57             (  55) EAELLNLTNLAL  27
Q8UBX7             ( 243) ERQRLRLFGEKI   6
Q8U8H9             ( 385) ARRTAELIQSDF  18
Q8U717             ( 273) ERQRLLADVARL  16
Q8U6T5             ( 203) EGARSIGLNHID  47
Q8VJU9             (  26) YQCRRHRPESCL  21
O67212             ( 309) IKSLEAVINGGF  15
O67226             ( 257) ARIRKRKRDTVL  11
Q55190             ( 134) ESNLKELIRVGP  13
Q9X2H5             (  55) KKNQVTDFGKVF  21
Q92PZ0             ( 281) IELAAHGIALQF  18
Q92N34             ( 137) SRFRLIGRERGY  20
Q92L22             ( 212) DRRRLRAFGDKI   8
Q92KZ6             (  59) AERAIAAARRAF  17
Q8YJN7             (   6) QSSMEAKLTAAF  22
Q8YDP9             (  26) NQLRKNSLGVAA  14
Q8XWW9             ( 176) DRIRVNCVNPVM  37
Q8XWH5             (  18) SSARIHAFGLAM  16
Q8XVB4             (  38) EEKTLIIVATAL  14
Q8XUI9             (   6) DREREAKLARKT  13
Q8XQE9             ( 191) VRGDAADAADAF  17
Q8R8L9             ( 198) ARRREINIMKYI  30
Q8R7I9             (  20) ERGNLLEETLVY  16
Q8R9W0             (  23) VRLAKDGFNIAI  10
Q8R805             (  17) SRGLGAAIAKAF  18
Q8PQX4             (  26) ERNRAAGVAAAA   9
Q8PN93             (  81) AQSFLGRIDLWF  44
Q8PLS9             (  55) ERAASDKIGQAL   6
Q8PLK3             ( 391) ARPLLGNFDQGF  20
Q8PLF0             (  23) QRLVADGGKVAL  17
Q8PJ52             ( 206) ERTLLLTGTIFM  18
Q8PEY1             ( 194) NRQLERRARLAN  15
Q8PEJ4             (   8) NRSTARAARTPF  16
Q8PED2             ( 123) RDAALADINASF  24
Q8PAS7             ( 211) ERPRMDYIGLIL  50
Q8PA03             (  55) ERAASDKIGQAL   6
Q8P9S2             ( 391) ARPLLGNFDQGF  20
Q8P9M2             (  30) GRVALFDVNADK  17
Q8P7U4             ( 206) ERTLLLTGTIFM  18
Q8P1F7             ( 300) PRQLMRLAERAF  26
Q8NZN2             ( 106) ERVLKINLTGAF   8
Q8NT37             (  31) DPELTARINDAM  47
Q8NSF7             (  15) ARGLGRALSESF  16
Q8NRK9             (  23) SRDIYRRRGRVF  28
Q93IG7             (  64) NRRRLLTARERL  11
Q8KCN0             (  11) ERAVLVGITSTP  27
Q8KAN9             (  20) VNKDQIKPESKF  21
Q8K7X8             ( 291) PRQLMRLAERAF  26
Q8K628             ( 106) ERVLKINLTGAF   8
P72392             ( 111) DKAAAFDISAGC  15
O86560             ( 161) ERRRVTAIGSRE  16
Q9Z4X2             ( 167) ERRAADPGDHSF  21
Q9XAP7             (  68) ARSLRRPAATVF  15
Q9L1T4             (  14) EQARRAPVRDRY  12
Q9KYC2             ( 153) ERKFVKVINSRP  41
Q9FC54             (  52) VRQLLESIDGPV  17
Q9KZV9             ( 274) VENATAAIGAAK  13
Q8ZDH6             ( 103) QSWLLFSIAIIY  16
Q8ZJH0             (  13) ARTLLLIVTLLF  11
P97309             (  85) EKLRMRTLARAL   6
O70241             ( 171) ERRRRFNINDRI   3
Q923F4             ( 388) ERQRRNDLRSSF   3
Q9EPW1             (  63) EKRRRDKMNSFI   4
Q99JK7             (  58) EKRYRSSINDKI   6
Q9D030             (  75) ERQRTQSLNEAF   3
Q8K3I5             ( 144) LRRTSARLELVF  11
Q8VHR1             (  23) ARSRRSQETEVL   5
O89006             (  34) EEEDTTTSNKVY  17
Q9R2A2             (  34) EEEDTTTSNKVY  17
Q9Z2I5             (  21) ARSRRSQETEVL   5
Q9QUM5             (  58) EKRRRDRINNSL   2
Q9JHC5             (  27) EKKRRARINVSL   4
Q8R4E5             ( 149) ERRRRDKINNWI   5
Q9EPJ1             ( 118) ERQRTQSLNEAF   3
Q8R3M6             ( 397) ERLRLSTWKVQL  32
Q925V5             ( 131) ERNRMHDLNAAL   3
Q9D2H4             ( 144) LRRTSARLELVF  11
Q8K1Z8             (  64) EKNRRAHLRLCL   5
Q9JK54             ( 127) EKLRMRTLADAL   6
Q9EQW5             (  77) ERKRMHDLNLAM   3
Q8VI53             ( 228) EQKRRFNIRMGF  10
O89012             (  34) EEEVTTTSNKVY  16
O89105             (  35) SKRHRDRLNTEL   7
Q9WTU9             (  27) ARSRRSKESEVF   4
Q99N33             ( 491) ERLRVRDINEAF   3
Q9QXJ5             (2373) ERRRRGEMRDLF   5
Q923L9             (  16) EKRRRDKMNHLI   5
P70366             (  32) EKRRREQENKYL   4
Q8VHZ2             (   0) XRRRLKKVNQAF   3
O08718             (  92) ERNRMHNLNSAL   3
Q8R385             (  26) ARSRRSKESEVF   4
Q91XJ5             (  57) EKRRRDKMNHLI   5
Q8R2J8             ( 207) ERRRRFNINDRI   3
O88295             (  81) EKRRRDKMNSFI   4
Q9ESZ4             ( 148) EKRYRSSINDKI   6
Q8K1X3             ( 367) ERLRVRDINEAF   3
Q62850             (  44) QRSRLTDLPIGL  31
O89007             (  34) EEEDTTTSNKVY  17
O09135             ( 208) ERRRRDKINNWI   5
Q9QX98             ( 169) ERRRMQSINDAF   3
Q8QZX6             (  35) SKRHRDRLNTEL   7
Q9R0U2             (  81) EKRRRDKMNSFI   4
P70365             (  32) EKRRREQENKYL   4
Q924H3             (  50) EKRRRDKMNHLI   5
Q9D8P5             (  62) EKHRRAKLRLYL  11
Q91XK1             ( 417) ERLRVRDINEAF   3
Q9DBX7             (  52) EKRRRDRINSSL   2
Q9D0R0             (  58) EKRRRDRINNSL   2
Q61202             (  32) EKRRREQENKYL   4
Q8VCY4             ( 556) ERLRVRDINEAF   3
Q9JHS2             (  21) ARSRRSQETEVL   5
Q9EPN2             ( 108) ERRRTQSINSAF   3
Q9CYA8             (  26) ARSRRSKESEVF   4
Q9WTL8             (  88) EKRRRDKMNSFI   4
Q9JL51             (  24) ERRRLSKVNEAF   2
Q99JA6             (  21) EKRRRDRINRSL   2
O35391             (   9) AKTRREKENGEF   6
O70425             (  90) EKRRLKKVNEAF   2
O55208             (  68) ERERIKNLNRGF  10
Q62065             ( 204) ENSRENLLHQAM  23
Q8R4S5             (  35) SKRHRDRLNTEL   7
O88810             (  81) EKRRRDKMNSFI   4
O88529             (  81) EKRRRDKMNSFI   4
Q9JIZ5             (  57) ERRRMQSINAGF   3
Q8VBZ0             (  22) LAQLLRRLRGDF  29
Q9QYC3             (  81) ERQRMHKLNNAF   3
Q8VIP2             ( 671) EQKRRFNIKLGF   5
O88930             (  35) SKRHRDRLNTEL   7
Q8K3Z5             (  88) ERQRRNELKRSF   2
Q9QX54             (  21) ARSRRSQETEVL   5
Q9D489             ( 209) EKLRRERIKSCC   9
Q8R4S7             (  35) SKRHRDRLNTEL   7
Q9CYJ4             ( 555) ERLRVRDINEAF   3
P70562             (  81) ERQRMHKLNNAF   3
Q8R4S3             (  35) SKRHRDRLNTEL   7
O35800             (  26) ARSRRSKESEVF   4
Q99KZ5             (  28) EKKVLYGYWSAF  81
Q8VE59             (  46) ERRRRDKINNWI   5
Q8K0H8             ( 138) EQKRRDAIKRGY   5
Q9QZQ0             (  67) ARSRRGKENFEF  12
Q9QY56             ( 363) ENSRENLLHQAM  23
Q921F3             (  98) ERRRRNKMTAYI   4
O89009             (  34) EEEDTTTSNKVY  17
Q9WTW4             ( 119) ERRRRYNINYRI  10
Q8R4S6             (  35) SKRHRDRLNTEL   7
Q923Z4             ( 112) ERKRMFNLNEAF   3
Q9QYE4             (  81) ERQRMHKLNNAF   3
Q921S4             (  68) EKRRRDKMNSFI   4
Q99MB8             ( 552) ERVRVRDINEAF   3
Q9EQX3             ( 217) ERRRRDKINNWI   5
Q8K3Z4             (  89) ERQRRNELKRSF   2
Q9QXW8             (  52) EKRRRDRINSSL   2
Q923F0             ( 158) ERWRQQHVNGAF   8
Q9QYF5             ( 169) ERRRMQSINDAF   3
Q9Z2W6             (  19) ERSLAIARGRGK  13
Q9JL05             ( 225) ERRRMHDLNDAL   3
O70284             (   9) ARTRREKENSEF   5
Q9JHS1             (  23) ARCRRSKETEVF   7
Q8R4S4             (  35) SKRHRDRLNTEL   7
O35410             ( 208) ERRRRDKINNWI   5
Q63643             ( 109) ERRRRNKMTQYI   4
Q9Z312             (  34) SKRHRDRLNTEL   7
Q91YA9             (  81) EKRRRDKMNSFI   4
Q9WTL9             (  81) EKRRRDKMNSFI   4
Q9JI41             (   9) ERQRTQSLNEAF   3
Q9JJR4             ( 129) IRDDEQYYNRIF  56
Q9QVY1             (  35) SKRHRDRLNTEL   7
Q9JL50             (  24) ERRRLSKVNEAF   2
Q9Z2E5             (  50) ERRRMQGLNTAF   3
O35434             (  23) ESQIRMALFIFF  28
Q9JJK7             (  35) SKRHRDRLNTEL   7
Q91YV0             ( 413) ERLRVRDINEAF   3
O70483             (  88) ERARMRVLSKAF   6
Q8VCH2             (  96) EDLRMSDAGIYW  92
O88337             (  76) EKRRRDKMNSFI   4
Q9QUS4             (  57) EKRRRDRINNSL   2
Q8JZK8             ( 144) LRRTSARLELVF  11
Q9WUJ7             ( 127) ERNRVKLVNLGF   4
Q91VN7             (  62) EKHRRAKLRLYL  11
Q923L8             (  50) EKRRRDKMNHLI   5
Q91XJ6             (  57) EKRRRDKMNHLI   5
Q8R4S2             (  35) SKRHRDRLNTEL   7
Q60763             ( 144) LRRTSARLELVF  11
Q922S2             ( 552) ERVRVRDINEAF   3
Q9JK33             ( 196) ERWRQQNVNGAF   7
Q99P79             (  35) SKRHRDRLNTEL   7
Q9CZ29             ( 257) IRHRRIHTGEKP  25
Q8VD56             (  82) ERQRVKCVNEGY   9
Q9D8I0             (  92) ERNRMHNLNSAL   3
Q99NA2             ( 240) ERTRVHTISAAF   6
Q9JLR5             (  84) ERTRVKTLRQAF   6
Q9JJV6             (  52) EKRRRDRINSSL   2
Q9JHE6             (  34) EKKRRARINESL   2
Q9CRT1             (  45) ERLRVRDINEAF   3
O08662             (  14) ERRRDAVIALGI  16
P97831             (  75) ERQRTQSLNEAF   3
Q99PF1             ( 144) LRRTSARLELVF  11
Q64305             ( 171) ERRRMQSINDAF   3
Q91W36             ( 131) HRKRKLLENSSL  19
Q8CIY4             (  35) SKRHRDRLNTEL   7
Q8CIY3             (  98) ERRRRNKMTAYI   4
Q8CHL8             (  35) SKRHRDRLNTEL   7
Q8CHG9             (  85) ERRRRNKMTQYI   4
Q8CH17             (  73) TRLRRLVPTIPP  24
Q8CGH4             (  53) EKKRRDRINECI   3
Q8CEI7             ( 110) ERNRMHGLNAAL   4
Q8CEC2             (  83) ERRRRNKMTAYI   4
Q8CE98             ( 572) ERLRVRDINEAF   3
Q8CD45             (  19) ERSLAIARGRGK  13
Q8CD44             (  51) EKRRRDRINNSL   2
Q8CC19             (  27) ARSRRSKESEVF   4
Q8CAH9             ( 553) ERVRVRDINEAF   3
Q8CAG7             (  35) EKRNREQENKYI  11
Q8C9W6             (  43) EKKRRDQFNVLI   6
Q8C9V3             (  98) ERRRRNKMTAYI   4
Q8C7Y3             (  35) EKRNREQENKYI  11
Q8C733             ( 326) EKRYRSSINDKI   6
Q8C6Y4             ( 304) ERRRRFNINDRI   3
Q8C6B1             ( 118) ERRRLSKVNEAF   2
Q8C6A8             ( 225) ERRRMHDLNDAL   3
Q8C5F1             ( 243) ERRRRFNINDRI   3
Q8C4Y1             (  23) ERKRRDHIKDSF   3
Q8C1I7             (  28) ERTRVHTISAAF   6
Q8BWA4             (  53) ERRRMQSINAGF   3
Q8BVI1             (  25) EKMRRDRINSSI   5
Q8BTI2             (   2) EKKRRARINVSL   4
Q8BRU1             (  43) EKKRRDQFNVLI   6
Q8BPE2             ( 158) ERWRQQHVNGAF   8
Q8BN74             (  35) EKRNREQENKYI  11
Q8BN29             ( 214) ERRRRFNINDRI   3
Q8BLP5             (   7) ERKRILDYNEAF  12
Q8BKT2             (  21) EKRRRDRINRSL   2
Q8BKA6             (  22) EKRRRARINESL   2
Q8BGW3             ( 107) ERRRMHDLNDAL   3
Q8BFV7             (  86) ERIRVEAFNLAF   6
Q8VAP6             (  50) FRCLELGIGSSF  24
Q65090             ( 545) QVQRRHHTDVAF  25
Q9E8G3             ( 227) EQSTTEHPTTAN  14
O42090             ( 116) DRQISDNISESS  21
O10469             ( 197) VRKRAEGFSHCA  13
Q9DTG3             ( 197) VRKRVEGFSHCA  12
Q9YN85             ( 197) VRKRAEGFSHCA  13
Q91TM1             ( 298) DRARLERVFEEL  17
Q00938             (  23) QVQRRHHTDVAF  25
P87593             ( 174) EKKRTTKAGTPH  45
Q89391             (   9) ARSVKKRPDSCS  24
Q91DH6             (  78) NDRTCAQINQRF  58
Q9YWN1             ( 846) WRSRADEINAIF  29
Q9IFW8             ( 197) VRKRAEGFSHCA  13
Q84636             (  62) DRKLSNSEVKKY  16
Q8QUM5             ( 147) ERVRRMQFKDDM  14
Q9Q8F5             ( 303) NRILQRRPGRTL  25
Q8QMT4             (  14) LRQRWPLITKMF  58
Q9E9R6             ( 146) EDLRRHGPGLSE  32
Q9PTN8             (  27) EKMRRDRINSSI   5
Q9W7B5             (  35) EKRRRDRINQSL   2
Q98T39             (  94) ERQRRNELKLSF   2
Q9PSF5             (   6) ERSRVRNLRQAF   4
Q98T40             (  94) ERQRRNELKLSF   2
Q98T13             (  94) ERQRRNELKLSF   2
Q8QFX4             (   7) VRSVRSCYEAVC  24
Q98T02             (  95) ERQRRNELKLSF   2
Q98TW1             (  12) ARSEAQKRKEGP  15
Q9W7E6             (  59) ERLRIRNLNTMF  11
Q8JH17             (  94) ERQRRNELKLSF   2
Q90466             (  26) EKIRRERINSSI   4
Q98T43             (  94) ERQRRNELKLSF   2
Q98927             ( 799) ERQRRNELKLRF   2
Q8JI94             (  95) ERQRRNELKLSF   2
Q9I8T7             (  88) EKRRRDKMNSFI   4
Q9PWP2             (  85) ERNRMHNLNAAL   3
Q9W7B6             (  21) EKQRRDRINRSL   2
P79832             (  74) ERRRRNKMTAYI   4
Q9PUL7             (  81) ERQRTQSLNEAF   3
O57562             ( 194) ERWRQQNVNGAF   7
Q8JH03             (  94) ERQRRNELKLSF   2
Q91207             ( 109) EKRRLKKVNEAF   2
Q9I8A3             (  53) EKRRRDRINNSL   2
Q8UV09             ( 101) ERQRRNELKLSF   2
Q90X12             (  58) SRLRRLVPTIPP  14
Q98T19             (  94) ERQRRNELKLSF   2
Q98T00             (  94) ERQRRNELKLSF   2
O42245             ( 127) ERRRMHGLNHAF   4
Q8UUZ7             ( 101) ERQRRNELKLSF   2
Q90464             (  -1) XXMRRDRINKCI   6
Q90X13             (  58) SRLRRLVPTIPP  14
Q98T16             (  94) ERQRRNELKLSF   2
Q98T45             (  94) ERQRRNELKLSF   2
O42180             ( 746) EQSRQRELVQCL  13
Q91558             (  53) ERNRVKLVNMGF   8
Q9W6C8             ( 116) ERTRMHDLNSAL   4
Q8JIA0             (  98) ERQRRNELKLSF   2
Q9I8K2             (  27) EKKRRDQFNVLI   6
Q98939             (  94) ERRRMHGLNHAF   4
Q8JGZ6             (  94) ERQRRNELKLSF   2
Q8JH04             (  94) ERQRRNELKLSF   2
Q8JIS0             (  87) ERNRMHSLNYAL   6
Q9I9C6             ( 242) RRARRLDPSEGT  12
Q8UVH3             (  31) EKRRREQENKYL   4
Q9DG56             (  87) GRHRMHNLNSAL  16
Q91606             (  65) ERLRVRDINGAF   4
Q8JH12             (  94) ERQRRNELKLSF   2
Q8UUJ7             (  60) EKLRMRRLAQAM   5
Q90ZD3             ( 118) ERRRLSKVNDAF   2
Q9DFB9             ( 314) ERQRRNELKLSF   2
Q8UW73             (  22) EKRRRERINNSL   2
Q9I9Q6             (  34) EKRRRDQFNILI   5
Q8JIX6             ( 107) EKRRLKKVNEAF   2
Q9W621             (  44) EKRRRARINESL   2
Q9PSL4             (  14) EKRRLKKVNEAF   2
Q9YH69             (  75) ERQRTQSLNEAF   3
Q98SZ9             (  92) ERQRRNELKLSF   2
Q98T38             (  94) ERQRRNELKLSF   2
Q98T04             (  94) ERQRRNELKLSF   2
Q8QGE4             ( 257) ERRRRFNINDRI   3
Q98904             (   6) ERRRMHGLNKAF   3
Q90W24             ( 193) ERWRQQNVNGAF   7
Q98T36             (  98) ERQRRNELKLSF   2
Q98T12             (  94) ERQRRNELKLSF   2
Q8JH16             (  94) ERQRRNELKLSF   2
Q98T34             (  98) ERQRRNELKLSF   2
Q9PTB3             (  23) ARCRRSKETEVF   7
O13126             (  42) ERRRMQGLNTAF   3
Q9DEU8             (  28) EKKRRERINSSL   2
Q98T06             (  94) ERQRRNELKLSF   2
Q98SW2             (  26) ARCRRGKESEVF   8
Q98T24             (  94) ERQRRNELKLSF   2
Q8JI93             (  95) ERQRRNELKLSF   2
Q91399             (  22) EQSLSIARGSSH  44
Q90XP4             ( 304) ERRRRFNINDRI   3
Q8QHA1             ( 101) ERQRRNELKLSF   2
Q9DE43             ( 105) ERSRMHGLNDAL   3
Q9W6G4             (  24) ERIRVEAFNLAF   6
Q9YH82             (  87) ERNRMHNLNAAL   3
Q8JGZ8             (  94) ERQRRNELKLSF   2
Q8UUZ9             ( 101) ERQRRNELKLSF   2
Q98T15             (  94) ERQRRNELKLSF   2
Q98T35             (  98) ERQRRNELKLSF   2
Q91631             (  16) ERLRVRDINEAF   3
Q8JI91             (  95) ERQRRNELKLSF   2
Q98SF2             (  53) ERNRVKLVNLGF   4
Q90467             (  15) EKRRRDRINQSL   2
Q8QGQ7             ( 101) EKRRRDKMNNLI   3
Q98SK3             (  54) ERRRRNKMTQYI   4
O12943             (  54) ERNRVRLVNLGF   4
Q98T09             (  92) ERQRRNELKLSF   2
O42448             (   5) SPVRSFRKNSSN  55
O73624             ( 104) EKMRMRKVSSAL   6
Q8JH08             (  94) ERQRRNELKLSF   2
Q98SJ5             (   9) GRTRREKENSEF  11
Q90Y91             (  28) SKRHRDRLNSEL   6
Q90X15             (  55) SRLRALVPTLPR  25
Q90692             (   9) ARTRREKENSEF   5
Q98T33             (  98) ERQRRNELKLSF   2
Q98T44             (  94) ERQRRNELKLSF   2
Q9W631             ( 196) ERLRVRDINEAF   3
Q8QFW6             ( 242) RRARRLDPSEGT  12
Q98SZ8             (  94) ERQRRNELKLSF   2
Q9W6C7             (  87) ERSRMHGLNDAL   3
Q8JI79             (  94) ERQRRNELKLSF   2
Q8JIA2             (  98) ERQRRNELKLSF   2
Q8JI97             (  95) ERQRRNELKLSF   2
Q9IAJ4             (  96) EKLRMRDLTKAL   4
Q98T41             (  94) ERQRRNELKLSF   2
Q98T03             (  94) ERQRRNELKLSF   2
Q9PTE4             ( 114) ERQRTQSLNDAF   3
Q98T29             (  94) ERQRRNELKLSF   2
Q8JI96             (  95) ERQRRNELKLSF   2
Q8JHA0             (  48) ERRRMQGLNTAF   3
Q91557             (  53) ERNRVKLVNLGF   4
Q8JH18             (  94) ERQRRNELKLSF   2
Q90WR7             ( 310) EKRYRSSINDKI   6
Q8JI81             (  94) ERQRRNELKLSF   2
Q90X20             (  26) ERRRRNKMTAYI   4
Q98T21             (  94) ERQRRNELKLSF   2
Q8UV03             ( 101) ERQRRNELKLSF   2
Q8JI98             (  95) ERQRRNELKLSF   2
Q90X22             (  60) ERKREKPVFESK  25
Q8QGM5             (  87) ERRRRNKMTQYI   4
Q8JIA1             (  98) ERQRRNELKLSF   2
Q98T25             (  94) ERQRRNELKLSF   2
Q9DDS7             ( 181) EHLRTNAVDCHT  35
Q98T37             (  98) ERQRRNELKLSF   2
Q9I8A9             (  26) ARCRRSNESEVF   7
Q8JI83             (  94) ERQRRNELKLSF   2
Q90260             (  75) ERNRVKQVNMGF   8
Q9DFB3             (  23) ERRRTQSINSAF   3
Q8JI87             (  95) ERQRRNELKLSF   2
Q8JIG1             (  83) EKRRRDKMNSFI   4
Q9DG11             (  72) ERRRRNKMTQYI   4
Q9PSH0             (  84) ERNRVKLVNMGF   8
Q8JH14             (  94) ERQRRNELKLSF   2
P79831             (  74) ERRRRNKMTAYI   4
Q9PUA3             (  34) EKRRRDQFNILI   5
Q98SZ2             (  94) ERQRRNELKLSF   2
Q8UV06             ( 101) ERQRRNELKLSF   2
Q9PWC2             ( 208) ERRRRFNINDRI   3
Q9DDU6             (   9) AKTRREKENGEF   6
Q91960             (  26) ERGRLKKINEAF   6
Q98SZ1             (  94) ERQRRNELKLSF   2
Q8JH11             (  94) ERQRRNELKLSF   2
Q9PTE3             (  86) ERQRTQSLNEAF   3
Q8JI86             (  95) ERQRRNELKLSF   2
Q90W03             (  28) SKRHRDRLNSEL   6
Q8QGE1             ( 119) ERRRLSKVNDAF   2
Q90764             ( 109) ERNRVKLVNLGF   4
Q9IAU1             (  42) EKRRRDKMNNLI   3
Q8QH97             ( 102) ERQRRNELKLSF   2
Q98T17             (  94) ERQRRNELKLSF   2
Q8JH20             (  94) ERQRRNELKLSF   2
Q98T46             (  94) ERQRRNELKLSF   2
Q9PWD7             (  62) ERRRRRRTTAKY   7
Q8QGI4             (  91) ERKRMHDLNIAM   5
Q8JH35             ( 105) ERSRMHGLNDAL   3
O73687             ( 193) ERWRQQNVNGAF   7
Q9DDQ8             ( 102) ERGRMHGLNDAL   7
Q9I9K1             (  22) ERRRRERMNRSL   3
Q8JH06             (  94) ERQRRNELKLSF   2
Q9DE55             (  76) ERRRLKKVNHAF   4
Q9W6B8             (  29) ERNRMHGLNAAL   4
Q98T07             (  94) ERQRRNELKLSF   2
Q8UUZ8             ( 101) ERQRRNELKLSF   2
O13125             (  42) ERRRMQGLNTAF   3
Q98SF1             (  28) ERNRVKLVNMGF   8
Q98T05             (  94) ERQRRNELKLSF   2
Q8QH98             ( 101) ERQRRNELKLSF   2
Q98T11             (  94) ERQRRNELKLSF   2
Q8JH01             (  94) ERQRRNELKLSF   2
Q8UVC4             ( 107) EKRRLKKVNEAF   2
Q98SZ6             (  94) ERQRRNELKLSF   2
Q98SZ3             (  94) ERQRRNELKLSF   2
Q8JI89             (  95) ERQRRNELKLSF   2
Q9PTN9             (   8) EKMRRDRINNSI   5
Q98SZ7             (  94) ERQRRNELKLSF   2
Q8JH15             (  94) ERQRRNELKLSF   2
Q9W690             ( 118) EKLRMRAIAEAL   4
Q8JH21             (  94) ERQRRNELKLSF   2
Q8UVC5             (  76) ERRRLKKVNHAF   4
Q8JI90             (  95) ERQRRNELKLSF   2
Q92001             ( 101) EKRRLKKVNEAF   2
Q98T30             (  94) ERQRRNELKLSF   2
Q9DGA9             (  37) ERKRMQGLNTAF   3
Q8JH02             (  94) ERQRRNELKLSF   2
Q8JH07             (  94) ERQRRNELKLSF   2
Q90YI8             ( 213) ERWRQQNVNGAF   7
Q98T32             (  94) ERQRRNELKLSF   2
Q8JI82             (  94) ERQRRNELKLSF   2
O57452             (   4) GRKRRKPVQRAL  24
Q98SS8             (  93) DRRRLIKINDAF   5
Q8QGM4             (  23) ARCRRSKETEVF   7
Q9W7C6             (  23) ARCRRSKETEVF   7
Q90259             (  87) ERNRVKLVNNGF   4
Q90465             (  25) EKKRRARINKCL   4
Q90ZK9             (  76) ERRRLKKVNHAF   4
Q98T27             (  94) ERQRRNELKLSF   2
Q98T10             (  94) ERQRRNELKLSF   2
Q98T23             (  94) ERQRRNELKLSF   2
Q9I9C9             ( 186) ERWRQQNVNGAF   7
Q8JIX7             ( 107) EKRRLKKVNEAF   2
Q9YIB9             (  26) ARCRRSKESEVF   7
Q8UV00             ( 101) ERQRRNELKLSF   2
Q9I8H6             (  93) EKRYRSSINDKI   6
Q8JI78             (  95) ERQRRNELKLSF   2
Q9DF73             (  22) ERRRRERMNRSL   3
Q8UV01             ( 101) ERQRRNELKLSF   2
Q8UV02             ( 101) ERQRRNELKLSF   2
Q90Y06             ( 207) ERWRQQNVNGAF   7
Q98SN3             (  98) ERRRRNKMTAYI   4
Q9YH15             (  79) ERIRVEAFNLAF   6
Q8JH19             (  94) ERQRRNELKLSF   2
Q9DG35             (   2) EKRRRDKMNSFI   4
Q8QHA0             ( 101) ERQRRNELKLSF   2
Q8JH13             (  94) ERQRRNELKLSF   2
O13150             (  92) ERNRVKQVNMGF   8
Q9W6C6             (  97) ERNRMHGLNNAL   4
Q90X14             (   7) VRSVRSCYEAVC  24
Q8JIA4             (  98) ERQRRNELKLSF   2
Q8JIA3             (  98) ERQRRNELKLSF   2
Q9IB70             (  96) EKLRMRDLTKAL   4
Q98SZ5             (  94) ERQRRNELKLSF   2
Q8JI92             (  95) ERQRRNELKLSF   2
Q8QG50             (  92) ERRRLKKVNQAF   3
Q8UV04             ( 101) ERQRRNELKLSF   2
Q9YHW4             (  71) ERRRRNKMTQYI   4
Q98T18             (  94) ERQRRNELKLSF   2
Q98T22             (  94) ERQRRNELKLSF   2
Q9IB69             (  75) EKLRMRDLTKAL   4
Q91959             (  26) ERRRLKKVNQAF   3
Q9I9H3             (  76) ERRRLKKVNHAF   4
Q9IAS2             (  87) ERRRRNKMTQYI   4
Q90Z13             (  52) EKMRRDRINSSI   5
Q91635             (  43) EKRRRARINESL   2
Q9I934             (  23) ERKRRDHIKDSF   3
Q9I9L0             (  57) EKRRRDRINNSL   2
Q90575             ( 110) ERNRVKLVNLGF   4
Q8JI88             (  95) ERQRRNELKLSF   2
Q9PTR9             (  87) ERNRMHNLNAAL   3
O73623             ( 104) EKMRMRNLSSAL   6
Q8JFY8             (  95) ERQRRNELKLSF   2
Q8JH00             (  94) ERQRRNELKLSF   2
Q98T31             (  94) ERQRRNELKLSF   2
Q8JGZ9             (  94) ERQRRNELKLSF   2
Q98T20             (  94) ERQRRNELKLSF   2
O57598             (  48) ERRRMQGLNTAF   3
Q9PRF6             (  35) ERNRVKQVNMGF   8
Q8UV08             ( 101) ERQRRNELKLSF   2
O93493             (  76) ERRRLKKVNHAF   4
Q8JI95             (  95) ERQRRNELKLSF   2
Q98T47             (  94) ERQRRNELKLSF   2
Q9DG13             (  87) ERRRRNKMTQYI   4
Q9I8H7             (  89) EKRYRSSINDKI   6
Q90491             ( 497) ERLRVRDINEAF   3
O93492             (  93) ERRRLSKVNDAF   2
Q98T01             (  94) ERQRRNELKLSF   2
Q8JH10             (  94) ERQRRNELKLSF   2
O93507             ( 194) ERWRQQNVNGAF   7
Q8UV07             ( 101) ERQRRNELKLSF   2
Q8UV10             ( 101) ERQRRNELKLSF   2
Q8JH05             (  94) ERQRRNELKLSF   2
Q98T28             (  94) ERQRRNELKLSF   2
Q9DGD0             ( 315) ERQRRNELKLSF   2
Q90ZM5             ( 308) EKRYRSSINDKI   6
Q98SH5             ( 185) EKRYRSSINDKI   6
Q98TI2             (  60) VRQVTSRANLPL  12
Q9I9D4             (  19) ERRRLSKVNDAF   2
Q98T14             (  94) ERQRRNELKLSF   2
Q9DF72             (  21) EKKRRDRINQRL   3
Q8JI85             (  95) ERQRRNELKLSF   2
Q9PVG4             ( 105) ERQRTQSLNEAF   3
Q8QGE0             ( 104) ERRRLSRVNDAF   3
Q9DDW0             (  76) ERRRLKKVNHAF   4
Q98SH6             (  76) EKRYRSSINDKI   6
Q98SW8             (  94) ERQRRNELKLSF   2
O73823             ( 271) ERWRQQNVNGAF   7
Q91151             (  78) ERRRLKKINEAF   2
Q98T42             (  94) ERQRRNELKLSF   2
Q8QGE5             ( 195) ERRRRFNINDRI   3
Q91608             (  61) ERLRVRDINEAF   3
Q8JGZ7             (  94) ERQRRNELKLSF   2
Q8QHA2             ( 101) ERQRRNELKLSF   2
Q98T08             (  94) ERQRRNELKLSF   2
Q91421             ( 319) ERQRRSEVKLNF  12
Q98SZ4             (  94) ERQRRNELKLSF   2
Q8UUX7             ( 101) EKRRLKKVNEAF   2
Q8JI99             (  95) ERQRRNELKLSF   2
Q8UW72             (  22) EKRRRERINNSL   2
Q8QH99             ( 101) ERQRRNELKLSF   2
Q9DEU7             (  28) EKKRRERINSSL   2
Q8JH09             (  94) ERQRRNELKLSF   2
Q8JH22             (  94) ERQRRNELKLSF   2
Q8QGQ3             (  50) SKRHRDRMNEVL   6
Q8UV05             ( 101) ERQRRNELKLSF   2
Q98T26             (  94) ERQRRNELKLSF   2
Q8UUX8             ( 100) EKRRLKKVNEAF   2
Q9YH81             (  51) ERNRMHHLNAAL   4
Q9DF41             (  43) EKRRRARINESL   2
O93491             ( 111) EKRRLKKVNEAF   2
Q91607             (  42) ERLRVRDINEAF   3
Q98TY7             (  93) ERRRLSKVNDAF   2
Q8JHA1             (  16) ERRRMHGLNHAF   4
Q9IBH7             ( 268) ERRRRFNINDRI   3
Q9PSG9             (  29) ERNRVKLVNMGF   8
Q8JI84             (  94) ERQRRNELKLSF   2
Q90Z14             (  25) EKMRRDRINNSI   5
Q9DG12             (  87) ERRRRNKMTQYI   4
Q90463             (  21) EKKRRDRINQRL   3
Q90Z12             (  43) EKRRRARINESL   2
Q8QH96             ( 105) ERQRRNELKLSF   2
Q9DG26             ( 111) EKRRLKKVNEAF   2
Q8JI80             (  94) ERQRRNELKLSF   2
Q90ZL0             ( 105) ERRRLKKINEAF   2
Q90468             ( 107) EKRRRARINESL   2
Q90VV1             (  43) EKRRRARINESL   2
Q9YHA3             (  73) ERDRTQSVNTAF   6
Q9PWP1             (  52) ERNRMHHLNAAL   4
Q91791             ( 104) ERRRLSKVNEAF   2
Q8UW74             (  22) EKRRRERINNSL   2
P70050             (  90) ERNRMHNLNSAL   3
P70051             (  94) ERNRMHHLNYAL   7
O42202             ( 105) ERNRMHGLNDAL   3
Q90ZL1             (  79) EKLRMRSLAEAL   4
Q9I879             (  85) EKRRRDKMNSFI   4
Q9PTS0             (  88) ERIRVEAFNLAF   6
Q90621             ( 188) ERLRVRDINEAF   3
Q91794             ( 255) ERQRRNELKLSF   2
Q90WI5             ( 103) EKRRLKKVNEAF   2
Q9DEQ9             ( 104) EKLRMRTLADAL   6
O73871             ( 262) ERRRRFNINDRI   3
O93439             (  76) EKLRMRRLAQAM   5
Q9IAU0             ( 179) ERRRRFNINDRI   3
Q8AXV6             (  57) EKRRRDRINNSL   2
Q8AXV5             (  52) EKRRRDRINHSL   3
Q8AXF5             (  18) EKKRRDQFNVLI   6
Q8AXF3             (  94) ERQRRNELKLSF   2
Q8AXF2             (  94) ERQRRNELKLSF   2
Q8AXF1             (  94) ERQRRNELKLSF   2
Q8AXF0             (  94) ERQRRNELKLSF   2
Q8AXE9             (  94) ERQRRNELKLSF   2
Q8AXE8             (  94) ERQRRNELKLSF   2
Q8AXE7             (  94) ERQRRNELKLSF   2
Q8AXE6             (  94) ERQRRNELKLSF   2
Q8AXE5             (  94) ERQRRNELKLSF   2
Q8AXE4             (  94) ERQRRNELKLSF   2
Q8AXE3             (  94) ERQRRNELKLSF   2
Q8AXE2             (  94) ERQRRNELKLSF   2
Q8AX95             (  95) ERKRMFSLNEAF   3
Q8AX94             (  97) ERQRTQSLNEAF   3
Q8AWF3             ( 100) ERRRLKKINEAF   2
Q8AW97             (  87) ERRRLGKVNDAF   4
Q8AW96             (  19) EKRRLKKVNEAF   2
Q8AW52             (  37) ERKRMQGLNTAF   3
Q8AVZ1             ( 348) ERQRRNELKLSF   2
Q8AVZ0             ( 104) ERRRLSKVNEAF   2
Q8AVU4             (  43) EKRRRARINESL   2
Q8AV42             ( 101) ERQRRNELKLSF   2
Q8AV41             ( 101) ERQRRNELKRSF   2
Q8AV40             ( 101) ERQRRNELKLSF   2
Q8AV39             ( 101) ERQRRNELKLSF   2
Q8AV38             ( 106) ERQRRNELKLSF   2
Q8AV37             ( 101) ERQRRNELKLSF   2
Q8AV36             ( 101) ERQRRNELKLSF   2
Q8AV35             ( 101) ERQRRNELKLSF   2
Q8AV34             (  97) ERQRRNELKLSF   2
Q8AV33             ( 101) ERQRRNELKLSF   2
Q8AV32             ( 101) ERQRRNELKLSF   2
Q995G8             ( 494) ERQRRNELKLSF   2
Q00089             ( 345) ERQRRNELKLSF   2
Q67004             ( 290) ERQRRNELKRSF   2
Q85523             ( 365) ERQRRNELKRSF   2
O56221             ( 799) ERQRRNELKLRF   2
Q90AP6             (  45) RKSVRIGPGQVF  12
Q85456             ( 347) ERQRRNELKLSF   2
//
ID   HLH_basic; BLOCK
AC   IPB001092B; distance from previous block=(-2,7069)
DE   Basic helix-loop-helix dimerization domain bHLH
BL   KYI;  width=15; seqs=1865; 99.5%=1032; strength=991
DEI_DROME|P41894   ( 136) KLTKITTLRLAMKYI   4

ESC1_SCHPO|Q04635  ( 368) KSSKWGLLTRAIQYI  13

HFR1_ARATH|Q9FE22  ( 166) KTDKVSVLDKTIEYM   3

INO4_YEAST|P13902  (  80) SRSELIIYLKSLSYL  17

MXI1_RAT|O09015    ( 102) RHTTLGLLNKAKAHI   8

MYCM_HUMAN|P12525  ( 309) RVSKVMILVKATEYL   6

NUC1_NEUCR|P20824  ( 740) PNSKASTVEMAIEYI   5

PHO4_YEAST|P07270  ( 289) APSKATTVEAACRYI   5

RTG1_YEAST|P32607  (  79) KPNKGQILTQAVEYI   5

SIMA_DROME|Q24167  ( 108) QLDKASVMRITIAFL   4

TCL5_HUMAN|Q9UL49  ( 385) ETDKATTLQWTTAFL  21

TT8_ARATH|Q9FT81   ( 391) KMDKVSILGDTIAYV   3

TWST_CAEEL|Q11094  (  54) KMSKIHTLRIATDYI  13

TYE7_YEAST|P33122  ( 248) KLNKSMILEKAVDYI   4

WS14_CAEEL|P41846  ( 900) VDSKTSLETFFDRYV  16

YAWC_SCHPO|Q10186  ( 119) EKNKGSILQRTAQYI   7

YNP2_CAEEL|P34555  (  39) RVSKLRILNAAITYI   9

YRY3_CAEEL|Q10007  ( 208) RISKVDTLRLAIRYI   3

Q58467             ( 197) YLLMAVVMIIIYGYI  17

Q10466             (5221) LKIKKADLKDKGEYV  26

Q03082             ( 251) SRFRELILGGVTQYL  14

Q60761             ( 225) AGKKHLIFGEPEEFI  18

ARLC_MAIZE|P13526  ( 444) RVNKASILAETIAYL   3
ARRS_MAIZE|P13027  ( 446) RVNKASILAETIAYL   3

ARN2_HUMAN|Q9HBZ2  ( 125) QELKHLILEAADGFL  11
ARN2_MOUSE|Q61324  ( 136) QELKHLILEAADGFL  11
ARNT_DROME|O15945  (  86) QELKHLILEAADGFL  11
ARNT_HUMAN|P27540  ( 162) QELKHLILEAADGFL  11
ARNT_MOUSE|P53762  ( 162) QELKHLILEAADGFL  11
ARNT_RABIT|O02748  ( 162) QELKHLILEAADGFL  11
ARNT_RAT|P41739    ( 162) QELKHLILEAADGFL  11

ASH1_HUMAN|P50553  ( 153) KMSKVETLRSAVEYI   2
ASH1_MOUSE|Q02067  ( 148) KMSKVETLRSAVQYI   2
ASH1_RAT|P19359    ( 150) KMSKVETLRSAVEYI   2
ASH1_XENLA|Q06234  ( 116) KMSKVETLRSAVEYI   2
ASH2_HUMAN|Q99929  (  85) KLSKVETLRSAVEYI   2
ASH2_MOUSE|O35885  ( 153) KLSKVETLRSAVEYI   2
ASH2_RAT|P19360    ( 153) KLSKVETLRSAVEYI   2
AST3_DROME|P09774  ( 128) KLSKVDTLRIAVEYI   2
AST4_DROME|P10084  ( 145) KISKVDTLRIAVEYI   4
AST5_DROME|P10083  (  73) KLSKVSTLKMAVEYI   2
AST8_DROME|P09775  ( 206) KLSKVETLRMAVEYI   2
O77028             ( 206) KLSKVETLRMAVEYI   2
O77026             (  73) KLSKVSTLKMAVEYI   2
Q24639             (  73) KLSKVSTLKMAVEYI   2
O77029             ( 133) KISKVDTLRIAVEYI   4
O77031             ( 145) KISKVDTLRIAVEYI   4
P91703             ( 152) KISKVDTLRIAVEYI   4
O77030             ( 127) KLSKVDTLRIAVEYI   2
O77032             ( 128) KLSKVDTLRIAVEYI   2

ASH3_HUMAN|Q9NQ33  ( 127) RLSKVETLRAAIKYI   2
ASH3_MOUSE|Q9JJR7  ( 127) RLSKVETLRAAIKYI   2

ATH1_HUMAN|Q92858  ( 194) KLSKYETLQMAQIYI   9
ATH1_MOUSE|P48985  ( 191) KLSKYETLQMAQIYI   9
ATO_DROME|P48987   ( 290) QLSKHETLQMAQTYI   8
LI32_CAEEL|Q10574  (  36) KLSKFETLQMAQKYI   9
ROI_DROME|Q9Y0A7   ( 173) RLSKYETLQMAQAYI   7

BET3_MESAU|O09029  ( 265) KLSKIATLLLAKNYI   3
HAN1_CHICK|Q90691  ( 118) KLSKIKTLRLATSYI   3
HAN1_HUMAN|O96004  ( 129) KLSKIKTLRLATSYI   3
HAN1_MOUSE|Q64279  ( 129) KLSKIKTLRLATSYI   3
HAN1_RAT|P97832    ( 129) KLSKIKTLRLATSYI   3
HAN1_SHEEP|Q28555  ( 135) KLSKIKTLRLATSYI   3
HAN1_XENLA|O73615  ( 115) KLSKIKTLRLATSYI   3
HAN2_BRARE|P57102  ( 125) KLSKIKTLRLATSYI   3
HAN2_CHICK|Q90690  ( 133) KLSKIKTLRLATSYI   3
HAN2_HUMAN|O95300  ( 134) KLSKIKTLRLATSYI   3
HAN2_MOUSE|Q61039  ( 134) KLSKIKTLRLATSYI   3
HAN2_XENLA|P57101  ( 127) KLSKIKTLRLATSYI   3
HEN1_HUMAN|Q02575  ( 110) KLSKIEILRLAICYI   4
HEN1_MOUSE|Q02576  ( 110) KLSKIEILRLAICYI   4
HEN2_HUMAN|Q02577  ( 112) KLSKIEILRLAICYI   4
HEN2_MOUSE|Q64221  ( 112) KLSKIEILRLAICYI   4
LYL1_HUMAN|P12980  ( 172) KLSKNEVLRLAMKYI   4
LYL1_MOUSE|P27792  ( 184) KLSKNEVLRLAMKYI   4
MUSC_HUMAN|O60682  ( 142) KLSKLDTLRLASSYI   3
MUSC_MOUSE|O88940  ( 137) KLSKLDTLRLASSYI   3
NDF2_HUMAN|Q15784  ( 156) KLSKIETLRLAKNYI   2
NDF2_MOUSE|Q62414  ( 157) KLSKIETLRLAKNYI   2
NDF2_RAT|Q63689    ( 156) KLSKIETLRLAKNYI   2
NDF4_HUMAN|Q9HD90  ( 122) KLSKIETLRLARNYI   3
NDF4_MOUSE|O09105  ( 122) KLSKIETLRLARNYI   3
NDF4_XENLA|P79920  ( 113) KLSKIETLRLARNYI   3
NDF6_HUMAN|Q96NK8  ( 129) KLSKIETLRLAKNYI   2
NDF6_MOUSE|P48986  ( 129) KLSKIETLRLAKNYI   2
NDFM_CHICK|P79766  ( 122) KLSKIETLRLARNYI   3
NGN1_BRARE|O42606  ( 105) KLTKIETLRFAHNYI   5
NGN1_HUMAN|Q92886  ( 127) KLTKIETLRFAYNYI   6
NGN1_MOUSE|P70660  ( 128) KLTKIETLRFAYNYI   6
NGN1_RAT|P70595    ( 128) KLTKIETLRFAYNYI   6
NGN2_HUMAN|Q9H2A3  ( 125) KLTKIETLRFAHNYI   5
NGN2_MOUSE|P70447  ( 147) KLTKIETLRFAHNYI   5
NGN3_HUMAN|Q9Y4Z2  ( 118) KLTKIETLRFAHNYI   5
NGN3_MOUSE|P70661  ( 118) KLTKIETLRFAHNYI   5
OLG1_HUMAN|Q8TAK6  ( 147) KLSKIATLLLARNYI   4
OLG1_MOUSE|Q9JKN5  ( 136) KLSKIATLLLARNYI   4
OLG1_RAT|Q9WUQ3    ( 137) KLSKIATLLLARNYI   4
OLG2_CHICK|Q90XB3  ( 143) KLSKIATLLLARNYI   4
OLG2_HUMAN|Q13516  ( 145) KLSKIATLLLARNYI   4
OLG2_MOUSE|Q9EQW6  ( 145) KLSKIATLLLARNYI   4
SCL_CHICK|P24899   ( 214) KLSKNEILRLAMKYI   4
SCX_CHICK|P59101   ( 102) KLSKIETLRLASSYI   3
SCX_MOUSE|Q64124   ( 113) KLSKIETLRLASSYI   3
TAL2_HUMAN|Q16559  (  37) KLSKNETLRLAMRYI   4
TAL2_MOUSE|Q62282  (  37) KLSKNETLRLAMRYI   4
TAL_HUMAN|P17542   ( 222) KLSKNEILRLAMKYI   4
TAL_MOUSE|P22091   ( 222) KLSKNEILRLAMKYI   4
TF15_CHICK|P79782  (  96) KLSKIETLRLASSYI   3
TF15_HUMAN|Q12870  ( 107) KLSKIETLRLASSYI   3
TF15_MESAU|Q60539  ( 105) KLSKIETLRLASSYI   3
TF15_MOUSE|Q60756  ( 105) KLSKIETLRLASSYI   3
TF21_HUMAN|O43680  ( 114) KLSKLDTLRLASSYI   3
TF21_MOUSE|O35437  ( 114) KLSKLDTLRLASSYI   3
TWST_DROME|P10627  ( 396) KLSKIQTLKLATRYI   2
TWST_HUMAN|Q15672  ( 142) KLSKIQTLKLAARYI   3
TWST_MOUSE|P26687  ( 146) KLSKIQTLKLAARYI   3
TWST_XENLA|P13903  ( 106) KLSKIQTLKLASRYI   3
YLB7_CAEEL|P46581  (  54) KLSKIETLRLARNYI   3
O96642             ( 129) KLSKIQTLKLAARYI   3

BHB3_MOUSE|Q99PV5  (  82) HLEKAVVLELTLKHL   4
BHB3_RAT|O35779    (  82) HLEKAVVLELTLKHL   4

CBF1_KLULA|P49379  ( 279) ETSKAAILSRAAEYI   5
CBF1_YEAST|P17106  ( 253) ESSKAAILARAAEYI   6

DPN_DROME|Q26263   (  80) KLEKADILEMTVKHL   3
ESM3_DROME|Q01068  (  51) RLEKADILELTVDHM   3
ESM7_DROME|P13097  (  51) KFEKADILEVTVQHL   8
ESMB_DROME|Q01069  (  53) RLEKADILELTVEHM   3
ESMC_DROME|Q01070  (  55) RLEKADILELTVTHL   3
ESMD_DROME|Q01071  (  55) KLEKADILELTVNYL   2
HAIR_DROVI|P29303  (  77) KLEKADILEKTVKHL   3
HES1_CHICK|O57337  (  75) KLEKADILEMTVKHL   3
HES1_HUMAN|Q14469  (  74) KLEKADILEMTVKHL   3
HES1_MOUSE|P35428  (  74) KLEKADILEMTVKHL   3
HES1_RAT|Q04666    (  74) KLEKADILEMTVKHL   3
HES3_MOUSE|Q61657  (  32) KLEKADILELSVKYM   3
HES3_RAT|Q04667    (  32) KLEKADILELSVKYV   3
HES5_MOUSE|P70120  (  55) KLEKADILEMAVSYL   2
HES5_RAT|Q03062    (  55) KLEKADILEMAVSYL   2
HEY1_CANFA|Q9TSZ2  (  87) KLEKAEILQMTVDHL   2
HEY1_HUMAN|Q9Y5J3  (  87) KLEKAEILQMTVDHL   2
HEY1_MOUSE|Q9WV93  (  87) KLEKAEILQMTVDHL   2

ID4_HUMAN|P47928   (  87) KVSKVEILQHVIDYI   4
ID4_MOUSE|P41139   (  87) KVSKVEILQHVIDYI   4

ESM5_DROME|P13096  (  56) RMDKAEMLEAALVFM   6
ESM8_DROHY|Q07291  (  48) RMDKAEMLESAVVFM   5

HIFA_HUMAN|Q16665  (  53) HLDKASVMRLTISYL   4
HIFA_MOUSE|Q61221  (  53) HLDKASVMRLTISYL   4
PAS1_MOUSE|P97481  (  50) HLDKASIMRLAISFL   4
SIM1_HUMAN|P81133  (  36) QVDKASIIRLTTSYL   3
SIM1_MOUSE|Q61045  (  36) QLDKASIIRLTTSYL   3
SIM_DROME|P05709   (  36) QLDKASVIRLTTSYL   3
TRH_DROME|Q24119   ( 122) QLDKASIIRLTISYL   3

HTF4_MESAU|Q60420  ( 368) PQTKLLILHQAVAVI   6
HTF4_PAPHA|Q28772  (  91) PQTKLLILHQAVAVI   6
HTF4_XENLA|Q91605  (  83) PQTKLLILHQAVAVI   6
ITF2_CHICK|Q90683  (  43) PQTKLLILHQAVAVI   6
ITF2_RAT|Q62655    ( 361) PQTKLLILHQAVAVI   6
TFE2_MOUSE|P15806  ( 212) AQTKLLILQQAVQVI   5

ID3_HUMAN|Q02535   (  63) QLSQVEILQRVIDYI   4
ID3_MOUSE|P41133   (  63) QLSQVEILQRVIDYI   4
ID3_RAT|P41138     (  63) QLSQVEILQRVIDYI   4

MAX_BRARE|P52161   (  62) QASRAQILDKATEYI   3
MAX_CHICK|P52162   (  57) KASRAQILDKATEYI   2
MAX_HUMAN|P25912   (  57) KASRAQILDKATEYI   2
MAX_MOUSE|P28574   (  57) KASRAQILDKATEYI   2
MAX_RAT|P52164     (  57) KASRAQILDKATEYI   2
MAX_XENLA|Q07016   (  57) KASRAQILDKATEYI   2

MF25_XENLA|P16076  ( 130) RLPKVDILRNAISYI   2
MYF5_BOVIN|P17667  ( 117) RLPKVEILRNAIRYI   2
MYF5_CHICK|Q08856  ( 119) RLPKVEILRNAIRYI   2
MYF5_COTJA|P34061  ( 107) RLPKVEILRNAIRYI   2
MYF5_HUMAN|P13349  ( 117) RLPKVEILRNAIRYI   2
MYF5_MOUSE|P24699  ( 117) RLPKVEILRNAIRYI   2
MYF5_NOTVI|Q91154  ( 117) RLPKVEILRNAISYI   2
MYF5_XENLA|P24700  ( 117) RLPKVEILRNAIQYI   2
MYF6_CHICK|Q01795  ( 127) RLPKVEILRSAISYI   2
MYF6_HUMAN|P23409  ( 127) RLPKVEILRSAISYI   2
MYF6_MOUSE|P15375  ( 127) RLPKVEILRSAISYI   2
MYF6_RAT|P19335    ( 127) RLPKVEILRSAINYI   2
MYF6_XENLA|Q92020  ( 125) RLPKVEILRSAINYI   2
MYO1_ONCMY|Q91205  ( 118) RLPKVDILRNAISYI   2
MYO2_ONCMY|Q91206  ( 118) RLPKVEILRNAISYI   2
MYOD_BRARE|Q90477  ( 118) RLPKVEILRNAISYI   2
MYOD_CAEBR|Q17295  ( 194) RLPKVEILRSAIDYI   2
MYOD_CHICK|P16075  ( 134) RLPKVEILRNAIRYI   2
MYOD_COTJA|P21572  ( 135) RLPKVEILRNAIRYI   2
MYOD_DROME|P22816  ( 195) RLPKVEILRNAIEYI   2
MYOD_HUMAN|P15172  ( 143) RLPKVEILRNAIRYI   2
MYOD_MOUSE|P10085  ( 143) RLPKVEILRNAIRYI   2
MYOD_PIG|P49811    ( 143) RLPKVEILRNAIRYI   2
MYOD_RAT|Q02346    ( 143) RLPKVEILRNAIRYI   2
MYOD_SHEEP|P29331  ( 143) RLPKVEILRNAIRYI   2
MYOD_XENLA|P13904  ( 129) RLPKVEILRNAIRYI   2
MYOG_CHICK|P17920  ( 116) RLPKVEILRSAIQYI   2
MYOG_COTJA|P34060  ( 116) RLPKVEILRSSIQYT   5
MYOG_HUMAN|P15173  ( 115) RLPKVEILRSAIQYI   2
MYOG_MOUSE|P12979  ( 115) RLPKVEILRSAIQYI   2
MYOG_PIG|P49812    ( 115) RLPKVEILRSAIQYI   2
MYOG_RAT|P20428    ( 115) RLPKVEILRSAIQYI   2
SUM1_LYTVA|Q00492  ( 146) RLPKVEILRNAIEYI   2

MITF_HUMAN|O75030  ( 347) RWNKGTILKASVDYI   5
MITF_MOUSE|Q08874  ( 347) RWNKGTILKASVDYI   5
MITF_RAT|O88368    (  56) RWNKGTILKASVDYI   5
TFE3_HUMAN|P19532  ( 382) RWNKGTILKASVDYI   5
TFE3_MOUSE|Q64092  ( 255) RWNKGTILKASVDYI   5
TFEB_HUMAN|P19484  ( 271) RWNKGTILKASVDYI   5
TFEB_MOUSE|Q9R210  ( 270) RWNKGTILKASVDYI   5

MLX_HUMAN|Q9UH92   ( 170) KLSKAIVLQKTIDYI   3
MLX_MOUSE|O08609   ( 170) KLSKAIVLQKTIDYI   3

MNT_HUMAN|Q99583   ( 254) KTSNLSVLRTALRYI   7
MNT_MOUSE|O08789   ( 256) KTSNLSVLRTALRYI   7

MYC1_XENLA|P06171  ( 370) KAPKVVILKKATEYA   3
MYC2_CYPCA|Q90342  ( 352) KAAKVVILKKATECI   5
MYC2_MARMO|P20389  ( 406) KAAKVVILKKACEYV   3
MYC2_SPEBE|Q64210  ( 406) KAAKVVILKKACEYV   3
MYC2_XENLA|P15171  ( 371) KAPKVVILKKATEYA   3
MYCL_HUMAN|P12524  ( 316) KAPKVVILSKALEYL   3
MYCL_MOUSE|P10166  ( 320) KAPKVVILSKALEYL   3
MYCN_CHICK|P18444  ( 393) KAAKVVILKKATEYV   2
MYCN_HUMAN|P04198  ( 416) KAAKVVILKKATEYV   2
MYCN_MARMO|Q61976  ( 412) KAAKVVILKKATEYV   2
MYCN_MOUSE|P03966  ( 414) KAAKVVILKKATEYV   2
MYCN_RAT|Q63379    ( 414) KAAKVVILKKATEYV   2
MYCN_SERCA|P26014  ( 379) KAAKVVILKKATEYV   2
MYCN_XENLA|P24793  ( 389) KAAKVVILKKATEYV   2
MYCS_MOUSE|Q9Z304  ( 383) KAAKVVILKKATEYI   2
MYCS_RAT|P23999    ( 381) KAAKVVILKKATEYI   2
MYC_ASTVU|Q17103   ( 356) RAAKVVILKKATDYV   2
MYC_AVIME|P06647   ( 373) KAPKVVILKRATEYV   2
MYC_BRARE|P52160   ( 357) KAAKVVILKKATECI   5
MYC_CALJA|P49032   ( 388) KAPKVVILKKATTYI   2
MYC_CANFA|Q28350   ( 389) KAPKVVILKKATAYI   2
MYC_CARAU|P49709   ( 350) KAAKVVILKKATECI   5
MYC_CHICK|P01109   ( 366) KAPKVVILKKATEYV   2
MYC_FELCA|P06877   ( 389) KAPKVVILKKATAYI   2
MYC_FLVTT|P21438   ( 389) KAPKVVILKKATAYI   2
MYC_HUMAN|P01106   ( 389) KAPKVVILKKATAYI   2
MYC_HYLLA|P49033   ( 389) KAPKVVILKKATAYI   2
MYC_MARMO|P22555   ( 389) KAPKVIILKKATAYI   3
MYC_MOUSE|P01108   ( 389) KAPKVVILKKATAYI   2
MYC_ONCMY|P06646   ( 359) KAAKVVILKKATECI   5
MYC_PANTR|P23583   ( 389) KAPKVVILKKATAYI   2
MYC_PIG|Q29031     ( 389) KAPKVVILKKATAYI   2
MYC_RAT|P09416     ( 389) KAPKVVILKKATAYI   2
MYC_SHEEP|Q28566   ( 389) KAPKVVILKKATAYI   2
Q91446             ( 141) KAPKVVILKKATEYV   2

MYCL_XENLA|Q05404  ( 296) KTPKVVVLSKATEFL   3
MYCM_XENLA|P35805  ( 296) KTPKVVVLSKATEFL   3

NPA1_HUMAN|Q99742  (  81) QLDKASIVRLSVTYL   4
NPA1_MOUSE|P97459  (  81) QLDKASIVRLSVTYL   4

PIF3_ARATH|O80536  ( 375) KVDKASMLDEAIEYL   2
PIF4_ARATH|Q8W2F3  ( 289) KTDKASILDEAIDYL   2

TAP4_HUMAN|Q01664  (  82) KLSKAAILQQTAEYI   3
YMH7_CAEEL|P34474  (  95) KLSKAAILQQTADMV   5

USF1_HUMAN|P22415  ( 237) GQSKGGILSKACDYI   6
USF1_MOUSE|Q61069  ( 237) GQSKGGILSKACDYI   6
USF1_RABIT|O02818  ( 237) GQSKGGILSKACDYI   6
USF1_XENBO|Q07957  ( 234) GQSKGGILSKACDYI   6
USF2_HUMAN|Q15853  ( 273) GASKGGILSKACDYI   5
USF2_MOUSE|Q64705  ( 273) GASKGGILSKACDYI   5
USF2_RAT|Q63665    ( 218) GASKGGILSKACDYI   5
USF_STRPU|Q07956   ( 228) GQSKGGILTKTCDYI   6

WS14_HUMAN|Q9NP71  ( 686) KVSKATTLQKTAEYI   3
WS14_MOUSE|Q99MZ3  ( 698) KVSKATTLQKTAEYI   3

AHR_MOUSE|P30561   (  62) KLDKLSVLRLSVSYL   2
AHR_RABIT|O02747   (  63) KLDKLSVLRLSVSYL   2
AHR_RAT|P41738     (  62) KLDKLSVLRLSVTYL   3
BHB2_HUMAN|O14503  (  90) HLEKAVVLELTLKHV   4
BHB2_MOUSE|O35185  (  90) HLEKAVVLELTLKHV   4
BHB2_RAT|O35780    (  90) HLEKAVVLELTLKHV   4
BHB3_HUMAN|Q9C0J9  (  82) HLEKAVVLELTLKHL   4
BMAL_HUMAN|O00327  (  65) KLDKLTVLRMAVQHM   3
CLOC_DROME|O61735  (  44) KMDKSTVLKSTIAFL   4
COE1_HUMAN|Q9UH73  ( 367) RLPKEVILKRAADLV   6
COE1_MOUSE|Q07802  ( 372) RLPKEVILKRAADLV   6
COE1_RAT|Q63398    ( 365) RLPKEVILKRAADLV   6
COE2_BRARE|O93375  ( 370) KLAKEMLLKRAADVV   7
COE2_MOUSE|O08792  ( 363) RLAKEMLLKRAADLV   9
COE2_XENLA|O73741  ( 364) RLAKEMLLKRAADLV   9
COE3_HUMAN|Q9H4W6  ( 373) RLPKEVLLKRAADLV   6
COE3_MOUSE|O08791  ( 373) RLPKEVLLKRAADLV   6
COE3_XENLA|O73742  ( 374) RLPKEVLLKRAADLV   6
COE4_HUMAN|Q9BQW3  ( 466) RLPKEVLLKRAADLA   7
COLL_DROME|P56721  ( 410) KLQKEIILKRAADLV  34
CYCL_DROME|O61734  (  66) KLDKLTVLRMAVQHL   2
DA_DROME|P11420    ( 590) PQTKLGILNMAVEVI   6
ESM8_DROME|P13098  (  48) RMDKAEMLESAVIFM   6
HAIR_DROME|P14003  (  71) KLEKADILEKTVKHL   3
HAN1_RABIT|P57100  ( 129) KLSKIKTLRLATSYI   3
HES2_HUMAN|Q9Y543  (  53) KLEKADVLEMTVRFL   3
HES2_MOUSE|O54792  (  53) KLEKADILEMTVRFL   3
HES2_RAT|P35429    (  53) KLEKADILEMTVRFL   3
HTF4_CHICK|P30985  ( 588) PQTKLLILHQAVAVI   6
HTF4_HUMAN|Q99081  ( 613) PQTKLLILHQAVAVI   6
HTF4_MOUSE|Q61286  ( 637) PQTKLLILHQAVAVI   6
HTF4_RAT|P51514    ( 638) PQTKLLILHQAVAVI   6
INO2_YEAST|P26798  ( 273) RIPKHILLTCVMNDI  20
ITF2_CANFA|P15881  ( 575) PQTKLLILHQAVAVI   6
ITF2_HUMAN|P15884  ( 600) PQTKLLILHQAVAVI   6
ITF2_MOUSE|Q60722  ( 603) PQTKLLILHQAVAVI   6
MAD4_MOUSE|Q60948  (  88) RHTTLSLLKRAKMHI  14
MAD_HUMAN|Q05195   (  91) RHTTLSLLTKAKLHI   8
MAD_MOUSE|P50538   (  90) RHTTLSLLTKAKLHI   8
MXI1_BRARE|P50541  ( 111) RHTTLGLLNKAKAHI   8
MXI1_HUMAN|P50539  ( 102) RHTTLGLLNKAKAHI   8
MXI1_MOUSE|P50540  ( 102) RHTTLGLLNKAKAHI   8
MYC1_CYPCA|Q90341  ( 345) KAAKVVILKKATECI   5
MYC_AVIM2|P10395   ( 371) KAPKVVILKKATEYV   2
MYC_AVIMC|P01110   ( 372) KAPKVVILKKATEYV   2
MYC_AVIMD|P06295   ( 372) KAPKVGILKKATEYV   2
MYC_AVIOK|P12523   ( 366) KAPKVVILKKATEYV   2
MYOD_CAEEL|P22980  ( 189) RLPKVEILRSAIDYI   2
NCO2_MOUSE|Q61026  (  66) KPDKCAILKETVKQI   8
NCO2_RAT|Q9WUI9    (  66) KPDKCAILKETVKQI   8
NCO3_HUMAN|Q9Y6Q9  (  65) KPDKCAILKETVRQI   8
NCO3_MOUSE|O09000  (  66) KPDKCAILKETVRQI   8
NCO3_XENLA|O57539  (  67) KPDKCAILKETVRQI   8
NDF1_CHICK|P79765  ( 139) KLSKIETLRLAKNYI   2
NDF1_HUMAN|Q13562  ( 136) KLSKIETLRLAKNYI   2
NDF1_MESAU|Q60430  ( 135) KLSKIETLRLAKNYI   2
NDF1_MOUSE|Q60867  ( 136) KLSKIETLRLAKNYI   2
NDF1_RAT|Q64289    ( 136) KLSKIETLRLAKNYI   2
NDF1_XENLA|Q91616  ( 137) KLSKIETLRLAKNYI   2
NPA2_HUMAN|Q99743  (  42) KMDKTTVLEKVIGFL   4
NPA2_MOUSE|P97460  (  42) KMDKTTVLEKVIGFL   4
PAS1_HUMAN|Q99814  (  50) HLDKASIMRLAISFL   4
PHT1_HUMAN|Q9UMS5  ( 612) VVSSVFLLTLSIAFI  19
PHT1_MOUSE|Q9QZ09  ( 611) VVSSVFLLTLSIAFI  19
PHTF_DROME|Q9V9A8  ( 552) KKAQLSVLEIASCII  17
RTG3_YEAST|P38165  ( 327) KPNKGIILDRTVEYL   5
SIM2_HUMAN|Q14190  (  36) QLDKASIIRLTTSYL   3
SIM2_MOUSE|Q61079  (  36) QLDKASIIRLTTSYL   3
SRE1_MOUSE|Q9WTN3  ( 350) KLNKSAVLRKAIDYI   3
SRE1_PIG|O97676    ( 129) KLNKSAVLRKAIDYI   3
SRE1_RAT|P56720    ( 326) KLNKSAVLRKAIDYI   3
SRE2_CRIGR|Q60429  ( 361) KMHKSGVLRKAIDYI   9
SRE2_HUMAN|Q12772  ( 363) KMHKSGVLRKAIDYI   9
TAP_DROME|O16867   ( 189) KLTKIEILRFAHNYI   5
TFE2_HUMAN|P15923  ( 585) PQTKLLILHQAVSVI   6
TFE2_MESAU|P98180  ( 580) PQTKLLILHQAVAVI   6
TFE2_RAT|P21677    ( 580) PQTKLLILHQAVAVI   6
TFE2_XENLA|Q01978  ( 591) PQTKLLILHQAVSVI   6
UNC3_CAEEL|Q93705  ( 383) RLPKDQILKRAAELA  14
O29330             ( 639) KGSKTLIFDSVERAA  17
O29978             ( 344) VVAKNLMLVIAAGYI   9
O28341             ( 653) VINAVNVLGKVTKYA  13
O57993             (  82) PVERSGVLIESADVL   7
O58295             ( 582) TVSKNETITKTITMT  11
O58924             (  58) YFERIGVMEASRIVV  14
Q9YFX5             ( 172) GPASHVLLTLVNAVI  23
Q9Y9X8             ( 158) DRERGLLLEDAVSYA  12
Q9HN79             ( 162) GDSRMSMLINVVAVL  20
Q9HJN2             ( 189) AEEQLLILYLVVAFI  13
Q9HHR8             ( 268) LAEIAVVLGIAVSYY  27
Q97YW9             ( 286) KLNKESMFKDANDSL  22
Q97C62             ( 476) PGTDIVWLSAVTKYI  28
Q97AQ0             ( 106) RPSKVEIIGIVIGFT   8
Q971A8             (  71) DVEKVEILEDAKVVT  14
Q96ZZ9             (1033) VGDKIIVINSTINVI   8
Q8ZW62             ( 186) VFNKSVLITETLKYA   9
O26447             ( 398) AVVTTEIIIGIIEYI  14
O27082             ( 817) VASLILILEAVLRFS  22
Q9YC30             ( 298) VVAKAALVTLAISFL   6
Q8U4C2             (  84) PVERSGVLIESADVL   7
Q8U2J9             ( 179) EKSKNSTVVITSHYL  13
Q8TK07             ( 117) LDARAGTLLDSTIYA  12
Q8TH72             ( 151) HTINHVIEEMNKNEI  30
Q8TH19             ( 225) EFSEVSTYKRILEAI  23
Q97Z77             ( 291) VDSRNLIVIAVLIFI  13
Q8PZ68             (  58) AGERVLMVYNALEHL  12
Q8PVU4             ( 280) AANKPAIEKIAVKAV  15
Q8PVS1             ( 281) PRAEGNVLNLAVLFI  16
Q8PU16             ( 784) PLPKIQTLIFTLVVI   7
Q8PT78             ( 273) FFEKNPDLRRIINFI  40
Q92242             ( 236) KLNKSMILEKAVDYI   4
Q96V45             ( 257) KLNKASVLTKATEYI   3
Q9UVN5             (1512) GLPKGAMLQHSAVHT  11
Q9UTA7             ( 313) TQPRLSTIQAALLYL   7
Q9C229             (1444) SGIRAEDIRLAREIV  20
Q9C0Y5             ( 770) KTSKKQILTNVSGYL   9
Q9P7B3             ( 720) SRSKSAIILLSATFL   8
Q9P8P8             ( 476) IQSRFVTLLQHYDYL  64
Q12398             ( 324) KLNKASILTKSIEYI   3
Q06859             ( 289) APSKATTVEAACRYI   5
Q9HEN9             ( 155) DTNKAQILQRAVEYI   9
O59677             ( 441) LVSSNVCLEKVDNYL  24
Q92280             (  97) VSTKAELLLKALDHV   6
Q9C1R9             ( 310) EYSKAGILNSAAALI  12
Q07896             ( 539) VSTKAELLLKALDHV   6
Q8TFJ8             ( 196) KSSKWETLTRAIEYI  13
O59704             ( 926) KEAQKEVLIIFAQYL  14
O60034             (1012) RAEKIEYVDKIIDLL  58
Q06860             ( 289) APSKATTVEAACRYI   5
Q8X074             ( 556) LPNKSVVVDLARGFL   7
Q9UUD1             ( 315) KLNKGTILAKATEYI   3
Q9HEX7             ( 125) EKNKGKILERTVSYI   8
Q9HDP4             (  90) ESSKATVLARRAEYI  23
O43019             ( 478) KLNKATILSKATEYI   3
Q8J1X7             ( 424) RVSKGEVLEMARRHI   4
Q8J0E0             (  46) DKNKGAILQRAIEYI  11
O14948             ( 175) RWNKGTILKASVEYI   5
Q9NY94             ( 224) KLSKNEILRLAMKYI   4
Q8N100             (  75) KLSKYETLQMALSYI   5
Q9HAP2             ( 752) LTSHAITLQKTVEYI  10
Q9NYQ5             (  92) KLDKLTVLRMAVQHL   2
Q96CY8             (  69) VLHRQSLMQKCHTFI  81
Q96QX4             ( 235) KNDAASVLEATVDYV   8
Q9UEC8             ( 136) KLSKIETLRLAKNYI   2
Q9NX45             ( 235) KNDAASVLEATVDYV   8
Q8WYA3             ( 129) KLDKLTVLRMAVQHL   2
Q9NTF6             (  48) HSARVVTVSSATHYV   9
Q8TAP5             (  50) HLDKASIMRLTISYL   4
Q96K34             (  50) HLDKASIMRLTISYL   4
O43392             ( 125) KPDKLTILRMAVSHM   3
Q8WYA1             (  95) KLDKLTVLRMAVQHL   2
Q8WZ51             (2026) VIDKVNTEDHQGEYV  33
Q9UPB1             (  53) HLDKASVMRLTISYL   4
Q9UPG2             ( 316) YLTMFKMLRDTLYYM  23
Q9NYQ4             (  79) KLDKLTVLRMAVQHL   2
Q9ULI6             (  72) KLDKLSVLRLSVSYL   2
Q8N6J9             ( 146) RWNKGTILKASVEYI   5
O43792             (  63) KPDKCKILKKTVDQI   9
Q8NAM2             (  91) KLEKAEILQMTVDHL   2
O94945             ( 359) LTSHAITLQKTVEYI  10
O43372             ( 310) RVSKVMILVKATEYL   6
Q9Y2N7             (  48) HLDKASIMRLTISYL   4
O43793             (  63) KPDKCKILKKTVDQI   9
Q8TAX8             (  48) KASRAQILDKATEYI   2
Q9HCC6             (  74) KLEKADILEMTVRHL   3
Q9NS70             (  58) KLDKLTVLRMAVQHL   2
Q8N416             ( 147) KLTKIETLRFAHNYI   5
Q9Y4L8             (  29) QLDKASIIRLTISYL   3
Q96SQ7             ( 265) KLSKLAILRIACNYI   3
O00146             ( 755) SSEDIEILEHAGELV  18
Q9Y4E9             (  42) KVSKSLILTRAFSEI  14
Q9Y6L9             ( 891) VIDKVNTEDHQGEYV  33
Q9UMQ5             ( 153) KAAKVVILKKATEYV   2
Q9Y5R3             (  83) KQSTAWMLHMAVRDL  61
Q8WYA5             ( 359) LTSHAITLQKTVEYI  10
Q8WVJ9             ( 100) KLSKIQTLKLAARYI   3
Q16509             ( 222) KLSKNEILRLAMKYI   4
Q96R32             (  73) LYAKLVILCWVCGFL  37
Q9NVW3             ( 597) KCIKLRTLNLGQNCI  29
Q96PR6             (  87) KLEKAEILQMTVDHL   2
Q8WYA2             ( 106) KLDKLTVLRMAVQHL   2
Q8N8Q0             ( 120) KLSKIATLLLARNYI   4
Q8WX40             ( 107) REDMASVLEMSVQFL   7
Q96T93             (  58) KLENAEVLELTVRRV   9
Q9BQ98             ( 711) KAEKQAAMSKALGFI  26
Q9BY81             (  57) QLDKASIIRLTISYL   3
Q9C0G2             ( 526) LVSGVAIFINIKEHI  25
Q96CP9             ( 594) LRTKGGCLLEVEELL  24
Q9P2S3             (  60) KLENAEVLELTVRRV   9
Q9UPH7             (  41) HLDKASIMRLTISYL   4
Q8NFJ8             ( 279) KLSKIATLLLAKNYI   3
Q9UQC6             ( 156) KLSKIETLRLAKNYI   2
Q9HC25             (  31) RLSKVDTLRLAIGYI   2
Q8N4N5             ( 412) TLTKAQILKLFLSYD  28
Q9BRJ9             ( 119) SLTKIETLRLAIRYI   3
Q96FL2             ( 116) KLSKAIVLQKTIDYI   3
Q14959             ( 122) KAAKVVILKKATEYV   2
Q8NDC7             ( 190) KPDKLTILRMAVSHM   3
Q96SB7             (1199) KKDKLQLLGATAFMI  10
Q96QM8             ( 293) TLTKAQILKLFLSYD  28
Q9HCA4             ( 115) RLPKVEILRSAIQYI   2
O95262             (  44) HLDKASIMRLTISYL   4
Q96J63             (  58) KLDKLTVLRMAVQHL   2
Q8WWL7             (1199) KKDKLQLLGATAFMI  10
Q8WU82             ( 504) LQEKAALLKKTLENL  13
Q96HZ4             (  60) KLENAEVLELTVRRV   9
Q9H2M4             ( 109) KLDKLTVLRMAVQHL   2
Q8NEE3             ( 111) REDMASVLEMSVQFL   7
Q96PT9             (  53) HLDKASVMRLTISYL   4
Q8NDY6             ( 137) KLSKIATLLLAKNYI   3
Q8N2J2             (  60) KLENAEVLELTVRRV   9
Q9H8R3             ( 627) KVSKSLILTRAFSEI  14
Q9NQ87             (  81) KLEKAEVLQMTVDHL   3
Q9BYE0             (  52) KLEKAEILEFAVGYL   3
O75321             ( 143) RLPKVEILRNAIRYI   2
Q8NGY2             ( 189) TDTRAIVMIQVVDVI  12
Q96HE1             ( 127) KLTKIETLRFAYNYI   6
Q8TBI7             ( 156) KLSKIETLRLAKNYI   2
Q8WXA1             (  50) HLDKASIMRLTISYL   4
Q9HAZ3             (  60) KLDKLSVLRLSVSYL   2
Q8TAT1             (  82) HLEKAVVLELTLKHL   4
O15074             (1426) LQEKAALLKKTLENL  13
Q96BZ0             ( 372) LLKRGFVLQDTVEQL  19
Q8WYA4             ( 143) KLDKLTVLRMAVQHL   2
Q14803             (  57) KASRAQILDKATEYI   2
Q9NX04             (  88) LGERLAILLKVRDMV   8
Q9H323             (  57) QLDKASIIRLTISYL   3
Q96RJ6             ( 136) RLSRIETLRLAIVYI   4
Q9BY83             (  81) QLDKASIVRLSVTYL   4
Q9UBP5             (  86) KLEKAEILQMTVDHL   2
O00150             (  63) KPDKCKILKKTVDQI   9
Q13804             (  59) KLDKLSVLRLSVSYL   2
Q8IYR9             ( 129) KLSKIETLRLAKNYI   2
Q8IYQ8             ( 108) RHTTLGLLNKAKAHI   8
Q8IYC6             (  57) KASRAQILDKATEYI   2
Q8IYC2             (  99) KPDKLTILRMAVSHM   3
Q8IXV0             (  71) KLEKADILEMTVKHL   3
Q8IXF2             (  57) QLDKASIIRLTISYL   3
Q8IXF0             (  87) QLDKASIIRLTISYL   3
Q8IW56             (  46) KLSKIETLRLARNYI   3
Q8IUT4             ( 103) KLDKLTVLRMAVQHM   3
Q23579             ( 123) KISKLATLKVASSYI   7
Q95NH3             (  71) KLEKADILEKTVKHL   3
Q18711             (  81) KSSRALILKRAVEFI   4
Q95ZK5             ( 274) KLNKGTILKASCDYI   4
Q8MNK7             (2355) LTDKEEILAAGTKYN  73
O77278             ( 143) KLSKIEILKLAICYI   4
Q9VJ16             (  97) KLEKADILELTVRHF  11
Q8TA56             (  27) KLDKLTVLRMAVQHL   2
Q9TVM0             ( 384) IVSKSMKELFAKGHI  17
Q9GRC7             ( 114) KLSKVETLRMAVEYI   2
Q21663             ( 130) RNTTLALLTRARDHI   8
Q9GS19             ( 274) KPDKAAILNQVVRTY  39
P91664             (  73) KASRAQILKKTTECI   5
Q9W4X2             ( 200) KLSKNEILRSAIKYI   3
Q8SYH4             ( 125) KYSKIESLRIAINYI  15
Q9VGZ5             ( 100) RIEKTEIIEMAIRHL   5
Q9VAS8             (1352) SPPDNAILNAPDQYI  17
Q9VG64             ( 218) LTKKMLLLSLAFFYT  28
Q24146             ( 316) KLNKSAVLRKSIDKI  14
Q9GRC6             ( 108) KLSKVETLRMAVEYI   2
Q9VJC1             ( 165) KLSKIATLLLAKNYI   3
Q23388             (1228) VGPRILIVEEAAEVL   5
Q9XZC7             ( 138) KLSKFETLQMAQSYI   9
Q9VE36             ( 131) LNSKTMLLPLVRDFA  14
Q8MRS4             ( 963) QAEKVRTLKATGDAA  19
Q9VWX7             (  61) KMDMGDVLELAVHHL   7
Q9TZ70             (  84) KTTNAAILFRACDFM  17
Q9N6Q1             (1789) KRSSYATLTVAEAVI  16
Q18053             (  48) KLSKEEVLFRIVKLL  16
O02219             (  80) KPDKLTILRMAVSHM   3
Q8MNH9             (  28) VKKQIEILDENKTMI  21
Q9NHD9             ( 248) KLSKVETLRMAVEYI   2
Q9V8N9             ( 973) QAEKVRTLKATGDAA  19
Q8WQQ7             ( 224) KFSKVDTLRMAVEYI   4
Q17326             ( 339) NQTKLGILYNAVSVI  13
Q9VZP3             ( 105) RPDKLLLVAITCLHI   8
O00947             ( 339) ILTNVVTMTEFTTMV  14
Q9VN30             ( 959) FHEKVEIMDVAKTFI  14
Q961H7             ( 136) KLTKITTLRLAMKYI   4
O77089             (1963) LSPKITVMEPVLRFL  12
Q8MQV4             ( 108) QLDKASVMRITIAFL   4
Q9VGC6             ( 186) ETNRIMILNFSAVFV  10
Q25124             ( 276) RLPKVEILRNAITYI   3
Q9NFW8             (  99) KLEKADILEMTVKHL   3
O44712             (  54) RLDKLSVLRLAVSFL   2
Q18590             (  67) KLSKIEILRFSIAYI   3
Q19918             ( 157) KLERVTVLQIILEYI   4
Q09961             ( 128) KWSKADTLREAVKYI   3
O17237             ( 798) MILKAKDEKNAEEWL  38
Q9N4M4             (7450) ELSRATMLNDAIAHL   6
Q9NCL3             (1579) KSSQLQVETFKVECL  17
Q95X77             ( 268) EWSKSSIVKYTSDFM  15
O76836             ( 754) SQNNAAVLKTNTDYY  40
Q9BKE5             ( 891) KLSKAAMLQKGADHI   7
Q9VID2             ( 191) RLSKIETLTLAKNYI   3
Q22060             ( 145) AAPKISVVTHSMGVT  11
Q8T3U8             ( 235) ETNRIMILNFSAVFV  10
O15984             ( 107) QLDKASIIRLTISYL   3
Q9VA43             ( 178) PNNKCEAEELFEGFT  23
Q9GSP7             (  34) KLSKIQTLKLATRYI   2
Q9BLX3             ( 124) KMSKVDTLRSAVEYI   2
O18374             (  66) KLSKLDTLRLATLYI   3
Q9VY43             (1579) KSSQLQVETFKVECL  17
Q8WSV7             ( 235) RWNKGSILKTTVDYV   7
Q9GNV2             (  85) KLSKIQTLRLAAMYI  11
Q18056             ( 185) KLERITILEIIIDYI   4
Q9XVQ0             ( 298) QLSRTLIIVTSTFVL  14
Q9W4I4             ( 143) KLSKIEILKLAICYI   4
Q8WQQ9             ( 117) KLSKIQTLKLASRYI   3
O96903             ( 660) RAPKVNILREAAKLC  39
Q9GYH2             ( 238) KDNKTTTMLLVMIFM  13
Q9U911             (  73) KLSKVSTLKMAVEYI   2
Q18612             (  60) SLPKIKTLRLAMQYI   6
Q8T1Q1             (  49) GIEKAGILETVMDVL   9
Q9VB47             ( 110) KLSKALILQKSIEYI   2
Q18054             ( 177) KLERITILEIIIDYI   4
Q9NCW7             (1579) KSSQLQVETFKVECL  17
Q9VXW7             (  43) RVDKTAVLRFAAHAL  12
O44538             ( 201) KHFDYVKMMKASNYL  30
Q9W4Q7             ( 297) KTSNLTILDTAHKYV  10
Q9VHG3             ( 215) KYSKIESLRIAINYI  15
Q9VGJ5             ( 121) RLSRIETLRLAITYI   3
Q9XZI1             ( 108) RLPKVEILRNAIEYI   2
Q95NU9             (  71) KLEKADILEKTVKHL   3
Q8MWP6             ( 334) RMPKVEILKNAIDYI   2
Q962X1             (1548) PTLKISLIQIFRAHL  11
Q24354             ( 220) KLSKNEILRSAIKYI   3
Q9V881             (  66) KLSKLDTLRLATLYI   3
Q963J8             ( 280) IVSKSMKELFAKGHI  17
Q26372             (  17) ASLRKSIPTMPSDKL  45
Q95U62             ( 105) RPDKLLLVAITCLHI   8
Q19917             ( 134) KLERVTVLQIILEYI   4
Q8SYL0             ( 132) LNSKTMLLPLVRDFA  14
Q9NHD8             (  60) KLSKVDTLRIAVEYI   2
Q9U910             ( 127) KLSKVDTLRIAVEYI   2
Q24159             ( 110) RPDKLLLVAITCLHI   8
Q9VW37             ( 316) KLNKSAVLRKSIDKI  14
Q25179             (  99) KLSKVEILRCAALYI   7
Q9NK61             ( 130) KLSKAAILQQTFQYI   7
Q9GPN7             (1746) VMSDTSFLRKIVEYP  39
Q9V406             ( 130) KLSKAAILQQTFQYI   7
Q24353             ( 138) KLSKIEILKLAICYI   4
O16380             ( 284) TWSKADDLIGNSDIV  29
Q26594             ( 479) EQEKVSDIIELDGHL  21
Q8N0R5             ( 177) KLDKLTVLRMAVQHL   2
Q9W4J8             ( 325) NDSKSQILIKACEYI  11
Q9GQP6             ( 110) KLSKALILQKSIEYI   2
Q9VBH3             ( 152) RLSQLQLMALVCVYV   8
P90982             (  65) QASRAVILKKAIESI   8
Q9N6W6             (  55) RLEKADILELTVTHL   3
Q8WQK4             ( 114) KTPKVDILRNAIAYI   3
O16853             (  61) KWEKADILEMAVEYL   4
Q9V758             ( 410) KLQKEIILKRAADLV  34
Q8SXE2             (  73) KASRAQILKKTTECI   5
Q94790             (  32) KLSKFETLQMAQTYX   9
P90977             (  62) KLSKVETLREAARYI   2
Q9N6W8             (  53) RLEKADILELTVEHM   3
Q9BLX4             (  92) KMSKVETLRSAVQYI   2
O46042             ( 297) KTSNLTILDTAHKYV  10
Q95VY6             ( 146) KLSKVDTLRLAVEYI   2
Q17358             ( 339) NQTKLGILYNAVSVI  13
Q23056             ( 253) YVPKAEVIIHVLQVV  11
Q9N6W7             (  55) KLEKADILELTVNYL   2
Q26649             ( 384) RAAKIVILKKATDYV   3
Q22805             ( 160) AKPRFQTEHQICKFF  24
O44875             ( 635) ASSQLSVLGSATRGI  12
Q9BLJ2             ( 570) YTPRSSILRSASGVA  10
Q9XV13             ( 121) KDTNKIILLSTVLFV  16
Q8SVU5             ( 292) ELEKANVLIDSSSMT  14
Q9W4S7             ( 660) RAPKVNILREAAKLC  39
O45320             (  77) RMSKANTLLLASNWI  21
Q25427             ( 228) GQSKGGILSKTCDYI   6
Q25428             ( 252) GQSKGGILSKTCDYI   6
Q95Q51             ( 398) AKDKTDTLKKALQVM   7
O02191             ( 427) RLPKVEILRNAITYI   3
Q8SXF5             ( 116) RLSKVDTLKLAISYI   2
Q8SSZ1             (  27) KLDKLTVLRMAVQHL   2
Q8SY46             ( 283) KTSNLTILDTAHKYV  10
Q9VEV9             (  61) KLDRLSILRLSVSYL   2
O76880             ( 200) KLSKNEILRSAIKYI   3
P91527             ( 273) KLNKGTILKASCDYI   4
Q94187             ( 297) KPEKLVDQHLAKQFI  67
Q9U450             ( 100) RIEKTEIIEMAIRHL   5
Q18277             (  48) RLSRVQILREATSYI   2
P90681             ( 238) YRLHNETLYLAVSYI  21
Q9NB27             ( 158) KLTKIETLRFAHNYI   5
O44118             (  72) RLDKTAVLRFATHGL  11
Q95WT6             ( 172) RNPKILILDEATSYL   4
Q8MQI7             (  60) QLDKASVIRLTTSYL   3
Q9VL05             (  93) KLSKIKTLKLAILYI   5
O61543             (  61) KLDRLSILRLSVSYL   2
Q9V7M2             ( 138) KLSKFETLQMAQSYI   9
Q9GR87             ( 177) KLDKLTVLRMAVQHL   2
Q95XG7             (  97) KMTKIETLRKAQEYI   5
Q8WQQ8             (  27) KLSKIQTLKLASRYI   3
Q8WQQ6             ( 138) KLSKVDTLRIAVEYI   2
Q9GNL5             ( 127) KLSKVDTLRIAVEYI   2
Q9VI67             ( 118) RLSKVDTLKLAISYI   2
Q9VID4             ( 948) KLSKAAMLQKGADHI   7
Q8MRA5             ( 128) KLSKVDTLRIAVEYI   2
Q9VYW2             (  72) RLDKTAVLRFATHGL  11
O96520             (  36) QLDKASVIRLTTSYL   3
Q9TX44             ( 420) KLSKIQTLKLATRYI   2
Q8MUL7             (  34) KLSKIQTLKLATRYI   2
Q9VSP0             ( 973) AADKSSLVDASKEVL   6
Q8MUL8             (  34) KLSKIQTLKLASRYI   3
Q8T8A9             (  52) KLEKADILEMTVRYL   3
Q8T0M7             ( 229) SLNRTSVLFVSISFI  18
Q8MT07             ( 395) KLSKIQTLKLATRYI   2
O76488             ( 120) KLSKVDTLRMVVEYI   2
Q8MQD2             ( 680) RHNKGQKVEQAPVFA  24
Q95VQ5             ( 247) KLSKIQTLKLATRYI   2
Q22717             (  95) KLSKVETLREAARYI   2
Q94816             ( 268) RLPKVEILRNAIEYI   2
Q9VBG4             ( 565) RISILVVVMFVVSYL  13
O02190             ( 427) RLPKVEILRNAITYI   3
Q8T804             ( 317) EGKKLATFQGVTSVV  12
Q9VEY3             ( 188) RLSKIDTLRLAIAYI   2
Q8T8Y9             ( 395) KLSKIQTLKLATRYI   2
Q94791             (  32) KLSKFETLQMAQTYX   9
O44711             (  80) KPDKLTILRMAVSHM   3
Q17588             ( 339) NQTKLGILHNAVSVI   8
Q20561             (  76) RLSKIDTLNLAIAYI   4
Q9NHE3             ( 139) KISKVDTLRIAVEYI   4
Q8WQQ5             ( 108) YKVKVDTLRIAVEYI  13
Q18076             ( 654) RHNKGQKVEQAPVFA  24
Q8T306             (  74) KLEKADILEMTVKHL   3
Q95UA9             (  71) KLEKADILEKTVKHL   3
Q9VPI8             ( 308) KLSKLSVLRVACSYI   5
Q962A3             ( 161) KLSKHEILRCTIRYI   7
Q960W6             ( 498) STAKAALVLPVLYYL  20
Q9N410             (  64) QLDKCFIIGSTVDII  23
O01591             ( 174) KHFDYVKMMKASNYL  30
Q9V7R8             ( 453) STAKAALVLPVLYYL  20
O46319             ( 391) AKTELEAEEKKDRYI  22
O45486             ( 384) IVSKSMKELFAKGHI  17
Q9VBW1             ( 609) GTARVSIMESVKEFI   7
O45489             (  83) KLSKIATLLLAKNHI   3
P90953             (  45) HIDKTTMVRLATAYI   6
O61528             (1963) AKDKTDTLKKALQVM   7
Q9U3E1             ( 146) KLSKAAILQQTADMV   5
Q8T0T6             ( 379) TINRHTDLSQSIGWL  25
Q9BKE4             ( 665) KLSKAAMLQKGADHI   7
Q9U9U4             ( 138) KLEKAEILQLTVEHL   2
Q8IU24             ( 112) RLPKVEILRNAISYI   2
Q8IU23             ( 114) KTPKVDILRNAIAYI   3
Q8IRS3             ( 325) NDSKSQILIKACEYI  11
Q8INT7             ( 899) KLSKAAMLQKGADHI   7
Q8INT6             ( 754) KLSKAAMLQKGADHI   7
Q8INP5             ( 125) KYSKIESLRIAINYI  15
Q8I812             (  44) QLDKASIIRLTIAFL   3
Q8I7T7             ( 102) KLSKVEILRYAMMYI  18
Q8I7T6             (  81) KPTQAEILMHTCEYV  12
Q8I7T5             (  58) RPRYLHILESAIAYI  79
Q8I7I9             ( 839) KPTNAVVLAKSADHI   6
Q8I710             ( 202) KLSKIQTLKLATRYI   2
Q8I1G0             ( 396) KLSKIQTLKLATRYI   2
Q8I066             ( 280) IVSKSMKELFAKGHI  17
Q9BE97             ( 125) KPDKLTILRMAVSHM   3
Q8MJ65             (  96) KAPKVVILKKATAYI   2
Q95MD1             ( 154) RWNKGTILKASVDYI   5
Q8MJ69             ( 110) KAPKVVILKKATAYI   2
Q8MJ74             ( 114) KAPKVVILKKATAYI   2
Q9MYY5             ( 117) KLNKSAVLRKAIXXX   2
Q8MJ72             ( 110) KAPKVVILKKATTYI   2
Q8MJ66             ( 112) KAPKVVILKKATAYI   2
Q9XTA4             (  50) HLDKASIMRLAISFL   4
Q95L20             (  84) RLPKVEILRNAIRYI   2
Q8SQA5             (  34) KLDKLSVLRLSVSYL   2
Q8MJ70             ( 110) KAPKVVILKXATAYI   2
Q9MZT9             ( 389) KAPKVVILKKATAYI   2
Q9MYY7             ( 113) KMHKSGVLRKAIDYI   9
Q9XTA5             (  53) HLDKASVMRLTISYL   4
Q9MYT3             (  63) KLSKIKTLRLATSYI   3
Q8MIH1             ( 143) KLSKIQTLKLAARYI   3
Q8MIH8             ( 147) KLSKIQTLKLAARYI   3
Q8MJ67             ( 113) KAPKVVILKKATAYI   2
O77790             (  77) RLPKVEILRSAIQYI   2
Q8MJ64             ( 109) KAPKVVILKKATTYI   2
O02811             (2001) RFSPNMTEREAANFI  22
Q95L69             ( 117) RLPKVEILRNAIRYI   2
Q8MJ68             ( 110) KAPKVVILKKATAYI   2
Q8MIE7             ( 144) KLSKIQTLKLAARYI   3
Q9MZT7             ( 389) KAPKVVILKKATAYI   2
Q9MYY6             ( 113) KMHKSGVLRKAIDYI   9
Q28925             (1424) RFSPNMTEREAANFI  22
Q8MIB5             ( 143) KLSKIQTLKLAARYI   3
Q8MJ71             ( 107) KAPKVVILKKATAYI   2
Q8MIF3             ( 138) KLSKIQTLKLAARYI   3
Q8MI03             ( 143) KLSKIQTLKLAARYI   3
Q9MZT8             ( 390) KAPKVVILKKATAYI   2
Q8MIB9             ( 143) KLSKIQTLKLAARYI   3
Q8MID5             ( 139) KLSKIQTLKLAARYI   3
Q8MHZ4             ( 141) KLSKIQTLKLAARYI   3
Q9MZT6             ( 388) KAPKVVILKKATAYI   2
Q95L21             (  94) RLPKVEILCSAIQYI  12
Q9MZU0             ( 389) KAPKVVILKKATAYI   2
Q8MI06             ( 143) KLSKIQTLKLAARYI   3
Q8MJ63             (  88) KAPKVVILKKATAYI   2
Q8MJ73             ( 112) KAPKVVILKKATAYI   2
Q28239             (  58) KAPKVVILKKAXXXX   1
Q95KC9             ( 412) TLTKAQILKLFLSYD  28
Q9BE11             ( 503) LVSGVAIFINIKEHI  25
Q95K45             ( 263) QASKSNLISGSVMYI  18
Q8HY55             ( 204) GASKGGILSKACDYI   5
Q30830             ( 124) FLTKGIIVGLVLLVL  13
Q9MJ75             (  53) RLIMLIIICSSYIYI  27
Q9T654             ( 422) RFKPYRLLEAKINYI  33
Q8WEV1             ( 159) TWDKIALLPCAICVT  19
Q9LGL7             (  96) QMDKATLLARVVDQV   7
Q9LQH2             (1642) EQAKKNIEEKTKQYA  16
Q9AW08             ( 612) ILSKIDMVQTSLTFL  10
Q93VJ4             ( 180) VTGKAGMLDEIINYV   6
Q8RV16             ( 195) QTNTSDMLDIAVTYI   6
Q8L994             ( 296) LLIQKSILRDAVTDL  19
Q9SFY5             ( 205) KVDISTMLEEAVHYV   8
Q9XIN0             ( 487) KCSIDALLERTIKHM  23
Q8LRU0             ( 465) EVEKISVLGGTIKYL   6
Q9M041             (  75) KMDTVSMLDEAISYV   3
Q94JL3             ( 302) KTDTASVLQEAIEYI   3
Q9M8K6             (  32) RGDQASIIGGVIEFI   6
Q94JE7             ( 355) KMDKASLLSDAIAYI   3
Q9LRJ4             ( 287) KMNLAMTLEESHKYI  12
Q8S3D6             ( 176) KTDKASMLDEIIDYV   3
Q9LUK7             ( 371) KMDKTSLLEDAVCYI   6
O22418             ( 434) KIDKVSILDDTIEYL   3
Q8LHY9             ( 352) ATSRTLVLANSAPVL  13
Q9LXA9             ( 179) KMDRTSILGDAIDYM   4
Q94HA7             ( 181) KSDTASVLHEALGYI   6
Q9FHA2             ( 125) KTDKASMLDEAIEYL   2
Q8LQW4             ( 726) TTPKKIDVRFIVVVI  15
Q9LT67             ( 176) KTDAASVLHEAMGYI   9
O64908             ( 466) KVDKISLLDETIEYL   3
Q9FIP9             ( 443) KMDKASLLGDAISYI   3
Q8LC47             (  78) KRDTASFLLEVIDYV  13
Q9SIR1             (1324) ARPVLAMLKKVVEHA  10
Q9M128             ( 146) RGDQASIVGGAIDFI   6
O82396             ( 154) KMDKASVLGDAIKHI   3
Q8LQZ5             ( 111) KVDKASSLAETIAYL  10
Q8S3D9             ( 211) ITGKAGMLDEIINYV   7
Q93Z71             (  83) KMDKASIIKDAISYI   3
O80482             ( 164) KVSVPNLLDEATDYI  14
Q9LGU4             ( 205) KEDRATVISDAIEYI   5
Q94LR3             (  33) KTDKASMLDEVIDYL   3
Q9LN89             ( 109) KRSSADHVLEAVNYI  22
Q9LND0             ( 244) KNDRASIVGEAIDYI   5
Q9M1K0             ( 111) KLSIPATVSRSLKYI  10
Q9ZW81             ( 270) QTSYADMLDLAVEHI  16
Q9LRN3             ( 228) RGDQASIIGGAIEFV   6
Q8S0N2             ( 313) KMDTASMLDEAASYL   3
Q948Y2             ( 406) KVDKASILAETITYL   3
Q9LET0             (  91) KELKQQTLEITDETI  38
Q9SS60             ( 655) LLSRSQKISKAEEFI  14
O64788             ( 170) KLLKTLSLMRTQVMV  24
Q40615             (  26) KVDKASILAETIAYL   3
Q9FKQ6             ( 133) PNDQASIIEGTISYL   7
O23696             ( 288) LISKEVLMGKAEYFE  82
Q41780             ( 413) KVDKASILAETIAYL   3
Q9FLZ1             ( 311) KKSFRRFLRSGIKHI  83
Q9AYK0             ( 541) KMDKASLLGDAISYI   3
Q9ZUV1             ( 111) ANDKTQTVVAVTTVV  11
Q9SA82             ( 166) KHNTAEMFNAAAKYV  10
Q8VXB1             ( 748) RPDSGIIKKVAVNYV  26
Q9FWE1             ( 224) KMDRTSILGDTIGYV   4
Q8S3F2             ( 147) KADKVTILDDAISRM   7
Q8S3E3             ( 184) KTDRAAMIDEIVDYV   4
Q8L9U3             ( 184) KTDRAAMIDEIVDYV   4
O82397             ( 147) KADKVTILDDAISRM   7
Q9SW10             ( 624) VHTKAEILACAKKML  11
Q9STJ6             ( 208) QQKLVEDLILSTGYX  15
Q9FK20             ( 133) RGDQASIIGGVVEYI   6
Q8LSP3             ( 315) KTDKISLLGSTIDYV   3
Q39903             ( 144) QNSTAEMIKLVRKYL   7
Q9SYA1             ( 231) KTDTASVLQEAIEYI   3
Q8LPT0             ( 423) KMDKASLLGDAISYI   3
Q9LPJ8             ( 480) KMDKASLLGDAIAYI   3
Q8S822             ( 179) EKAEAVVEKAADEVV  13
Q9SKX1             ( 122) GMETSKLMEETAHYI  10
Q9ZPY8             ( 423) KMDKASLLGDAISYI   3
Q9LV21             ( 296) LLIQKSILRDAVTDL  19
Q8S3F5             ( 461) KMDKASLLGDAVSYI   3
Q8S0C6             ( 294) KKDKTTVLINAAKYL   6
Q8LB18             ( 119) KGDQASIVGGAIDFI   6
Q9FUA5             ( 234) KFPKDGSSPKSLRYI  85
Q9ZUG9             ( 176) KTDKASMLDEIIDYV   3
Q9C988             ( 126) KWSAPSIIDNVITYI  12
Q41101             ( 490) KMDKASLLGDAISYI   3
Q94D62             ( 278) KKDKTSILIRAREYV   6
Q9FIQ6             ( 119) KGDQASIVGGAIDFI   6
Q9CAD0             ( 433) KIDKVSILDDTIEYL   3
Q8S470             ( 408) KVDKASILAETIAYL   3
Q9ASJ3             ( 236) KVDLVTMLEKAINYV   7
Q9LYM0             (  27) AESETSIIVDASKYI  13
Q9FFU7             ( 448) VFAKAEMLQRTSKHV   8
Q9SRT2             ( 297) VTGKALMLDEIINYV   6
Q9ASL3             ( 612) EEERAATLIATTTMI   9
Q8LQF2             ( 316) VVGKAVMLDEIINYV   5
Q8LM97             ( 179) EKAEAVVEKAADEVV  13
Q8LIB9             ( 202) SMSKAAVVGMVRTVA   8
Q9FRI0             (  98) QSDINAILDCVIEYT  14
Q9LV17             ( 192) IIGKALVLDEIINYI   8
Q9ZV87             ( 240) QEVKWPVLTSAGQVL  50
Q9FYJ6             ( 227) KTDTASVLQEAITYI   4
Q9LU04             ( 484) QGERVEVEEKFGIVL  17
Q9LSE2             ( 335) KMDRASILGDAIDYL   3
Q40614             (  26) KVDKASILAETIAYL   3
Q8L7J0             ( 576) KCSIDSLLERTIKHM  23
Q8S3E7             ( 342) VTGKAVMLDEIINYV   5
Q40834             (  30) KVDKASILAETIAYL   3
Q9ARY0             ( 686) QIDKASMLDEAIEYL   4
Q38736             ( 471) KVDKVSILDHTIDYL   4
Q9ZPW3             ( 224) VTGKAGMLDEIINYV   6
Q8LQN1             ( 302) KTDTASVLHEAIEYI   4
Q40599             (  26) KVDKASILAETIAYL   3
Q8LG13             ( 176) KTDAASVLHEAMGYI   9
Q9ZSQ9             ( 146) KMDKASILGDAAKYL   3
Q8SB96             ( 473) KLAMLEQLQDSVDNL  25
Q8S3D3             ( 304) KVDISTMLEEAVHYV   8
Q94I55             ( 179) LVSRNQMILLVILFL   8
Q8S3D8             ( 207) VTGKAGMLDEIINYV   6
Q9ZRX1             ( 293) LLIQKSILRDAVTDL  19
Q9LQ08             ( 108) KRSTSDHIVQAVNYI  21
Q94ED0             ( 415) KMDTASMLDEAANYL   4
Q9SP39             ( 174) VTGKAVMLDEIINYV   5
Q8S3D4             ( 340) VTGKALMLDEIINYV   6
Q8W2F4             ( 480) KMDKASLLGDAIAYI   3
Q8W2F5             ( 443) KMDKASLLGDAISYI   3
Q8VY82             (  59) KTDTASVLLDAMHYI   7
Q9FLI0             (  66) KRAMSDHVNGAVSFI  23
Q9SJX4             ( 264) KIDRASIVGEAIDYI   4
Q9C7T4             ( 156) RGDQASIVGGAINYL   6
Q93W88             ( 175) VTGKALMLDEIINYV   6
Q9LH76             ( 593) VVSHNEILEMYKSYI  27
Q8LJ97             ( 403) LHDRATLLTKVITMV   9
O81900             (  60) NMTKASIVEDAITYI   7
Q9LS08             ( 163) KTDKASLLAEVIQHM   4
Q8VZA6             (  38) KNDKATILTDTVQLL   7
Q9XII8             ( 292) KLNKIGIFSDAVDYI   6
Q8S3D5             ( 168) KTDKASMLDEIIDYV   3
Q9XIJ2             (  46) KLPVPHLIDQATSYM  22
Q9LIG3             ( 336) KMDTASMLDEAANYL   4
Q9LU71             (  83) KMDKASIIKDAISYI   3
Q9LQ51             ( 169) VIGKALVLDEIINYI   6
Q9LPQ6             (1078) AMGMATMLDEIINYV   8
Q8LCW3             ( 175) VIGKALVLDEIINYI   6
Q8S3E8             ( 167) KTDKSAILDDAIRVV   4
Q9SM95             ( 108) KTDKVSMLDEAIDYL   2
Q8LRT9             ( 423) EVEKISVLGDTIQYL   5
Q9XIJ1             (  46) RLPVPQLIDQAVSYM  12
Q9SVP7             ( 798) MLTRAGLLSRAKEFI  15
Q9XEF0             (  94) KLDKAALLATVIEQV   8
Q9FXG5             ( 252) QMNTACVLDEAVQYL  29
Q9M2R7             ( 243) IQGTALVLDEIINHV   8
Q8LAF0             (  49) KTDTASVLLDAMHYI   7
Q8LCD1             (  82) KMDKASIIKDAISYI   3
Q9FHA7             ( 160) KMDTASMLDEAIHYV   5
Q9SND4             ( 157) KMDTASMLDEAIHYV   5
Q8L9T3             ( 146) RGDQASIVGGAINYV   6
Q9LYT0             ( 288) RTDKASILDEAIDYL   2
Q9FSQ4             (  54) RGSAARVLQETCSYI  12
Q9LK48             ( 230) ITGKAVMLDEIINYV   7
Q9FT09             ( 268) KTDTASVLSEAIGYI   4
Q9LTS4             ( 317) KKDKASVLSIAREQL   8
Q9SGY8             ( 217) QLNKIGIFSDAVDYI   6
Q40752             (  30) KVDKASILAETIAYL   3
Q9LPG6             ( 596) VVSHNEILEMYKNYI  27
Q9FXA3             ( 102) KADKSTIVDEAVSSI   8
Q8L851             ( 211) ITGKAGMLDEIINYV   7
Q8L8P6             ( 143) AMGMAVMLDVIIDYV  10
Q9M270             ( 209) RGDQASIVGGAINYV   6
Q8LBK8             ( 271) ALSDVLLLSKVFQKL  24
Q40616             (  26) KVDKASILSETIDYL   3
Q9FMB6             (  68) KRDKASFLLEVIEYI  12
O65531             (1463) QGSAADIIKIAMINI  20
Q9FLK6             ( 110) KADKVSILDDVIEHL   3
Q94D54             ( 316) KKDKTSILIRAREYV   6
Q40602             (  26) KVAKASILAEPIAYL   7
Q8S483             ( 419) RVNKASILAETIAYL   3
Q8VZ22             ( 212) KTDTASVLHDAIDYI   4
Q8W0Q8             ( 252) VAVAVAVLLGITVYV  16
Q8LDA7             ( 322) QTSYSDMLDLAVQHI  17
Q9FJ00             ( 171) KVDLVTMLEKAIGYV   8
Q39204             ( 480) KMDKASLLGDAIAYI   3
Q8S7J7             ( 142) RGDQASIVGGAINYV   6
Q8S235             (  72) KMDTVSMLEQAIHYV   6
Q9M0R0             ( 223) QTNTADMLEEAVEYV   4
Q9SLT6             ( 175) VIGKALVLDEIINYI   6
Q9AYI8             ( 220) KTDKVSVLGSTIEYV   3
Q9SA66             ( 177) KTDRAAMIDEIVDYV   4
Q9SJW8             ( 548) KCSIDSLLERTIKHM  23
O81756             ( 301) KVDISTMLEEAVHYV   8
Q8LFU9             ( 125) KTDKASMLDEAIEYL   2
Q8S3E4             ( 180) VTGKAGMLDEIINYV   6
Q9SJX5             ( 242) KGDRASILQDGIDYI   7
Q9C8Z9             ( 180) KQSVPVILEEATDYI  10
Q9LRW0             ( 216) ELEVVEGMKLARGYI  23
O82599             ( 158) NGDQASIVGGAIDFI   9
Q8VZJ4             ( 624) VHTKAEILACAKKML  11
Q9SYM5             ( 598) VVSHNEILEMYRDYI  27
Q9SA36             ( 153) KLVLFSTFAMSITSI  25
Q41285             (  30) KVDKASILTETIAYL   3
O23192             ( 229) KTDKASMLDEAIEYL   2
Q8RYL7             ( 252) KMDRASILGDAIEYL   3
O48644             ( 480) KMDKASLLGDAIAYI   3
Q40644             (  26) KVDKASILAEPIPYL  12
Q93Y53             ( 146) SPCTLSVLPLTLGYI  27
O65678             ( 211) ITGKAGMLDEIINYV   7
Q9SVU6             ( 309) KTDRSSMLDDVIEYV   4
Q40643             ( 427) KVDKASILAETIAYL   3
Q9FLI1             (  36) KRSTSDQVNEAVNYI  17
Q9FE77             ( 231) QLDTASVIEEAVRYL   4
Q9LSQ3             ( 137) KTDKASMLDEIIEYV   3
Q9M4A8             ( 446) RVNKASILAETIAYL   3
Q94D59             ( 246) KKDKASILIRAREHI   6
Q8LG61             ( 349) FHDIALALKKIDTCI  21
Q9SN74             (  60) NSGKASILCEATRFL  18
O48535             ( 339) QTNTSDMLDLAVDYI   5
Q40835             (  30) KVDKASILAETIAYL   3
Q9FRI2             (  86) AMGMAVMLDVIIDYV  10
Q93ZM7             ( 216) ELEVVEGMKLARGYI  23
Q8LEG1             ( 205) KVDISTMLEEAVHYV   8
Q8S3F1             ( 160) KTDKATVLEDAIKHL   3
Q8L5W8             ( 261) KDDKASLLDEAIKYM   6
Q8S3F3             ( 154) KMDKASVLGDAIKHI   3
Q93ZB9             ( 206) KLDQLRVIGAAPETI  30
Q9LPF4             (  90) LYARLVTMVTSRDFL  16
Q9LI31             ( 436) KMDKASLLGDAITYI   3
O80727             ( 239) RDDKASLLDEAIKYM   7
Q8W5G3             ( 248) KVDISTMLEEAVHYV   8
Q9SL63             ( 316) KSDKASMLDEAIEYM   4
Q8L5W7             ( 220) KDDNESMLDEAINYM  11
Q9T072             ( 156) KMDKASVLGDALKHI   3
Q9FIX5             ( 117) KNDKNSIVEKAVDEI  11
Q9LEZ3             ( 309) KRDKASFLLEVIEYI  12
Q9ZPN6             ( 552) KMDKASLLGDAISYI   3
Q9XGZ1             ( 142) TVSKMATLTKKVRIA  29
Q942Q3             ( 408) KMDTASMLDEAANYL   4
Q41102             ( 462) KMDKASLLGDAISYI   3
Q40603             (  26) KVDKASIFAETIAYL   5
Q9ZUV8             ( 159) KMDKASIVGDAVLYV   4
Q8LJC5             ( 889) KCSIDTLLEKTIKHM  22
Q9LTC7             ( 196) KTDKSAILDDAIRVV   4
O24438             (1117) FLNKGGILMFVLVYV  17
Q8S3E6             ( 166) KHNTAEMFNAAAKYV  10
Q8S3D7             ( 288) RTDKASILDEAIDYL   2
Q9LSL1             ( 206) KMDRTSILGDAIDYM   4
Q9SZR4             (  82) KLDKASVIKDSIDYM   3
Q9FJL4             ( 340) VTGKALMLDEIINYV   6
Q9C707             ( 233) KVDLVTMLEKAISYV   7
Q8L8Y1             ( 209) RGDQASIVGGAINYV   6
Q8W0P3             (  72) SRTQLGSLDEAAAYI  14
Q8S490             ( 108) QTNTADMLDLAVDYI   4
Q9FN69             ( 469) KIDKVSILDDTIEYL   3
Q8S3E2             ( 243) IQGTALVLDEIINHV   8
Q9LPE2             ( 148) GPDKTVTLGDVSDML   8
Q8S3E0             ( 291) VTGKALMLDEIINYV   6
O81313             ( 150) KMDTASMLDEAIRYT   6
Q9LXD8             ( 157) KMDTASMLDEAIRYV   3
O64746             ( 170) KLNTAEMFQAAAKYV   6
Q93Y00             ( 182) KTDRAAMIDEIVDYV   4
Q9LJD1             ( 727) DENMWMIYGHATNHM  31
O80668             ( 361) KFNKAVITCFIICVL  48
Q9LY78             ( 289) KQSKIEIVEQIMREI  12
Q9LNJ5             ( 461) KMDKASLLGDAVSYI   3
Q9S7Y1             ( 205) KTDKASLLAEVIQHV   4
O81348             ( 200) KMDKASVLGEAIKYL   2
Q9FMQ9             ( 301) KVTRISTLARFRVYT  12
O81901             ( 190) KTDTASVLHDAIDYI   4
Q8LJF6             ( 383) SGGKNTIVAAAANYI   8
Q8LD53             ( 105) KTDKAAILVDAVRMV   7
Q41875             ( 496) KMDRASILGDTIEYV   3
Q8LEZ5             ( 206) KMDRTSILGDAIDYM   4
O81306             ( 175) KTDKASMLDEVIEYL   3
Q8LF81             ( 164) VTGKAGMLDEIINYV   6
Q948Y3             ( 427) RVDKASILAETIAYL   3
O65643             (  77) KSDKASVLTDTIQML   6
Q9SFZ3             ( 441) KTDTASVLMEAIGYI   9
O65552             ( 225) KTDKASMLDEIIDYV   3
Q8S9Z4             (  58) DKERNSTIISVVDFT  16
Q40902             ( 325) RLSKVMLIVAVCLVV  10
Q9FP06             ( 431) VTGKAVMLDEIINYV   5
Q8S3E1             ( 179) KMDRTSILGDAIDYM   4
Q8S3E5             ( 170) KLNTAEMFQAAAKYV   6
Q9FUA4             ( 229) KTDKASMLDEAIEYL   2
Q9M0X8             ( 193) KTDTASVLNEAVEYI   4
Q9SZK7             (1363) QQDKASVLGETVRYF  12
Q9LT23             (  91) KNDKATILTDTVQLL   7
Q9C690             ( 343) QTNTADMLDLAVQYI   4
Q9SQ79             ( 508) TVNIADMLDEAVEYV   7
Q9ASX9             ( 218) QMNTACVLDEAVQYL  29
Q8W2F2             (  77) KSDKASVLTDTIQML   6
O81072             ( 685) EEGKEEIFDFPEQYS  30
Q9SUP3             ( 136) VNDKNQLLSLVRKYL   8
Q40836             (  30) RMDKVSILAQTIAYL   3
Q9C9S9             ( 175) TMGMATMLDEIINYV   8
Q8S9M5             (  90) KTDKATLLAKVVQRV   8
Q9C8P8             ( 220) QTNTADMLEEAVEYV   4
Q9FTF3             ( 564) QGEKETVRQLAIVAL  72
Q9T079             ( 554) PKTTVVVLSRSEKCI  12
Q8L8X9             ( 180) KQSVPVILEEATDYI  10
Q8S3D2             ( 307) KMDTASMLDEAANYL   4
Q8S3F4             ( 245) KTDKASMLDEVIEYL   3
O23226             ( 176) VTGKAGMLDEIINYV   6
Q9M1K1             ( 106) KLSIPETVSKSLKYI   9
Q41514             (  30) RGEQASILAETIAYL   5
Q40833             (  30) KVDKASILAETIAYL   3
Q8LBH9             ( 146) SPCTLSVLPLTLGYI  27
Q9ZVX2             ( 238) KLDRASILGDAINYV   2
O49687             ( 444) KMDKASLLGDAISYI   3
Q9ZQS4             ( 450) KVDKVSILDHTIEYL   4
Q9SQK8             ( 200) KMDKASLLGDAISYI   3
Q941Z7             ( 103) KLSIPTTVSRVLKYI  10
Q8W2F6             ( 444) KMDKASLLGDAISYI   3
Q41854             ( 450) RVNKASILAETIAYL   3
Q9LN95             ( 109) KRSSADHVLEAVNYI  22
O81037             ( 224) RGDQASIVGGAIDFV   6
Q8L467             ( 164) KTDKPAILDDAIRIL  14
Q8S3E9             ( 159) KVDKASIVGDAVLYV   5
Q41286             (  30) KVAKVSLLAETIAYL   4
Q948F6             (  64) KTDKASMLDDAIEYL   3
Q8LQ30             (  58) RASTTRIVEEAIACV  11
O82398             ( 160) KTDKATVLEDAIKHL   3
Q8S3F0             ( 156) KMDKASVLGDALKHI   3
Q9ZVB5             (  96) KLSVSATVSQALKYI   9
Q8LE61             ( 302) KTDTASVLQEAIEYI   3
Q9FTJ0             (  23) LLLRIVVLGLVGEFG  73
Q9FTQ1             ( 109) KMDKAALLAEVVGHV   4
Q9AWY1             ( 286) KVDKASILSETIAYL   3
Q9CAL3             ( 311) LNFKYSTLEKATGSF  28
O80674             (  98) KTDKATLLAKVVQRV   8
Q9LND7             ( 194) FSSRLDLIVMAASVV  13
Q9SJM1             ( 349) FHDIALALKKIDTCI  21
Q8LIB8             ( 202) SMSKAAIVGMVRAVA   7
O23090             ( 277) RMDKASLLSDAVSYI   3
Q9LPW3             ( 295) KMDRASILGDAIDYL   3
Q9C682             ( 100) KTDKVAIINDAIRMV   6
Q9FYE6             ( 100) KLSIPMTVARVVKYI  11
Q9M5P3             ( 146) SPCTLSVLPLTLGYI  27
Q944L0             ( 298) AEKTKLTMNDVKAVL  16
Q9FH37             ( 105) KTDKAAILVDAVRMV   7
O23487             ( 348) KMDKASLLADAITYI   4
Q940I6             ( 180) VTGKAGMLDEIINYV   6
Q8LID5             ( 182) SVSKAAVLGLVRAVA   7
Q8RX65             (  59) KSDKASVLTDTIQML   6
Q9CAA9             ( 342) VTGKAVMLDEIINYV   5
Q9CAA4             (  78) KRDTASFLLEVIDYV  13
Q9C670             ( 262) VTGKAVMLDEIINYV   5
Q9LXG5             (  43) TVSASKVLQETCNYI  11
Q9SEY5             ( 254) SRPKGVVYSHRGAYL  35
O22768             ( 184) KTDRAAMIDEIVDYV   4
Q9STJ7             (  36) KRSTSDQVKGAVNYI  16
Q8LIC5             ( 176) GVSKAAVLGVVRAVA   9
Q8VWV9             ( 838) VVEKLMILGLSKSHL   6
Q9ATD7             ( 464) KADKVSILDVTIEYL   4
Q9FEA1             ( 503) KMDKASILGDTIEYV   2
O23297             ( 158) KTDKPAILDDAIRIL  14
Q9ATD8             ( 452) KADKVSILDDTIEYL   2
O50002             ( 218) KYNGGLDTEAAYPYV  67
Q8L5G8             (  80) RGDIHAQLKMLISYV  27
Q9SLX2             ( 450) KVDKVSILDHTIEYL   4
Q8H8H9             ( 148) RGDQATVVGGAIDYV   6
Q8H8E4             ( 210) KMDRTSILGDTIDYV   4
Q8H7N8             ( 142) RGDQASIVGGAINYV   6
Q8H6X2             ( 146) KMDKASIIGDAILYV   4
Q8H102             ( 322) QTSYSDMLDLAVQHI  17
Q8GZV6             ( 667) ITGKAMMLDEIINYV   8
Q8GZM7             ( 316) KSDKASMLDEAIEYM   4
Q8GZ38             ( 245) KTDKASMLDEVIEYL   3
Q8GZ13             ( 184) AMGMATMLDEIINYV   8
Q8GYC3             (  82) KLDKASVIKDSIDYM   3
Q8GY61             ( 211) ITGKAGMLDEIINYV   7
Q8GX46             ( 242) KGDRASILQDGIDYI   7
Q8GWZ9             ( 158) RGDQASIVGGAINYV   6
Q8GWK7             ( 186) TMGMATMLDEIINYV   8
Q8GVF0             ( 242) KGDRASILQDGIDYI   7
Q8GRJ1             ( 260) KTDKASILDEAIEYL   2
Q8VSD2             ( 422) TLSKHAEMAKAFDYI  24
Q9AMU0             (  60) DAFVALLLSFTVVCL  24
Q934L1             (  72) PVLLLSLLGATLDYA  12
Q8KWC2             ( 512) HTPMAYLLKPFTDYF  73
Q99QK1             ( 239) TLSKHAEMAKAFDYI  24
Q93SJ3             ( 164) AASKGGVVSMTLPMA  14
Q52181             ( 371) KVNQAKIDGFTFNQV  72
Q93QG8             ( 192) EGLTAATATDALSHL  23
Q93LQ4             ( 307) ARTKLQLVKATARHL   7
Q8VSI6             ( 422) TLSKHAEMAKAFDYI  24
O07845             ( 399) EVGKGLGLGLSISYS  31
Q9RMV6             (  66) RGITHSLFGLVLVLI  16
Q45828             ( 151) LKEKIDIVNNSVKVA   9
Q06074             ( 162) LFSMLMILSIGISRI  18
Q93HE5             ( 875) VHDRGSLLDLVRTHL   8
Q54812             ( 166) GFTKAVALELAKTGI  17
Q9AE31             ( 249) RGLNAITLGEAAAFH  41
Q9FA97             ( 199) LMDKASTLDFVVEVV   4
Q9AIT7             ( 199) LMDKASTLDFVVEVV   4
Q93EX7             ( 267) RRNRLAVLVATVKVL   8
Q9FDK7             (  56) PKKNIETLQKADIVV  14
Q8KWW8             ( 641) RAPRILVLDEATSHL   3
Q9S488             ( 171) KWGREDVLEQTIKNL  16
O07469             ( 218) IGDRVLIVSFVVVVI  10
O06468             ( 252) IRLATEMMSEADGYL  15
Q55221             ( 167) GFTKAVALELARTGI  17
Q937Y1             ( 269) NMERITIYKEAVDFI  13
Q93QX7             ( 323) AMLSALTLLPALLFV  17
Q54206             ( 130) TLAKGMIVEGSAEYV   8
Q8VSD7             ( 422) TLSKHAEMAKAFDYI  24
Q93NY1             ( 425) RELDPSVMAAAVGYV  16
Q9EZI2             ( 133) QLGQTADIAHAVAFL  12
O51656             ( 203) VNYKLNDINKSIEYI  40
P72627             ( 491) RFPRLLVLILSVVVM   9
O07744             ( 150) PHDRVGIMWPSLLVI  39
Q9PDI9             ( 119) KPLQSDIKPITIEVV  26
Q9KN09             ( 398) LLINALMVALAIALL  13
Q9KEL2             (  82) SVTKVQLLGIVLIVV   9
Q9KC74             ( 486) LEEKLSTLQNVKSYV   6
Q9K9K1             ( 332) RVSKGRTIREFVIGV  19
Q9K718             (  61) LAVLFFVLTIAVAYF  38
Q9K0Z5             ( 231) QRAKLAILGISSKVV   7
Q9JYW1             (  21) SYSKSSIIIFSSYVV  21
Q9JXR1             ( 112) QVNLKSVFRASKAVL  15
Q9JSY4             ( 231) QRAKLAILGISSKVV   7
Q9I2R3             (  81) KQAKKHPEQKSRVYV  48
Q9I201             ( 264) KTERGLTVLGTSGYL   8
Q9I1Q7             ( 323) GLLTVSGLAALVAFL  30
Q9HYP7             ( 204) EMTALNDGRQALEYL  34
Q9HVI8             (1241) RVPKVSVNLSARQFA  35
Q9HUF4             ( 226) KLIKALDAITVDGFV  30
Q9AB09             ( 351) KLSRILWLGPAVVLI  29
Q9AA40             ( 469) ALYKVLTVTIEMRHA  84
Q9A7Z6             ( 163) GASKAGLLHMTKRMA   8
Q9A0C0             ( 519) LKDKLVTIGDAAFHI  10
Q99YD6             ( 154) AASKAGMIGFTKSVA   7
Q99SP1             ( 139) NVAKADIIDNSIFYA  12
Q98ND6             ( 170) VRSRGVVVFLAVWMI  67
Q98HM4             ( 160) SASKGGVVGMTLPVA  13
Q98H05             ( 326) REERGGVLASVLSVM   8
Q98FG7             ( 286) YGDRAALLKEAATFV   9
Q98DE7             ( 362) EIPRIVVLGLSLIVI   8
Q98D51             ( 141) LQERLAIIDTAQGNI  19
Q98BY8             ( 306) PFEKVDLVAIARGVI   9
Q986S8             ( 255) VNDRVGMMIDSLAHV   9
Q9FBC3             ( 154) AASKAGLIGFTKSVA   7
Q97PK5             (  31) MANRILTILASIFFV  19
Q97MM6             ( 149) NNPKLLILDEPTVGI  18
Q97L06             ( 108) SEAKLDVIANAVGYT  11
Q97KQ0             ( 320) NIEKNLIIMVVVSFV  17
Q97DR7             ( 154) HNPKLIIMDEPTVGI  18
Q97DA6             ( 158) AAAKAGIIGMTKSVA   6
Q930R6             ( 417) YKAKTVVNEVLDRYT  55
Q92UI5             ( 476) YLAMLADYREATDVL  18
Q92JC5             ( 322) FQFQVGMYKIVTAFL  23
Q92JA3             ( 173) ETVKATVESAVREVI  14
Q92FV1             (  37) VNDEGVTLTGSDSDI  19
Q92DA6             ( 100) YRFHHTTLQWKREKI  54
Q8ZN33             ( 332) KESARSVLRVWLKFA  74
Q8ZLD6             ( 456) VFSKIGLVTLAVTVV   8
Q8ZAZ2             ( 346) AKNKGETIYEALNYI  12
Q8Z269             ( 456) VFSKIGLVTLAVTVV   8
Q8YDB5             ( 174) RDMEIHIKDVSDKYL  92
Q8YAW1             (  37) VNDEGVTLTGSDSDI  19
Q8Y8J1             ( 110) KRDKIEAGEISTNSI  33
Q8XJS0             ( 214) CNNKIVLMRITKEMI  34
Q8XG63             ( 293) QAATEITLADAPKFA  18
Q8XDS3             ( 458) CVAIIVVLAFATRFL  33
Q8XBY1             ( 532) HWPKTTLLVAALSVL   9
Q8XBW4             ( 372) RSDMLSTIEYAPVWI  36
Q8X731             ( 274) IEECNAIIEQFIDYL  37
Q935B7             (  67) KFTRSDVIRAAIFHL  10
Q8UK57             ( 172) GLDKWRWMIGTGVYL  43
Q8UBX7             ( 316) YGEKAAILIAAARFI   9
Q8U8H9             ( 494) EQAPWATLAHSTQFV  29
Q8U717             ( 303) RRERVDLVDITRTVV   7
Q8U6T5             ( 257) APSWGSMLNTAKNFL  34
Q8VJU9             ( 232) PHDRVGIMWPSLLVI  39
O67212             ( 380) MYEKIIILGVALNFL  23
O67226             ( 832) KEKKGEILLHVNDFP  41
Q55190             ( 320) EDLEEQILPLADFFV  24
Q9X2H5             (  69) VSDKILVISTAVAML  10
Q92PZ0             ( 317) SGDMVGVKRAAIAVL  22
Q92N34             ( 244) ICTKHGILLIFDEVI  21
Q92L22             ( 285) YGPRSAILAETARFI   9
Q92KZ6             (  80) ASERSLILLRAADMI   8
Q8YJN7             (  18) APEKLEVINESRLHA  10
Q8YDP9             ( 430) PLVTGTILGLLVIYI  22
Q8XWW9             ( 217) RLSTPQDVANACLYL  13
Q8XWH5             ( 449) AESRALIVAHVTRFT  11
Q8XVB4             ( 281) DSDKVLTLDEALEGA  17
Q8XUI9             ( 199) LMDKASTLDFVVEVV   4
Q8XQE9             ( 400) MLSMVMMLSMSLGVA  20
Q8R8L9             ( 232) ALLSVGVLALMYGYT  67
Q8R7I9             ( 278) KATMVGAAKLIIDYL  24
Q8R9W0             ( 156) AASKAGIIGLTKSVA   6
Q8R805             ( 220) KVTAHEDLADVVLFF  22
Q8PQX4             ( 126) RGVKVRILIDQLSAI  37
Q8PN93             ( 306) TRDKVLIGAAAAAVT  29
Q8PLS9             ( 112) FAPRAAMLEQAAGVV  10
Q8PLK3             ( 428) RANEAGALTAAIGSV  17
Q8PLF0             ( 163) AASKGGVVGMTLPMA  14
Q8PJ52             ( 251) SAPKLAAFGMAYRLL  16
Q8PEY1             ( 470) TQPKILVLDEATSHL   5
Q8PEJ4             ( 279) KNARAVTVVSAISHV   8
Q8PED2             ( 186) KGLMALTLLQRPDYS  46
Q8PAS7             ( 282) RNFRAGTLAMVVAYA  12
Q8PA03             ( 112) FAPRASMLEQAAAVV   9
Q8P9S2             ( 428) RANEAGALTAAIGSV  17
Q8P9M2             ( 163) AASKGGVVGMTLPMA  14
Q8P7U4             ( 251) SAPKLAAFGMAYRLL  16
Q8P1F7             ( 519) LKDKLVTIGDAAFHI  10
Q8NZN2             ( 154) AASKAGMIGFTKSVA   7
Q8NT37             ( 194) IREKTGVLIASAGYL   9
Q8NSF7             ( 100) KAEDITIERFNQQYT  26
Q8NRK9             ( 233) HGDKTMQVADAAAEI  24
Q93IG7             ( 162) SPTRASVVGEVAEML   7
Q8KCN0             ( 247) KINKLVLLSDTVGFI   6
Q8KAN9             (  61) DAEKIGTVQQAIDYI  10
Q8K7X8             ( 510) LKDKLVTIGDAAFHI  10
Q8K628             ( 154) AASKAGMIGFTKSVA   7
P72392             ( 130) TLAKGMVVEGSAEYV   8
O86560             (1173) RLARLDTLPTAATVL  11
Q9Z4X2             ( 369) PLSRTSLPEIAQPHL  34
Q9XAP7             ( 281) RLDRLVTVFNARAVT  17
Q9L1T4             ( 298) RWDRLITLLNSRAVT  11
Q9KYC2             ( 253) HRARLAILKAAVDYA   6
Q9FC54             ( 204) ERAKATVVHVTASHA  11
Q9KZV9             ( 320) KGNKADTLPATKSFL   9
Q8ZDH6             ( 125) KSNRTAIITLSCLVI   9
Q8ZJH0             ( 274) IEECNAIIEQFIDYL  37
P97309             ( 113) NLTKIETLRLAIRYI   5
O70241             ( 198) RWNKGTILKASVDYI   5
Q923F4             ( 414) KAAKVVILKKATEYV   2
Q9EPW1             (  90) KLDKLTVLRMAVQHM   3
Q99JK7             (  82) KLNKSAVLRKAIDYI   3
Q9D030             ( 100) KLSKIQTLKLAARYI   3
Q8K3I5             ( 225) AGKKHLIFGEPEEFI  18
Q8VHR1             (  50) HLDKASIMRLTISYL   4
O89006             ( 182) GMPKTGILIAVLSVI   7
Q9R2A2             ( 182) GMPKTGILIAVLSVI   7
Q9Z2I5             (  48) HLDKASIMRLTISYL   4
Q9QUM5             (  87) KLEKAEILQMTVDHL   2
Q9JHC5             (  57) KLEKADILELSVKYM   3
Q8R4E5             ( 178) GQSKGGILSKACDYI   6
Q9EPJ1             ( 143) KLSKIQTLKLAARYI   3
Q8R3M6             ( 504) LQEKASVLKKTLESL   9
Q925V5             ( 157) KLSKIETLRLAKNYI   2
Q9D2H4             ( 225) AGKKHLIFGEPEEFI  18
Q8K1Z8             (  90) RHTTLSLLTKAKLHI   8
Q9JK54             ( 155) PLTKIQTLKYTIKYI  11
Q9EQW5             ( 105) KLSKIATLLLARNYI   4
Q8VI53             ( 252) QTSHAITLQKTMEYI  11
O89012             ( 182) GMPKTGILIAVLSVI   7
O89105             (  62) KLDKLSVLRLSVSYL   2
Q9WTU9             (  54) HLDKASVMRLTISYL   4
Q99N33             ( 518) PQTKLLILHQAVAVI   6
Q9QXJ5             (2398) KVSKSLILNRAFSEI  15
Q923L9             (  43) KLDKLSVLRRAVQYL   2
P70366             (  63) KPDKCKILKKTVDQI   9
Q8VHZ2             (  25) RLPKVEILRNAIRYI   2
O08718             ( 118) KLTKIETLRFAHNYI   5
Q8R385             (  53) HLDKASVMRLTISYL   4
Q91XJ5             (  84) KLDKLSVLRRAVQYL   2
Q8R2J8             ( 234) RWNKGTILKASVDYI   5
O88295             ( 108) KLDKLTVLRMAVQHM   3
Q9ESZ4             ( 172) KMHKSGVLRKAIDYI   9
Q8K1X3             ( 394) PQTKLLILHQAVAVI   6
Q62850             ( 227) LSPKASPEQRATRSI  39
O89007             ( 182) GMPKTGILIAVLSVI   7
O09135             ( 237) GQSKGGILSKACDYI   6
Q9QX98             ( 195) RLSKVDTLRLAIGYI   2
Q8QZX6             (  62) KLDKLSVLRLSVSYL   2
Q9R0U2             ( 108) KLDKLTVLRMAVQHM   3
P70365             (  63) KPDKCKILKKTVDQI   9
Q924H3             (  77) KLDKLSVLRRAVQYL   2
Q9D8P5             (  88) RHTTLSLLKRAKMHI  14
Q91XK1             ( 444) PQTKLLILHQAVAVI   6
Q9DBX7             (  81) KLEKAEVLQMTVDHL   3
Q9D0R0             (  87) KLEKAEILQMTVDHL   2
Q61202             (  63) KPDKCKILKKTVDQI   9
Q8VCY4             ( 583) PQTKLLILHQAVAVI   6
Q9JHS2             (  48) HLDKASIMRLTISYL   4
Q9EPN2             ( 134) KLSKIKTLRLATRYI   3
Q9CYA8             (  53) HLDKASVMRLTISYL   4
Q9WTL8             ( 115) KLDKLTVLRMAVQHM   3
Q9JL51             (  49) RLPKVEILRNAIRYI   2
Q99JA6             (  52) KLEKAEILEFAVGYL   3
O35391             (  36) QLDKASIIRLTTSYL   3
O70425             ( 115) RLPKVEILRSAIQYI   2
O55208             (  94) KPSKVDILKGATEYI   4
Q62065             ( 434) LRTKGGCLLEVEELL  24
Q8R4S5             (  62) KLDKLSVLRLSVSYL   2
O88810             ( 108) KLDKLTVLRMAVQHM   3
O88529             ( 108) KLDKLTVLRMAVQHM   3
Q9JIZ5             (  82) KLSKAAILQQTAEYI   3
Q8VBZ0             ( 174) RGSRVVTVGSATQYV   5
Q9QYC3             ( 107) KLSKIETLTLAKNYI   3
Q8VIP2             ( 699) KVSKATTLQKTAEYI   3
O88930             (  62) KLDKLSVLRLSVSYL   2
Q8K3Z5             ( 114) KAPKVVILKKATAYI   2
Q9QX54             (  48) HLDKASIMRLTISYL   4
Q9D489             ( 234) KSDVASVIEATVDYV   9
Q8R4S7             (  62) KLDKLSVLRLSVSYL   2
Q9CYJ4             ( 582) PQTKLLILHQAVAVI   6
P70562             ( 107) KLSKIETLTLAKNYI   3
Q8R4S3             (  62) KLDKLSVLRLSVSYL   2
O35800             (  53) HLDKASVMRLTISYL   4
Q99KZ5             ( 718) PQERVQMVRVALKHI   8
Q8VE59             (  75) GASKGGILSKACDYI   5
Q8K0H8             ( 170) KLSKAIVLQKTIDYI   3
Q9QZQ0             (  94) QLDKASIIRLTISYL   3
Q9QY56             ( 593) LRTKGGCLLEVEELL  24
Q921F3             ( 125) KPDKLTILRMAVSHM   3
O89009             ( 182) GMPKTGILIAVLSVI   7
Q9WTW4             ( 146) RWNKGTILKASVDYI   5
Q8R4S6             (  62) KLDKLSVLRLSVSYL   2
Q923Z4             ( 138) RLSRIETLRLAIVYI   4
Q9QYE4             ( 106) KLSKIETLTLAKNYI   3
Q921S4             (  95) KLDKLTVLRMAVQHM   3
Q99MB8             ( 579) AQTKLLILQQAVQVI   5
Q9EQX3             ( 246) GASKGGILSKACDYI   5
Q8K3Z4             ( 115) KAPKVVILKKATAYI   2
Q9QXW8             (  81) KLEKAEVLQMTVDHL   3
Q923F0             ( 184) KLSKNEVLRLAMKYI   4
Q9QYF5             ( 195) RLSKVDTLRLAIGYI   2
Q9Z2W6             (  63) QLSQVEILQRVIDYI   4
Q9JL05             ( 253) KLSKIATLLLAKNYI   3
O70284             (  36) QLDKASIIRLTTSYL   3
Q9JHS1             (  50) HLDKASIMRLAISFL   4
Q8R4S4             (  62) KLDKLSVLRLSVSYL   2
O35410             ( 237) GQSKGGILSKACDYI   6
Q63643             ( 136) KPDKLTILRMAVSHM   3
Q9Z312             (  61) KLDKLSVLRLSVSYL   2
Q91YA9             ( 108) KLDKLTVLRMAVQHM   3
Q9WTL9             ( 108) KLDKLTVLRMAVQHM   3
Q9JI41             (  34) KLSKIQTLKLAARYI   3
Q9JJR4             ( 182) GMPKTGLLIIALGVM   9
Q9QVY1             (  62) KLDKLSVLRLSVSYL   2
Q9JL50             (  49) RLPKXEILRNAIRXI   2
Q9Z2E5             (  76) KLSKYETLQMALSYI   5
O35434             ( 103) QMFIFLVLGIAECVL  21
Q9JJK7             (  62) KLDKLSVLRLSVSYL   2
Q91YV0             ( 440) PQTKLLILHQAVAVI   6
O70483             ( 114) KLSKLDTLRLASSYV   3
Q8VCH2             ( 127) QAPKSSMMTTTATVL   9
O88337             ( 103) KLDKLTVLRMAVQHM   3
Q9QUS4             (  86) KLEKAEILQMTVDHL   2
Q8JZK8             ( 225) AGKKHLIFGEPEEFI  18
Q9WUJ7             ( 153) KLSKVETLRSAVEYI   2
Q91VN7             (  88) RHTTLSLLKRAKMHI  14
Q923L8             (  77) KLDKLSVLRRAVQYL   2
Q91XJ6             (  84) KLDKLSVLRRAVQYL   2
Q8R4S2             (  62) KLDKLSVLRLSVSYL   2
Q60763             ( 225) AGKKHLIFGEPEEFI  18
Q922S2             ( 579) AQTKLLILQQAVQVI   5
Q9JK33             ( 222) KLSKNEILRLAMKYI   4
Q99P79             (  62) KLDKLSVLRLSVSYL   2
Q9CZ29             ( 423) SLIKHQRFHTAAKHH 100
Q8VD56             ( 108) RLSKVETLRAAIKYI   2
Q9D8I0             ( 118) KLTKVETLRFAHNYI   5
Q99NA2             ( 266) KLSKLAILRIACNYI   3
Q9JLR5             ( 110) KLSKLDVLVLATSYI   5
Q9JJV6             (  81) KLEKAEVLQMTVDHL   3
Q9JHE6             (  60) KLENAEVLELTVRRV   9
Q9CRT1             (  72) PQTKLLILHQAVAVI   6
O08662             ( 316) YLTMFKMLRDTLYYM  23
P97831             ( 100) KLSKIQTLKLAARYI   3
Q99PF1             ( 225) AGKKHLIFGEPEEFI  18
Q64305             ( 197) RLSKVDTLRLAIGYI   2
Q91W36             ( 491) TVTDEETVGKAKAYI  12
Q8CIY4             (  62) KLDKLSVLRLSVSYL   2
Q8CIY3             ( 125) KPDKLTILRMAVSHM   3
Q8CHL8             (  62) KLDKLSVLRLSVSYL   2
Q8CHG9             ( 112) KPDKLTILRMAVSHM   3
Q8CH17             (  87) KVSKVEILQHVIDYI   4
Q8CGH4             (  82) HLEKAVVLELTLKHL   4
Q8CEI7             ( 136) KLSKIETLRLAKNYI   2
Q8CEC2             ( 110) KPDKLTILRMAVSHM   3
Q8CE98             ( 599) PQTKLLILHQAVAVI   6
Q8CD45             (  63) QLSQVEILQRVIDYI   4
Q8CD44             (  80) KLEKAEILQMTVDHL   2
Q8CC19             (  54) HLDKASVMRLTISYL   4
Q8CAH9             ( 580) AQTKLLILQQAVQVI   5
Q8CAG7             (  66) KPDKCAILKETVKQI   8
Q8C9W6             (  67) KMDKSTVLQKSIDFL   4
Q8C9V3             ( 125) KPDKLTILRMAVSHM   3
Q8C7Y3             (  66) KPDKCAILKETVKQI   8
Q8C733             ( 350) KLNKSAVLRKAIDYI   3
Q8C6Y4             ( 331) RWNKGTILKASVDYI   5
Q8C6B1             ( 143) RLPKVEILRNAIRYI   2
Q8C6A8             ( 253) KLSKIATLLLAKNYI   3
Q8C5F1             ( 270) RWNKCTILKASVDYI   7
Q8C4Y1             (  48) KASRAQILDKATEYI   2
Q8C1I7             (  54) KLSKLAILRIACNYI   3
Q8BWA4             (  78) KLSKAAILQQTAEYI   3
Q8BVI1             (  55) KLEKADILEMAVSYL   2
Q8BTI2             (  32) KLEKADILELSVKYM   3
Q8BRU1             (  67) KMDKSTVLQKSIDFL   4
Q8BPE2             ( 184) KLSKNEVLRLAMKYI   4
Q8BN74             (  66) KPDKCAILKETVKQI   8
Q8BN29             ( 241) RWNKGTILKASVDYI   5
Q8BLP5             (  33) RLSKIATLRRAIHRI   9
Q8BKT2             (  52) KLEKAEILEFAVGYL   3
Q8BKA6             (  53) KLEKADILEMTVRFL   3
Q8BGW3             ( 135) KLSKIATLLLAKNYI   3
Q8BFV7             ( 112) KLSKIEILRLAICYI   4
Q8VAP6             ( 109) TISRTGIVKGTTQFL   8
Q65090             ( 586) ALLRAATYYFSDSEI  26
Q9E8G3             ( 293) SMSKLTLITLVCLVA   9
O42090             ( 187) VQDRNVLLLITSKYI   7
O10469             ( 269) TRSRISLIRRVCCYA  10
Q9DTG3             ( 269) TRSRISLIRRVCCYA  10
Q9YN85             ( 269) TRSRISLIRRVCCYA  10
Q91TM1             ( 417) GQLRLLTLEQAAAAV  13
Q00938             (  64) ALLRAATYYFSDSEI  26
P87593             ( 204) EHERGIILRASASML  10
Q89391             (  44) RPPRAVLMMTAVFFI  16
Q91DH6             ( 252) EIEKTVVVAGSTQHI   9
Q9YWN1             (2255) AANELGMLEKTKEDL  15
Q9IFW8             ( 269) TRSRISLIRRVCCYA  10
Q84636             ( 119) SPEKIMIILAVLFVI  12
Q8QUM5             ( 174) RRTKREIIASAIQCL  20
Q9Q8F5             ( 333) NMTKMDILESVVHYA  19
Q8QMT4             (  31) RYTRSIIIKMSIHYI  12
Q9E9R6             ( 665) ELSRAGTLGCSCGVA  11
Q9PTN8             (  57) KLEKADILEMTVTYL   3
Q9W7B5             (  66) KTEKADILKKTVHFL   5
Q98T39             ( 120) KAPKVVILKKATEYV   2
Q9PSF5             (  32) KLSKLDVLVLGTNYI   9
Q98T40             ( 120) KAPKVVILKKATEYV   2
Q98T13             ( 120) KAPKVVILKKATEYV   2
Q8QFX4             (  61) SVSQVEILQHVIDYI   7
Q98T02             ( 121) KAPKVVILKKATEYV   2
Q98TW1             (  67) KPDKCAILKETVKQI   8
Q9W7E6             (  85) KPSKVDTLKAATEYI   3
Q8JH17             ( 120) KAPKVVILKKATEYV   2
Q90466             (  56) RQEKADILEMTLDFL   4
Q98T43             ( 120) KAPKVVILKKATEYV   2
Q98927             ( 825) KAPKVVILKKATEYV   2
Q8JI94             ( 121) KAPKVVILKKATEYV   2
Q9I8T7             ( 115) KLDKLTVLRMAVQHM   3
Q9PWP2             ( 111) KLTKIETLRFAHNYI   5
Q9W7B6             (  52) KMEKAEILELAVIYI   4
P79832             ( 101) KPDKLTILRMAVSHM   3
Q9PUL7             ( 106) KLSKIQTLKLASRYI   3
O57562             ( 220) KLSKNEILRLAMKYI   4
Q8JH03             ( 120) KAPKVVILKKATEYV   2
Q91207             ( 134) RLPKVEILRSAIQYI   2
Q9I8A3             (  82) KLEKAEILQMTVDHL   2
Q8UV09             ( 127) KAPKVVILKKATEYV   2
Q90X12             (  72) RVSKVEILQHVIDYI   4
Q98T19             ( 120) KAPKVVILKKATEYV   2
Q98T00             ( 120) KAPKVVILKKATEYV   2
O42245             ( 153) KLSKYETLQMAQIYI   9
Q8UUZ7             ( 127) KAPKVVILKKATEYV   2
Q90464             (  29) KLEKADILEMAVIYL   5
Q90X13             (  72) RVSKVEILQHVIDYI   4
Q98T16             ( 120) KAPKVVILKKATEYV   2
Q98T45             ( 120) KAPKVVILKKATEYV   2
O42180             (1494) LLPKTQVIDRAVKVL   6
Q91558             (  80) KMSKVETLRSAVEYI   2
Q9W6C8             ( 142) KLSKIETLRLAKNYI   2
Q8JIA0             ( 124) KAPKVVILKKATEYV   2
Q9I8K2             (  51) KMDKSTILQKSIDFL   3
Q98939             ( 120) KLSKYETLQMAQIYI   9
Q8JGZ6             ( 120) KAPKVVILKKATEYV   2
Q8JH04             ( 120) KAPKVVILKKATEYV   2
Q8JIS0             ( 113) KLTKIETLRFANNYI  13
Q9I9C6             ( 372) RLPKEVILKRAADLV   6
Q8UVH3             (  62) KPDKCKILKKTVDQI   9
Q9DG56             ( 113) KLTKIETLRFARNYI   4
Q91606             (  92) PQTKLLILHQAVSVI   6
Q8JH12             ( 120) KAPKVVILKKATEYV   2
Q8UUJ7             (  88) NLTKIETLRLATRYI   5
Q90ZD3             ( 143) RLPKVEILRNAISYI   2
Q9DFB9             ( 340) KAAKVMILKKAAECI   7
Q8UW73             (  53) KVEKAEILECTVQFL   7
Q9I9Q6             (  58) RIDKSTVLQKSIDFL   5
Q8JIX6             ( 132) RLPKVEILRSAIQYI   2
Q9W621             (  75) KLEKADILEMTVKHL   3
Q9PSL4             (  26) EALKRSTLLNPNQRL  37
Q9YH69             ( 100) KLSKIQTLKLAARYI   3
Q98SZ9             ( 118) KAPKVVILKKATEYV   2
Q98T38             ( 120) KAPKVVILKKATEYV   2
Q98T04             ( 120) KAPKVVILKKATEYV   2
Q8QGE4             ( 284) RWNKGTILKASVDYI   5
Q98904             (  32) KLSKYDTLQMAQTYI   8
Q90W24             ( 219) KLSKNEILRLAMKYI   4
Q98T36             ( 124) KAPKVVILKKATEYV   2
Q98T12             ( 120) KAPKVVILKKATEYV   2
Q8JH16             ( 120) KAPKVVILKKATEYV   2
Q98T34             ( 124) KAPKVVILKKATEYV   2
Q9PTB3             (  50) HLDKASIMRLAISFL   4
O13126             (  68) KLSKYETLQMALSYI   5
Q9DEU8             (  56) KLEKADVLEITVQHM   4
Q98T06             ( 120) KAPKVVILKKATEYV   2
Q98SW2             (  53) NLDKASIMRLAISYL   5
Q98T24             ( 120) KAPKVVILKKATEYV   2
Q8JI93             ( 121) KAPKVVILKKATEYV   2
Q91399             (  67) KLSQVEILQHVIDYI   5
Q90XP4             ( 331) RWNKGTILKASVDYI   5
Q8QHA1             ( 127) KAPKVVILKKATEYV   2
Q9DE43             ( 131) KLSKIETLRLARNYI   3
Q9W6G4             (  50) KLSKIEILRLAICYI   4
Q9YH82             ( 113) KLTKIETLRFAHNYI   5
Q8JGZ8             ( 120) KAPKVVILKKATEYV   2
Q8UUZ9             ( 127) KAPKVVILKKATEYV   2
Q98T15             ( 120) KAPKVVILKKATEYV   2
Q98T35             ( 124) KAPKVVILKKATEYV   2
Q91631             (  43) PQTKLLILHQAVAVI   6
Q8JI91             ( 121) KAPKVVILKKATEYV   2
Q98SF2             (  80) KMSKVETLRSAVEYI   2
Q90467             (  46) KVEKAEILESVVHFL   5
Q8QGQ7             ( 128) KLDKLTVLRMAVQHL   2
Q98SK3             (  81) KPDKLTILRMAVSHM   3
O12943             (  80) KLSKVETLRSAVEYI   2
Q98T09             ( 118) KAPKVVILKKATEYV   2
O42448             (  60) NVSKMEILQHVIDYI  17
O73624             ( 132) TLTKIETLRLTIRYI   4
Q8JH08             ( 120) KAPKVVILKKATEYV   2
Q98SJ5             (  36) QSDKASIIRLTTSYL   4
Q90Y91             (  55) SLDKLSILRLSVSYL   3
Q90X15             (  69) RVSKVELLQHVIDYI   5
Q90692             (  36) QLDKASIIRLTTSYL   3
Q98T33             ( 124) KAPKVVILKKATEYV   2
Q98T44             ( 120) KAPKVVILKKATEYV   2
Q9W631             ( 223) PQTKLLVLHQAVNVI   6
Q8QFW6             ( 372) RLPKEVILKRAADLV   6
Q98SZ8             ( 120) KAPKVVILKKATEYV   2
Q9W6C7             ( 113) KLSKIETLRLAKNYI   2
Q8JI79             ( 120) KAPKVVILKKATEYV   2
Q8JIA2             ( 124) KAPKVVILKKATEYV   2
Q8JI97             ( 121) KAPKVVILKKATEYV   2
Q9IAJ4             ( 124) TLTKIETLRLAIKYI   3
Q98T41             ( 120) KAPKVVILKKATEYV   2
Q98T03             ( 120) KAPKVVILKKATEYV   2
Q9PTE4             ( 139) KLSKIQILKLASRYI   3
Q98T29             ( 120) KAPKVVILKKATEYV   2
Q8JI96             ( 121) KAPKVVILKKATEYV   2
Q8JHA0             (  74) KLSKYETPQMALSYI  25
Q91557             (  80) KMSKVETLRSAVEYI   2
Q8JH18             ( 120) KAPKVVILKKATEYV   2
Q90WR7             ( 334) KMHKSGVLRKAIDYI   9
Q8JI81             ( 120) KAPKVVILKKATEYV   2
Q90X20             (  53) KPDKLTILRMAVSHM   3
Q98T21             ( 120) KAPKVVILKKATEYV   2
Q8UV03             ( 127) KAPKVVILKKATEYV   2
Q8JI98             ( 121) KAPKVVILKKATEYV   2
Q90X22             (1052) KASTKEMLSPVVEMV  14
Q8QGM5             ( 114) KPDKLTILRMAVSHM   3
Q8JIA1             ( 124) KAPKVVILKKATEYV   2
Q98T25             ( 120) KAPKVVILKKATEYV   2
Q9DDS7             ( 201) KISLIGIAALVVAVI  24
Q98T37             ( 124) KAPKVVILKKATEYV   2
Q9I8A9             (  53) HLDKASIMRLDHQLP  79
Q8JI83             ( 120) KAPKVVILKKATEYV   2
Q90260             ( 101) KMSKVETLRSAVEYI   2
Q9DFB3             (  49) KLSKIKTLRLATSYI   3
Q8JI87             ( 121) KAPKVVILKKATEYV   2
Q8JIG1             ( 110) KLDKLTVLRMAVQHM   3
Q9DG11             (  99) KPDKLTILRMAVSHM   3
Q9PSH0             ( 111) KMKSVETLRSAVEYI   9
Q8JH14             ( 120) KAPKVVILKKATEYV   2
P79831             ( 101) KPDKLTILRMAVSHM   3
Q9PUA3             (  58) RMDKSTVLHKSIDYL   4
Q98SZ2             ( 120) KAPKVVILKKATEYV   2
Q8UV06             ( 127) KAPXVVILKKATEYV   2
Q9PWC2             ( 235) RWNKGTILKASVDYI   5
Q9DDU6             (  36) QLDKASIIRLTTSYL   3
Q91960             (  51) RLPKVEILSSAINYX   3
Q98SZ1             ( 120) KAPKVVILKKATEYV   2
Q8JH11             ( 120) KAPKVVILKKATEYV   2
Q9PTE3             ( 111) KLSKIQTLKLAARYI   3
Q8JI86             ( 121) KAPKVVILKKATEYV   2
Q90W03             (  55) SLDKLSILRLSVSYL   3
Q8QGE1             ( 144) RLPKVEILRNAISYI   2
Q90764             ( 135) KMSKVETLRSAVEYI   2
Q9IAU1             (  69) KLDKLTVLRMAVQHL   2
Q8QH97             ( 128) KAPKVVILKKATEYV   2
Q98T17             ( 120) KAPKVVILKKATEYV   2
Q8JH20             ( 120) KAPKVVILKKATEYV   2
Q98T46             ( 120) KAPKVVILKKATEYV   2
Q9PWD7             ( 107) KLSKIEILRLAICYI   4
Q8QGI4             ( 119) KLSKIATLLLARNYI   4
Q8JH35             ( 131) KLSKIETLRLARNYI   3
O73687             ( 219) KLSKNEILRLAVKYI   2
Q9DDQ8             ( 128) KLSKIETLRLAKNYI   2
Q9I9K1             (  53) RLEKAEILEYTVLFL  11
Q8JH06             ( 120) KAPKVVILKKATEYV   2
Q9DE55             ( 101) RLPKVEILRNAIQTS  28
Q9W6B8             (  55) KLSKIETLRLAKNYI   2
Q98T07             ( 120) KAPKVVILKKATEYV   2
Q8UUZ8             ( 127) KAPKVVILKKATEYV   2
O13125             (  68) QLSKYETLQMALSYI   5
Q98SF1             (  55) KMSKVETLRSAVEYI   2
Q98T05             ( 120) KAPKVVILKKATEYV   2
Q8QH98             ( 127) KAPKVVILKKATEYV   2
Q98T11             ( 120) KAPKVVILKKATEYV   2
Q8JH01             ( 120) KAPKVVILKKATEYV   2
Q8UVC4             ( 132) RLPKVEILRSAIQYI   2
Q98SZ6             ( 120) KAPKVVILKKATEYV   2
Q98SZ3             ( 120) KAPKVVILKKATEYV   2
Q8JI89             ( 121) KAPKVVILKKATEYV   2
Q9PTN9             (  38) KLEKADILEMAVSYL   2
Q98SZ7             ( 120) KAPKVVILKKATEYV   2
Q8JH15             ( 120) KAPKVVILKKATEYV   2
Q9W690             ( 146) PLTKIQTLKCTINYI   7
Q8JH21             ( 120) KAPKVVILKKATEYV   2
Q8UVC5             ( 101) RLPKVEILRNAIQYI   2
Q8JI90             ( 121) KAPKVVILKKATEYV   2
Q92001             ( 126) RLPKVEILRSAIQYI   2
Q98T30             ( 120) KAPKVVILKKATEYV   2
Q9DGA9             (  63) KLSKYETLQMALSYI   5
Q8JH02             ( 120) KAPKVVILKKATEYV   2
Q8JH07             ( 120) KAPKVVILKKATEYV   2
Q90YI8             ( 239) KLSKNEILRLAMKYI   4
Q98T32             ( 120) KAPKVVILKKATEYV   2
Q8JI82             ( 120) KAPKVVILKKATEYV   2
O57452             (  55) SLDKLSILRLSVSYL   3
Q98SS8             ( 116) RLPKVEILRNAISYI   2
Q8QGM4             (  50) HLDKASIMRLAISFL   4
Q9W7C6             (  50) HLDKASIMRLAISFL   4
Q90259             ( 113) KMSKVETLRSAVEYI   2
Q90465             (  55) KLEKADILELTVKHL   3
Q90ZK9             ( 101) RLPKVEILRNAIQYI   2
Q98T27             ( 120) KAPKVVILKKATEYV   2
Q98T10             ( 120) KAPKVVILKKATEYV   2
Q98T23             ( 120) KAPKVVILKKATEYV   2
Q9I9C9             ( 212) KLSKNEILRLAMKYI   4
Q8JIX7             ( 132) RLPKVEILRSAIQYI   2
Q9YIB9             (  53) HLDKASIMRLTISYL   4
Q8UV00             ( 127) KAPKVVILKKATEYV   2
Q9I8H6             ( 117) KLNKSAVLRKAIXXX   2
Q8JI78             ( 121) KAPKVVILKKATEYV   2
Q9DF73             (  53) RLEKAEILEYTVLFL  11
Q8UV01             ( 127) KAPKVVILKKATEYV   2
Q8UV02             ( 127) KAPKVVILKKATEYV   2
Q90Y06             ( 233) KLSKNEILRLAMKYI   4
Q98SN3             ( 125) KPDKLTILRMAVSHM   3
Q9YH15             ( 105) KLSKIEILRLAICYI   4
Q8JH19             ( 120) KAPKVVILKKATEYV   2
Q9DG35             (  29) KLDKLTVLRMAVQHM   3
Q8QHA0             ( 127) KAPKVVILKKATEYV   2
Q8JH13             ( 120) KAPKVVILKKATEYV   2
O13150             ( 118) KMSKVETLRSAVEYI   2
Q9W6C6             ( 123) KLSKIETLRLAKNYI   2
Q90X14             (  67) KLSQVEILQHVIDYI   5
Q8JIA4             ( 124) KAPKVVILKKATEYV   2
Q8JIA3             ( 124) KAPKVVILKKATEYV   2
Q9IB70             ( 124) TLTKIETLRLAIQYI   4
Q98SZ5             ( 120) KAPKVVILKKATEYV   2
Q8JI92             ( 121) KAPKVVILKKATEYV   2
Q8QG50             ( 117) RLPKVEILRNAIKYI   2
Q8UV04             ( 127) KAPKVVILKKATEYV   2
Q9YHW4             (  98) KPDKLTILRMAVSHM   3
Q98T18             ( 120) KAPKVVILKKATEYV   2
Q98T22             ( 120) KAPKVVILKKATEYV   2
Q9IB69             ( 103) TLTKIETLRLTIQYI   4
Q91959             (  51) RLPKVEILSSAIHYX   5
Q9I9H3             ( 101) RLPKVEILRNAIQYI   2
Q9IAS2             ( 114) KPDKLTILRMAVSHM   3
Q90Z13             (  82) KPEKADILELAVKFL   3
Q91635             (  74) KLEKADILEMTVKHL   3
Q9I934             (  53) QASRAQILDKATEYI   3
Q9I9L0             (  86) KLEKAEILQMTVDHL   2
Q90575             ( 136) KMSKVETLRSAVEYI   2
Q8JI88             ( 121) KAPKVVILKKATEYV   2
Q9PTR9             ( 113) KLTKIETLRFAHNYI   5
O73623             ( 132) TLTKIEILRLTIRYI   4
Q8JFY8             ( 121) KAPKVVILKKATEYV   2
Q8JH00             ( 120) KAPKVVILKKATEYV   2
Q98T31             ( 120) KAPKVVILKKATEYV   2
Q8JGZ9             ( 120) KAPKVVILKKATEYV   2
Q98T20             ( 120) KAPKVVILKKATEYV   2
O57598             (  74) KLSKYETLQMALSYI   5
Q9PRF6             (  61) KMSKVETLRSAVEYI   2
Q8UV08             ( 127) KAPKVVILKKATEYV   2
O93493             ( 101) RLPKVEILRNAIQYI   2
Q8JI95             ( 121) KAPKVVILKKATEYV   2
Q98T47             ( 120) KAPKVVILKKATEYV   2
Q9DG13             ( 114) KPDKLTILRMAVSHM   3
Q9I8H7             ( 113) KMHKSGVLRKAIDYI   9
Q90491             ( 524) PQTKLLILHQAVNVI   6
O93492             ( 118) RLPKVEILRNAISYI   2
Q98T01             ( 120) KAPKVVILKKATEYV   2
Q8JH10             ( 120) KAPKVVILKKATEYV   2
O93507             ( 220) KLSKNEILRLAMKYI   4
Q8UV07             ( 127) KAPKVVILKKATEYV   2
Q8UV10             ( 127) KAPKVVILKKATEYV   2
Q8JH05             ( 120) KAPKVVILKKATEYV   2
Q98T28             ( 120) KAPKVVILKKATEYV   2
Q9DGD0             ( 341) KAAKVVILKKATECI   5
Q90ZM5             ( 332) KLNKSAILRKAIEYI   2
Q98SH5             ( 209) KMHKSGVLRKAIDYI   9
Q98TI2             ( 196) SRSKLQLVGVTSLFI  11
Q9I9D4             (  44) RLPKVEILRNAISYI   2
Q98T14             ( 120) KAPKVVILKKATEYV   2
Q9DF72             (  52) KLEKAEILELAVEYI   2
Q8JI85             ( 121) KAPKVVILKKATEYV   2
Q9PVG4             ( 130) KLSKIQTLKLAARYI   3
Q8QGE0             ( 129) RLPKVDILRNAISYI   2
Q9DDW0             ( 101) RLPKVEILRNAIQYI   2
Q98SH6             ( 100) KLNKSAILRKAIEYI   2
Q98SW8             ( 120) KAPKVVILKKATEYV   2
O73823             ( 297) KLSKNEILRLAMKYI   4
Q91151             ( 103) RLPKVEILRSAISYI   2
Q98T42             ( 120) KAPKVVILKKATEYV   2
Q8QGE5             ( 222) RWNKGTILKASVDYI   5
Q91608             (  88) PQTKLLVLHQAVSVI   6
Q8JGZ7             ( 120) KAPKVVILKKATEYV   2
Q8QHA2             ( 127) KAPKVVILKKATEYV   2
Q98T08             ( 120) KAPKVVILKKATEYV   2
Q91421             ( 346) KASKVVILEKAIECI   4
Q98SZ4             ( 120) KAPKVVILKKATEYV   2
Q8UUX7             ( 126) RLPKVEILRSAIQYI   2
Q8JI99             ( 121) KAPKVVILKKATEYV   2
Q8UW72             (  53) KVEKAEILECTVQFL   7
Q8QH99             ( 127) KAPKVVILKKATEYV   2
Q9DEU7             (  56) KLEKADVLEITVQHM   4
Q8JH09             ( 120) KAPKVVILKKATEYV   2
Q8JH22             ( 120) KAPKVVILKKATEYV   2
Q8QGQ3             (  77) TLDKLTILRLSVSYL   4
Q8UV05             ( 127) KAPKVVILKKATEYV   2
Q98T26             ( 120) KAPKVVILKKATEYV   2
Q8UUX8             ( 125) RLPKVEILRSAIQYI   2
Q9YH81             (  77) KLTKIETLRFAYNYI   6
Q9DF41             (  74) KLEKADILEMTVKHL   3
O93491             ( 136) RLPKVEILRSAIQYI   2
Q91607             (  69) PQTKLLILHQAVAVI   6
Q98TY7             ( 118) RLPKVEILRNAISYI   2
Q8JHA1             (  42) KLSKYETLQMAQIYI   9
Q9IBH7             ( 295) RWNKGTILKASVDYI   5
Q9PSG9             (  56) KMKSVETLRSAVEYI   9
Q8JI84             ( 120) KAPKVVILKKATEYV   2
Q90Z14             (  55) KLEKADILEMAVNYL   2
Q9DG12             ( 114) KPDKLTILRMAVSHM   3
Q90463             (  52) KLEKAEILELAVEYI   2
Q90Z12             (  74) KLEKADILEMTVKHL   3
Q8QH96             ( 131) KAAKVVILKKATEYV   2
Q9DG26             ( 136) RLPKVEILRSAIQYI   2
Q8JI80             ( 120) KAPKVVILKKATEYV   2
Q90ZL0             ( 130) RLPKVEILRSAISYI   2
Q90468             ( 138) KLEKADILEMTVKHL   3
Q90VV1             (  74) KLEKADILEMTVKHL   3
Q9YHA3             (  99) KLSKIETLRLASSYI   3
Q9PWP1             (  78) KLTKIETLRFAYNYI   6
Q91791             ( 129) RLPKVEILRNAIRYI   2
Q8UW74             (  53) KVEKAEILECTVQFL   7
P70050             ( 116) KLTKIETLRFAYNYI   6
P70051             ( 120) KLTKIETLRFAHNYI   5
O42202             ( 131) KLSKIETLRLAKNYI   2
Q90ZL1             ( 107) PLTKIQTLKYTIQYI  11
Q9I879             ( 112) KLDKLTVLRMAVQHM   3
Q9PTS0             ( 114) KLSKIEILRLAICYI   4
Q90621             ( 215) PQTKLLILHQAVSVI   6
Q91794             ( 281) KAPKVVILKKATEYA   3
Q90WI5             ( 128) RLPKVEILRSAIQYI   2
Q9DEQ9             ( 132) PLTKIQTLKCTIKYI   7
O73871             ( 289) RWNKGTILKASVDYI   5
O93439             ( 104) SLTKIETLRLATRYI   3
Q9IAU0             ( 206) RWNKGTILKASVDYI   5
Q8AXV6             (  86) KLEKAEILQMTVDHL   2
Q8AXV5             (  81) KLEKAEILQMTVDHL   2
Q8AXF5             (  42) KMDKSTILQKSIDFL   3
Q8AXF3             ( 120) KAPKVVILKKATEYV   2
Q8AXF2             ( 120) KAPKVVILKKATEYV   2
Q8AXF1             ( 120) KAPKVVILKKATEYV   2
Q8AXF0             ( 120) KAPKVVILKKATEYV   2
Q8AXE9             ( 120) KAPKVVILKKATEYV   2
Q8AXE8             ( 120) KAPKVVILKKATEYV   2
Q8AXE7             ( 120) KAPKVVILKKATEYV   2
Q8AXE6             ( 120) KAPKVVILKKATEYV   2
Q8AXE5             ( 120) KAPKVVILKKATEYV   2
Q8AXE4             ( 120) KAPKVVILKKATEYV   2
Q8AXE3             ( 120) KAPKVVILKKATEYV   2
Q8AXE2             ( 120) KAPKVVILKKATEYV   2
Q8AX95             ( 121) RLSRIDTLRLAIVYI   4
Q8AX94             ( 122) KLSKIQTLKLAARYI   3
Q8AWF3             ( 125) RLPKVEILRSAINYI   2
Q8AW97             ( 112) RLPKVEILRNAISYI   2
Q8AW96             (  44) RLPKVEILRSAIQYI   2
Q8AW52             (  63) KLSKYETLQMALSYI   5
Q8AVZ1             ( 374) KAPKVVILKKATEYA   3
Q8AVZ0             ( 129) RLPKVEILRNAIRYI   2
Q8AVU4             (  74) KLEKADILEMTVKHL   3
Q8AV42             ( 127) KAPKVVILKKATEYV   2
Q8AV41             ( 127) KAPKVIILKKATEYV   3
Q8AV40             ( 127) KAPKVVILKKATEYV   2
Q8AV39             ( 127) KAPKVVILKKATEYV   2
Q8AV38             ( 132) KAPKVVILKKATEYV   2
Q8AV37             ( 127) KAPKVVILKKATEYV   2
Q8AV36             ( 127) KAPKVVILKKATEYV   2
Q8AV35             ( 127) KAPKVVILKKATEYI   1
Q8AV34             ( 123) KAPKVVILKKATEYV   2
Q8AV33             ( 127) KAPKVVILKKATEYV   2
Q8AV32             ( 127) KAPKVVILKKATEYV   2
Q995G8             ( 520) KAPKVVILKKATEYV   2
Q00089             ( 371) KAPKVVILKKATEYV   2
Q67004             ( 316) KAPKVVILKKATAYI   2
Q85523             ( 391) KAPKVVILKKATAYI   2
O56221             ( 825) KAPKVVILKKATEYV   2
Q90AP6             (  75) KSAWNETLQQVVTQL  34
Q85456             ( 373) KAPKVVILKRATEYV   2
//
ID   C5_DNA_meth; BLOCK
AC   IPB001525A; distance from previous block=(0,1325)
DE   C-5 cytosine-specific DNA methylase
BL   DGG;  width=14; seqs=222; 99.5%=909; strength=1176
MTA1_ARTLU|P31974  (  11) VDLFAGIGGFHAAL  12

MTB6_BACSP|P43420  (   5) ASLFAGVGGIDLGF  10

MTD2_HERAU|P25265  (   6) IDLFCGVGGLTHGL  12

O13369             ( 230) GDTFCGGGGVSLGA  31

DCM_ECOLI|P11876   (  90) IDLFAGIGGIRRGF   7
DNM1_ARATH|P34881  (1096) LDIFAGCGGLSHGL   7
DNM1_CHICK|Q92072  (1057) LDVFSGCGGLSEGF   7
DNM1_HUMAN|P26358  (1142) LDVFSGCGGLSEGF   7
DNM1_MOUSE|P13864  (1145) LDVFSGCGGLSEGF   7
DNM1_PARLI|Q27746  (1134) LDVFAGCGGLSEGF   7
DNM1_RAT|Q9Z330    (1147) LDVFSGCGGLTEGF   9
MTA1_RUEGE|P94147  (   4) IDLFCGAGGLGEGF  13
MTB1_BACSH|P13906  (  61) LSLFCGAGGLDLGF   8
MTB1_BREEP|P10283  (   4) LSLFSGCGGMDLGL   6
MTB1_HERAU|P25262  (   7) IDLFAGIGGFRLGL   6
MTB1_NEIGO|Q59603  (   5) IDLFSGIGGIRLGF   6
MTB5_NEIGO|Q59605  (   7) IDLFSGMSGIRKGF  28
MTBA_BACAR|P19888  (   6) VDLFAGIGGIRIGF   8
MTBF_BACSU|P17044  ( 104) IDLFAGIGGIRLGF   6
MTBR_BACSU|P06530  (  62) LSLFSGCGGLDLGF   6
MTC1_HERAU|P25263  (   5) IDLFAGIGGMRLGF   6
MTC2_HERAU|P25264  (   7) IDLFAGIGGFRLGL   6
MTD1_DESDN|P05302  (   4) IDLFAGCGGFSHGF   7
MTD1_HERAU|P24600  (   4) IDLFAGCGGMSLGF   5
MTD1_NEIMC|Q9RLM4  (  59) FSFFSGAGFLDLGF  13
MTD5_DACSA|P50185  (   9) IDLFAGIGGMRIPF  46
MTE1_HERAU|P25266  (   7) IDLFAGIGGFRLGL   6
MTE8_ECOLI|P50196  (  84) LELFAGAGGMALGL   8
MTF1_FUSNU|P34906  (   4) LSLFSGAGGLDLGF   6
MTF7_NEIGO|Q59606  (  19) LSLFSGCGGLDLGF   6
MTH1_HAEHA|P05102  (  15) IDLFAGLGGFRLAL  13
MTH2_HAEPA|P15446  (  35) IDLFAGIGGFRIAM  12
MTH3_HAEAE|P20589  (   4) ISLFSGAGGLDLGF   6
MTH5_HAEIN|P45000  (   4) VDLFSGCGGLSLGF   6
MTHA_HAEPH|P50192  (  48) IDLFSGAGGFSLGF   5
MTHT_METTF|P29567  (   6) ASFFSGAGGLDLGF   8
MTM1_MORSP|P11408  ( 108) IDLFSGIGGIRQSF  18
MTM4_NEIGO|P31033  (   6) LEICAGAGGQALGL  21
MTN1_NOCAE|P50188  (   7) VEICAGAGGQALGL  22
MTN4_NEILA|P50182  (   7) IDLFSGMSGIRKGF  28
MTNX_NEILA|P24581  (   5) IDLFAGIGGIRLGF   6
MTP1_PSYTA|O33481  (  80) VELFAGAGGLALGL   8
MTP2_NEIGO|P08455  (   4) ISLFSGCGGLDLGF   6
MTS1_SALIN|P09795  (  78) LSFFSGAMGLDLGI  34
MTS2_SHISO|P34879  (  75) IDLFAGIGGTRLGF  11
MTS3_STAAU|P16668  (   7) VELFAGVGGFRLGL   9
MTS9_STAAU|P23737  ( 102) FETFAGAGGLALGL  13
MTSA_LACLC|P34877  (  82) IDLFAGIGGTRLGF  11
MTX2_XANOR|P52311  (   7) IDLFAGAGGLSLGF   5

DNM2_HUMAN|O14717  (   7) LELYSGVGGMHHAL  18
DNM2_MOUSE|O55055  (   7) LELYSGIGGMHHAL  16
PMT1_SCHPO|P40999  (  10) LELYSGIGGMHYAL  15

MTBP_BACSU|P05795  (   7) MSLFSGIGAFEAAL  15
MTBR_BPRH1|P09915  (   7) MSLFSGIGAFEAAL  15
MTBS_BPSPR|P00476  (   7) MSLFSGIGAFEAAL  15

MTSB_LACLC|P34878  (   5) FEAFAGYGSQRLAL  59
MTSI_SPISQ|P15840  (  14) FEAFAGIGAQRKAL  25

MT52_METJA|Q58600  (   8) IDLFCGCGGFSRGF   8
MTA1_ACEPA|O52702  (   8) VSLFAGAGGFSSGF  10
MTB1_BACBR|P34905  (   6) GELFCGPGGLALGA  36
MTE2_ECOLI|P05101  (  99) IDLFAGIGGIRKGF   7
MTG1_HAEGA|P25282  (   8) LSLFSSAGIGEYFL  92
MTG2_HAEGA|P25283  (   6) MSLFSSAGIGELDL  94
MTH2_HAEAE|O30868  (   7) IDLFAGIGGIRLGF   6
MTS1_STRAH|O31073  (   8) ISLFSGAGGLDCAI  20
O26595             (   7) IDIFAGAGGLTEGF   8
Q9YAD7             (   8) ADVFAGGGGFSRGF  11
Q9V2M5             (  11) LDLFAGAGGFSLGF   5
Q980M6             (   7) IDLFSGAGGFSLGF   5
Q975T7             (   6) VDLFSGAGGFSLGF   6
Q8ZWR3             (   5) VDLFAGGGGFGLGF  14
Q8ZTL3             (   7) VSLFSGAGGLDLGF   6
Q8TV73             (   6) VDLFCGAGGFSRGF   9
Q8U4N2             (   5) IDLFAGAGGFSLGF   5
Q8Q059             (   8) LDMFSGAGGLTEGF  37
O42803             ( 787) LDIFAGCGGLTLGL   8
Q8NJW0             ( 287) GDTFAGAGGASRGI  21
Q96W73             ( 843) MDLYCGGGNFGRGL  53
Q8NJV8             ( 284) GDTFAGAGGASRGI  21
Q9HFI8             ( 287) GDTFAGAGGASRGI  21
Q8NJV9             ( 291) GDTFAGAGGASRGI  21
O42731             ( 787) LDIFAGCGGLTLGL   8
Q8IAJ7             (1135) LDVFAGCGGLSEGF   7
Q8IAJ6             ( 983) LDVFAGCGGLSEGF   7
Q8MJ28             (1040) LDVFSGCGGLSEGF   7
Q38652             (  17) LELFCGGGLGATGF  29
Q8W6H6             (  15) FHLFCGLGAGAKGF  33
Q94M66             (   4) LDLFAGIGGFRIGM  10
Q02778             (   7) MSLFSGIGAFEAAL  15
Q9ZXI4             (   9) FHFCCGLGGGAAGF  43
Q8LPU5             ( 348) LDLYSGCGGMSTGL   9
Q94F87             ( 679) LDLYSGCGGMSTGL   9
Q9C9L8             ( 272) LDLYSGCGAMSTGL  10
O48867             (1326) LDIFAGCGGLSEGL   6
O23273             (1081) LDIFAGCGGLSHGL   7
O49022             (1120) LDIFAGCGALSEGL   7
O50037             ( 212) LDLYSGCGAMSTGF  10
Q8S921             ( 732) LDIFAGCGGLSEGL   6
Q9SEG3             (1079) LDIFAGCGGLSHGL   7
O49139             ( 228) LDLYSGCGAMSTGF  10
Q9FR60             (1026) SGVFSGCGGLSEGF  78
Q9M0S8             (1074) LDIFAGCGGLSHGL   7
O50073             ( 228) LDLYSGCGAMSTGF  10
Q94FN4             ( 272) LDLYSGCGAMSTGL  10
Q9MB97             (1121) LDIFAGCGGLSEGL   6
Q8LQY1             (  10) LEFYSGIGGMRYSL  22
Q9ARI6             ( 348) LDLYSGCGGMSTGL   9
O49137             ( 228) LDLYSGCGAMSTGF  10
Q9T0I1             ( 972) LDIFAGCGGLSYGL   7
Q8LPU6             (1016) LDIFAGCGGLSEGL   6
Q9AXT8             ( 344) LDLYSGCGGMSTGL   9
O48866             (1111) LDIFAGCGGLSEGL   6
O65343             (1084) LDIFAGCGGLSEGL   6
Q94IR0             (  10) LEFYSGIGGLRYSL  22
Q9FVA3             ( 343) LDIFAGCGGLSEGL   6
Q94F88             ( 272) LDLYSGCGAMSTGL  10
Q8LER4             (  18) LEFYSGIGGMRYSL  22
Q8S4C3             (1090) LDIFAGCGGLSEGL   6
O49415             ( 679) LDLYSGCGGMSTGL   9
O49144             ( 228) LDLYSGCGAMSTGF  10
O49889             (1124) LDIFAGCGGLSEGL   6
Q8H854             ( 456) LDLYSGCGAMSTGL  10
Q8H0H2             ( 179) LDLYSGCGAMSTGL  10
Q9EUV5             (   6) VDLFCGVGGLTCGV  28
Q9L5I8             (  95) IDLFAGIGGLRSGF   9
Q8RT52             (   5) ASLFSGAGFLDLGF  11
Q9KJH1             (   6) VSLFSGGGGLDLGF   9
O53067             (   5) ASFFAGVGGIDLGF  11
O52849             (  11) IDLFAGAGGMSLGF   5
Q9X5I9             (  41) ATVFSGIGAVEQAF  30
O30357             (   8) IDLFSGAGGLSLGF   5
Q93LM5             (   8) FSFFAGSGFLDLGF  22
Q59380             (   4) LEIFSGAGGLAKGL   9
Q59958             (   4) IDLFSGIGGFRLGM   9
Q93LL9             (  13) VDLFAGAGGMTLGF   8
P77950             (  75) IDLFAGIGGTRLGF  11
O52850             (   5) LDLFSGAGGFTLGL   7
Q9RQS3             (   7) FELFAGIGSQYKAC  81
O31098             (  13) ASLFCGCGGMDVGI  22
Q8RLK9             (   4) LEIFSGAGGLAKGL   9
Q9ZHP3             (  63) VDLFCGAGGITQGL  12
P70750             (   8) VSLFAGAGGFSSGF  10
Q9ACM3             (   4) LELFAGVGGFRIGL  10
Q9X9M1             (   5) ASFFAGVGGIDLGF  11
Q9RPJ2             (   7) ISLFSGAMGLDLGL  28
Q59245             (  33) LSLFCGAGGLDLGF   8
Q9F658             (   4) LEIFSGAGGLAKGL   9
Q9WVZ8             (   6) LEICAGAGGQALGL  21
O08431             (  75) IDLFAGIGGTRLGF  11
Q8VMN0             (  10) FHFCCGLGGGAKGF  43
Q59612             (  15) ISLFSGCGGLDLGF   6
Q59604             (  15) ISLFSGCGGLDLGF   6
Q9F6L2             (  27) VSLFSGCGGFCEGV  19
Q9ZHP1             (  63) VDLFCGAGGITQGL  12
Q8RT54             (   7) FSFFSGAGFLDLGF  13
Q8VLC7             (   6) LDLFCGAGGFSAGL   9
P94630             (   8) VSTFSGCGGLDLGL  10
Q8VTD8             (   6) LDLFCGAGGFSAGL   9
Q9FDE0             (   5) ASLFSGAGFLDLGF  11
Q93K37             (  13) IEGFCGAGGMSLGL  38
Q9EXA5             (  43) ISLFSSAGVGCYGF  61
Q60171             (  17) AELFAGGGLMAVGL  34
O87350             (   4) LELFAGVGGFRIGL  10
Q8GMC3             (   4) LDLFCGAGGLSYGF   8
Q8GGA1             (  61) IDLFAGIGGFRIAM  12
Q8GC38             (  52) VSLFSGAGGLDLGL   6
Q8GA84             (   4) VSLFSGAGGLDLGF   6
Q8GA83             (   4) VSLFSGAGGLDLGL   6
O34939             (  87) ADLFSGCGGLSLGV  14
O34680             (   4) VSLFSGIGGIELGL   9
O24892             (   6) LDLFCGAGGFSAGL   9
O24895             (  10) ISLFSGAGVGCYGL  28
O25746             (   1) MDFCSGIGGGRLGL  21
Q59995             (   7) IDLFAGCGGMSLGL   6
Q9ZLZ0             (   5) ADIFCGAGGLSYGF  11
Q9ZK91             (   7) MDFCSGIGGGRLGL  21
Q9XAZ7             (   5) ASLFSSAGIAETYL  94
Q9PCK4             (  20) GSVCSGIEAVSLAW  75
Q9KMW8             (  20) FSFFAGSGFLDLGF  22
Q9K765             (   9) VSLFSGAGGLDMGF  15
Q9K003             (  41) ATVFSGIGAVEQAF  30
Q9JZI7             (   7) IDLFSGMSGIRKGF  28
Q9JWD8             (   9) VDFFCGGGGMSYGM  16
Q9JU80             (   7) IDLFSGMSGIRKGF  28
Q9JRF0             (  23) IDLFAGIGGFRIAM  12
Q9JQR8             (  41) ATVFSGIGAVEQAF  30
Q9A9F5             (   4) LSLFCGAGGLDQGF  10
Q9A2D9             (  10) LEFFAGGGMARLGL  43
Q982S6             (  29) IVLFAGMGGGCDGL  71
Q8ZNT0             (  94) IDLFAGIGGIRRGF   7
Q8Z5Q6             (  94) IDLFAGIGGIRRGF   7
Q8YYB6             (  76) ISFFSGAMGLDLGF  29
Q8YUQ9             (  20) VDLFAGAGGMSLGF   6
Q8YMV9             (  10) IDLFAGAGGFGLGF  11
Q9KIV6             (   8) FSFFAGSGFLDLGF  22
Q8X8S5             (   4) IDLFSGVGGLSLGA  18
Q935J8             (  95) IDLFAGIGGLRSGF   9
Q92LC3             (   7) ADLFSGCGGLSLGL   6
Q8XTV8             (   3) LSLFCGAGGLDKGF   8
Q97JQ1             (  10) LELFGGIGAPRKAF 100
Q97IY5             (   9) GSLFAGVGGICLGF  16
Q8PKG0             (  14) GSVCSGIEAVSLAW  75
Q8NPN5             (   8) VSTFSGCGGLDLGL  10
Q9L1W7             (   3) LDLFAGPGGWSRAV  52
Q8FGJ2             (  90) IDLFAGIGGIRRGF   7
Q8EVR5             (  14) FEAFAGIGSQFKAL  57
Q8EUE9             (   7) IDLFAGIGGFHKAL  11
Q8EL98             (   6) ASLFAGIGGIDIGF  10
Q8EL95             (  18) VDLFSGCGGLALGF   7
Q8ECW6             (   6) VDNFAGGGGASTGM  45
Q8E4N1             (   4) LDLFAGIGGFRLGL   6
Q8DZ25             (   4) LDLFAGIGGFRLGM   9
Q8DXI1             (   4) LDLFAGIGGFRLGM   9
Q8CXP0             (  15) IDLFAGAGGLSNGF  22
Q8CWG2             (   7) ADLFAGIGGIRMGM  19
Q8CE27             (   7) LELYSGIGGMHHAL  16
Q8C7F0             (   7) LELYSGIGGMHHAL  16
Q9YQY1             ( 279) MDVFSGCGGLSLGL  10
P79922             (1017) LDVFSGCGGLSEGF   7
Q9I8X6             (1028) LDVFSGCGGLSEGF   7
Q9YHD9             ( 226) LDVFSGCGGLSEGF   7
Q8QGB8             (1025) LDVFSGCGGLSEGF   7
//
ID   C5_DNA_meth; BLOCK
AC   IPB001525B; distance from previous block=(42,187)
DE   C-5 cytosine-specific DNA methylase
BL   PCQ;  width=16; seqs=222; 99.5%=928; strength=1211
MTD2_HERAU|P25265  (  71) KILVGCAPCQDFSQYT  39

MTF7_NEIGO|Q59606  (  80) DIILGGFPCQDFSMIW  12

MTS3_STAAU|P16668  (  77) DMIVGGFPCQDYSVAR  10

MTSB_LACLC|P34878  ( 119) DFFTYSFPCQDISVAG  15

MTSI_SPISQ|P15840  ( 133) DLLTYSFPCQDLSQQG  18

PMT1_SCHPO|P40999  (  73) KLWTMSPSCQPFTRIG  86

O13369             ( 293) DILHLSPPCQTFSRAH  18

DCM_ECOLI|P11876   ( 169) DVLLAGFPCQPFSLAG   5
MTA1_ARTLU|P31974  (  76) DVLTGGFPCQPFSKSG   8
MTA1_RUEGE|P94147  (  72) DVVMGGPPCQGFSTYG  10
MTB1_BREEP|P10283  ( 107) DVVTGGFPCQDFSFAG   7
MTB1_NEIGO|Q59603  (  63) DILLAGFPCQPFSIAG   5
MTB5_NEIGO|Q59605  (  72) DILLAGFPCQAFSFAG   6
MTB6_BACSP|P43420  (  65) DVLLSGFPCTSFSVAG  18
MTBA_BACAR|P19888  (  68) DFLLAGFPCQPFSYAG   7
MTBF_BACSU|P17044  ( 162) DVLLAGFPCQPFSNIG   7
MTBP_BACSU|P05795  (  70) DLLTSGFPCPTFSVAG  16
MTBR_BPRH1|P09915  (  70) DLLVGGSPCQSFSVAG   7
MTBS_BPSPR|P00476  (  70) DLLVGGSPCQSFSVAG   7
MTC1_HERAU|P25263  (  67) DFLLAGFPCQPFSYAG   7
MTD1_DESDN|P05302  (  68) DGIIGGPPCQGFSLSG   7
MTD1_HERAU|P24600  (  67) ELIIGGPPCQDFSSAG   7
MTD1_NEIMC|Q9RLM4  ( 140) VGFIGGPPCPDFSIAG  11
MTD5_DACSA|P50185  (  67) DLLLAGFPCQAFSQGG   7
MTE8_ECOLI|P50196  ( 145) DVLAGGFPCQAFSYAG   7
MTF1_FUSNU|P34906  (  63) DGIIGGPPCQSWSEAG   8
MTH1_HAEHA|P05102  (  73) DILCAGFPCQAFSISG   7
MTH2_HAEPA|P15446  (  95) DILCAGFPCQAFSIAG   5
MTH3_HAEAE|P20589  (  63) DGIIGGPPCQSWSEGG   9
MTH5_HAEIN|P45000  (  67) DLIMGGPPCQDFSSAG  10
MTHA_HAEPH|P50192  ( 114) DVVIGGPPCQGFSMAG   5
MTHT_METTF|P29567  (  65) VGFIGGPPCQSWSLAG  12
MTM1_MORSP|P11408  ( 166) DILCAGFPCQPFSHIG  15
MTM4_NEIGO|P31033  (  66) DLLAGGVPCPPFSKAG  12
MTN1_NOCAE|P50188  (  70) SLLAGGVPCPPFSIAG  14
MTN4_NEILA|P50182  (  72) DILLAGFPCQAFSFAG   6
MTNX_NEILA|P24581  (  66) DILSAGFPCQPFSQAG   8
MTP1_PSYTA|O33481  ( 141) DLLTGGFPCQPFSYAG   7
MTP2_NEIGO|P08455  (  65) DGIIGGPPCQSWSEAG   8
MTS1_SALIN|P09795  ( 146) DLIMGGPPCQAFSTAG   9
MTS2_SHISO|P34879  ( 134) EILVGGFPCVAFSQAG  12
MTS9_STAAU|P23737  ( 166) DILSGGYPCQTFSYAG  35
MTSA_LACLC|P34877  ( 141) DILVGGFPCQAFSQAG   5
MTX2_XANOR|P52311  (  75) DIVIGGAPCQGFSLIG  11

DNM1_ARATH|P34881  (1190) DFINGGPPCQGFSGMN   6
DNM1_CHICK|Q92072  (1133) EMLCGGPPCQGFSGMN   6
DNM1_HUMAN|P26358  (1218) EMLCGGPPCQGFSGMN   6
DNM1_MOUSE|P13864  (1221) EMLCGGPPCQGFSGMN   6
DNM1_PARLI|Q27746  (1210) ELLCGGPPCQGFSGMN   5
DNM1_RAT|Q9Z330    (1223) EMLCGGPPCQGFSGMN   6

DNM2_HUMAN|O14717  (  71) DMILMSPPCQPFTRIG  16
DNM2_MOUSE|O55055  (  71) NMILMSPPCQPFTRIG  17

MTB1_BACSH|P13906  ( 148) NLVIGGFPCPGFSEAG   8
MTBR_BACSU|P06530  ( 149) NLILGGFPCPGFSEAG   8

MTB1_HERAU|P25262  (  67) DVLVGGVPCQPWSIAG   9
MTC2_HERAU|P25264  (  67) DLVVGGVPCQPWSIAG  10
MTE1_HERAU|P25266  (  67) DVLVGGVPCQPWSIAG   9

MT52_METJA|Q58600  ( 125) DVIIGGPPCEGYTGAN  14
MTA1_ACEPA|O52702  (  73) FVVIGGPPCQGFSTAG  11
MTB1_BACBR|P34905  (  84) DAFTFGFPCNDYSIVG  46
MTE2_ECOLI|P05101  ( 178) DVLLAGFPCQPFSLAG   5
MTG1_HAEGA|P25282  (  75) DFLIASPPCQGMSVAG  11
MTG2_HAEGA|P25283  (  73) KFLLATPPCQGLSSVG  31
MTH2_HAEAE|O30868  (  65) DILLAGFPCQPFSIAG   5
MTS1_STRAH|O31073  (  88) TLVIGGPPCTPFSKSG  22
O26595             ( 114) DGIIGGPPCQAYSYAG   8
Q9YAD7             (  76) DVVIASPPCEPFTGAN  15
Q9V2M5             (  71) DVIIGGPPCEPFTAIN  15
Q980M6             (  72) DVVIGGPPCEGYTAAN  15
Q975T7             (  71) DIVIGSPPCEPYTGAN  15
Q8ZWR3             (  69) DVIIGSPPCEPFTAAN  16
Q8ZTL3             (  82) DVVVGGPPCQDFSIVR  10
Q8TV73             (  70) DVIIGGPPCEPFTAAN  14
Q8U4N2             (  65) DVIIGGPPCEPFTAIN  15
Q8Q059             ( 117) DVVIGGPPCQAYSVAG   6
O42803             ( 873) DFIYGGPPCQGFSGVN  13
Q8NJW0             ( 351) DILHLSPPCQVWSPAH  21
Q96W73             ( 918) DFIAAGSPCPGFSLLT  18
Q8NJV8             ( 348) DILHLSPPCQVWSPAH  21
Q9HFI8             ( 351) DILHLSPPCQVWSPAH  21
Q8NJV9             ( 353) DILHLSPPCQVWSPAH  21
O42731             ( 873) DFIYGGPPCQGFSGVN  13
Q8IAJ7             (1211) ELLCGGPPCQGFSGMN   5
Q8IAJ6             (1059) ELLCGGPPCQGFSGMN   5
Q8MJ28             (1116) EMLCGGPPCQGFSGMN   6
Q38652             (  76) DVIFGGPPCQDFSVAG   7
Q8W6H6             ( 107) DIVFLSAPCKGFSGLL  28
Q94M66             (  68) DVICGGFPCQAFSIAG   5
Q02778             (  70) DLLVGGSPCQSFSVRG  20
Q9ZXI4             ( 101) DAVFISSPCKGASGLL  42
Q8LPU5             ( 513) DVICGGPPCQGISGFN   7
Q94F87             ( 856) GVICGGPPCQGISGYN  12
Q9C9L8             ( 452) DVVCGGPPCQGISGHN  10
O48867             (1420) DFINGGPPCQGFSGMN   6
O23273             (1175) DFINGGPPCQGFSGMN   6
O49022             (1214) DFINGGPPCQGFSGMN   6
O50037             ( 393) YSVCGGPPCQGISGYN  27
Q8S921             ( 842) ELLVGGPPCQGFSGLN   6
Q9SEG3             (1173) DFINGGPPCQGFSGMN   6
O49139             ( 409) YTVCGGPPCQGISGYN  13
Q9FR60             (1102) EMLCGGPPCQGFSGMN   6
Q9M0S8             (1168) DFISGGPPCQGFSGMN   7
O50073             ( 409) YTVCGGPPCQGISGYN  13
Q94FN4             ( 452) DVVCGGPPCQGISGHN  10
Q9MB97             (1215) DFINGGPPCQGFSGMN   6
Q8LQY1             (  73) QAWLLSPPCQPYTRQG  30
Q9ARI6             ( 513) DVICGGPPCQGISGFN   7
O49137             ( 409) YTVCGGPPCQGISGYN  13
Q9T0I1             (1077) DFISGGPPCQGFSRLN   9
Q8LPU6             (1110) EFINGGPPCQGFSGMN   6
Q9AXT8             ( 509) DVICGGPPCQGISGFN   7
O48866             (1205) DFINGGPPCQGFSGMN   6
O65343             (1178) EFINGGPPCQGFSGMN   6
Q94IR0             (  73) HAWLLSPPCQPYTRQG  35
Q9FVA3             ( 437) EFINGGPPCQGFSGMN   6
Q94F88             ( 452) DVVCGGPPCQGISGHN  10
Q8LER4             (  81) DAWLLSPPCQPYTRQG  24
Q8S4C3             (1184) EFINGGPPCQGFSGMN   6
O49415             ( 881) GVICGGPPCQGISGYN  12
O49144             ( 409) YTVCGGPPCQGISGYN  13
O49889             (1218) DFINGGPPCQGFSGMN   6
Q8H854             ( 628) DVICGGPPCQGISGFN   7
Q8H0H2             ( 362) QVICGGPPCQGVSGFN  32
Q9EUV5             (  72) RLLMGCAPCQPFSAYS  49
Q9L5I8             ( 174) DVLLAGFPCQPFSIAG   5
Q8RT52             (  72) RGIIGGPPCQDFSIGN   8
Q9KJH1             (  65) DVVIGGPPCQSFSLVG   7
O53067             (  64) DIMLAGFPCQAFSIAG  10
O52849             (  74) DAVIGGPPCQGFSISA  16
Q9X5I9             ( 105) DILVGGSPCQAFSMVG   8
O30357             (  74) DLVIGGPPCQGFSMAG   5
Q93LM5             (  92) VGFIGGPPCPDFSIGG  13
Q59380             (  64) DIVAGGPPCQPFSLGG   7
Q59958             (  69) DVICGGFPCQAFSIAG   5
Q93LL9             (  81) DVVICGSPCQGFSLIG  15
P77950             ( 134) EILVGGFPCVAFSQAG  12
O52850             (  69) DIITGGPPCQGFSVAG   5
Q9RQS3             ( 146) DILTYSFPCQDISQQG  14
O31098             (  83) DILLGGFPCQSFSISA  16
Q8RLK9             (  64) DIVAGGPPCQPFSLGG   7
Q9ZHP3             ( 129) NLVVGGPPCQGFSVAG   6
P70750             (  73) FVVIGGPPCQGFSTAG  11
Q9ACM3             (  74) DMIVGGFPCQDYSVAR  10
Q9X9M1             (  64) DVMLAGFPCQAFSIAG  10
Q9RPJ2             (  76) DLVAGGPPCQAFSVFG   8
Q59245             ( 120) NLVIGGFPCPGFSEAG   8
Q9F658             (  64) EVIAGGPPCQPFSLGG   7
Q9WVZ8             (  66) DLLAGGVPCPPFSKAG  12
O08431             ( 134) EILVGGFPCVAFSQAG  12
Q8VMN0             ( 102) DVVFISSPCKGASGLL  40
Q59612             (  76) DGIIGGPPCQSWSEAG   8
Q59604             (  76) DGIIGGPPCQSWSEAG   8
Q9F6L2             ( 102) DLLFGGPPCQGYSQIG   8
Q9ZHP1             ( 129) NLVVGGPPCQGFSVAG   6
Q8RT54             (  86) VGFIGGPPCPDFSVGG  13
Q8VLC7             (  74) NMIIGGPPCQGFSNKG  10
P94630             (  70) DLVTGGFPCQDFSMIW  13
Q8VTD8             (  74) NMIIGGPPCQGFSNKG  10
Q9FDE0             (  72) RGIIGGPPCQDFSIGN   8
Q93K37             (  79) DLFSGGPPCQGFSKQR  15
Q9EXA5             ( 115) DVVIATPPCQGMSVAN  25
Q60171             (  76) DVIAGGPPCQDYSVAG   7
O87350             (  74) DIIVGGFPCQDYSVAR   9
Q8GMC3             (  71) RAVLGGPPCQGFSLKG  11
Q8GGA1             ( 121) DVLCAGFPCQAFSIAG   5
Q8GC38             ( 139) DIMIGGFPCPGFSSAG  13
Q8GA84             (  63) DVVIGGFPCQGFSQAN   5
Q8GA83             (  63) DVVVGGFPCQGFSVAN   5
O34939             ( 168) DFILAGPPCQGHSDLN  36
O34680             (  61) DLVAAGFPCQDLSQAG  12
O24892             (  74) NMIIGGPPCQGFSNKG  10
O24895             (  87) DLVVATPPCQGMSVAN  25
O25746             (  60) DALISGFPCQAFSING  17
Q59995             (  77) DLIAGGPPCQGFSLMG   6
Q9ZLZ0             (  68) DILLGGPPCQSYSTLG   9
Q9ZK91             (  66) DVLVSGFPCQAFSING  15
Q9XAZ7             (  71) DFLIASPPCQGMSVAG  11
Q9PCK4             (  83) DILVGGTPCQSFSVAG  17
Q9KMW8             ( 100) TGFIGGPPCPDFSVAG  15
Q9K765             (  68) DILLGGWPCQGFSLAG  16
Q9K003             ( 105) DILVGGSPCQAFSMVG   8
Q9JZI7             (  72) DILLAGFPCQAFSFAG   6
Q9JWD8             (  77) LILIGCSPCQYWSVIQ  64
Q9JU80             (  72) DILLAGFPCQAFSFAG   6
Q9JRF0             (  83) DVLTAGFPCQPFSIAG   5
Q9JQR8             ( 105) DILVGGSPCQAFSMVG   8
Q9A9F5             (  72) SGVIGGPPCQSFSQAN  10
Q9A2D9             (  71) DLAWASSPCQDFSLAG  27
Q982S6             (  92) RALHASPDCTHFSVAK  68
Q8ZNT0             ( 173) DVLLAGFPCQPFSLAG   5
Q8Z5Q6             ( 173) DVLLAGFPCQPFSLAG   5
Q8YYB6             ( 143) DIMLGGPPCQAFSTAG  11
Q8YUQ9             (  88) DVIICGSPCQGFSLMG  14
Q8YMV9             (  76) DIIIGGPPCQGFSIAG   4
Q9KIV6             (  92) VGFIGGPPCPDFSIGG  13
Q8X8S5             (  71) DGIIGGPPCQGFSSIG   7
Q935J8             ( 174) DVLLAGFPCQPFSIAG   5
Q92LC3             (  87) DVLAGGPPCQGFSFAG   6
Q8XTV8             (  71) SGIIGGPPCQSFSRAN  10
Q97JQ1             (  69) DVLIHGSPCQDFSIAG  22
Q97IY5             ( 120) DVLNGGFPCQAFSIAG   5
Q8PKG0             (  77) DILVGGTPCQSFSVAG  17
Q8NPN5             (  70) DLVTGGFPCQDFSMIW  13
Q9L1W7             (  61) RGVIASPPCQAWSMAG  11
Q8FGJ2             ( 169) DVLLAGFPCQPFSLAG   5
Q8EVR5             ( 127) DIFTYSFPCQDLSVQG  20
Q8EUE9             (  75) DFLFAGFPCQTFSNAG  13
Q8EL98             (  65) DIITAGWPCVAFSIAG  23
Q8EL95             (  89) LIVIGGPPCQAYSKIG  13
Q8ECW6             (  70) ALAWFSPDCKHFSKAK 100
Q8E4N1             (  69) DIICVGFPCQAFSLAG  21
Q8DZ25             (  69) DIICGGFPCQAFSLAG   5
Q8DXI1             (  68) DVICGGFPCQAFSIAG   5
Q8CXP0             (  91) IVVIGGPPCQGFSNAN  17
Q8CWG2             (  70) DLLLAGFPCQPFSIAG   5
Q8CE27             (  71) NMILMSPPCQPFTRIG  17
Q8C7F0             (  71) NMILMSPPCQPFTRIG  17
Q9YQY1             ( 352) ECMVGGPPCQGYSILN  30
P79922             (1093) EMLCGGPPCQGFSGMN   6
Q9I8X6             (1104) EMLCGGPPCQGFSGMN   6
Q9YHD9             ( 302) EMLCGGPPCQGFSGMN   6
Q8QGB8             (1101) EMLCGGPPCQGFSGMN   6
//
ID   C5_DNA_meth; BLOCK
AC   IPB001525C; distance from previous block=(5,41)
DE   C-5 cytosine-specific DNA methylase
BL   GPV;  width=28; seqs=222; 99.5%=1671; strength=1170
DNM1_ARATH|P34881  (1216) QCEMILAFLSFADYFRPRYFLLENVRTF  12

MTA1_ARTLU|P31974  ( 100) RGTLFWNIARIIEEREPTVLILENVRNL  14

MTA1_RUEGE|P94147  (  95) RNQLYVPYFGFVEEFRPKAFLIENVVGL  27

MTB1_BREEP|P10283  ( 146) RGQLYLWLKKVVEITKPKVFIAENVKGL  23

MTB6_BACSP|P43420  (  90) SGDLFFETLRLIVAKKPQVIFLENVKNL  16

MTBF_BACSU|P17044  ( 186) RRNIIFDVLRILKKKQPKMFLLENVKGL  11

MTBP_BACSU|P05795  ( 127) RGTLFFETALLAEEKKPKFVILENVKGL  10

MTD1_DESDN|P05302  (  91) RNSLFVDFVRFVKFFSPKFFVMENVLGI  22

MTD1_HERAU|P24600  (  90) RANLTLDFAKIVLAIQPAWVIMENVERA  28

MTD1_NEIMC|Q9RLM4  ( 164) NGKLSQSYVDLICKNQPDFFVFENVKGL  15

MTD2_HERAU|P25265  (  94) KWQLLTEFSRLIREIEPDIISMENVPEV  42

MTD5_DACSA|P50185  (  91) RGQLFFQVAKILNDHRPQAILLENVKGL  13

MTF7_NEIGO|Q59606  ( 104) RGNLYKSFLRFVNAKKPKVFVAENVKGL   9

MTH1_HAEHA|P05102  (  97) RGTLFFDIARIVREKKPKVVFMENVKNF   8

MTH2_HAEPA|P15446  ( 119) RGTLFFDVAEIIRRHQPKAFFLENVKGL  10

MTH5_HAEIN|P45000  (  90) RADLTYSFANIVCNIRPKWFVMENVEQI  20

MTHA_HAEPH|P50192  ( 140) RNHLFKEFVRVVKLTQPKFFVMENVARL  16

MTHT_METTF|P29567  (  89) RGKTFYAYVDLVKEKDPLFFLAENVPGI  24

MTM1_MORSP|P11408  ( 191) QGTMFHEIVRIIETKKTPVLFLENVPGL  47

MTM4_NEIGO|P31033  (  89) ERDLFPEAIRLAKETDPKAIMLENVRGL  20

MTN1_NOCAE|P50188  (  93) MRDLFAWAVELCDVMKPRALMLENVRGL  38

MTS1_SALIN|P09795  ( 170) RGNVFIKYLDVALDIRPKYIVIENVRGL  24

MTS3_STAAU|P16668  ( 104) KGVLFWQIIRYIQNTFPKYLLLENVDRL  28

MTS9_STAAU|P23737  ( 190) RGTLFYPYSKILSKLKPKAFIAENVRGL  14

MTSB_LACLC|P34878  ( 146) RSSLLWECCKIIEHKKPKYLMMENVKNL  18

MTSI_SPISQ|P15840  ( 164) LWEIERALDSTEKNDLPKYLLMENVGAL  52

MTX2_XANOR|P52311  (  98) RNQLVHHYVRVVMELKPKYFVFENVKGL  12

PMT1_SCHPO|P40999  (  99) QAFLNILNVLPHVNNLPEYILIENVQGF  38

O13369             ( 318) NEASFFAVVNLIKAVRPRLFTVEETDGI  80

DCM_ECOLI|P11876   ( 202) QGTLFFDVVRIIDARRPAMFVLENVKNL   9

DNM1_CHICK|Q92072  (1159) KNSLVVSFLSYCDYYRPRFFLLENVRNF   8
DNM1_HUMAN|P26358  (1244) KNSLVVSFLSYCDYYRPRFFLLENVRNF   8
DNM1_MOUSE|P13864  (1247) KNSLVVSFLSYCDYYRPRFFLLENVRNF   8
DNM1_PARLI|Q27746  (1236) KNSLISSYLSYCDYYRPRFFLLENVRNF   9
DNM1_RAT|Q9Z330    (1249) KNSLVVSFLSYCDYYRPRFFLLENVRNF   8

DNM2_HUMAN|O14717  (  97) NSFLHILDILPRLQKLPKYILLENVKGF  27
DNM2_MOUSE|O55055  (  97) TSFLYILDILPRLQKLPKYILLENVKGF  18

MTB1_BACSH|P13906  ( 171) RNFLYIHFIRCLMQVQPEIFVAENVKGM  16
MTBR_BACSU|P06530  ( 172) RNFLYLHFIRSLIQAQPEIFVAENVKGM  32

MTB1_HERAU|P25262  (  91) RGQLWADVIRLVQINQPKAFIFENVKGL  13
MTC2_HERAU|P25264  (  91) RGQLWADVIRLVRINQPKAFIFENVKGL  12
MTE1_HERAU|P25266  (  91) RGQLWADVIRLVQINQPKAFIFENVKGL  13

MTB1_NEIGO|Q59603  (  87) RGTLFFNIAEILKTKQPKAFLLENVKRL   8
MTNX_NEILA|P24581  (  90) RGTLFFDIERILLAKKPQAFLLENVKQL  11
MTS2_SHISO|P34879  ( 158) RGTLFFDIARIIKEKKPHAFLLENVKNL   9
MTSA_LACLC|P34877  ( 165) RGTLFFEIARIIKEKRPKAFLLENVKNL   5

MTB5_NEIGO|Q59605  (  96) RGTLFFDVARILKAKKPKGFILENVEGL   9
MTN4_NEILA|P50182  (  96) RGTLFFDVARILKAKKPKGFILENVEGL   9

MTBA_BACAR|P19888  (  92) RGTLFFEVERVLRDNRPKAFLLENVRGL   9
MTC1_HERAU|P25263  (  91) RGTLFFEIERILKAYRPKGFLLENVRGL   9

MTBR_BPRH1|P09915  (  94) RGTLFFQYIDTLKEKQPRYFVFENVKGL   8
MTBS_BPSPR|P00476  (  94) RGTLFFQYVETLKEKQPKFFVFENVKGL   8

MTE8_ECOLI|P50196  ( 169) RGTLFFEFARAAKEINPKVLLAENVRGL   9
MTP1_PSYTA|O33481  ( 165) RGTLVFEMARAIKEIKPKVFLAENVKGL   8

MTF1_FUSNU|P34906  (  87) RGKLFYEYIRILKDIQPKFFLAENVKGM   8
MTH3_HAEAE|P20589  (  87) RGKLFYEYIRILKQKKPIFFLAENVKGM  17
MTP2_NEIGO|P08455  (  89) RGQLFFDYIRILKSKQPKFFLAENVSGM  11

MT52_METJA|Q58600  ( 156) TGRLVLEYIRIVGDLQPKIFVMENVPGI  10
MTA1_ACEPA|O52702  (  96) RNLLIFNYLNIVERLSPRWLIFENVEGL  18
MTB1_BACBR|P34905  ( 108) YGPLYSYGVKILNEYNPLVFIAENVGGL  48
MTE2_ECOLI|P05101  ( 211) QGTLFFDVARIIRAKKPAIFVLENVKNL   7
MTG1_HAEGA|P25282  ( 103) RNYLIMYVIAMIKKLKPAYILIENVPFL  23
MTG2_HAEGA|P25283  ( 101) RNFLIFEVFEFIDVLNLDFILIENVPRF  32
MTH2_HAEAE|O30868  (  89) RGTLFFNIEAILKAKKPKAFLLENVKRL  10
MTS1_STRAH|O31073  ( 116) NASLLDEYVRVVRESKPEAFILENVQGL  19
O26595             ( 140) RNYLYLLYIKFLKEFQPEFFVFENVPGM  11
Q9YAD7             ( 107) AGQLFLHAIRLIGLLKPRFFVIENVPGI  14
Q9V2M5             ( 102) IGRLVLEFVRFVERLKPKVFVMENVPQI  12
Q980M6             ( 103) RGNLTLEFIRIVDEVKPKIFVMENVPAI  10
Q975T7             ( 102) DGQLTLEYIRIVGELRPKIFVMENVPSI  22
Q8ZWR3             ( 100) AGQLTLEFIRLVGEIGPKVFVMENVAAL  27
Q8ZTL3             ( 108) RGRLYAHFIRALAVLQPKAFVFENVPGL  10
Q8TV73             ( 101) VGRLVLHFVRIIGDLQPEVFVMENVPAI  16
Q8U4N2             (  96) IGRLVLEFIRFVKEIKPKVFVMENVPQI  12
Q8Q059             ( 145) RNYLYRHYISFLKSFEPKIFVFENVPGI  14
O42803             ( 897) KNSLVATFLSYVDHYKPRFVLLENVKGL  10
Q8NJW0             ( 376) NLAILFSCTHLIEKIRPRLFTVEQTFGI  53
Q96W73             ( 944) NQSLVASFASFVDFYRPKYGVLENVSGI  48
Q8NJV8             ( 373) NLAILFSCTHLIEKIRPRLFTVEQTFGI  53
Q9HFI8             ( 376) NLAILFSCTHLIEKIRPRLFTVEQTFGI  53
Q8NJV9             ( 378) NLAILFSCTHLIEKIRPRLFTVEQTFGI  53
O42731             ( 897) KNSLVATFLSYVDHYKPRFVLLENVKGL  10
Q8IAJ7             (1237) KNSLISSYLSYCDYYRPRFFLLENVRNF   9
Q8IAJ6             (1085) KNSLISSYLSYCDYYRPRFFLLENVRNF   9
Q8MJ28             (1142) KNSLVVSFLSYCDYYRPRFFLLENVRNF   8
Q38652             ( 100) RGKLVWRYLEIIERKQPKAFVFENVKGL   9
Q8W6H6             ( 139) TLRGVWLMLEAFKDKLPKLIIFENVPRI  37
Q94M66             (  92) RGTLFFEIARFASILKPRYLFLENVKGL   9
Q02778             (  94) RGTLFFQYIDTLKEKKPRYFVFENVKGL   8
Q9ZXI4             ( 133) TLRCIWLMGEAWADDPVPLIVFENVPRL  53
Q8LPU5             ( 541) KNKQMVTFMDIVAYLKPKYVLMENVVDI  14
Q94F87             ( 884) RNQQIIVFMDIVEYLKPSYVLMENVVDI  12
Q9C9L8             ( 480) KNKQLLVYMNIVEYLKPKFVLMENVVDM  12
O48867             (1446) QCEMILAFLSFADYYRPKYFLLENVRNF   9
O23273             (1201) QCEMILAFLSFADYFRPKYFLLENVKKF  12
O49022             (1240) QCEMILAFLSFADYFRPRYFLLENVRNF   9
O50037             ( 421) KNQQLLVFLDIIDFLKPSYVLMENVVDL  11
Q8S921             ( 868) NNSLVGSYLSYCDFYRPRYFILENVMGF  28
Q9SEG3             (1199) QCEMILAFLSFADYFRPKYFLLENVKKF  12
O49139             ( 437) KNQQLLVFLDIIDFLKPNYVLMENVVDL  11
Q9FR60             (1129) NNSLVVSFLSYCDYYRPRFFLLENVRNF   8
Q9M0S8             (1194) QCEMILAFLSFADYFRPKYFLLENVKKF  12
O50073             ( 437) KNQQLLVFLDIIDFLKPNYVLMENVVDL  11
Q94FN4             ( 480) KNKQLLVYMNIVEYLKPKFVLMENVVDM  12
Q9MB97             (1241) QCEMILAFLSFADYYRPKFFLLENVRNF   9
Q8LQY1             (  99) FSFIKILNLMKNMCFPPQMLFVENVVGF  46
Q9ARI6             ( 541) KNKQMVTFMDIVAYLKPKYVLMENVVDI  14
O49137             ( 437) KNQQLLVFLDIIDFLKPNYVLMENVVDL  11
Q9T0I1             (1103) QCQMILAFLSFADYFRPKYFLLENVKTF  12
Q8LPU6             (1136) QCEMILAFLSFAEYFRPRFFLLENVRNF   9
Q9AXT8             ( 537) KNKQMVTFMDIVAYLKPKYVLMENVVDI  14
O48866             (1231) QCEMILAFLSFADYYRPKYFLLENVRTF  12
O65343             (1204) QCEMILAFLSFAEYFRPRFFLLENVRNF   9
Q94IR0             (  99) FSFIKILNLMQDMSYPPQMLFVENVVGF  46
Q9FVA3             ( 463) QCEMILAFLSFAEYFRPRFFLLENVRNF   9
Q94F88             ( 480) KNKQLLVYMNIVEYLKPKFVLMENVVDM  12
Q8LER4             ( 107) SSFLRILELIPHTTKPPQMLFVENVVGF  57
Q8S4C3             (1210) QCEMILAFLSFAEYFRPRFFLLENVRNF   9
O49415             ( 909) RNQQIIVFMDIVEYLKPSYVLMENVVDI  12
O49144             ( 437) KNQQLLVFLDIIDFLKPNYVLMENVVDL  11
O49889             (1244) QCEMILAFLSFADYYRPKFFLLENVRNF   9
Q8H854             ( 656) KNKQLVVFMDIVKYLRPKYVLMENVVDI  10
Q8H0H2             ( 390) KNKQLETFMDIVEFLNPRFVLMENVVDL  14
Q9EUV5             (  99) KMDLLDYFGKQVELVQPEIVSMENVPQL  37
Q9L5I8             ( 207) QGTLFFDVARIIRAKQPAIFVLENVKNL   7
Q8RT52             (  97) RGRLVWNFLEKIAYLQPDFFLFENVEGL  12
Q9KJH1             (  88) RGQLVWQYLRIINEIRPKCFVFENVVGL  13
O53067             (  90) RGNLFFELVRILETKKPRVAFFENVKNL  18
O52849             (  99) RNYLYRQFLRVIKLVKPRIVFMENVKEI  15
Q9X5I9             ( 129) RGTLFYEFSRVVDEVQPKIFIYENVKGL  14
O30357             ( 100) RNHLFKEFVRIVKIVQPYFFVMENVARL  24
Q93LM5             ( 116) NGKLSASYVELICRNLPDFFLFENVKGL  15
Q59380             (  87) SRDMFPFAIKAIEVLQPKAFIFENVKGL  18
Q59958             (  93) RGTLFFEIARAAKQIQPRFLFLENVKGL   8
Q93LL9             ( 104) RNSLVFHFHRLVFELKPKFFVMENVRGI  20
P77950             ( 158) RGTLFFDIARIIKEKKPHAFLLENVKNL   9
O52850             (  94) RNNLIMEMYRFASILKPNLVILENVKGI  17
Q9RQS3             ( 174) LLYEVERILKLNRDNLPKVLLLENVKAL  28
O31098             ( 110) RGKLFFEMIKVLKEKKPRFFIGENVKGL  16
Q8RLK9             (  87) SRDMFPFAIKAIEVLQPKAFIFENVKGL  18
Q9ZHP3             ( 152) RNRLFYEFVRVVSEIRPWYVVMENVPGI  14
P70750             (  96) RNLLIFNYLNIVERLSPRWFIFENVEGL  17
Q9ACM3             ( 101) KGVLFWEIIRATRIIKPKYLILENVDRL  18
Q9X9M1             (  90) RGNLFFELVRILKAKKPRIAFFENVKNL  17
Q9RPJ2             ( 100) RGQLIFEYVRMIKELNPKVFVMENVRGL   9
Q59245             ( 143) RNFLYIHFIRCLMQVQPEIFVAENVKGM  16
Q9F658             (  87) RRDMFPHAVRYVEYYRPKAFIFENVKGL  12
Q9WVZ8             (  89) ERDLFPEAIRLAKETDPKAIMLENVRGL  20
O08431             ( 158) RGTLFFDIARIIKEKKPHAFLLENVKNL   9
Q8VMN0             ( 134) TLRCVWLMCEAWQHNPPGLIVFENVPRL  36
Q59612             ( 100) RGQLFFDYIRILKSKQPKFFLAENVSGM  11
Q59604             ( 100) RGQLFFDYIRILKSKQPKFFLAENVSGM  11
Q9F6L2             ( 125) RNQLYAEYVRVLKTLRPRVFLMENVPNM  10
Q9ZHP1             ( 152) RNRLFYEFVRVVSEIRPWYVVMENVPGI  14
Q8RT54             ( 110) NGVLTKAYVDTILEFTPDFFVFENVKGL  24
Q8VLC7             (  98) RNFLFLEYIEIVKAIKPEIFIIENVKNL   8
P94630             (  94) RGTLYQNFRDFVAAKKPKAFIAENVKGL  13
Q8VTD8             (  98) RNFLFLEYIEIVKAIKPEIFIIENVKNL   8
Q9FDE0             (  97) RGKLVWNFLEKIAYLQPDFFLFENVEGL  11
Q93K37             ( 104) RNKLVLEYSRLVNELKPRAFLFENVEIF  21
Q9EXA5             ( 139) RNSLVVESIKIVREVQPKFFIFENVKAF  14
Q60171             ( 100) RGKLVWAYLRIIEAKRPKAFIFENVKGL   7
O87350             ( 101) KGVLFWEIIRATRIIKPKYLILENVDRL  18
Q8GMC3             (  95) RNFLFQEYLEIVRQVNPDFIVMENVKAL  13
Q8GGA1             ( 145) RGTLFFDVAEIIRRHRPKAFFLENVKGL  10
Q8GC38             ( 162) RNFLYVHFIRALVETQPAFFVAENVKGL  11
Q8GA84             (  87) RNQLYLEFLRVVNAKKPKFFFAQNVRGI  86
Q8GA83             (  87) RNKLYLEMVRIIRDKRPAYFIAENVKGI  10
O34939             ( 192) RNALLMRVSRVIELFQPSSVLVENVPGI  31
O34680             (  89) VKKLFELIEKKEHANRPPWILIENVPYM  54
O24892             (  98) RNFLFLEYIEIVKAIKPEIFIIENVKNL   8
O24895             ( 112) RNSLVVESIDLIKQIKPRFFILENVPSF  15
O25746             (  84) RGTIIYGLIRILKVKQPECFLLENVKGL  17
Q59995             ( 100) RNSLVFEYVRMIRDLKPKYFLFENVPGM  10
Q9ZLZ0             (  90) KANLFKEYLRILDLVKPKIFVFENVVGL  11
Q9ZK91             (  90) RGTIIYGLIRILKVKQPKCFLLENVKGL  16
Q9XAZ7             (  99) RNHLIFRVIEFILLKRPTFVLIENVPFF  23
Q9PCK4             ( 115) ELANAIDQIRHQDRRSPATLVWENVPGV  59
Q9KMW8             ( 124) NGILTRVYIDAIVQNQPDFFLFENVKGL  15
Q9K765             (  91) RNTLYKYYVKYLEEKKPLAFVGENVKGM  21
Q9K003             ( 129) RGTLFYEFARVVDEVQPKIFIYENVKGL  12
Q9JZI7             (  96) RGTLFFDVARILKAKKPKGFILENVEGL   9
Q9JWD8             ( 101) SKSLLLEFQRFVEYFNPGYVVVENVPGI  31
Q9JU80             (  96) RGTLFFDVARILKAKKPKGFILENVEGL   9
Q9JRF0             ( 116) QGTLFFDVAEIIGKHRPKIFLLENVKNL  10
Q9JQR8             ( 129) RGTLFYEFARVVDEVQPKIFIYENVKGL  12
Q9A9F5             ( 100) PMAYARLVAALHSRSPLDFFVMENVVGL  50
Q9A2D9             ( 100) FGFWSLMRSLSAEGRAPSVIVIENVVGL  67
Q982S6             ( 116) RRSLAWVICRWAGTVRPETITMENVQEI  32
Q8ZNT0             ( 206) QGTLFFDVVRIIDARRPALFVLENVKNL   8
Q8Z5Q6             ( 206) QGTLFFDVVRIIDARRPALFVLENVKNL   8
Q8YYB6             ( 167) RGNIFLKYIELILQIRPKYAVIENVRGL  20
Q8YUQ9             ( 111) RNSLVFHFHRLVLELQPKFFVMENVRGI  11
Q8YMV9             ( 101) RNGLFINFAQWIKFLEPKAFVMENVKGL  27
Q9KIV6             ( 116) NGKLSSAYIELICQNLPDFFLFENVKGL  15
Q8X8S5             (  94) RNQLYMHFYRLVSELQPLFFLAENVPGI  15
Q935J8             ( 207) QGTLFFDVARIIRAKQPAIFVLENVKNL   7
Q92LC3             ( 110) RNLLFKKYVEMVEALQPQALVIENVPGM  19
Q8XTV8             (  99) PFVYADLIRTLNKRSPVPFFVFENVVGL  71
Q97JQ1             (  99) LMWETISIIKQMGIWKPRVVVWENVKNV  63
Q97IY5             ( 149) ISIIKLIRLLDSVHGKPRVLFLENVKNL  48
Q8PKG0             ( 110) EIANAIDQVRNRAHRPPATLVWENVPGV  61
Q8NPN5             (  94) RGTLYQNFRDFVAAKKPKAFIAENVKGL  13
Q9L1W7             ( 116) AAEPMRYLYALNTVGEPDWVAMEEVPDV 100
Q8FGJ2             ( 202) QGTLFFDVVRIIDARRPAMFVLENVKNL   9
Q8EVR5             ( 162) ERILEEIKNSFSKEEMPKYLLMENVKNL  64
Q8EUE9             ( 100) RGTLFFDIAKILKNKKPKYILLENVKHL  19
Q8EL98             ( 122) RGTLFFDVIRFIRAKNPEAIFLENVKNL   9
Q8EL95             ( 122) RGKLYENFLDYALHVDANVIVMENVPEA  62
Q8ECW6             (  94) IRGLAWVTIRWAMKVRPRVIMLENVEEF  31
Q8E4N1             (  93) RGTLFFELARAAQQIQPRFLFLENVKGL  10
Q8DZ25             (  93) RGTLFFEIARAAKQIQPRFLFLENVKGL   8
Q8DXI1             (  92) RGTLFFEIARFASILRPKYLFLENVKGL   9
Q8CXP0             ( 116) NNQLVKQYVRAIDEIKPTAFLLENVRSM  16
Q8CWG2             ( 103) QGTLFFDVARIIKAKQPKAFLLENVKNL   6
Q8CE27             (  97) TSFLYILDILPRLQKLPKYILLENVKGF  18
Q8C7F0             (  97) TSFLYILDILPRLQKLPKYILLENVKGF  18
Q9YQY1             ( 378) KNTLVNLYIALALYYKPAVLIMENVRNL  19
P79922             (1119) KNSLVVSYLSYCDYYRPKYFLLENVRNF   8
Q9I8X6             (1130) KNSLVVSYLSYCDYYRPKFFLLENVRNF   8
Q9YHD9             ( 328) KNSLVVSYLSYCDYYRPRFFLLENVRNF   8
Q8QGB8             (1127) KNSLVVSYLSYCDYYRPKFFLLENVRNF   8
//
ID   C5_DNA_meth; BLOCK
AC   IPB001525D; distance from previous block=(13,213)
DE   C-5 cytosine-specific DNA methylase
BL   YQR;  width=27; seqs=222; 99.5%=1615; strength=1179
DCM_ECOLI|P11876   ( 321) KYILTPVLWKYLYRYAKKHQARGNGFG  39

DNM1_ARATH|P34881  (1263) GYQVRFGILEAGAYGVSQSRKRAFIWA   7

MTA1_ARTLU|P31974  ( 154) PAIFSPHLLPAWMGGTPQVRERVFITA  54

MTA1_RUEGE|P94147  ( 142) GYAADVVTLDACEYGVPQHRRRVFIFG  25

MTB1_BREEP|P10283  ( 194) YVVLDAQVLNAKNYGVAQNRERVIFIG  11

MTB1_NEIGO|Q59603  ( 134) GYTVYFKVLNTLDFGLPQKRERIYIVG   9

MTB6_BACSP|P43420  ( 138) YHIKYQVLNAKDFGNIPQNRERIYIVG  42

MTBA_BACAR|P19888  ( 139) GYGVSYLLLNSSTFGVPQNRVRIYILG  19

MTBF_BACSU|P17044  ( 233) GYSVFYEVMDAQNFGLPQRRERIVIVG  12

MTC1_HERAU|P25263  ( 137) LNYGVYLILNSSNFQVPQNRLRVYIVG  31

MTD1_DESDN|P05302  ( 141) GYKVCVIILNACDYGVPQSRQRVFFIG  21

MTD1_HERAU|P24600  ( 134) GYSLAQVVLDASLCGVPQLRKRTFVIG  25

MTD1_NEIMC|Q9RLM4  ( 212) GYVCTEKLINAIEYGVPQDRERIILVG   9

MTD2_HERAU|P25265  ( 141) GYHVSHSVVHCPDYGIPQQRDRLVLFA  34

MTD5_DACSA|P50185  ( 138) NYVVSWKIISATDFNLPQKRERIFIVG  12

MTE8_ECOLI|P50196  ( 217) YTLFEPRVLKAIFYKVPQKRERLIIVA  32

MTF7_NEIGO|Q59606  ( 151) GYYVQANVYNFAEFGVPQFRERVLIVG  10

MTH1_HAEHA|P05102  ( 144) DYSFHAKVLNALDYGIPQKRERIYMIC  18

MTH2_HAEPA|P15446  ( 168) YFVPEPAIVNAKNFGVPQNRERIYIVG  12

MTH5_HAEIN|P45000  ( 134) GYGLTSAILDASYCGVPQSRTRFSLIG  33

MTHA_HAEPH|P50192  ( 187) GYKVKCKVLNAADFGVPQLRSRIVFIG  13

MTHT_METTF|P29567  ( 136) GYNVEYKVLNAKDYGVPQDRKRVFIVG   5

MTM1_MORSP|P11408  ( 238) GYKVHHTVLDASHFGIPQKRKRFYLVA  12

MTM4_NEIGO|P31033  ( 136) GYLGQWKLLYAADYGVSQLRPRVLFVA  17

MTN1_NOCAE|P50188  ( 140) GYVAEWRLLHASDFGVPQLRPRFVLVA  13

MTNX_NEILA|P24581  ( 137) GYKVYTEVLKARDFGIPQNRERIYLVG   9

MTP1_PSYTA|O33481  ( 213) YKILEKEVYKAIFYKVPQKRERLIIIG  25

MTP2_NEIGO|P08455  ( 136) GYDVTLTMANAKDYGVAQERKRVFYIG  14

MTS1_SALIN|P09795  ( 238) GYSVSFNLYNSANFGVPQIRERVIIIC  14

MTS2_SHISO|P34879  ( 205) NYTVYYNIFAAKDFGVPQNRERIYIVG   9

MTS3_STAAU|P16668  ( 154) GYNVEWRVINAADYGNAQRRRRVFIFG  11

MTS9_STAAU|P23737  ( 237) GYEVYWNILNSWNYDVAQKRERIVIIG  20

MTSA_LACLC|P34877  ( 212) DYEVHTALFKARDFGLPQNRERIYIVG  13

MTSB_LACLC|P34878  ( 193) GYTNYWDILNARDFGIPQNRERVFCIS  18

MTSI_SPISQ|P15840  ( 211) GYQNSIEVLNAADFGSSQARRRVFMIS  26

MTX2_XANOR|P52311  ( 147) DVVTDYRVLNAADYGVPQDRRRLILMG  18

PMT1_SCHPO|P40999  ( 143) GYNLIEGILSPNQFNIPNSRSRWYGLA  41

O13369             ( 365) GYSFRICVLNAIEYGVCQNRKRLIIIG  22

DNM1_CHICK|Q92072  (1206) GYQCTFGVLQAGQYGVAQTRRRAIVLA   8
DNM1_HUMAN|P26358  (1291) GYQCTFGVLQAGQYGVAQTRRRAIILA   7
DNM1_MOUSE|P13864  (1294) GYQCTFGVLQAGQYGVAQTRRRAIILA   7
DNM1_PARLI|Q27746  (1283) GYQCTFGILQAGQYGVPQTRRRAIILA   7
DNM1_RAT|Q9Z330    (1296) GYQCTFGVLQAGQYGVAQTRRRAIILA   7

DNM2_HUMAN|O14717  ( 141) GFQYQEFLLSPTSLGIPNSRLRYFLIA  25
DNM2_MOUSE|O55055  ( 141) GFQYQEFLLSPSSLGIPNSRLRYFLIA  23

MTB1_BACSH|P13906  ( 218) GYRVEARLLNARDYGVPQIRERVIIVG   7
MTBR_BACSU|P06530  ( 219) GYRVQFKLLNARDYGVPQLRERVIIEG  19

MTB1_HERAU|P25262  ( 138) GYSVFYKLLNSFDFGVAQNRDRVFIVG   9
MTC2_HERAU|P25264  ( 138) GYNVYYKLLNSFDYGVAQNRDRVFIIG   9
MTE1_HERAU|P25266  ( 138) GYSVFYKLLNSFDFGVAQNRDRVFIVG   9

MTB5_NEIGO|Q59605  ( 150) GYYVSWKVLNAKEFGIPQNRKRIYLTG   9
MTN4_NEILA|P50182  ( 150) GYYVSWKVLNAKDFGIPQNRKRIYLTG   9

MTBP_BACSU|P05795  ( 174) GYRIDLELLNSKFFNVPQNRERVYIIG  10
MTBR_BPRH1|P09915  ( 141) GYRIDLELLNSKFFNVPQNRERIYIIG  10
MTBS_BPSPR|P00476  ( 141) GYRIDLELLNSKFFNVPQNRERLYIIG  10

MTF1_FUSNU|P34906  ( 134) GYNVFIKLLNAFDYGVAQDRERVFYVG  12
MTH3_HAEAE|P20589  ( 134) GYDVHIILLNANDYGVAQDRKRVFYIG  15

MT52_METJA|Q58600  ( 199) YEDVYFNTLRAEDYGNPSVRRRVFVSN  31
MTA1_ACEPA|O52702  ( 143) GYSVRLQKVNLAAYGVPQTRKRVLIIG  16
MTB1_BACBR|P34905  ( 158) GYKLVPHLYKFEEYGVPQRRHRIIIVG  19
MTE2_ECOLI|P05101  ( 330) KYILTPKLWEYLYNYAKKHAAKGNGFG 100
MTG1_HAEGA|P25282  ( 155) EYHIHFDILDAADYGTPQRRKRAIIRL  42
MTG2_HAEGA|P25283  ( 153) KYQIDIVILNAKDYGICQSRPRAIIKM  35
MTH2_HAEAE|O30868  ( 136) GYTVYHKVLNTLDFGLPQKRERIYIVG  11
MTS1_STRAH|O31073  ( 163) GYNPTFRVLLAAEYGVPQLRRRVFVVG  19
O26595             ( 187) EYKLDFEVRDAYNFGVPQRRRRIIVIG  30
Q9YAD7             ( 152) YRRVYFNLLRAEEHGTPSRRLRVFVSN  30
Q9V2M5             ( 144) GYDIYFNVLNALDYGAPQVRRRVFISN  12
Q980M6             ( 149) YGNIFFNILHAEDYGNPSKRSRVFISN  24
Q975T7             ( 147) GYKIFFNFLNAEDYGNPSKRTRVFISN  22
Q8ZWR3             ( 144) GYEVYFNILHAEDYGVPSRRRRVFVSN  16
Q8ZTL3             ( 177) YEIVFSDIVDFAAAGVPQKRERLIIIG  27
Q8TV73             ( 146) YDEIHFNVLQAVHYGVPSYRRRVFISN  35
Q8U4N2             ( 138) GYPIEFNILNALDYGVPQIRRRVFISN  13
Q8Q059             ( 192) GYKTEAHMLNAKDFSVLQERNRIIFIG  38
O42803             ( 959) NYQCRIGLVQSGEYGVPQSRPRVIFLA   9
Q8NJW0             ( 423) GYSVRWKVVNFSHYGLPQPRRRLIMIG  10
Q96W73             ( 994) GYQAQLILGDAWAHGAPQSRERVFLYF  55
Q8NJV8             ( 420) GYSVRWKVVNFSHYGLPQPGRRLIMIG  51
Q9HFI8             ( 423) GYSVRWKVVNFSHYGLPQPRRRLIMIG  10
Q8NJV9             ( 425) GYSVRWKVVNFSHYGLPQPRRRLIMIG  10
O42731             ( 959) NYQCRIGLVQSGEYGVPQSRPRVIFLA   9
Q8IAJ7             (1284) GYQCTFGILQAGQYGVPQTRRRAIILA   7
Q8IAJ6             (1132) GYQCTFGILQAGQYGVPQTRRRAIILA   7
Q8MJ28             (1189) GYQCTFGVLQAGQYGVAQTRRRAIILA   7
Q38652             ( 147) GYEISWEVVNAWDYGVAQKRERVFIVG   8
Q8W6H6             ( 186) FAVAETTHDCGQIGGLGQSRKRFLLVA  73
Q94M66             ( 139) GYDVEWQVLNSKNFGVPQNRERVFIIG   6
Q02778             ( 141) GYRIDLELLNSKFFNVPQNRERIYIIG  10
Q9ZXI4             ( 180) YAVAETTHDCGELGGLAQSRKRFLLVA  32
Q8LPU5             ( 588) KYQARLGMMVAGCYGLPQFRMRVFLWG  13
Q94F87             ( 931) RYQARLGIMTAGCYGLSQFRSRVFMWG  15
Q9C9L8             ( 527) NYQVRNGMMAAGAYGLAQFRLRFFLWG  13
O48867             (1493) GYQVRFGILEAGAFGVPQSRKRAFIWA   6
O23273             (1248) GYQVRFGILEAGTYGVSQPRKRVIIWA  10
O49022             (1287) GYQVRFGILEAGAFGVSQSRKRAFIWA   7
O50037             ( 468) NYQTRLGMMTAGSYGLPQVRNRVFLWA  13
Q8S921             ( 998) GYQVRFGALNAGNYGVPQSRKRVFIIA  19
Q9SEG3             (1246) GYQVRFGILEAGTYGVSQPRKRVIIWA  10
O49139             ( 484) NYQTRLGMMAAGSYGLPQLRNRVFLWA  11
Q9FR60             (1176) GYQCTFGVLQAGQYGVAQTRRRAIILA   7
Q9M0S8             (1241) GYQVRFGILEAGTYGVSQPRKRVIIWA  10
O50073             ( 484) NYQTRLGMMAAGSYGLPQLRNRVFLWA  11
Q94FN4             ( 527) NYQVRNGMMAAGAYGLAQFRLRFFLWG  13
Q9MB97             (1288) GYQVRFGILEAGAFGVPQSRKRAFIWA   6
Q8LQY1             ( 143) NFNTQEFILSPLQFGIPYSRPRYFCLA  24
Q9ARI6             ( 588) KYQARLGMMVAGCYGLPQFRMRVFLWG  13
O49137             ( 484) NYQTRLGMMAAGSYGLPQLRNRVFLWA  11
Q9T0I1             (1150) GYQVRFGLLEAGAYGISQPRKRAFIWA   8
Q8LPU6             (1183) GYQVRFGILEAGAFGVAQSRKRAFIWA   6
Q9AXT8             ( 584) KYQARLGMMVAGCYGLPQFRMRVFLWG  13
O48866             (1278) GYQVRFGILEAGAYGVPQSRKRAFIWA   6
O65343             (1251) GYQVRFGILEAGAFGVAQSRKRAFIWA   6
Q94IR0             ( 143) NFNTQEFILSPLQFGVPYSRPRYFCLA  23
Q9FVA3             ( 510) GYQVRFGILEAGAFGVAQSRKRAFIWA   6
Q94F88             ( 527) NYQVRNGMMAAGAYGLAQFRLRFFLWG  13
Q8LER4             ( 151) DYVTQEFILSPLQFGVPYSRPRYFCLA  24
Q8S4C3             (1257) GYQVRFGILEAGAYGVAQSRKRAFIWA   6
O49415             ( 956) RYQARLGIMTAGCYGLSQFRSRVFMWG  15
O49144             ( 484) NYQTRLGMMAAGSYGLPQLRNRVFLWA  11
O49889             (1291) GYQVRFGILEAGAYGVPQSRKRAFIWA   6
Q8H854             ( 703) NYQARLGMMAAGYYGLPQFRMRAFLWG  11
Q8H0H2             ( 437) NYQARMGMMVAGAYGLPQFRRRASMWG  28
Q9EUV5             ( 143) NYFVDWKIVYAPEYGVPQKRKRLLLLA  18
Q9L5I8             ( 326) RYILSPKLWEYLYNYAKKHQAKGNGFG  67
Q8RT52             ( 164) GYKTYFKVLNALEFGIPQDRARVFIIG   8
Q9KJH1             ( 138) GYEVQWSVLNAADYGVPQRRKRIFIVG   9
O53067             ( 138) YKYLFQVFNASEYGNIPQNRERIYIVA  25
O52849             ( 149) GYSIKPFIINAADFGIPQERIRFFMVA  20
Q9X5I9             ( 176) GYDLYFQIMNSKDYGIPQHRERIFVVG   8
O30357             ( 147) GYSVECKILSAADFGVPQIRSRVIFIG  11
Q93LM5             ( 164) GYILTERLINAIEYGVPQDRERIILIG   9
Q59380             ( 162) TYDVSFKLINAADYGVPQIRERVIIVG  12
Q59958             ( 140) GFDVEWQMLNSKDFGVPQNRERVFIIG   7
Q93LL9             ( 153) KVEENYQILNAANYGVPQSRERLFLIG  16
P77950             ( 205) NYTVYYNIFAAKDFGVPQNRERIYIVG   9
O52850             ( 144) GYKIKVFVLNTSDFGVPQGRQRVFVIA  22
Q9RQS3             ( 221) GYKSIWKVVNSTDYGSCQNRERVFCIS  32
O31098             ( 157) GYHINYKLLNSSEFGVPQKRERVFIVG   9
Q8RLK9             ( 162) TYDVSFKLINAADYGVPQIRERVIIVG  12
Q9ZHP3             ( 200) YPHVSVAILESADYGVPQIRPRAIFIA  17
P70750             ( 143) GYSVRLQKVNLAAYGVPQTRKRVLIIG  16
Q9ACM3             ( 151) GYSVEWRVINAADYGRSQRRRRVFFFV  27
Q9X9M1             ( 138) YKYLFQVMNAADYGNIPQNRERIYIVA  22
Q9RPJ2             ( 167) GYHVDCFVVNAANYGAPQIRERVILIG  12
Q59245             ( 190) GYRVEARLLNARDYGVPQIRERVIIVG   7
Q9F658             ( 162) KYKVSYQLLNAADYGVPQKRERVVIVG   9
Q9WVZ8             ( 136) GYLGQWKLLYAADYGVSQLRPRVLFVA  17
O08431             ( 205) NYTVYYNIFAAKDFGVPQNRERIYIVG   9
Q8VMN0             ( 181) YAVSETTHDCGELGGLAQSRKRFLLVA  34
Q59612             ( 147) GYDVTLTMANAKDYGVAQERKRVFYIG  14
Q59604             ( 147) GYDVTLTMANAKDYGVAQERKRVFYIG  14
Q9F6L2             ( 173) YSNCGVTVVAASDHGVPQLRRRAIFFG  33
Q9ZHP1             ( 200) YPNISVAILESADYGIPQIRPRAIFIA  16
Q8RT54             ( 157) KYNLTDRLTNCIEYGPPFDRDRIFLFG  61
Q8VLC7             ( 145) GYQLSYQILNAKDYGVPQNRERAFIVG   5
P94630             ( 143) GYIVKPRLYNFAEYGVPQFRERVLIVG  10
Q8VTD8             ( 145) GYQLSYQILNAKDYGVPQNRERAFIVG   5
Q9FDE0             ( 166) GYKTYFKVLNALEFGIPQDRTRVFVVG   9
Q93K37             ( 149) DYNIYTYFICSSDFGVAQKRGRFLMIG  31
Q9EXA5             ( 192) HYNILSNVLNFKDYGANSSRTRTLVIG  44
Q60171             ( 147) GYNVSWKLINAWDYGVAQKRERVFIVG   8
O87350             ( 151) GYSVEWRVINAAEYGRSQRRRRVFFFV  27
Q8GMC3             ( 142) GYFVNYQVLNAKDYGVPQSRERIFIIA   9
Q8GGA1             ( 194) YFVPEPEIVNAKDFGVPQNRERIFIVG  10
Q8GC38             ( 209) GYDVQAKLVNARDYGVPQSRERVFLVG   7
Q8GA84             ( 134) GYKVKKQLFNVADYGVPQMRYRVIIVG  34
Q8GA83             ( 134) GYNVKYSLLNCADYGVPQTRMRVIILG  13
O34939             ( 238) GYYFDEIVLNAEKLGVSQARRRYFIFA  23
O34680             ( 136) GYTWAYRTVDARCFGLPQRRHRVILLA  29
O24892             ( 145) GYQLSYQILNAKDYGVPQNRERAFIVG   5
O24895             ( 165) DYMLYDEVINFKNFGANSSRTRTLVIG  41
O25746             ( 131) GYTTYYKILNSADFQLAQNRERLYIVG  11
Q59995             ( 149) HIEKPILVLDASLYGAPQKRKRLIILG  32
Q9ZLZ0             ( 137) GYILEHAILNALDYGVPQVRERVILVG  10
Q9ZK91             ( 137) GYTTHYQILNSADFQLAQKRERLYIVG  12
Q9XAZ7             ( 151) EYYIQTHIFDSADYGVAQHRKRAIIRM  29
Q9PCK4             ( 181) RRRIAWRVLDAQYFGVAQRRKRVFLVA  17
Q9KMW8             ( 172) GYVLTDRLTNSIEFGVPQDRDRILMFG  19
Q9K765             ( 138) GYTLFYKLLNAKDYSVPQNRERVIIVG  12
Q9K003             ( 176) GYDLYFQIMNSKDYGIPQHRERIFVVG   8
Q9JZI7             ( 150) GYYVSWKVLNAKDFGIPQNRKRIYLTG   9
Q9JWD8             ( 148) GFTVHFGIHNTADYGIPQSRKRFTLIA  39
Q9JU80             ( 150) GYYVSWKVLNAKDFGIPQNRKRIYLTG   9
Q9JRF0             ( 162) LDYQIFYQVMNAKYYVPQNRERIFIVG  66
Q9JQR8             ( 176) GYDLYFQIMNSKDYGIPQHRERIFVVG   8
Q9A9F5             ( 147) GFKVARLLLNAKDHGTPQNRPRLFLLG  26
Q9A2D9             ( 146) EGYRFGALEIDAGAFVPQSRPRVFVVA  78
Q982S6             ( 203) GYSFEYRVLVCADYGVPTIRKRFFGVA  22
Q8ZNT0             ( 325) KYILTPVLWKYLYRYAKKHQARGNGFG  39
Q8Z5Q6             ( 325) KYILTPVLWKYLYRYAKKHQARGNGFG  39
Q8YYB6             ( 235) GYSISFNLYNTANYGVPQIRERVVMIC  19
Q8YUQ9             ( 160) QVEENYQVLNAAHYGVPQARERLFLIG  31
Q8YMV9             ( 151) GYFVEVWVLNAAEYGIPQIRERIFIVG  18
Q9KIV6             ( 164) GYLLTERVINAIEYGVPQDRERIILLG  10
Q8X8S5             ( 141) YDILDPIKVKASDYGAPTIRTRYFFIG  29
Q935J8             ( 326) RYILSPKLWEYLYNYAKKHQAKGNGFG  67
Q92LC3             ( 173) GYDVDAMLVDSASFGVPQKRSRLIAIG  34
Q8XTV8             ( 146) GFSVQEAILNAANYSVPQNRERLIMVG  15
Q97JQ1             ( 146) GYTNNYEILNAMDFGLPQRRERVFTIS  38
Q97IY5             ( 197) YIIKEKVLNTMDFSHLPQNRERIYIVG  60
Q8PKG0             ( 176) RRRIAWRVLDAQYFGVAQRRKRVFLVA  17
Q8NPN5             ( 143) GYIVKPRLYNFAEYGVPQFRERVLIVG  10
Q9L1W7             ( 158) GFSVWYGILNAADFGVPQTRKRAILLA  15
Q8FGJ2             ( 321) KYILTPVLWKYLYRYAKKHQARGNGFG  39
Q8EVR5             ( 209) GYKSKTYLLNSKNFDNCQNRERVFCLS  35
Q8EUE9             ( 149) LIPKEPLILSPHEFGIPQERYRVFIPG  48
Q8EL98             ( 170) YYIDSKIMNTMDYGNIPQNRERIFIVG  33
Q8EL95             ( 169) GYDAIWTVLNAADFGVPQTRVRLFVMA  20
Q8ECW6             ( 185) GYKVEFRELRACDYGAPTIRKRLFMIA  36
Q8E4N1             ( 140) GYDVEWQVLNSKDFQVPQNRERVFLIG   9
Q8DZ25             ( 140) GYDVEWQVLNSKDFQVPQNRERVFIIG   9
Q8DXI1             ( 139) GYNVEWQIFNSKNFGVPQNRERVFIIG   7
Q8CXP0             ( 358) DYKIDDNVLDASFFGVPQRRKRFMVLG  31
Q8CWG2             ( 150) LGYHVTYKLIDAAGFVPQHRERTYIVG  55
Q8CE27             ( 141) GFQYQEFLLSPSSLGIPNSRLRYFLIA  23
Q8C7F0             ( 141) GFQYQEFLLSPSSLGIPNSRLRYFLIA  23
Q9YQY1             ( 425) GYDVMLNILQAGHYGVPQTRQRVIVVA  19
P79922             (1166) GYQCTFGVLQAGQYGVAQTRRRAIVLA   8
Q9I8X6             (1177) GYQCTFGVLQAGQYGVAQTRRRAIILA   7
Q9YHD9             ( 375) GYQCTFGVLQAGQYGVAQTRRRAIILA   7
Q8QGB8             (1174) GYQCTFGVLQAGQYGVAQTRRRAIILA   7
//
ID   C5_DNA_meth; BLOCK
AC   IPB001525E; distance from previous block=(51,434)
DE   C-5 cytosine-specific DNA methylase
BL   RTF;  width=18; seqs=222; 99.5%=1066; strength=1216
MTA1_ARTLU|P31974  ( 437) RRLSPRETARLQGLPEWF   9

MTB1_BREEP|P10283  ( 339) RRLTVRECALIQSFPPDY   6

MTB6_BACSP|P43420  ( 263) RKLTPRECFNFQGYPEDF  12

MTBF_BACSU|P17044  ( 349) RLFSELELKRLMGFPVDF  22

MTD1_DESDN|P05302  ( 312) RNFTAREGARIQSFPDTY  10

MTD1_NEIMC|Q9RLM4  ( 356) RRISAAEALAIQSLPKEF  14

MTD2_HERAU|P25265  ( 287) RAISLREAALLQTFPRSY  11

MTH1_HAEHA|P05102  ( 272) RKLHPRECARVMGYPDSY  40

MTM1_MORSP|P11408  ( 351) RLLTTNECKAIMGFPKDF  19

MTM4_NEIGO|P31033  ( 258) PRLTVRMTARIQGFPDDW  33

MTN1_NOCAE|P50188  ( 263) PKLTCEMVARIQGWRDGE  93

MTS1_SALIN|P09795  ( 382) RPLSVQEYKVIQQFPEEW  39

MTS3_STAAU|P16668  ( 349) RTLTPIEAERLNGFPDNW  36

MTSB_LACLC|P34878  ( 306) RRLTPRETWRFMGVEDTN  29

MTSI_SPISQ|P15840  ( 332) RKMNSDETFLYIGFDSQD  83

MTX2_XANOR|P52311  ( 314) RVITVREAARLHSYPDWF   9

PMT1_SCHPO|P40999  ( 275) RYFTAREVARLMGFPESL  15

O13369             ( 478) RKFTVRELACIQGFPDEY  26

DCM_ECOLI|P11876   ( 400) RRLTPRECARLMGFEAPG  14

DNM1_ARATH|P34881  (1474) RILTVRECARSQGFPDSY   5
DNM1_CHICK|Q92072  (1460) RVVSVRECARSQGFPDTY   6
DNM1_HUMAN|P26358  (1546) RVVSVRECARSQGFPDTY   6
DNM1_MOUSE|P13864  (1548) RVVSVRECARSQGFPDSY   6
DNM1_PARLI|Q27746  (1537) RVVSVRECARSQGFPDTY   6
DNM1_RAT|Q9Z330    (1550) RVVSVRECARSQGFPDTY   6
MTA1_RUEGE|P94147  ( 378) RFVSVREAARFQSFPDTY  11
MTB1_HERAU|P25262  ( 378) RKITVSEAARLQGFPGSF  27
MTB1_NEIGO|Q59603  ( 249) RRLTGREMLRLQGFPDDF   9
MTBA_BACAR|P19888  ( 364) RRITPRECARLQGFPDDF   4
MTC1_HERAU|P25263  ( 364) RRITPRECARLQGFPDSF   4
MTC2_HERAU|P25264  ( 378) RPITVNEAARIQGFPATF  14
MTD5_DACSA|P50185  ( 259) RVLTPRECARLQGFPESF   4
MTE1_HERAU|P25266  ( 378) RPITVSEAARLQGFPSTF  14
MTF1_FUSNU|P34906  ( 276) RRLSIRECARIQGFPDTF   5
MTH2_HAEPA|P15446  ( 303) RKMTPREWARLQGFPDSY  15
MTH3_HAEAE|P20589  ( 273) RRLTVRECARVQGFPDDF   7
MTHT_METTF|P29567  ( 274) RRLSVRECARIQGFPDDF   4
MTNX_NEILA|P24581  ( 255) RKITPPEAARLQGFPDSF  11
MTP2_NEIGO|P08455  ( 277) RRMTVREVARIQGFPDNF   9
MTS2_SHISO|P34879  ( 327) RKITPREASRLQGFPSDF   9
MTSA_LACLC|P34877  ( 334) RKITPREAARLQGFPENF   5

DNM2_HUMAN|O14717  ( 341) RYFTPKEIANLLGFPPEF  35
DNM2_MOUSE|O55055  ( 341) RYFTPKEIANLQGFPPEF  11

MTB1_BACSH|P13906  ( 345) RRLSVKEIKRIQTFPDWY   9
MTBR_BACSU|P06530  ( 346) RRLSVKEIARVQTFPDWF  11

MTB5_NEIGO|Q59605  ( 373) RTLTGKEGLRLFGYPDDY  17
MTN4_NEILA|P50182  ( 373) RTLTGKEGLRLFGYPDDY  17

MTBP_BACSU|P05795  ( 382) RKLSPLECWRLQAFDDED  18
MTBR_BPRH1|P09915  ( 442) RKLTPLECWRLQAFDEED  19
MTBS_BPSPR|P00476  ( 378) RRLTPLECFRLQAFDDED  16

MTD1_HERAU|P24600  ( 244) RPLTTKERSLIQTFPLDF  21
MTH5_HAEIN|P45000  ( 246) RPLTTIERSYIQTFPKSF  36

MTE8_ECOLI|P50196  ( 361) RPLTVREYARIQTFPDEW   8
MTP1_PSYTA|O33481  ( 357) RPLTTREYARIQTFPDDW  10
MTS9_STAAU|P23737  ( 376) RPFSIREYARIQSFPDEW   9

MTF7_NEIGO|Q59606  ( 291) RAFTNRERARLQSFPDDF  11
MTHA_HAEPH|P50192  ( 319) RALTVRELAALQSFPDDF   6

MT52_METJA|Q58600  ( 315) RLLTPREQARLMSYPDYH  11
MTA1_ACEPA|O52702  ( 330) RPLTIRECARIQTFPDKY   9
MTB1_BACBR|P34905  ( 294) RALTNRERARLQTFPDDY  11
MTE2_ECOLI|P05101  ( 409) RRLTPRECARLMGFEKVD  22
MTG1_HAEGA|P25282  ( 305) RVLSVLELMRLTGLPDNW  24
MTG2_HAEGA|P25283  ( 303) RVLSLLETFIVSSIDENI  74
MTH2_HAEAE|O30868  ( 251) RRLTGPEMLRLQGFPDTF  16
MTS1_STRAH|O31073  ( 318) RRFRVAEMKRIMTFPDEF  43
O26595             ( 359) RSLTVREAARIQSFPDNY   6
Q9YAD7             ( 271) RLLTVREQARLMGFPDYH   9
Q9V2M5             ( 254) RPLTVREQARLMGFPDDF   6
Q980M6             ( 266) RFLTVREQARLMSYPDDH  10
Q975T7             ( 264) RFLTVREQARLMSYPDDH  10
Q8ZWR3             ( 261) RVLTVREQARLMGYPDGY   9
Q8ZTL3             ( 408) ATLTLRERARLQTFPDLF  49
Q8TV73             ( 264) RLLTVREQARLMSYPDDH  10
Q8U4N2             ( 248) RPLTVREQARIMGFPDDF   6
Q8Q059             ( 369) RSLTVREVARIQSFPDNY   8
O42803             (1209) RVYTVRELARAQGFPDWF  21
Q8NJW0             ( 528) RQFTPQEYALLQGFPMHH  19
Q96W73             (1186) RPYTVQEMRRAQGYLDEE  58
Q8NJV8             ( 525) RQFTLQEYALLQGFPMHH  21
Q9HFI8             ( 528) RQFTPQEYALLQGFPMHH  19
Q8NJV9             ( 530) RQFTPQEYALLQGFPMHH  19
O42731             (1209) RVYTVRELARAQGFPDWF  21
Q8IAJ7             (1538) RVVSVRECARSQGFPDTY   6
Q8IAJ6             (1386) RVVSVRECARSQGFPDTY   6
Q8MJ28             (1443) RVVSVRECARSQGFPDTY   6
Q38652             ( 269) RRFTVRECLRIQSAPDTY  33
Q8W6H6             ( 648) RPFTTLELAALQSLVDPD  22
Q94M66             ( 332) RKLTPRECWRLQGFPDWA   9
Q02778             ( 442) RKLTPLECWRLQAFDEED  19
Q9ZXI4             ( 504) RPFTTLELAALQSLVDPE  24
Q8LPU5             ( 823) RVLTIRENARLQGFPDYY   6
Q94F87             (1164) RVLTIRESARLQGFPDYF   7
Q9C9L8             ( 760) RVLSIRENARLQGFPDDY   5
O48867             (1705) RIVTVRECARSQGFPDSY   6
O23273             (1459) RIITVRECARSQGFPDSY   5
O49022             (1498) RILTVRECARSQGFPDHY   7
O50037             ( 700) RVLSVRENARLQGFPDCY   7
Q8S921             (1259) RTVSVREVARSQGFPDQH  16
Q9SEG3             (1457) RIITVRECARSQGFPDSY   5
O49139             ( 715) RVLSVRENARLQGFPDCY   7
Q9FR60             (1429) RVVSVRECARSQGFPDSY   6
Q9M0S8             (1452) RIITVRECARSQGFPDSY   5
O50073             ( 715) RVLSVRENARLQGFPDCY   7
Q94FN4             ( 760) RVLSIRENARLQGFPDDY   5
Q9MB97             (1499) RIVTVRECARSQGFPDSY   6
Q8LQY1             ( 307) RFFTPREVANLHSFPSSF  14
Q9ARI6             ( 823) RVLTIRENARLQGFPDYY   6
O49137             ( 715) RVLSVRENARLQGFPDCY   7
Q9T0I1             (1349) RIISVRECARSQGFPDSY   5
Q8LPU6             (1394) RIITVRECARSQGFPDSY   5
Q9AXT8             ( 819) RVLTIRENARLQGFPDYY   6
O48866             (1489) RIVTVRECARSQGFPDSY   6
O65343             (1462) RIITVRECARSQGFPDSY   5
Q94IR0             ( 305) RFFTPREVANFHSFPSNF  17
Q9FVA3             ( 721) RIITVRECARSQGFPDSY   5
Q94F88             ( 760) RVLSIRENARLQGFPDDY   5
Q8LER4             ( 332) RYFTPREVANFHSFPEDF  16
Q8S4C3             (1468) RIITVRECARSQGFPDSY   5
O49415             (1091) RVLTIRESARLQGFPDYF   7
O49144             ( 715) RVLSVRENARLQGFPDCY   7
O49889             (1502) RIVTVRECARSQGFPDSY   6
Q8H854             ( 938) RVLTIRENARLQGFPDYY   6
Q8H0H2             ( 661) RVLTIRENARLQGFPDYY   6
Q9EUV5             ( 290) RALSLREGAILQTFPKDY  16
Q9L5I8             ( 405) RRLTPRECARLMGFEQPG  17
Q8RT52             ( 316) RRLTVREALRLQSVPDWY  11
Q9KJH1             ( 312) RLITVREALRLQGFPDNY   6
O53067             ( 264) RKLTPRECFNVQGFPKEY  12
O52849             ( 324) RNLTVREAARIQSFPDNY   7
Q9X5I9             ( 358) RKLTPRECLRLMGFRDDF   9
O30357             ( 280) RALTVRELAALQSFPDNF   7
Q93LM5             ( 324) RRLSVAEALAIQSLPVNF  13
Q59380             ( 319) RYFTVYEGKLLQTFPREF  14
Q59958             ( 391) RRITPKECFRLQGFPDWA   9
Q93LL9             ( 338) RCITVREAARLHSYPDWF  13
P77950             ( 327) RKITPREASRLQGFPSDF   9
O52850             ( 315) RNLTAREGARLQSFPDKF  11
Q9RQS3             ( 346) KYISPRQAFLYMGFGKND  74
O31098             ( 277) RRLTPREAANIQSFPQSF  11
Q8RLK9             ( 319) RYFTVYEGKLLQTFPREF  14
Q9ZHP3             ( 323) RVISSREMARLQSFPDSF  12
P70750             ( 330) RPLTIRECARIQTFPDKY   9
Q9ACM3             ( 361) RLLTPIEAERLQDFPDDW  24
Q9X9M1             ( 264) RKLTPRECFNVQGFPKDY  11
Q9RPJ2             ( 314) RAISVGEAAAIQEFPDYW  47
Q59245             ( 317) RRLSVKEIKRIQTFPDWY   9
Q9F658             ( 319) RYFTSYEAKLLQTFPEEF  19
Q9WVZ8             ( 258) PRLTVRMTARIQGFPDDW  33
O08431             ( 327) RKITPREASRLQGFPSDF   9
Q8VMN0             ( 471) RPFTTLEMAALQSLVDPE  25
Q59612             ( 288) WRMTVREVARIQGFPDNF  37
Q59604             ( 288) RRMTVREVARIQGFPDNF   9
Q9F6L2             ( 355) RWITVREAARLQSFHDGF  37
Q9ZHP1             ( 323) RVISAREMARLQTFPDSF   8
Q8RT54             ( 304) RRISAAEAMAIQSLPKEF  16
Q8VLC7             ( 303) RSITPREAARIQSFSDDY  11
P94630             ( 280) RALTNRQRARIQSFPDDF  38
Q8VTD8             ( 303) RSITPREATRIQSFSDDY  31
Q9FDE0             ( 318) RRLTVREALRLQSVPDWY  11
Q93K37             ( 298) RAITLREGAMLQGFPVNY  30
Q9EXA5             ( 346) RVFSVRELMRMMSIPPSF  42
Q60171             ( 453) RRFTVRECLRIQSVPDWY  13
O87350             ( 361) RFITPIEAERLQDFPDDW  24
Q8GMC3             ( 300) RAITPREAARLQSFPDDF   5
Q8GGA1             ( 329) RKMTPREWARLQGFPETF  17
Q8GC38             ( 337) RRLSVREISRIQTFPDWF   9
Q8GA84             ( 259) RRMSVRESAIIQTFPLDY  25
Q8GA83             ( 256) RRMTVREIAAAQSFPDDF  15
O34939             ( 378) RTITPHEAARIQFFPDFF  49
O34680             ( 239) GTINIRDAERLQGFPEDW 100
O24892             ( 303) RSITPREAARIQSFSDNY  12
O24895             ( 319) RVFSIRELMLLMNIPSRF  52
O25746             ( 256) KRLNAIESLLLQGFPRDL  35
Q59995             ( 337) RCITVREAARLHTYPDWF  13
Q9ZLZ0             ( 296) RALSIREGARLQSFPDNY   6
Q9ZK91             ( 262) KRLNAVESLLLQGFPRDL  40
Q9XAZ7             ( 302) RVLTPLELMLLTSLPIDW  40
Q9PCK4             ( 472) RRLMPVECERLQGMPDDY  43
Q9KMW8             ( 328) RRLSAAEALAIQSLPKEF  13
Q9K765             ( 259) RRFSWQEAAAIQTFPRDM  45
Q9K003             ( 358) RKLTPRECLRLMGFRDDF   9
Q9JZI7             ( 373) RTLTGKEGLRLFGYPDDY  17
Q9JWD8             ( 298) RALSLREGATLQSFPRNY  30
Q9JU80             ( 373) RTLTGKEGLRLFGYPDDY  17
Q9JRF0             ( 283) RKLTPRECSRLMGFPKDF   8
Q9JQR8             ( 358) RKLTPRECLRLMGFRDDF   9
Q9A9F5             ( 277) RRLSVYEALLLQGFPRDY  10
Q9A2D9             ( 313) RLISPREAARLMGLPDSY   8
Q982S6             ( 601) RMLEPEEGAAAHGFKPGA  67
Q8ZNT0             ( 404) RRLTPRECARLMGFEAPQ  18
Q8Z5Q6             ( 404) RRLTPRECARLMGFEAPQ  18
Q8YYB6             ( 379) RPLSIQEYKRIQQFPDSW  19
Q8YUQ9             ( 345) RCITVREAARLHSYPDWF  13
Q8YMV9             ( 336) RNLTAREGARIQSFPDNY   9
Q9KIV6             ( 324) RRISVAEALAIQSLPAKF  16
Q8X8S5             ( 315) RVITPREAARLQGFPDWF   4
Q935J8             ( 405) RRLTPRECARLMGFEQPG  17
Q92LC3             ( 358) RILTVRECARLQSFPDRF  10
Q8XTV8             ( 276) RRLSVYEAMLLQGFPTEY  26
Q97JQ1             ( 253) RFLTEKECWLLQGFSEED  26
Q97IY5             ( 354) RKLTPKETFKLQGFPVGN  26
Q8PKG0             ( 427) RRLMPRECERLQGMPDDH  37
Q8NPN5             ( 280) RALTNRERARIQSFPDDF  11
Q9L1W7             ( 363) IRITAREAGLLQTFPADY  56
Q8FGJ2             ( 400) RRLTPRECARLMGFEAPG  14
Q8EVR5             ( 336) RYLTPLECFKYMQFDVND  36
Q8EUE9             ( 370) RHLTPRETANLQSFPEDF  20
Q8EL98             ( 294) RKITPKEALKFQGFLVGE  33
Q8EL95             ( 405) RGISVREAARLQSFPDDF  16
Q8ECW6             ( 494) RMLEPHELFACQGFNPEY  79
Q8E4N1             ( 388) RRLTPRECFRLQGFPDWA   8
Q8DZ25             ( 388) RRLTPRECFRLQGFPDWA   8
Q8DXI1             ( 386) RKLTPRECWRLQGFPDWA   9
Q8CXP0             ( 530) VALSIREAARLQSFRDGY  38
Q8CWG2             ( 271) RRLTPRECARLMGYPDSF   6
Q8CE27             ( 341) RYFTPKEIANLQGFPPEF  11
Q8C7F0             ( 341) RYFTPKEIANLQGFPPEF  11
Q9YQY1             ( 667) RVLSARESARGQGFPDSY  29
P79922             (1420) RVVSVRECARSQGFPDTY   6
Q9I8X6             (1431) RVVSVRECARSQGFPDTY   6
Q9YHD9             ( 629) RVVSVRECARSQGFPDTY   6
Q8QGB8             (1428) RVVSVRECARSQGFPDTY   6
//
ID   C5_DNA_meth; BLOCK
AC   IPB001525F; distance from previous block=(6,348)
DE   C-5 cytosine-specific DNA methylase
BL   GNV;  width=13; seqs=222; 99.5%=833; strength=1111
MTA1_ARTLU|P31974  ( 465) YKQMGNGVNVGVV  16

MTBA_BACAR|P19888  ( 391) YKQLGNSVTVKVV   7

MTD1_NEIMC|Q9RLM4  ( 385) FKTIGNGVPFLAA  20

MTF7_NEIGO|Q59606  ( 318) RRQIGNAVPPQGV  11

MTH1_HAEHA|P05102  ( 299) YKQFGNSVVINVL  11

MTS1_SALIN|P09795  ( 409) YRQLGNAVPIGLG  13

MTS3_STAAU|P16668  ( 388) ITRIGNQIEKIDS  97

MTSI_SPISQ|P15840  ( 365) IFVCGNSISVEVL  26

DCM_ECOLI|P11876   ( 431) YRQFGNSVVVPVF   7
MTB1_NEIGO|Q59603  ( 276) RKVAGNSVSVPVI   8
MTB6_BACSP|P43420  ( 291) YKQAGNSVVVPVI   5
MTBF_BACSU|P17044  ( 376) YRQFGNSVAVPMI   6
MTBP_BACSU|P05795  ( 414) YKQAGNSITVSVL  11
MTBR_BPRH1|P09915  ( 474) YKQAGNSITVTVL  10
MTBS_BPSPR|P00476  ( 410) YKQTGNSITVTVL  31
MTC1_HERAU|P25263  ( 391) YRQFGNSVSVPVV   5
MTD5_DACSA|P50185  ( 286) WRQFGNSVPVSVI  10
MTH2_HAEPA|P15446  ( 330) YKQFGNSVAVPAI   5
MTM1_MORSP|P11408  ( 378) YRQMGNSVVVPVV   8
MTNX_NEILA|P24581  ( 282) YRQFGNSVCVPVI  23
MTS2_SHISO|P34879  ( 354) YKQFGNSVAVPVI   4
MTSA_LACLC|P34877  ( 361) YKEFGNSVAVPTI  25
MTSB_LACLC|P34878  ( 337) YKQSGNSIVVPVL  28

DNM1_ARATH|P34881  (1501) HRQIGNAVPPPLA   3
DNM1_CHICK|Q92072  (1487) HRQVGNAVPPPLA   3
DNM1_HUMAN|P26358  (1573) HRQVGNAVPPPLA   3
DNM1_MOUSE|P13864  (1575) HRQVGNAVPPPLA   3
DNM1_PARLI|Q27746  (1564) HRQIGNAVPPPMA   4
DNM1_RAT|Q9Z330    (1577) HRQVGNAVPPPLA   3
MTA1_RUEGE|P94147  ( 405) FRQIGNAVPPLLG   4
MTB1_BACSH|P13906  ( 382) YKQIGNAVPVFLT  19
MTB1_BREEP|P10283  ( 374) YKIIGNAVPPLLG   5
MTBR_BACSU|P06530  ( 383) YKQIGNAVPVLLA   3
MTD1_DESDN|P05302  ( 347) YQQIGNAVPPLLA   3
MTD1_HERAU|P24600  ( 271) EQMIGNAVPVNLA  11
MTD2_HERAU|P25265  ( 318) SRQIGNAVPVALG  17
MTE8_ECOLI|P50196  ( 388) YKQIGNAVPVNLS   4
MTF1_FUSNU|P34906  ( 304) YKMVGNAVPVDLA   5
MTH3_HAEAE|P20589  ( 301) YKMIGNAVPVNLA   4
MTH5_HAEIN|P45000  ( 273) EQMIGNAVPVNLA  11
MTHA_HAEPH|P50192  ( 346) QQQVGNAVPPLLA   6
MTHT_METTF|P29567  ( 302) YTMVGNAVPVKLA   6
MTM4_NEIGO|P31033  ( 285) YRQIGNAFPPPVA   8
MTN1_NOCAE|P50188  ( 291) YRQIGNAFPPPVA   8
MTP1_PSYTA|O33481  ( 384) YKQIGNAVPVNLA   3
MTP2_NEIGO|P08455  ( 305) YKMIGNAVPVNLA   4
MTS9_STAAU|P23737  ( 403) YRQIGNAVPVNLA   3
MTX2_XANOR|P52311  ( 341) FRQIGNSVPPLLA   3
O13369             ( 505) RRIIGNAVPPPLS   5

DNM2_HUMAN|O14717  ( 370) YRLLGNSLNVHVV  14
DNM2_MOUSE|O55055  ( 370) YRLLGNSLNVHVV  14
PMT1_SCHPO|P40999  ( 305) YRLLGNSINVKVV  10

MTB1_HERAU|P25262  ( 405) FRLIGNSVAPPVI   5
MTC2_HERAU|P25264  ( 405) FRLIGNSVAPPVI   5
MTE1_HERAU|P25266  ( 405) FRLIGNSVAPPVI   5

MTB5_NEIGO|Q59605  ( 400) CDLLGNTVAVPVI  15
MTN4_NEILA|P50182  ( 400) YDLLGNTVAVPVI  13

MT52_METJA|Q58600  ( 342) YNQIGESVPVALS   9
MTA1_ACEPA|O52702  ( 357) IQQIGNAVPPLAA   6
MTB1_BACBR|P34905  ( 321) RKQIGMAVPPDGA  57
MTE2_ECOLI|P05101  ( 440) YRQFGNSVVVPVF   7
MTG1_HAEGA|P25282  ( 334) RQIIGECIPPLLI  38
MTG2_HAEGA|P25283  ( 332) RTIIGEAIPPKLL  13
MTH2_HAEAE|O30868  ( 278) RKVAGNSVSVPVI   8
MTS1_STRAH|O31073  ( 345) QRQIGNPVPVELG  36
O26595             ( 386) YRQIGNAVPPLMS   5
Q9YAD7             ( 298) YNMVGEAVPPPLA   8
Q9V2M5             ( 281) FDSVGEAVPPPLA  14
Q980M6             ( 293) YNQVGESVPVALS   9
Q975T7             ( 291) YNQVGEAVPVVLS  10
Q8ZWR3             ( 288) YNQVGESVPPPLS   8
Q8ZTL3             ( 435) RAQIGEAVPPLAA   9
Q8TV73             ( 291) YDQVGESVPPELA   9
Q8U4N2             ( 275) FDSVGEAVPPPLA  14
Q8Q059             ( 396) YAQIGNAVPPLMA   6
O42803             (1244) HRNIGNAVPVPLG  11
Q8NJW0             ( 553) KKQIGNAFPPIFV  15
Q96W73             (1213) WKLVGNSVSRHMA  33
Q8NJV8             ( 550) KKQIGNAFPPIFV  15
Q9HFI8             ( 553) KKQIGNAFPPIFV  15
Q8NJV9             ( 555) KKQIGNAFPPIFV  15
O42731             (1244) HRNIGNAVPVPLG  11
Q8IAJ7             (1565) HRQIGNAVPPPMA   4
Q8IAJ6             (1413) HRQIGNAVPPPMA   4
Q8MJ28             (1470) HRQVGNAVPPPLA   3
Q38652             ( 298) YRIVGNGIASRVA  17
Q8W6H6             ( 679) RERIGNAVPPDAA  12
Q94M66             ( 363) YKQAGNSVTVNVI   6
Q02778             ( 474) YKEAGNSITVTVL  15
Q9ZXI4             ( 535) RERIGNAVPPAAA  12
Q8LPU5             ( 850) YIQVGNAVAVPVA   4
Q94F87             (1191) YCQIGNAVAVSVS  11
Q9C9L8             ( 787) YIQVGNAVAVPVA   4
O48867             (1732) HRQIGNAVPPPLA   3
O23273             (1486) HRQIGNAVPPPLA   3
O49022             (1525) HRQIGNAVPPPLA   3
O50037             ( 727) YIQVGNAVAVPVG   5
Q8S921             (1286) YKQVGNAVPPPLA   3
Q9SEG3             (1484) HRQIGNAVPPPLA   3
O49139             ( 742) YIQVGNAVAVPVG   5
Q9FR60             (1456) HRQVGNAVPPPLA   3
Q9M0S8             (1479) HRQIGNAVPPPLA   3
O50073             ( 742) YIQVGNAVAVPVG   5
Q94FN4             ( 787) YIQVGNAVAVPVA   4
Q9MB97             (1526) HRQIGNAVPPPLA   3
Q8LQY1             ( 336) YAMLGNSLSVAVV  14
Q9ARI6             ( 850) YIQVGNAVAVPVA   4
O49137             ( 742) YIQVGNAVAVPVG   5
Q9T0I1             (1376) HRQVGNAVPPPLA   3
Q8LPU6             (1421) HRQIGNAVPPPLA   3
Q9AXT8             ( 846) YIQVGNAVAVPVA   4
O48866             (1516) HQQIGNAVPPPLA   3
O65343             (1489) HRQIGNAVPPPLA   3
Q94IR0             ( 334) YAMLGNSLSIAVV  18
Q9FVA3             ( 748) HRQIGNAVPPPLA   3
Q94F88             ( 787) YIQVGNAVAVPVA   4
Q8LER4             ( 361) YAMLGNSLSVAVV  14
Q8S4C3             (1495) HRQIGNAVPPPLA   3
O49415             (1118) YCQIGNAVAVSVS  11
O49144             ( 742) YIQVGNAVAVPVG   5
O49889             (1529) HRQIGNAVPPPLA   3
Q8H854             ( 965) YIQVGNAVAIPVA   8
Q8H0H2             ( 688) YMQVGNAVAVPVA  14
Q9EUV5             ( 322) AVQIGNAVPVKLG  21
Q9L5I8             ( 436) YRQFGNSVIVDVF  17
Q8RT52             ( 345) FKMVSNGVPYKLA  23
Q9KJH1             ( 340) HTIVGNAVPPILS   9
O53067             ( 292) YKQAGNSVVVPVI   5
O52849             ( 369) FNQVGNAVPPLLA   4
Q9X5I9             ( 385) YRQAGNSIVVDVL   9
O30357             ( 307) QQQVGNAVPPLLA   6
Q93LM5             ( 353) FKTIGNGVPYLAS  14
Q59380             ( 346) MRQIGNAVPVLLA   4
Q59958             ( 422) YKQAGNSVTVPVI   5
Q93LL9             ( 365) FRQVGNSVPPLLA   3
P77950             ( 354) YKQFGNSVAVPVI   4
O52850             ( 360) YNQIGNAVPPLLA   4
Q9RQS3             ( 379) LFLCGNSISIEVX  27
O31098             ( 305) YKAIGNAVPPVLM  15
Q8RLK9             ( 346) MRQIGNAVPVLLA   4
Q9ZHP3             ( 350) MWQIGNAVPPRLA  11
P70750             ( 357) IQQIGNAVPPLAA   6
Q9ACM3             ( 398) MFFMGNALVTEIV  35
Q9X9M1             ( 292) YKQAGNSVTVPVI   5
Q9RPJ2             ( 341) FRQIGNAVPVRLG   5
Q59245             ( 354) YKQIGNAVPVFLT  19
Q9F658             ( 346) MRQIGNAVPVKLS   5
Q9WVZ8             ( 285) YRQIGNAFPPPVA   8
O08431             ( 354) YKQFGNSVAVPVI   4
Q8VMN0             ( 502) RERIGNAVPPKAA  11
Q59612             ( 316) YKMIGNAVPVNLA   4
Q59604             ( 316) YKMIGNAVPVNLA   4
Q9F6L2             ( 382) LKQIGNAVPPLMA   6
Q9ZHP1             ( 350) MWQIGNAVPPRLA  11
Q8RT54             ( 333) FKTIGNGVPYLAA  13
Q8VLC7             ( 330) CKQIGNAVPPLLA   4
P94630             ( 307) RRQIGNAVPPVGM  15
Q8VTD8             ( 330) CKQIGNAVPPLLA   4
Q9FDE0             ( 347) FKMVSNGVPYKLA  23
Q93K37             ( 325) RLQIGNAVPPPVS   9
Q9EXA5             ( 393) RHCIGESVPTAVL  28
Q60171             ( 482) YRIVGNGIASRVA  17
O87350             ( 398) MFFMGNALVTEIV  35
Q8GMC3             ( 327) CKQIGNAVPPRLA   6
Q8GGA1             ( 356) YKQFGNSVAVPAV   6
Q8GC38             ( 373) YKQIGNAVPVQLA   6
Q8GA84             ( 286) YRQVGNAVPVLFA   5
Q8GA83             ( 283) YRQIANAVPPKLG  52
O34939             ( 406) QDVIGNAVPSKLS  18
O34680             ( 273) WRLVGNAVSVRVS  11
O24892             ( 330) CKQIGNAVPPLLA   4
O24895             ( 686) DRQITNSVLVKNG 100
O25746             ( 289) LSQAGNAMSVNVI  21
Q59995             ( 364) FREIGNSVVPLLA   9
Q9ZLZ0             ( 323) RLQIGNAVPPLLS   9
Q9ZK91             ( 295) LSQAGNAMSVNVI  21
Q9XAZ7             ( 331) RQCIGESIPPLLI  17
Q9PCK4             ( 505) YKAIGNSMAVPCM  30
Q9KMW8             ( 357) FKTIGNGVPFLAS  21
Q9K765             ( 286) YKQIGNAVPVKLA   3
Q9K003             ( 385) YRQAGNSIVVDVL   9
Q9JZI7             ( 400) YDLLGNTVAVPVI  13
Q9JWD8             ( 326) ARLIGNAVPPMYA  36
Q9JU80             ( 400) CDLLGNTVAVPVI  15
Q9JRF0             ( 311) YKQFGNSIAVPLV   6
Q9JQR8             ( 385) YRQAGNSIVVDVL   9
Q9A9F5             ( 304) IDQVSEAVPPPLA  20
Q9A2D9             ( 340) LQVMGDGVAVPVV  64
Q982S6             ( 638) YHLVGNSVPPHMI  12
Q8ZNT0             ( 435) YRQFGNSVVVPVF   7
Q8Z5Q6             ( 435) YRQFGNSVVVPVF   7
Q8YYB6             ( 406) YRQIGNAVPVGFG   9
Q8YUQ9             ( 372) FRQVGNSVPPLLA   3
Q8YMV9             ( 381) YNQIGNAVPPLLA   4
Q9KIV6             ( 353) FKTIGNGVPYLAS  14
Q8X8S5             ( 342) FRQIGNSVSPIVA   6
Q935J8             ( 436) YRQFGNSVIVDVF  17
Q92LC3             ( 395) YTQVGNAVPPLLA   4
Q8XTV8             ( 303) ITQISEAVPPPLA  21
Q97JQ1             ( 284) YKQAGNSIPVTIL  11
Q97IY5             ( 390) YKQAGNAVSVPII   7
Q8PKG0             ( 460) YRAIGNSMAVPCI  26
Q8NPN5             ( 307) RRQIGNAVPPVGM  15
Q9L1W7             ( 390) FSQIGNAVPPLLA   6
Q8FGJ2             ( 431) YRQFGNSVVVPVF   7
Q8EVR5             ( 369) IYIAGNSIPVKIL  23
Q8EUE9             ( 403) YKQFGNSINVKIA  11
Q8EL98             ( 325) YKQAGNAVSVPVI   5
Q8EL95             ( 432) FKQIGNAVPPLLA   3
Q8ECW6             ( 526) VARVGNSVPPQFA  25
Q8E4N1             ( 419) YKQAGNSVTVNVI   6
Q8DZ25             ( 419) YKQAGNSVTVTVI   8
Q8DXI1             ( 417) YKQAGNSVTVNVI   6
Q8CXP0             ( 557) YQQVGNAVPPLLA   3
Q8CWG2             ( 298) YRQFGNSVAVPVI   4
Q8CE27             ( 370) YRLLGNSLNVHVV  14
Q8C7F0             ( 370) YRLLGNSLNVHVV  14
Q9YQY1             ( 694) YKQVGNAVPPPMA   4
P79922             (1447) HRQVGNAVPPPLS   4
Q9I8X6             (1458) HRQVGNAVPPPLS   4
Q9YHD9             ( 656) HRQVGNAVPPPLS   4
Q8QGB8             (1455) HRQVGNAVPPPLS   4
//
   ( 341) RYFTPKEIANLQGFPPEF  11
Q9YQY1             ( 667) RVLSARESARGQGFPDSY  29
P79922             (1420) RVVSVRECARSQGFPDTY   6
Q9I8X6             (1431) RVVSVRECARSQGFPDTY   6
Q9YHD9             ( 629) RVVSVRECARSQGFPDTY   6
Q8QGB8             (1428) RVVSVRECARSQGFPDTY   6
//
ID   C5_DNA_meth; BLOCK
AC   IPB001525F; distance from previous block=(6,348)
DE   C-5 cytosine-specific DNA methylase
BL   GNV;  width=13; seqs=222; 99.5%=833; strength=1111
MTA1_ARTLU|P31974  ( 465) YKQMGNGVNVGVV  16

blimps-3.9/examples/blimps/sample.pros000064400001460000012000000043350776373110200204530ustar00jorjastaff00000400000027>CMT1 u53501 predicted by Goodman et al$
MAARNKQKKRAEPESDLCFAGKPMSVVESTIRWPHRYQSKKTKL
QAPTKKPANKGYNFTGGKKEDEEIIKQAKCHFDKALVDGVLINLNDDVYVTVSFLSIC
VYILCCYAFCFVEMLRGSDASSSLSSDSALNCFENLHKDEKFLLDLYSGCGAMSTGFC
MGASISGVKLITKWSVDINKFACDSLKLNHPETEVRNEAAEDFLALLKEWKRLCEKFS
LVSSTEPVESISELEDEEVEENDDIDEASTGAELEPGEFEVEKFLGIMFGDPQGTGEK
TLQLMVRWKGYNSSYDTWEPYSGLGNCKEKLKEYVIDGFKSHLLPLSGTVYTVCGGPP
CQGISGYNRYRNNEAPLEDQKNQQLLVFLDIIDFLKPNYVLMENVVDLLRFSKGFLAR
HAVASFVAMNYQTRLGMMAAGSYGLPQLRNRVFLWAAQPSEDLQVGRIQMEFLKLDNA
LTLADAISDLPPVTNYVANDVMDYNDAAPKTEFENFISLKRSETLLPAFGGDPTRRLF
DHQPLVLGDDDLERVSYIPKQKGANYRDMPGVLVHNNKAEINPRFRAKLKSGKNVVPA
YAISFIKGKSKKPFGRLWGDEIVNTVVTRAEPHNQVSPFAFISHVSGYVPLRIL
>CMT2 composite N-term from gi|2832630, C=term from Luca$
MLSPAKCESEEAQAPLDLHSSSRSEPECLSLVLWCPNPEEAAPSSTRELIKLPDNGEMSLRRSTTLNCNS
PEENGGEGRVSQRKSSRGKSQPLLMLTNGCQLRRSPRFRALHANFDNVCSVPVTKGGVSQRKFSRGKSQP
LLTLTNGCQLRRSPRFRAVDGNFDSVCSVPVTGKFGSRKRKSNSALDKKESSDSEGLTFKDIAVIAKSLE
MEIISECQYKNNVAEGRSRLQDP
AKRKVDNDTLLYSSINSSKQSLGSNKRMRRSQRFMKGTENEGEENLGKSKGKGMSLASCSFRRSTRLSGTVETGNT
ETLNRRKDCGPALCGAEQVRGTERLVQISKKDHCCEAMKKCEGDGLVSSKQELLVFPSGCIKKTVNGCRDRTLGKP
RSSGLNTDDIHTSSLKISKNDTSNGLTMTTALVEQDAMESLLQGKTSACGAADKGKTREMHVNSTVIYLSDSDEPS
SIEYLNGDNLTQVESGSALSSGGNEGIVSLDLNNPTKSTKRKGKRVTRTAVQEQNKRSICFFIGEPLSCEEAQE
RWRWRYELKERKSKSRAQQSEDDEDKIVANVECHYSQAKVDGHTFSLGDFAYIKGEEEETHVGQIVEFFKTTDGE
SYFRVQWFYRATDTIMERQATNHDKRRLFYSTVMNDNPVDCLISKVTVLQVSPRVGLKPNSIKSDYYFDMEYCVE
YSTFQTLRNPKTSENKLECCADVVPTESTESILKKKSFSGELPVLDLYSGCGGMSTGLSLGAKISGVDVVTKWAV
DQNTAACKSLKLNHPNTQVRNDAAGDFLQLLKEWDKLCKRYVFNNDQRTDTLRSRKFNKETSGSSSSSDDDSDS
EEYEVEKLVDICFGDHDKTGKNGLKFKVHWKGYRSDEDTWELAEELSNCQDAIREFVTSGFKSKILPLPGRVGVI
CGGPPCQGISGYNRHRNVDSPLNDERNQQIIVFMDIVEYLKPSYVLMENVVDILRMDKGSLGRYALSRLVNMRY
QARLGIMTAGCYGLSQFRSRVFMWGAVPNKNLPPFPLPTHDVIVRYGLPLEFERNVVAYAEGQPRKLEKALVLK
DAISDLPHVSNDEDREKLPYESLPKTDFQRYIRSTKRDWTGSAMDNRNKRTMLLHDHRPFHINEDDYARVGQIP
KRKGANFRDLPGLIVRNNTVCRDPSMEPVILPSGKPLLTWALLGTRIRFTFQQGKSKKSLWIYKIRKPFARLWW
DETVPTVLTVPTCHSQALLHPEQDRVLTIRESARLQGFPDYFQFCGTIKERYCQIGNAVAVSVSRALGYSLGMA
FRGLARDEHLIKLPQNFSHSTYPQLQETIPH
>DMT000107   DMT107 [Zea mays] protein sequence 
GISRTERYRSLGNSFQVDTVAYHLSVLKDRYPQGMNVLSLFTGIGGAEVALHRLGIRMNT
VISVEKSEVNRTILKSWWDQTQTGTLIEINDVQTLTADRIEAYIRRIGGFDLVIGGSPCN
NLAGSNRHHRDGLEGDHSSLFYHYFRILDSVKSIMERL
blimps-3.9/examples/blimps/www-search.pl000075500001460000012000000045740773637446600207410ustar00jorjastaff00000400000027#!/usr/bin/perl -w

#	Sample script to do bulk Block Searches
#	Replaces Email Block Searcher
#	Arguments are  
#	Requires libwww-perl         (http://www.linpro.no/lwp/)

#       Form                            Mail
#       database=plus | minus | prints  #DB PLUS | MINUS | PRINTS
#       ty=auto | AA | DNA              #TY AUTO | AA | DNA
#       st=0 | 1 | -1                   #ST BOTH | FORWARD | REVERSE
#       ge=0 to 16                      #GE 0 to 16
#       ou=all | sum | gff | old | raw  #OU ALL | SUM | GFF | OLD | RAW
#                                       #FO TEXT | HTML
#       ex=n                            #EX n
#       sequence=                       #SQ

use lib '/usr/local/perl';
use LWP 5.63;
use HTTP::Request::Common;
use strict;

# URL of Blockmaker script
my $script_url = 'http://blocks.fhcrc.org/blocks-bin/blocks_search';

# Defaults for the form fields
#	Other possible values at http://blocks.fhcrc.org/www/blocks_search.html
my %form_data = (
	database 	=>	'plus',
	ex		=>	1,
	ou		=>	'all',
	ty		=>	'auto',
	st		=>	2,
	ge		=>	0);



# HTML named entities to convert
my %convert = (
	amp		=>	'&',
	lt		=>	'<',
	gt		=>	'>',
	quot		=>	'"');


unless ($#ARGV == 1) {
	die "Usage: $0 seq_file email_address\n";
}

# Create the user agent
my $ua = LWP::UserAgent->new();
$ua->agent('Batch Blocks Searcher');
$ua->from($ARGV[1]);


# Read in the sequences (in FASTA format), one at a time, and then
# call block searcher.
open(SEQS, $ARGV[0]);

my $seq;

my $count = 0;

for ( ; ; ) {
	$_ = ;

	if ($seq && ((! $_) || (/^>/))) {
		++$count;
		
		if ($count > 1) {
			print '#' x 80;
		}
		
		$form_data{'sequence'} = $seq;
		my $response = $ua->request(POST $script_url, \%form_data);
		
		if ($response->is_success()) {
			my $data = $response->content;

			# Strip out the header
			$data =~ s/^.*BLKPROB/BLKPROB/s;

			# and the footer
			$data =~ s/<\/PRE>//;
			$data =~ s/<\/PRE>.*//s;

			# Strip out HTML Tags
			$data =~ s/<[^>]+>//g;

			foreach (keys(%convert)) {
				$data =~ s/&$_;/$convert{$_}/g;
			}
			
			if ($data =~ /Here are your search results/) {
				print $data;
			} else {
				warn "Blockmaker request #$count failed: $data\n";
			}
		} else {
			warn "Blockmaker request #$count failed, ", $response->status_line(), "\n";
		}

		undef $seq;
	}

	if (! $_) {
		last;
	}
	
	$seq .= $_;
}

close(SEQS);
exit;
blimps-3.9/examples/blimps/distribution/000075500001460000012000000000001043043273200207675ustar00jorjastaff00000400000027blimps-3.9/examples/blimps/distribution/example.bli000064400001460000012000001372501041506445700231320ustar00jorjastaff00000400000027BLIMPS (BLocks IMProved Searcher)   Version 3.8  2006/04
(C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center


Probe Sequence: HAIR_DROME  HAIRY PROTEIN 

Probe Size: 337 Amino Acids

Probe File: /d0/local/blimps-3.8/examples/blimps/example.pro

Target File (s) : sample.blocks

Records Searched:   9

Scores Done:                    3205

Alignments Done:                3205

AC#         Description                                         Strength  Score RF    AA#
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991   1107  0     70 KLEKADILEKTVKHL
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960   1104  0     39 EKRRRARINNCL
IPB000953   Chromo domain                                           1126    956  0     40 KRRRARINNCLNElKTLILdaTKKDPARHSkLEKADIL
IPB000953   Chromo domain                                           1126    941  0    139 INGVKTELHQQQRQQQQqsIHaQmLPSPPSSPEQDSQq
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    941  0    128 RRRLLQHLSNCI
IPB000953   Chromo domain                                           1126    935  0    302 DIKpSVIQRVPMEQQPLSLVikKQiKEEEQpWRPW
IPB000953   Chromo domain                                           1126    925  0     38 MEKRRRARINNCLNELKtLILdATKKDPARHSKLEKAD
IPB000953   Chromo domain                                           1126    925  0     50 LNELKTLILDATKKDPArHsKlEKaDILEKTVKHLQEL
IPB000953   Chromo domain                                           1126    922  0     34 NKPImEKRRRARINNcLnELKTLiLDATKKDPARHSKL
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    918  0    171 EqDSQQGAAAPYLFGIqQTASgYFLPN
IPB000953   Chromo domain                                           1126    916  0     75 DILEKTVKHLQELQRQQAAMQqAaDPKIVNkFKAGFAD
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    912  0     50 LNELKTLILDATKKDPARhskLEkaDIL
IPB000953   Chromo domain                                           1126    910  0     36 PIMEKRRRARINNcLNELKTLILDaTKKDpaRhSKLEK
IPB000953   Chromo domain                                           1126    909  0     25 TPLKSDRRSNKPImEKRrRARINNCLNELKTLILDATK
IPB000953   Chromo domain                                           1126    908  0    209 GSIALVLPQSLPQQQQQqLLQhQQQqQQLAVaAAAAAa
IPB000953   Chromo domain                                           1126    906  0     22 LKETPLKSDRRSNKPIMeKrRrARiNNCLNELKTLILD
IPB000953   Chromo domain                                           1126    905  0     63 KDPARHSKLEKADiLEKtvKHlQELqRQQAamQQAADP
IPB000953   Chromo domain                                           1126    901  0     39 EKRRRARINNCLNELKTLiLDaTKKDPARHSKLEKADI
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    900  0     51 NELKTLILDATKKDP
IPB000953   Chromo domain                                           1126    894  0    114 VNEVSRFPGIEPAQRRRLLqHlSNCiNGVKTELHQQQR
IPB000953   Chromo domain                                           1126    893  0     66 ARHSKLEKADILEKTVKHLqElQRQqAAMQQaADPKIV
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    893  0    126 AQRRRLLQHLSN
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    891  0     99 DPKIVNKFKAGF
IPB000953   Chromo domain                                           1126    889  0     32 RSNKPIMEKRRRARINnCLnElKTLiLDATkKDPARHS
IPB000953   Chromo domain                                           1126    889  0     92 AAMQQAADPKIVNKFKAgFADcVNEvSRFpGIEPAQRR
IPB000953   Chromo domain                                           1126    888  0     62 KKDpARHSKLEKADILEkTVKhLQELQRQQaaMQQAAD
IPB000953   Chromo domain                                           1126    886  0     89 RQQAAMQQAADPKiVNKFKAGFADCvNEVSRFpGIEPa
IPB000953   Chromo domain                                           1126    885  0    267 SASSHSSAGYESAPGSSSsCSYApSSPANSSYEPMDIK
IPB000953   Chromo domain                                           1126    882  0     20 AQLKETPLKSDRRSNKpIMeKrRRaRINNClnELKTLI
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    882  0     73 KADILEKTVKHLQELQrQqAAMQQaADp
IPB000953   Chromo domain                                           1126    881  0    141 GVKTELHQQQRQQQQQSIHAQmLpSPPSSpEQDSQQGa
IPB000953   Chromo domain                                           1126    880  0      3 GVtAANMTNVLGTAVVpAQLKeTpLKSDRRSnKPImEK
IPB000953   Chromo domain                                           1126    880  0     52 ELKTLILDATKKDPARHSKLEkADiLEKTVkhLQELQR
IPB000953   Chromo domain                                           1126    880  0     55 TLILDATKKDPARhSKLeKADILEKTVKHLQELQRQQa
IPB000953   Chromo domain                                           1126    880  0     86 ELQRQQAAMQQAADPKIVnKfkAGFADCVNEVsRFpGI
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    880  0     40 KRRRARINNCLN
IPB000953   Chromo domain                                           1126    879  0    213 LVLpQSLPQQQQQQLLQHQqQqQQLAVAAAaaAAAAAq
IPB000953   Chromo domain                                           1126    877  0    292 SPANSSYEPMDIKPSVIqRVpmEQQPLSLVIKKQIKEE
IPB000953   Chromo domain                                           1126    877  0    305 PSVIQRVPMEQQPlSLVIKKQIKEEEQPWRpW
IPB000953   Chromo domain                                           1126    876  0    165 SPPSSpEQDSQQGAAApYLFGIQQTASGYflPnGMQVI
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    876  0     32 RSNKPIMEKRRRARI
IPB000953   Chromo domain                                           1126    874  0     16 AVVpAQLKETPLKSDRRSnKpImEKRRRARInncLNEL
IPB000953   Chromo domain                                           1126    874  0     42 RRARINNCLNELKTLILDATKkDpaRHSKLEKADILEK
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    874  0     90 QQAaMQQAADPkIVNKfKAGFAdcVnEV
IPB000953   Chromo domain                                           1126    873  0     98 ADPKIVNKFKAGFADcVnEVSrFpGiEPAQRRRLLQHL
IPB000953   Chromo domain                                           1126    872  0     19 PAQLKETPLKSDRRSNKpiMEkRRRARINNcLnELKTL
IPB000953   Chromo domain                                           1126    872  0     69 SKLEKADILEKTvKHLQeLqRqQaamQQAADPKIVNKF
IPB000953   Chromo domain                                           1126    870  0      1 VTGVTAANMTNVLGTAVVpAQlKETPLKSDRRsNKpIM
IPB000953   Chromo domain                                           1126    870  0    144 TELHQQQRQQQQQSIHAqMLpSppSSPEQDSQQGAAAP
IPB000953   Chromo domain                                           1126    869  0      5 TAANmTNVLGTAvVPAQLKetpLKSDRRSNkPIMEKRR
IPB000953   Chromo domain                                           1126    869  0     11 NVLGTAVVPAQLKETPLksdRrSNKPIMEKRRRARINN
IPB000953   Chromo domain                                           1126    869  0    262 TASTGSASSHSSAGYESApgSSSSCSYAPSSPANSSYE
IPB000953   Chromo domain                                           1126    868  0    195 LPNGmQVIPTKLPNGSIALVLpQSLPQQQQQQLLQHQq
IPB000953   Chromo domain                                           1126    868  0    237 LAVAAAAAAAAAAQQQpmLVSmpQRTASTgSasSHSSa
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    868  0     34 NKPIMEKRRRAR
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    868  0     93 AMQQAADpKIVNKFKAgfAdcVnEVSRF
IPB000953   Chromo domain                                           1126    867  0     79 KTVKHLQELQRQQAAMQqAADpKiVNKfKAGFADCVNE
IPB000953   Chromo domain                                           1126    866  0     60 ATKKDpARHSKLEKADILEKtVKhLqELQRQQAAMQQa
IPB000953   Chromo domain                                           1126    866  0     85 QELQRQQAAMQQAADPKIvnKFKaGfADcVNEVSRFPg
IPB000953   Chromo domain                                           1126    866  0     96 QAADPKIVNKFKAGFADCvnEVSRFPGIEpaQRRRLLq
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    866  0      6 AANMTNVLGTAVVpA
IPB000953   Chromo domain                                           1126    865  0     21 QLKETpLKSDRRSNKPImEKRrRaRiNNcLNELKTLIL
IPB000953   Chromo domain                                           1126    864  0      9 MTNVLGTAVVPAQlKETpLKSdRRSNKPiMEKRRRARI
IPB000953   Chromo domain                                           1126    864  0    115 NEVSRFPGIEPAQRRRLLQhLSNciNGVKTELhQQQRq
IPB000953   Chromo domain                                           1126    864  0    118 SRfpGIEPAQRRRlLQHLsnCINGVKTELHQQQRQQQq
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    864  0     64 DPARHSKLEKADILE
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    864  0    169 SPEQDSQQGAAAPYL
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    864  0     22 LKETPLKsDRrSNkpImeKRRRArInN
IPB000953   Chromo domain                                           1126    863  0     27 LKSDRRSNKPIMEKRRRARInnCLnELKTLILDATKKD
IPB000953   Chromo domain                                           1126    863  0     93 AMQQAADPKIVNKfKAGFAdCVNEVSRfPgIEpAQRRR
IPB000953   Chromo domain                                           1126    863  0    109 GFADCVNEVSRFPGIEpAQrRrLLQHLSNCInGVKTEL
IPB000953   Chromo domain                                           1126    863  0    113 CVNEVSRfPGIEPAQRRrLLQhLSncINGVkTELHQQq
IPB000953   Chromo domain                                           1126    863  0    117 VSRFPGIEPAQRRRLLQHLsncINGvKTELHQQQRQQq
IPB000953   Chromo domain                                           1126    863  0    257 SMPQRTASTGSASSHSSAgYESApGSSSSCSYAPSSPa
IPB000953   Chromo domain                                           1126    863  0    296 SSYEPMDIKPSVIQRVpmEqQpLSLvIKKQIKEEEQPw
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    863  0    127 QRRRLLQHLSNC
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    863  0     88 QRQQAAMQQAADPKI
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    863  0    232 QqQQQLAVAAAAAAaAAaQQQpmLVSM
IPB000953   Chromo domain                                           1126    862  0     35 KPIMEKRRRARINNcLneLKtlILDATKKDpaRHSKLE
IPB000953   Chromo domain                                           1126    862  0    125 PAQRRRLLQHLSNcINGVKTElHQQqRQQQQQsIHAQM
IPB000953   Chromo domain                                           1126    862  0    252 QPMLVSMPQRTASTGSASshSSAGYESAPgSSsSCSYa
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    861  0    124 EPAQRRRLLQHL
IPB000953   Chromo domain                                           1126    860  0    131 LLQHLSNCINGVKTELHqQqRqQQQqSIHAQmLPSpPS
IPB000953   Chromo domain                                           1126    860  0    234 QQQLAVAAAAAAAAAAQqQpMlVSMPQRTASTGSASSh
IPB000953   Chromo domain                                           1126    860  0    298 YEPMDIKPSVIQRVPMEqQpLSLviKKQiKEEEQPWRP
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    860  0    132 LQHLSNCINGVK
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    860  0     67 RHSKLEKADILEKTV
IPB001525F  C-5 cytosine-specific DNA methylase                     1111    860  0     10 tNVLGtAVVPAqL
IPB000953   Chromo domain                                           1126    859  0     12 VLGTAVVPAQLKETPLKSdrRSNKpiMEKRRRARINNC
IPB000953   Chromo domain                                           1126    859  0     48 NCLNELKTLILDATKKDpArHSKLEKADiLEKTVKHLq
IPB000953   Chromo domain                                           1126    858  0      4 VTAANMTNVLGTAVVPAqLKETpLKSDRRSNKpIMEKR
IPB000953   Chromo domain                                           1126    858  0    101 KIVNKFKAGFADCVNEVSRFpgIEpAQRRRlLQHLSNC
IPB000953   Chromo domain                                           1126    858  0    121 PGIEPAQRRRLLQhLSnCinGVKTELHQQQRQQQQQSI
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    858  0    231 QqQQQQLAVAAAAAaAAaAQQqpMLVS
IPB000953   Chromo domain                                           1126    857  0     70 KLEKADILEKTVKhLQELQrQqAaMqQAADpKIVNKFK
IPB000953   Chromo domain                                           1126    857  0    111 ADcVNEVSRFPGIEPAQrRrLlQhLSNCiNGVKTELHq
IPB000953   Chromo domain                                           1126    857  0    129 RRLLQHLSNCINGVKTELHqQqRQQqQQSiHaQMLpSP
IPB000953   Chromo domain                                           1126    857  0    201 VIPTKLPNGSIALVLPQSLpQqQQQqLLQHQQQQQQLa
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    857  0    129 RRLLQHLSNCIN
IPB000953   Chromo domain                                           1126    856  0     47 NNcLNELKTLILDATKKDpARhSKLEKADilEKTVKHL
IPB000953   Chromo domain                                           1126    856  0     59 DAtKKDPARHSKLEKADILeKTVKHLQELQRQQAAmQq
IPB000953   Chromo domain                                           1126    856  0     68 HSKLEKADILEKTVKHLqELQrQQaAMQQAadpKIVNK
IPB000953   Chromo domain                                           1126    856  0    243 AAAAAAAQQQPMLVSMpqRTaSTGSASSHSSaGyESAP
IPB000953   Chromo domain                                           1126    856  0    281 GSSSSCSYAPSSPANSSYEpMdIKpSVIQRVPMEQQPL
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    856  0    109 GFADCVNEVSrFpGiePaQRRRLLqhL
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    856  0    110 FADCVNEVsRFPGiePAQRRRlLqhLS
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    856  0    275 GYESAPGssSSCSYaPSSPANssYePM
IPB000953   Chromo domain                                           1126    855  0     -2   MVTGVTAANMTNVLGtAVvpAQLKETPLkSDRRSNK
IPB000953   Chromo domain                                           1126    855  0    210 SIALVLPQSLPQQQQQQLLqHqQQQqQLAVaaAAAAAa
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    855  0    107 KAGFADCVNEVSRFP
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    855  0    125 PAQRRRLLQHLSNCI
IPB000953   Chromo domain                                           1126    854  0     53 LKtLILDATKKDPARHSkLeKaDiLEKTVKHLQELQRq
IPB000953   Chromo domain                                           1126    854  0     56 LILDATKKDPARHSKLEkAdilEKTvKHLQELQRQQAa
IPB000953   Chromo domain                                           1126    854  0    143 KTELHQQQRQQQQQSIHAQMLpSppSSPEQDSQQGAAa
IPB001525F  C-5 cytosine-specific DNA methylase                     1111    854  0    173 DSQqGaAaPYLFG
IPB000953   Chromo domain                                           1126    853  0     76 ILEKTVKHLQELQRQQAAMqQaADpKIVNKFKAGFADC
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    853  0     98 aDPKIVNKFKAGFADcvNEvSRFpGIe
IPB000953   Chromo domain                                           1126    852  0    127 QRRRLLQHLSNCINGVKtELHqQQRqQQQQSIhAQmLP
IPB000953   Chromo domain                                           1126    852  0    240 AAAAAAAAAAQQQPMLVSMpQrTaSTGSASShsSAGYE
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    852  0     37 IMEkRRRARINNCLNELKTLILdaTKKd
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    852  0    165 SpPSSPEQDSQQGAAAPYLFgIQQTASg
IPB000953   Chromo domain                                           1126    851  0      8 NMtNVLGTAVVPAQLKEtpLKSDRRSNKPiMEKRRRAR
IPB000953   Chromo domain                                           1126    851  0    134 HLSNCINGVKTELhQQQrQqQqQSiHAQMLpSpPSSPE
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    851  0    294 ANSSYEPMDIKPSVI
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    851  0    100 PKIVNKFKAgFADCvNevSRfpGIePA
IPB000953   Chromo domain                                           1126    850  0     31 RRSNKpIMEKRRRARInnCLneLKTLILDATKKDPARh
IPB000953   Chromo domain                                           1126    850  0     67 RhSKLEKADILEKTVKHLQeLqRQQAAMQQaaDPKIVN
IPB000953   Chromo domain                                           1126    850  0    185 GIQQTASGYFLPNGMQVIpTKlpNGSIALVlPQSLpQq
IPB000953   Chromo domain                                           1126    849  0     57 ILDATKKDPARHSKLEKAdILeKTVKHLQElQRQQAAM
IPB000953   Chromo domain                                           1126    849  0    128 RRRLLQHLSNCINGVKTeLhQqQRQqQQQSIhAQMLPS
IPB000953   Chromo domain                                           1126    848  0     97 AADpKIVNKFKAGfADCVnevSRFpGIEPAQRRRLLQh
IPB000953   Chromo domain                                           1126    848  0    126 AQRRRLLQHLSNCiNGVkTeLhQQQRQQQQQSIHAQML
IPB000953   Chromo domain                                           1126    848  0    220 PQQQQQQLLQHQQQQQQLAVaaAaaAAAAAQQQPMLVS
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    848  0     42 RRARINNCLNEL
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    848  0    205 KLPNGSIALVLPQSL
IPB001525E  C-5 cytosine-specific DNA methylase                     1216    848  0    121 PGIEPAQRRRLLQhLSNc
IPB000953   Chromo domain                                           1126    847  0     18 VPAQLKETPLKSDRRSnkpIMeKRRRARiNNcLNELKT
IPB000953   Chromo domain                                           1126    847  0     41 RRRARINNCLNELKTLILdAtkKDpARHSKlEKADILE
IPB000953   Chromo domain                                           1126    847  0     58 LDATKKDPARHSKlEKADiLEkTvKHLQELQRQQAAMq
IPB000953   Chromo domain                                           1126    847  0     65 PARHSKLEKADILEKTVkHLQeLQRqQAAMQQAADpKI
IPB000953   Chromo domain                                           1126    847  0     83 HLQELQRQQAAMQQAADpKIvnKFKAGfADcVnEVSRF
IPB000953   Chromo domain                                           1126    847  0    140 NGVKTELHQQQRQQQQQSihaqmLpSPPSSpEQDSQQg
IPB000953   Chromo domain                                           1126    847  0    167 PSSpEQDSQQGAAAPYLFgIQqTaSGYfLpNgMQVIPT
IPB000953   Chromo domain                                           1126    846  0     49 CLNELKTLILDATKKDpARhSkLEKADILEkTVKHLQE
IPB000953   Chromo domain                                           1126    846  0     51 NELKTLILDATKKDPARHsKLeKaDiLEKTVKhLQELq
IPB000953   Chromo domain                                           1126    846  0     74 ADILEKTVKHLQElQRQqAAMqQaaDPKiVNKfKAGFa
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    846  0    237 LAVaAAAAAAAAAQqQPmLVSMpQrtAs
IPB000953   Chromo domain                                           1126    845  0     71 LEKADILEKTVKHlQELqRqQaAmQqAADpkIVNKFKa
IPB000953   Chromo domain                                           1126    845  0     95 QQAADpKIVNKFKAGFADCVneVSRfPGiEpaQRRRLL
IPB000953   Chromo domain                                           1126    845  0    211 IALVLpQSLPQQQQQQLLQhQqQQQqLAVAaaAAAAAa
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    845  0    147 HQQQRQQQQQSI
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    845  0     34 NKPIMEKrRRARINNcLNElKtLILdA
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    845  0    253 PmLVSMpQRTASTGSASSHsSaGYeSA
IPB000953   Chromo domain                                           1126    844  0     72 EKADILEKTVKHLQELQrQqaamQQAADPKIVnKFKAg
IPB000953   Chromo domain                                           1126    844  0     82 KhLQELQRQQAAMQQAADpKiVNKFKAGFADcVNEVSR
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    844  0    233 QqQQLAVAAAAAAAaAAQQQPmLVsMp
IPB001525E  C-5 cytosine-specific DNA methylase                     1216    844  0     36 PIMEkRrRARINNcLnEL
IPB000953   Chromo domain                                           1126    843  0    289 APSSPANSSYEPMDIKpSvIQrVpMEQQPLSLVIKKQI
IPB000953   Chromo domain                                           1126    842  0    112 DCVNEVSRFPGIEPAQRrRLLqHLSNcINgVKTELHQq
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    842  0    200 QvIPTKLpNGSIALVLPQSLpqQQqQQL
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    841  0    315 QQPLSLVIKKQIKEE
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    841  0     87 LqRQQAAMqQAADpKIvNKfKaGFAdC
IPB000953   Chromo domain                                           1126    840  0    301 MDIKPSVIQRVPMEQQpLsLvIKKQiKEEEQPWRPW
IPB001525B  C-5 cytosine-specific DNA methylase                     1211    840  0    252 QpMLVSmPqrTASTGS
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    839  0    148 QQQRQQQQQSIH
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    839  0    180 APYLFGIQQTASGYF
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    839  0    188 QTASGYFLPNGMQVI
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    839  0    128 RRRLLQHLSNCINGVKTELhqqQrqQQq
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    839  0    228 LQHQqQQQQLAVAAAAAAAAAAQQqPmL
IPB000953   Chromo domain                                           1126    838  0    145 ELHQQQRQQQQQSiHAQmLpSppSSPEQDSQQGAAAPy
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    838  0     38 MEKRRRARINNC
IPB000953   Chromo domain                                           1126    837  0    120 FPGIEpAQRRRLLQHLSnCIngVKTELHQQQRQQQQQS
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    837  0     73 KADILEKTVKHLQEL
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    837  0     57 ILDaTKKDpArHSKLEkAdILektVKHL
IPB000953   Chromo domain                                           1126    836  0     23 KEtpLKSDRRSNKPIMEkRrRaRinNcLNElKTLILDa
IPB000953   Chromo domain                                           1126    836  0    197 NGMQVIPTKLPNGSIALVLpQSLpQqQQQQlLQHQQQq
IPB000953   Chromo domain                                           1126    836  0    255 LVSMPQRTASTGSASSHSsAGYESaPGSSSScsyApSS
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    836  0    309 QRVPMEQQPLSL
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    836  0    315 QQPLSLVIKKQI
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    836  0    307 VIQRVPMEQQPLSLV
IPB000953   Chromo domain                                           1126    835  0    132 LQHLSNCINGVKTELHQqQrQqQQQSIHAQMLpSPpSS
IPB000953   Chromo domain                                           1126    835  0    239 VAAAAAAAAAAQQQPMLVsMpqRTaSTGSASShSSAGy
IPB000953   Chromo domain                                           1126    835  0    307 VIQRVpMEQQPLSlVIKkQIKeEEQPWRPW
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    835  0    108 aGFADCVnEVSRFpGIepAQRRrLLqh
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    835  0    116 EVSRFPGIEPAQrRrLLQHlSncIngV
IPB000953   Chromo domain                                           1126    834  0     73 KADILEKTVKHLQELQRqQAamQQaADPKiVnKFKAGF
IPB000953   Chromo domain                                           1126    834  0     84 LQELQRQQAAMQQAADpkiVnkFKaGFADCVnEVSRFP
IPB000953   Chromo domain                                           1126    834  0    266 GSASSHSSAGYESAPGSSssCSYapSSPANSSyEPmDI
IPB000953   Chromo domain                                           1126    833  0     15 TAVVPAQLKETPLKSDRrsnKpImEKRRRARInNCLNE
IPB000953   Chromo domain                                           1126    833  0     17 VVPAQLKETPLKSDRRSnKpimEKRRRARiNncLNELK
IPB000953   Chromo domain                                           1126    833  0     30 DRRSNKPIMEKRRRARInnCLnELKTLILDaTKKDpAR
IPB000953   Chromo domain                                           1126    833  0    123 IEPAQRRRLLQHLSNcIngVKTELHqQQRQQQQQSIHa
IPB000953   Chromo domain                                           1126    833  0    235 QQLAVAAAAAAAAAAQQqpMLVSmpqRTASTgsASSHS
IPB000953   Chromo domain                                           1126    833  0    244 AAAAAAQQQPMLvSMPQrTASTGSaSSHSSagyESAPg
IPB000953   Chromo domain                                           1126    833  0    299 EPMDIKPSVIQRvPMEQqpLSlViKKQIKEEEQPWRPw
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    833  0     64 DPARHSKLEKAD
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    833  0    302 DIKPSVIQRvPMEQqPLSLVIkkQiKEe
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    833  0    180 aPYLFGIQqTASGYFLPNGmQvIpTKL
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    833  0    230 HqQQQQQLAVAAAAaAAaAAQqqpMLV
IPB000953   Chromo domain                                           1126    832  0     44 ARINNCLNELKTLiLDAtKKDpARHSKLEKadILEKTV
IPB000953   Chromo domain                                           1126    832  0    208 NGSIALVLPQSLPQQQQqQLLqHQQqQQQLaVAAAAAa
IPB000953   Chromo domain                                           1126    832  0    238 AVAAAAAAAAAAQQQPMLvsMpQRTASTGSaSsHSSAg
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    832  0    251 QQPMLVSMPQRTAST
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    832  0    316 QPLSLVIKKQIKEEE
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    832  0    159 HAQmLPSppSSPEqDSqQGAAapYLFG
IPB000953   Chromo domain                                           1126    831  0     64 DPARHSKLEKADIlEKTVKhLqELQRQQAAMQQAADPK
IPB000953   Chromo domain                                           1126    831  0    108 AGfADCVNEVSRFPGIEpAqRrRLLqHLSNcInGVKTE
IPB000953   Chromo domain                                           1126    831  0    110 FADCVNEVSRFPGiEPAqRrRlLQHLSNciNgVKTELh
IPB000953   Chromo domain                                           1126    831  0    130 RLLQHLSNCINGvKTELHQqQrQQQqQSiHaQMLPSPP
IPB000953   Chromo domain                                           1126    831  0    142 VKtELHQQQRQQQQQSIHAqMlpSpPSSPEQdsQQGAa
IPB000953   Chromo domain                                           1126    831  0    247 AAAQQQPMLVSMPQRTASTgSaSSHSSAGyESAPGSSS
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    831  0     29 SDRRSNKPIMEK
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    831  0     95 QQAADPKIVNKF
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    831  0     43 RARINNCLNELKTLI
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    831  0    191 SGYfLPNGMQVIpTKLPNGsIAlvlPQs
IPB000953   Chromo domain                                           1126    830  0     43 RARINNCLNELKTlILDATKKdpaRHSKLEkaDILEKT
IPB000953   Chromo domain                                           1126    830  0    138 CINGVKTELHQQQRQQQqQsihAQMLPSPpSSpEQDSq
IPB000953   Chromo domain                                           1126    830  0    222 QQQQQLLQHQQQQQQLAVAAaaAaaAAAQQQPMLVSMP
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    830  0     90 QQAAMQQAADPK
IPB000953   Chromo domain                                           1126    829  0     61 TKKDPARHSKLEKADILeKTvkHLQELQRQQaAMQQAa
IPB000953   Chromo domain                                           1126    829  0    178 AAApYLFGIQQTASGYFLpnGmQviPTKLpNgsIALVL
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    829  0    233 QQQQLAVAAAAAAAA
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    828  0     62 KKDPARHSKLEKADI
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    828  0    128 RRRLLQHLSNCINGV
IPB000953   Chromo domain                                           1126    827  0     81 VKHLQELQRQQAAmQQAAdpKIVNKfKAGfadcVNEVS
IPB000953   Chromo domain                                           1126    827  0    261 RTASTGSASSHSSAGYESApGSSSScSYApSSpANSSy
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    827  0     79 KTVKHLQELQRQQAA
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    827  0     26 PLKSdRRSNKPIMEKRrRArInnclnEL
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    827  0    170 PEQDSQQgAAAPYLFgiQQtAsGYFLp
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    827  0    187 QqTASGYFLPNGMqvIPTKlPnGSIaL
IPB000953   Chromo domain                                           1126    826  0     94 MQQAADPKIVNKFKAGFAdCvnEvSRFPGiEPAQRRRL
IPB000953   Chromo domain                                           1126    826  0    133 QhLSNCINGVKTElHQQqRqQqQQSiHAQMlPsPPSSP
IPB000953   Chromo domain                                           1126    826  0    136 SNcINGVKTELHQQQRQqQqQSIhaqMLPSpPsSPEQD
IPB000953   Chromo domain                                           1126    826  0    172 QDSQQGAAAPYLFGIQQtAsGYFLpNGMQVIPTKLpNg
IPB000953   Chromo domain                                           1126    826  0    284 SScSYAPSSPANSSYEpmdIKpSviqRVPMEQQPLSLV
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    826  0     46 INNCLNELKTLI
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    826  0     97 AADPKIVNKFKAGFA
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    826  0     49 cLNELKTLILDATKKDPArhSklEkADI
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    826  0    236 QLAVAAAAAAAAAAqQqPMLVsmpqRTA
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    826  0    179 aAPYLFGIqQTASGYfLpNGMqVIpTk
IPB000953   Chromo domain                                           1126    825  0      7 ANMTNVLGTAVVPAQLKeTpLkSDRRSNKpImEKRRRa
IPB000953   Chromo domain                                           1126    825  0     87 LQRQQAAMQQAADPKIVnKFKaGFaDcVNEVSRFPGIE
IPB000953   Chromo domain                                           1126    825  0    212 ALVLPQSLPQQQQQQLLqHqQqQQQLAVAAaaAAAAAa
IPB000953   Chromo domain                                           1126    825  0    265 TGSASSHSSAGYESAPGSssScSYaPSSPANSsyEpMD
IPB000953   Chromo domain                                           1126    825  0    293 PANSSyEPMDIKPSVIQrvpMeQQpLSLVikKQIKEEE
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    825  0    226 QLLQHQQQQQQLAVA
IPB001525B  C-5 cytosine-specific DNA methylase                     1211    825  0    112 DCVNevSrfPGIePAQ
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    825  0     95 QqAADPKIVNKFKAGfAdcvNeVSrFp
IPB000953   Chromo domain                                           1126    824  0    106 FKAGFADCVNEVSRFPGIEpaqRRRLLQHLSncINGVK
IPB000953   Chromo domain                                           1126    824  0    137 NCINGVKTELHQQQRQQqQqSIHaQmLPSppSsPEQDS
IPB000953   Chromo domain                                           1126    824  0    286 CSYAPSSPANSSyEPMDIKpSVIQRvPMEQQPLSLVIK
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    824  0     43 RARINNCLNELK
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    824  0    260 QRTASTGSASSH
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    824  0    208 NGSIALVLPQSLPQq
IPB000953   Chromo domain                                           1126    823  0      2 TGVTAANMTNVLGTAVVpAqLkETpLKSDRRSnKPIME
IPB000953   Chromo domain                                           1126    823  0    303 IKPSVIQRVPMEQQPLSLvIKkQiKEEEQpwRpw
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    823  0     27 LKSDRRSNKPIM
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    823  0    151 RQQQQQSIHAQM
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    823  0    115 NEVSRFPGIEPAQRRRLLqhLsncinGV
IPB000953   Chromo domain                                           1126    822  0     28 KSDRRSNKPIMEKRRRArinncLNELKTLildATKKDP
IPB000953   Chromo domain                                           1126    822  0     99 DPKIVNKfKAGFADcVnevsRFpGiEPAQRRRLLQHLS
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    822  0     24 ETPLKSDrRSNKpimeKrRRARINncL
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    822  0    234 QqQLAVAAAAAAAAaAqQQpMlVSMPq
IPB000953   Chromo domain                                           1126    821  0     29 SDRRSNKPIMEKRRRARInnClNELKTLiLDaTKKDPa
IPB000953   Chromo domain                                           1126    821  0    228 LQHQQQQQQLAVAAAAAAAAaaQQQPMLVSMPQRTAST
IPB000953   Chromo domain                                           1126    821  0    242 AAAAAAAAQQQPMlVSMpQrtaSTGSASSHSSAGYESa
IPB000953   Chromo domain                                           1126    821  0    253 PMLVSMPQRTASTGSASSHsSaGYESAPGSSSscSyAP
IPB000953   Chromo domain                                           1126    821  0    271 HSSAGyESAPGSSSScSYApSSpanSSYEpMdIKPSVI
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    821  0      4 VTAANMTNVLGTAVV
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    821  0    297 SYEPMDIKPSVIQRV
IPB000953   Chromo domain                                           1126    820  0     24 ETPLKSDRRSNKPiMEKrRrarINncLNELkTLILDAT
IPB000953   Chromo domain                                           1126    820  0     37 IMEKRRRARINNClNELkTLilDaTKKDPARhsKLEKa
IPB000953   Chromo domain                                           1126    820  0     88 QRQQAAMQQAADPKIVnkFKagFaDcVNEVSRfPGIEP
IPB000953   Chromo domain                                           1126    820  0    218 SLPQQQQQQLLQHQQQQqQLaVAaaAAAAAaaQQQpML
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    820  0    150 QRQQQQQSIHAQ
IPB001525B  C-5 cytosine-specific DNA methylase                     1211    820  0    280 pGsSSScSyaPsSPAN
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    820  0     11 NvLGTAVVpAQLKETPLKSdrrsNkPIM
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    820  0     56 LILdATKKDpARHSKLeKAdILEkTVKh
IPB000953   Chromo domain                                           1126    819  0    107 KAGFADCVNEVSRfPGIepAQrRRLLQHLSNcINGVKT
IPB000953   Chromo domain                                           1126    819  0    250 QQQpmLVSMPQRTASTGSAsShSSaGYESApgsSSScS
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    819  0    258 MPQRTASTGSAS
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    819  0     84 LQELqRQQAAMQQAADPKIVnkfkaGFA
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    819  0    210 SIALVLPQSLPQQQqQqLLqhqQQqQQL
IPB000953   Chromo domain                                           1126    818  0    156 QSIHAQMLPSPPSSPEQDsqQgAaaPYLFgIQQTASGy
IPB000953   Chromo domain                                           1126    818  0    169 SPEQDSQQGAAAPYLFGIQqtaSGYfLPNgMQVIPTKL
IPB000953   Chromo domain                                           1126    818  0    182 YLfGIQQTASGYFlPNGmQVipTKLPNGSiaLVLPQSL
IPB000953   Chromo domain                                           1126    818  0    245 AAAAAQQQPMLVSmPQRtAstgSaSSHSSAGYESApGS
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    818  0    116 EVSRFPGIEPAQ
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    818  0     83 HLQELQRQQAAMQQA
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    818  0    230 HQQQQQQLAVAAAAA
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    818  0     92 AAmQqAADpKIVNKFKAGFAdcvNeVSr
IPB000953   Chromo domain                                           1126    817  0     10 TNVLGTAVVPAQLKETpLKsDrRSnKPIMEkRRRARIN
IPB000953   Chromo domain                                           1126    817  0    183 LFGIQQTASGYFLPNGMqvIpTKLpNGSiAlVLPQSLP
IPB000953   Chromo domain                                           1126    817  0    270 ShSSAGYESAPGSSSSCSYApSSpaNSSYEpmDIKpSV
IPB000953   Chromo domain                                           1126    817  0    274 AGYESAPGSSSSCSYApSspanSSYEPMDikPsVIQRV
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    817  0    228 LQHQQQQQQLAVAAA
IPB001525B  C-5 cytosine-specific DNA methylase                     1211    817  0    160 AqMLpSPPssPeqDSQ
IPB001525B  C-5 cytosine-specific DNA methylase                     1211    817  0    260 QrtASTgSasSHSSAG
IPB000953   Chromo domain                                           1126    816  0     54 KTLILDATKKDPARHSKLEKadILEKTVKHlQELQRQq
IPB000953   Chromo domain                                           1126    816  0    168 SSPEQDSQQGAAAPYLFgiqQTASGyFLPNGmQVIpTK
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    816  0    230 HQQQQQQLAVAA
IPB000953   Chromo domain                                           1126    815  0    148 QQQRQQQQQSIHAQMLpSppSSpEQDSQQgaaAPYLFg
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    815  0     87 LQRQQAAMQQAA
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    815  0    232 QQQQQLAVAAAA
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    815  0     63 KdPaRHSKLEKADILEkTVkhLQElQRq
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    815  0     66 ARHSKLEKADILEKTvkHLqeLQrqQAA
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    815  0    126 AQRrRLLQHLSNCINGVKTeLhQQqRQq
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    815  0     71 LEKADILEkTVKHLQeLQRQQaAMqqA
IPB000953   Chromo domain                                           1126    814  0    200 QVIpTKLPNGSIAlVLpqsLpqQQQqQLLQHQQQQQQL
IPB000953   Chromo domain                                           1126    814  0    236 QLAVAAAAAAAAAAQQQpMLvSmpQRTASTGSASSHSS
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    814  0     12 VLGTAVVPAQLKETP
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    814  0    180 ApYLFGIQQTASGYFLPNGmqVipTKlp
IPB001525E  C-5 cytosine-specific DNA methylase                     1216    814  0    129 RRLlqHlSnCINGVKTEL
IPB000953   Chromo domain                                           1126    813  0      6 AANMTNVLGTAVvPAQLkETplKSDRRSNKpIMEKRRR
IPB000953   Chromo domain                                           1126    813  0    259 PQRTASTGSASSHSSAGYEsapGSSSSCSyaPsSPANS
IPB001525B  C-5 cytosine-specific DNA methylase                     1211    813  0    253 pMLVSmPqrTAsTGSA
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    813  0    175 QQGaAAPYLfgIQQTAsGYFLpngmQvI
IPB001525F  C-5 cytosine-specific DNA methylase                     1111    813  0    230 HQQqqqQLAVAAA
IPB000953   Chromo domain                                           1126    812  0    180 APYLFGIQQTASGYFLpngMQVIpTKLPNgSIALVLPq
IPB000953   Chromo domain                                           1126    812  0    194 FLPNGMQVIPTKLPNGSIALvlpQSLPQQQQQQLLQHq
IPB000953   Chromo domain                                           1126    812  0    206 LPNGSIALVLPQSlPQQqQqQlLQHqQQQQQLAVAAAa
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    812  0     41 RRRARINNCLNE
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    812  0     55 TLILDATKKDPARHS
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    812  0    156 QSIHAQMLPSPPSSP
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    812  0    107 KAGFADCVNEVSrFpgiePAQRrrLLq
IPB000953   Chromo domain                                           1126    811  0     80 TVKHLQELQRQQAAMQQAAdpkIvnKFKAgFaDcVNEV
IPB000953   Chromo domain                                           1126    811  0    102 IVNKFKAGFADCvNEVSrFpGIEpaqRRRLlQhLSNcI
IPB000953   Chromo domain                                           1126    811  0    264 STGSASSHSSAGyESApgssSSCSYAPSSpansSYEPM
IPB001525B  C-5 cytosine-specific DNA methylase                     1211    811  0    277 ESApGSSSscSYaPSS
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    811  0    104 NKFkAGFADcVNEVSRfPGIepaQrRRL
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    811  0    229 QhQQqQQQLAVAAAAAAAAAAqQQpMlV
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    811  0     33 sNKPIMEKRRrAriNNClNeLKTLILd
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    811  0    248 aAQQQPMLVSMPQRtASTGsAsshsSA
IPB001525F  C-5 cytosine-specific DNA methylase                     1111    811  0      6 AANMTNvLgTAVV
IPB000953   Chromo domain                                           1126    810  0    219 LPQQQQQQLLQHQQQQQqLAvaAaaAAAAAaQQQPmLV
IPB000953   Chromo domain                                           1126    810  0    249 AQQQPMLVSMPQRTASTgsASSHSSAGYESaPGSSSSC
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    810  0     30 DRRSNKPIMEKR
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    810  0    171 EQDSQQGAAAPY
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    810  0    104 NKFKAGFADCVNEVS
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    810  0    214 VLPQSLPQQQQQQLL
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    810  0     47 NNcLNELKTLILDATKkDpArhsklEKA
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    810  0    208 NGSIALVLpQSLpQqQqQqLLqhQqQQq
IPB000953   Chromo domain                                           1126    809  0    116 EVSRFpGIEPAQRRRLLqHLSnCinGVKTElhQQQRQq
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    809  0    135 LSNCINGVKTEL
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    809  0    235 QQLAVAAAAAAA
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    809  0     20 AQLKETPLKSDRRSN
IPB000953   Chromo domain                                           1126    808  0      0 MVtGVTAANMTNvlGTAVvpaqLKETPLKSDRRSNKPI
IPB000953   Chromo domain                                           1126    808  0    119 RFPGIEPAQRRRLlQHLSnCinGvKTELHQQQRQQQQq
IPB000953   Chromo domain                                           1126    808  0    199 MQVIPTKLPNGSIALVLpQsLpQQQqQQLLQhQQQQQq
IPB000953   Chromo domain                                           1126    808  0    215 LPQSLpQQQQQQLlQHQqQqQqLaVAAAAAaaAAAQQq
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    808  0     31 RRSNKPIMEKRRRAr
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    808  0     96 QAADPKIVNKFKAGF
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    808  0      2 TGVTAANMTNVLGTAvVPAqLkEtpLKs
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    808  0    215 LPQSLPQQqQqQLLQhqQQQQqLaVaA
IPB000953   Chromo domain                                           1126    807  0    122 GIEpAQRRRLLQHlSNCIngvkTELHQQQRQQQQQSIh
IPB000953   Chromo domain                                           1126    807  0    258 MPQRTASTGSASShSSAgYeSapGSSSScSYapSSpAN
IPB001525B  C-5 cytosine-specific DNA methylase                     1211    807  0    213 LVLpqSlPqQqqqQLL
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    807  0    234 QQQLAVAAAAAAAAAAqQqpMLvsmPQr
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    807  0     96 QAADPKIVNKFKAGFAdcVnEvsrFPG
IPB000953   Chromo domain                                           1126    806  0    241 AAAAAAAAAQQQPmLVSmpqRTASTGSASSHSsAGyES
IPB000953   Chromo domain                                           1126    806  0    260 QRtASTGSASSHSSAGYesApgSSSScSYApSsPANSS
IPB000953   Chromo domain                                           1126    806  0    277 ESApGSSSSCSYAPSSpAnsSYEpMDIKPSVIQRVpME
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    806  0     50 LNELKTLILDATKKD
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    806  0    235 QQLAVAAAAAAAAAA
IPB001525B  C-5 cytosine-specific DNA methylase                     1211    806  0    284 SScSYaPSsPAnSSYe
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    806  0    131 LLQhLSNCINgVKTELhQqqrqQQqQSI
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    806  0    174 SQQGAAApYLFgIQqTASGyFLpNgMQV
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    806  0     79 KTVKHLQELQrQQAamqQAADpkIVnk
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    806  0    296 sSYEPMDIkPSVIqrVPmEQQpLSLVi
IPB000953   Chromo domain                                           1126    805  0     26 PLKSDRRSNKPIMEKRRrArinNcLNELKTlILDATKK
IPB000953   Chromo domain                                           1126    805  0    104 NKfKAGFADCVNEVSRFpgIEpAQRRRLLQHLsNCINg
IPB000953   Chromo domain                                           1126    805  0    177 GAAAPyLfGIQQTASGYFLpngmQViPTKLpnGSIALV
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    805  0     78 EKTVKHLQELQR
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    805  0    232 QQQQQLAVAAAAAAA
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    805  0      3 GVTAANMTNVLGTAvVPaQlKeTpLKS
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    805  0     78 EKTVKHLQELqRQqaAmQQAAdpkIVN
IPB000953   Chromo domain                                           1126    804  0     -1  MVTGVTAANMTNVLGTAvVpaQLKETPLKSdRRSNKP
IPB000953   Chromo domain                                           1126    804  0    124 EPAQRRRLLQHLSNcIngvKteLhQqQRQQQQQSIHAq
IPB000953   Chromo domain                                           1126    804  0    193 YFLpNGMQVIPTKlPNGSiALVLpQSLPQQQQQQLLQh
IPB000953   Chromo domain                                           1126    804  0    300 PMDIKpSVIQRVPmEQQpLsLVIKKqIKEEEQpwRpw
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    804  0     80 TVKHLQELQRQQAAM
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    804  0    175 QQGAAAPYLFGIQQT
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    804  0    252 QPMLVSMPQRTASTG
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    804  0     10 TNVLGTAVVPAQLkeTPlKsDRrSnKp
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    804  0     84 LqELQRQQAAMQQAadPKIvNKFkAgF
IPB000953   Chromo domain                                           1126    803  0    294 ANSSYEPMDIKPSVIQRVpMEqQpLSLViKkQIKEEEq
IPB000953   Chromo domain                                           1126    803  0    304 KPSVIQRVPMEQQPLSLViKKqIKEEEQPWRPW
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    803  0     24 ETPLKSDRRSNK
IPB001092A  Basic helix-loop-helix dimerization domain bHLH          960    803  0    233 QQQQLAVAAAAA
IPB001525D  C-5 cytosine-specific DNA methylase                     1179    803  0    212 alVLPQSLpQqQQqQLLQHQQqqqqLA
IPB000953   Chromo domain                                           1126    802  0     13 LGtAVVPAQLKETPLKSDRrSnKpimEKRRRaRINNcL
IPB000953   Chromo domain                                           1126    802  0    176 QGAAApYLFGIQQTASGYFLpnGmQvIPTKlPnGSIAL
IPB000953   Chromo domain                                           1126    802  0    207 PNGSIALVLPQSLPQQQqQqLlQhQqQQQQlaVAAAAa
IPB000953   Chromo domain                                           1126    802  0    297 SYEpmDIKPSVIQRVPMeQqplSLViKKQikEEEQpwR
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    802  0     -1  MVTGVTAANMTNVL
IPB001092B  Basic helix-loop-helix dimerization domain bHLH          991    802  0    312 PMEQQPLSLVIKKQI
IPB001525C  C-5 cytosine-specific DNA methylase                     1170    802  0    139 INGVKTELHQQQRQqQqQSIhAQmlPSp
IPB000953   Chromo domain                                           1126    801  0    100 PKIVNKFKAGFADcVNEVsrfpGiEPAQRRRLLQHLSN
IPB000953   Chromo domain                                           1126    801  0    191 SGYFLpNGMQVIPTKLpngsiaLvLPQSLpQQQQQQLL
IPB000953   Chromo domain                                           1126    801  0    290 PSSpANSSYEPMDiKPSViqRVpmEqQPLSlVIKKQIK
              1126    813  0      6 AANMTNVLGTAVvPAQLkETplKSDRRSNKpIMEKRRR
IPB000953   Chromo domain                                           1126    813  0    259 PQRTASTGSASSHSSAGYEsapGSSSSCSyaPsSPANS
IPB001525B  C-5 cytosine-specific DNA methylase                     1211    813  0    253 pMLVSmPqrTAsTGSA
IPB001525C  C-5 cytosine-specificblimps-3.9/examples/blimps/distribution/example.blkprob000064400001460000012000000116351041506445700240150ustar00jorjastaff00000400000027
BLKPROB Version  8/22/03.1
Database=sample.blocks
        ___________               ___________               ___________ 
       |\ __________\            |___________|            /__________ /|
       | |           |           |           |           |           | |
       | | **********|           |***********|           |********** | |
       | | * BLOCKS  |           |EMAIL & WWW|           |SEARCHER * | |
       | | **********|           |***********|           |********** | |
        \|___________|___________|___________|___________|___________|/
                     |\ __________\         /__________ /|
                     | |  blocks@  |       | http://   | |
                     | |   blocks. |       |  blocks.  | |
                     | |   fhcrc.  |       |  fhcrc.   | |
                     | |   org     |       |  org      | |
                      \|___________|       |___________|/


Here are your search results. The database searched was Blocks+ (10 June 00)
which includes: BLOCKS 12.0 consisting of 4071 blocks representing 998 groups
documented in InterPro 1.0/PROSITE, plus 3141 blocks from 498 groups documented 
in PRINTS 26.0 but not represented in BLOCKS, plus 2382 blocks from 569 groups 
documented in PFAM 5.3 but not represented in BLOCKS or PRINTS, plus
962 blocks from 250 groups documented in PRODOM 99.1 but not represented in
BLOCKS, PRINTS or PFAM, plus 282 blocks from 76 groups documented in DOMO 2.0
but not represented in BLOCKS, PRINTS, PFAM or PRODOM for a total of 10,838
blocks from 2391 groups.  Get more information at http://blocks.fhcrc.org.
If you found the Blocks Searcher useful, please cite:
   S Henikoff & JG Henikoff, "Protein family classification
   based on searching a database of blocks", Genomics 19:97-107 (1994).
Please report problems to:  webmaster@blocks.fhcrc.org
==============================================================================
Each hit consists of one or more blocks from a protein group found
in the query sequence. One set of the highest-scoring blocks that are in the 
correct order and separated by distances comparable to the Blocks database is 
selected for analysis. If this set includes multiple blocks the probability 
that the lower scoring blocks support the highest scoring block is reported. 
Maps of the database blocks and query sequence are shown:
AAA represents a block roughly in proportion to its width.
  : represents the minimum distance between blocks in the database.
  . represents the maximum distance between blocks in the database.
< > indicate the sequence has been truncated to fit the page.
The query map is aligned on the highest scoring block. Multiple block hits 
that are consistent with the highest scoring block are separated by colons.
Block hits that are not consistent are mapped below. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database is
shown. The distance between detected blocks is listed as (min, max): for the
database entry followed by the distance in the query. Upper case in the query
indicates at least one occurrence of the residue in that column of the block.

=============================================================================
Note: For searches using DNA queries, "Location" refers to the position
in the query in base pairs from 5' to 3' on the + strand, whereas the map and 
alignment show the translated position in amino acid residues.
============================================================================= 

Query=HAIR_DROME  HAIRY PROTEIN  
Size=337 Amino Acids
Blocks Searched=9
Alignments Done=            3205
Cutoff combined expected value for hits=  1
Cutoff block expected value for repeats/other=  1
==============================================================================
                                                             Combined
Family                                       Strand  Blocks   E-value
IPB001092  Basic helix-loop-helix dimerization   1   2 of 2   5.7e-11

==============================================================================
>IPB001092 2/2 blocks Combined E-value= 5.7e-11: Basic helix-loop-helix dimerization domain bHLH
Block    Frame    Location (aa)      Block E-value
IPB001092A  0         40-51             9.8e-06
IPB001092B  0         71-85             1.8e-06
Other reported alignments:

                         |--- 2957 amino acids---|
         IPB001092 A............................................................B
        HAIR_DROME                                                             AB

IPB001092A          <->A   (-2,3229):39
HAIR_DROVI|P29303  46      EKRRRARINNCL
                           ||||||||||||
HAIR_DROME         40      EKRRRARINNCL

IPB001092B         A<->B   (-2,7069):19   
HAIR_DROVI|P29303  77      KLEKADILEKTVKHL
                           |||||||||||||||
HAIR_DROME         71      KLEKADILEKTVKHL

------------------------------------------------------------------------------

1 possible hits reported
your search results. The database searched was Blocks+ (10 June 00)
which includes: BLOCKS 12.0 conblimps-3.9/examples/blimps/distribution/example.cs000064400001460000012000000003261041506445600227610ustar00jorjastaff00000400000027ER      2
FR   ../../docs/default.amino.frq
SQ   /d0/local/blimps-3.8/examples/blimps/example.pro
DB   sample.blocks
OU   /d0/local/blimps-3.8/examples/blimps/example.bli
ST      2
RE      1
NU      0
CO      3
//
blimps-3.9/examples/blimps/distribution/example.err000064400001460000012000000000701041506445600231400ustar00jorjastaff00000400000027Warning: Using default.qij

Warning: Using default.qij

blimps-3.9/examples/blimps/distribution/example.blksort000064400001460000012000000341621041506454500240400ustar00jorjastaff00000400000027
BLKSORT Version  8/21/02.1
Database=sample.blocks
        ___________               ___________               ___________ 
       |\ __________\            |___________|            /__________ /|
       | |           |           |           |           |           | |
       | | **********|           |***********|           |********** | |
       | | * BLOCKS  |           |EMAIL & WWW|           |SEARCHER * | |
       | | **********|           |***********|           |********** | |
        \|___________|___________|___________|___________|___________|/
                     |\ __________\         /__________ /|
                     | |  blocks@  |       | http://   | |
                     | |   blocks. |       |  blocks.  | |
                     | |   fhcrc.  |       |  fhcrc.   | |
                     | |   org     |       |  org      | |
                      \|___________|       |___________|/

==============================================================================
      Attention Blocks E-mail users: See new searching options at
	      http://blocks.fhcrc.org/help/email.html
==============================================================================
Here are your search results. The database searched was Blocks+ (10 June 00)
which includes: BLOCKS 12.0 consisting of 4071 blocks representing 998 groups
documented in InterPro 1.0/PROSITE, plus 3141 blocks from 498 groups documented 
in PRINTS 26.0 but not represented in BLOCKS, plus 2382 blocks from 569 groups 
documented in PFAM 5.3 but not represented in BLOCKS or PRINTS, plus
962 blocks from 250 groups documented in PRODOM 99.1 but not represented in
BLOCKS, PRINTS or PFAM, plus 282 blocks from 76 groups documented in DOMO 2.0
but not represented in BLOCKS, PRINTS, PFAM or PRODOM for a total of 10,838
blocks from 2391 groups.  Get more information at http://blocks.fhcrc.org.
If you found the Blocks Searcher useful, please cite:
   S Henikoff & JG Henikoff, "Protein family classification
   based on searching a database of blocks", Genomics 19:97-107 (1994).
Please report problems to:  webmaster@blocks.fhcrc.org
==============================================================================
Each numbered result consists of one or more blocks from a Prosite group found
in the query sequence. One set of the highest-scoring blocks that are in the 
correct order and separated by distances comparable to the Blocks database is 
selected for analysis. If this set includes multiple blocks the probability 
that the lower scoring blocks support the highest scoring block is reported. 
Maps of the database blocks and query sequence are shown:
AAA represents the first block roughly in proportion to its width.
  : represents the minimum distance between blocks in the database.
  . represents the maximum distance between blocks in the database.
< > indicate the sequence has been truncated to fit the page.
The query map is aligned on the highest scoring block. Multiple block hits 
that are consistent with the highest scoring block are separated by colons.
Block hits that are not consistent are mapped below. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database is
shown. The distance between detected blocks is listed as (min, max): for the
database entry followed by the distance in the query. Upper case in the query
indicates at least one occurrence of the residue in that column of the block.

The following nomogram is provided to aid interpretation of scores and 
probability estimates. It summarizes results from 7,082 searches using 
shuffled protein queries. "Shuffled percentiles" are calculated from scores
obtained for the top-scoring block in each search:

   1400 *-----------|-----------|-----------|-----------|100.00  
        |\                                              |        
        | \                                             |        
   1350 -  \                                            - 99.99  
        |   \                                           |        
        |    \               < 1/7000 searches          |        
   1300 -     \                                         - 99.96 S
 A      *      \                                        |       H
 N      | \     \                                       |       U
 C 1250 -  \     \                                      - 99.82 F
 H      |   \     \                                     |       F
 O      |    \     \                                    |       L
 R 1200 -     \     * \ \ \ \                           - 99.60 E
        |      \              \ *  \                    |       D
 B      |        \   < 1/1000         \                 |
 L 1150 *           *   searches        \               - 98.80 P
 O      | \           \ \                 \             |       E
 C      |    \            \ \               *           |       R
 K 1100 -       \             \ * \ \ \ \ \   \         - 92.28 C
        |           *   < 1/100 searches    *   \       |       E
 S      |              \                     \    \     |       N
 C 1050 -                 \ \ \ * \            \    \   - 53.16 T
 O      |                           \ \ \         \  \  |       I
 R      |                                 \          \\ |       L
 E 1000 |-----------|-----------|-----------|-----------|  0.00 E
        0          -1          -2          -3          -4 
                             LOG(P)

For example, a first hit with anchor block score of 1150 (98.80th percentile)
and estimated P-value of .01 (log(P) = -2) is expected to occur by chance
less than once in 1000 searches but more than once in 7000 searches
using protein queries of typical length and composition. It is not appropriate
to apply this nomogram to hits other than the first hit reported.

For interpretation of block hits, you might find it worthwhile to obtain the
full set of blocks and documentation for a group. To do this, send a blank
message to blocks@blocks.fhcrc.org with the subject heading: GET BL????? e.g.,  
'Subject: GET BL00044' (0s are zeros) for full information on this group.
=============================================================================
Note: For searches using DNA queries, "Location" refers to the position
in the query in base pairs from 5' to 3' on the + strand, whereas the map and 
alignment show the translated position in amino acid residues as before.
============================================================================= 

Query=HAIR_DROME  HAIRY PROTEIN 
, 
 Size=337 Amino Acids
Blocks Searched=9

1.------------------------------------------------------------------------
Block     Rank Frame Score Strength   Location (aa) Description
IPB001092A     2   0   1104   960          40-     51 Basic helix-loop-helix d
IPB001092A     5   0    941   960         129-    140 Basic helix-loop-helix d
IPB001092A    22   0    893   960         127-    138 Basic helix-loop-helix d
IPB001092A    23   0    891   960         100-    111 Basic helix-loop-helix d
IPB001092A    36   0    880   960          41-     52 Basic helix-loop-helix d
IPB001092A    55   0    868   960          35-     46 Basic helix-loop-helix d
IPB001092A    76   0    863   960         128-    139 Basic helix-loop-helix d
IPB001092A    82   0    861   960         125-    136 Basic helix-loop-helix d
IPB001092A    86   0    860   960         133-    144 Basic helix-loop-helix d
IPB001092A    99   0    857   960         130-    141 Basic helix-loop-helix d
IPB001092A   134   0    848   960          43-     54 Basic helix-loop-helix d
IPB001092A   151   0    845   960         148-    159 Basic helix-loop-helix d
IPB001092A   165   0    839   960         149-    160 Basic helix-loop-helix d
IPB001092A   171   0    838   960          39-     50 Basic helix-loop-helix d
IPB001092A   178   0    836   960         310-    321 Basic helix-loop-helix d
IPB001092A   179   0    836   960         316-    327 Basic helix-loop-helix d
IPB001092A   196   0    833   960          65-     76 Basic helix-loop-helix d
IPB001092A   212   0    831   960          30-     41 Basic helix-loop-helix d
IPB001092A   213   0    831   960          96-    107 Basic helix-loop-helix d
IPB001092A   219   0    830   960          91-    102 Basic helix-loop-helix d
IPB001092A   236   0    826   960          47-     58 Basic helix-loop-helix d
IPB001092A   252   0    824   960          44-     55 Basic helix-loop-helix d
IPB001092A   253   0    824   960         261-    272 Basic helix-loop-helix d
IPB001092A   257   0    823   960          28-     39 Basic helix-loop-helix d
IPB001092A   258   0    823   960         152-    163 Basic helix-loop-helix d
IPB001092A   275   0    820   960         151-    162 Basic helix-loop-helix d
IPB001092A   281   0    819   960         259-    270 Basic helix-loop-helix d
IPB001092A   288   0    818   960         117-    128 Basic helix-loop-helix d
IPB001092A   301   0    816   960         231-    242 Basic helix-loop-helix d
IPB001092A   303   0    815   960          88-     99 Basic helix-loop-helix d
IPB001092A   304   0    815   960         233-    244 Basic helix-loop-helix d
IPB001092A   322   0    812   960          42-     53 Basic helix-loop-helix d
IPB001092A   337   0    810   960          31-     42 Basic helix-loop-helix d
IPB001092A   338   0    810   960         172-    183 Basic helix-loop-helix d
IPB001092A   344   0    809   960         136-    147 Basic helix-loop-helix d
IPB001092A   345   0    809   960         236-    247 Basic helix-loop-helix d
IPB001092A   373   0    805   960          79-     90 Basic helix-loop-helix d
IPB001092A   388   0    803   960          25-     36 Basic helix-loop-helix d
IPB001092A   389   0    803   960         234-    245 Basic helix-loop-helix d
IPB001092B     1   0   1107   991          71-     85 Basic helix-loop-helix d
IPB001092B    19   0    900   991          52-     66 Basic helix-loop-helix d
IPB001092B    41   0    876   991          33-     47 Basic helix-loop-helix d
IPB001092B    61   0    866   991           7-     21 Basic helix-loop-helix d
IPB001092B    66   0    864   991          65-     79 Basic helix-loop-helix d
IPB001092B    67   0    864   991         170-    184 Basic helix-loop-helix d
IPB001092B    77   0    863   991          89-    103 Basic helix-loop-helix d
IPB001092B    87   0    860   991          68-     82 Basic helix-loop-helix d
IPB001092B   110   0    855   991         108-    122 Basic helix-loop-helix d
IPB001092B   111   0    855   991         126-    140 Basic helix-loop-helix d
IPB001092B   124   0    851   991         295-    309 Basic helix-loop-helix d
IPB001092B   135   0    848   991         206-    220 Basic helix-loop-helix d
IPB001092B   161   0    841   991         316-    330 Basic helix-loop-helix d
IPB001092B   166   0    839   991         181-    195 Basic helix-loop-helix d
IPB001092B   167   0    839   991         189-    203 Basic helix-loop-helix d
IPB001092B   173   0    837   991          74-     88 Basic helix-loop-helix d
IPB001092B   180   0    836   991         308-    322 Basic helix-loop-helix d
IPB001092B   203   0    832   991         252-    266 Basic helix-loop-helix d
IPB001092B   204   0    832   991         317-    331 Basic helix-loop-helix d
IPB001092B   214   0    831   991          44-     58 Basic helix-loop-helix d
IPB001092B   222   0    829   991         234-    248 Basic helix-loop-helix d
IPB001092B   223   0    828   991          63-     77 Basic helix-loop-helix d
IPB001092B   224   0    828   991         129-    143 Basic helix-loop-helix d
IPB001092B   227   0    827   991          80-     94 Basic helix-loop-helix d
IPB001092B   237   0    826   991          98-    112 Basic helix-loop-helix d
IPB001092B   246   0    825   991         227-    241 Basic helix-loop-helix d
IPB001092B   254   0    824   991         209-    223 Basic helix-loop-helix d
IPB001092B   269   0    821   991           5-     19 Basic helix-loop-helix d
IPB001092B   270   0    821   991         298-    312 Basic helix-loop-helix d
IPB001092B   289   0    818   991          84-     98 Basic helix-loop-helix d
IPB001092B   290   0    818   991         231-    245 Basic helix-loop-helix d
IPB001092B   296   0    817   991         229-    243 Basic helix-loop-helix d
IPB001092B   311   0    814   991          13-     27 Basic helix-loop-helix d
IPB001092B   323   0    812   991          56-     70 Basic helix-loop-helix d
IPB001092B   324   0    812   991         157-    171 Basic helix-loop-helix d
IPB001092B   339   0    810   991         105-    119 Basic helix-loop-helix d
IPB001092B   340   0    810   991         215-    229 Basic helix-loop-helix d
IPB001092B   346   0    809   991          21-     35 Basic helix-loop-helix d
IPB001092B   351   0    808   991          32-     46 Basic helix-loop-helix d
IPB001092B   352   0    808   991          97-    111 Basic helix-loop-helix d
IPB001092B   363   0    806   991          51-     65 Basic helix-loop-helix d
IPB001092B   364   0    806   991         236-    250 Basic helix-loop-helix d
IPB001092B   374   0    805   991         233-    247 Basic helix-loop-helix d
IPB001092B   381   0    804   991          81-     95 Basic helix-loop-helix d
IPB001092B   382   0    804   991         176-    190 Basic helix-loop-helix d
IPB001092B   383   0    804   991         253-    267 Basic helix-loop-helix d
IPB001092B   395   0    802   991           0-     14 Basic helix-loop-helix d
IPB001092B   396   0    802   991         313-    327 Basic helix-loop-helix d

1107=94.06th percentile of anchor block scores for shuffled queries
P< 0.047 for IPB001092A in support of IPB001092B
                         |--- 2957 amino acids---|
         IPB001092 A............................................................B
        HAIR_DROME                                                             AB
        HAIR_DROME                                                             
        HAIR_DROME                                                             

IPB001092A          <->9   (-2,3229):39
HAIR_DROVI|P29303  46      EKRRRARINNCL
                           ||||||||||||
HAIR_DROME         40      EKRRRARINNCL

IPB001092B         9<->9   (-2,7069):19   
HAIR_DROVI|P29303  77      KLEKADILEKTVKHL
                           |||||||||||||||
HAIR_DROME         71      KLEKADILEKTVKHL

1 possible hits reported
blimps-3.9/examples/blimps/distribution/example.blocks000064400001460000012000000051151062461201400236210ustar00jorjastaff00000400000027ID   EXAMPLE; BLOCK
AC   exampleA; distance from previous block=(52,155)
DE   EXAMPLE
BL   WDF motif=[8,0,17] motomat=[1,80,-10] width=46 seqs=8
TC1A_CAEBR (  53) KKPLVSLKNRKARVEWAKQHLSWGPREWANHIWSDESKFNMFGTDG  45

TC3A_CAEEL ( 110) KLRPAPLLSADHKLKRLEFAKNNMGTNWSKVVFSDEKKFNLDGPDG 100

       HB1 (  98) KVPLPSPRHIKARLSLAKTYLNWPVSKWRNILWTDGSKIMLFGGTG  72

       Uhu (  82) KKPFISTKNKGTRMTFAKTHLDKDLEFWNTIIFEDESKFIIFGSDG  61

    Bari-1 ( 120) KTIEITPTNKTKRLRFALEYVKKPLDFWFNILWTDESAFQYQGSYS  80

     Minos ( 156) EKPLLTLRQKKKRLQWARERMSWTQRQWDTIIFSDEAKFDVSVGDT  78

TC1A_CAEEL (  53) KKPFISKKNRMARVAWAKAHLRWGRQEWAKHIWSDESKFNLFGSDG  42
TC2A_CAEBR (  53) KKPSISKKNRIARVAWARAHLHWGRQDWANHVFSDESKFNLFGTDG  45
//
ID   EXAMPLE; BLOCK
AC   exampleB; distance from previous block=(20,24)
DE   EXAMPLE
BL   GMW motif=[8,0,17] motomat=[1,80,-10] width=11 seqs=8
       HB1 ( 168) GGPKIMVWACF  79

     Minos ( 224) FPASTMVWGCM 100

TC1A_CAEBR ( 122) GGGSVMVWGCF  36
TC1A_CAEEL ( 122) GGGSVMVWGCF  36
TC2A_CAEBR ( 122) GGGSVMVWGCF  36
TC3A_CAEEL ( 176) GGGTVMVWGAF  59
       Uhu ( 150) HGGSVMVWACI  64
    Bari-1 ( 187) GGGTVMFWGCL  68
//
ID   EXAMPLE; BLOCK
AC   exampleC; distance from previous block=(39,40)
DE   EXAMPLE
BL   QDN motif=[8,0,17] motomat=[1,80,-10] width=11 seqs=8
TC3A_CAEEL ( 226) FRFQQDNATIH  77

     Minos ( 275) FTFQQDGASSH 100

TC1A_CAEBR ( 172) WVFQQDNDPKH  54
TC1A_CAEEL ( 172) FVFQQDNDPKH  50
TC2A_CAEBR ( 172) FVFQQDNDPKH  50
       HB1 ( 218) WTFQQDNDQKR  82
       Uhu ( 200) FRFYQDNDQKH  79
    Bari-1 ( 238) WILQQDNAPCH 100
//
ID   EXAMPLE; BLOCK
AC   exampleD; distance from previous block=(18,18)
DE   EXAMPLE
BL   SIW motif=[8,0,17] motomat=[1,80,-10] width=15 seqs=8
       HB1 ( 247) WQAPPSHLNPIENLY 100

       Uhu ( 229) XPAQSPDVNVIXNLW  78

     Minos ( 304) WPSNSPDLSPIENIW  56

TC1A_CAEBR ( 201) WPSQSPDLNPIEHMW  39
TC1A_CAEEL ( 201) WPSQSPDLNPIEHLW  34
TC2A_CAEBR ( 201) WPSQSPDLNPIEHLW  34
TC3A_CAEEL ( 255) WPARSPDLNPIENLW  38
    Bari-1 ( 267) WPPQSPDLNIIENVW  53
//
ID   EXAMPLE; BLOCK
AC   exampleE; distance from previous block=(17,23)
DE   EXAMPLE
BL   WSR motif=[8,0,17] motomat=[1,80,-10] width=37 seqs=8
TC1A_CAEBR ( 237) LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY  56

TC1A_CAEEL ( 237) LENAWKAIPMSVIHKLIDSMPRRCQAVIDANGYATKY  65

TC2A_CAEBR ( 237) LQDVWQAIPMSVIDTILDSMPRRCQTVIDAKGFPTKY  66

TC3A_CAEEL ( 293) ILDAWKSIPDNQLKSLVRSMEDRLIEIIRTQGNPINY 100

       HB1 ( 283) VQDTWAKIPPKPCXDLVDFMPRGCKAVLANKGYPAKY  94

       Uhu ( 261) LLDEWSKISPETTRKLVSSMNNRLMEDIKAKGYHTKY  80

    Bari-1 ( 303) IAEIWSKLTLEFAQTLVRSIPKRLQAVIDAKGGVTKY  84

     Minos ( 340) LQEMWDSISQEHCKNLLSSMPKRVKCVMQAKGDVTQF  92

//
( 187) GGGTVMFWGCL  68
//
ID   EXAMPLE; BLOCK
AC   exampleC; distance from previous block=(39,40)
DE   EXAMPLE
BL   QDN motif=[8,0,17] motomat=[1,80,-10] width=11 seqs=8
TC3A_CAEEL ( 226) FRFQQDNATIH  77

     Minos ( 275) FTFQQDGASSH 100

TC1A_CAEBR ( 172) WVFQQDNDPKH  54
TC1A_CAEEL ( 172) FVFQQDNDPKH  50
TC2A_CAEBR ( 172) FVFQQDNDPKH  50
       HB1 ( 218) WTFQQDNDQKR  82
       Uhu ( 200) FRFYQDNDQKH  79
    Bari-1 ( 238) WILQQDNblimps-3.9/examples/blimps/distribution/multimat.example.cs000064400001460000012000000001641041506464700246160ustar00jorjastaff00000400000027BLock  			exampleE.blk
DBase			example.pros
OUtput_file		exampleE.blk.bli
REpeats_allowed		NO
NUmber_to_report	0
//
blimps-3.9/examples/blimps/distribution/exampleA.blk.bli000064400001460000012000000331311062461201400237610ustar00jorjastaff00000400000027BLIMPS (BLocks IMProved Searcher)   Version 3.8  2006/04
(C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center



Block File: exampleA.blk

Target File (s) : example.pros

Records Searched:   89

Scores Done:                      89

Alignments Done:               62773

AC#                    Description                                                Score RF  AA# Length
TC1A_CAEBR|P35072     TRANSPOSABLE ELEMENT TCB1 TRANSPOSASE (TRANSPOSABLE ELEM      2915  0    52    273 KKPLVSLKNRKARVEWAKQHLSWGPREWANHIWSDESKFNMFGTDG
TC1A_CAEEL|P03934     TRANSPOSABLE ELEMENT TC1 TRANSPOSASE                          2914  0    52    273 KKPFISKKNRMARVAWAKAHLRWGRQEWAKHIWSDESKFNLFGSDG
TC2A_CAEBR|Q04202     TRANSPOSABLE ELEMENT TCB2 TRANSPOSASE                         2879  0    52    273 KKPSISKKNRIARVAWARAHLHWGRQDWANHVFSDESKFNLFGTDG
TC3A_CAEEL|P34257     TRANSPOSABLE ELEMENT TC3 TRANSPOSASE                          2670  0   109    329 KLRPAPLLSADHKLKRLEFAKNNMGTNWSKVVFSDEKKFNLDGPDG
OE66_NPVOP|O10305     OCCLUSION-DERIVED VIRUS ENVELOPE PROTEIN E66 (ODV-E66)        2056  0   437    682 KTaLAkTRtAGAiLvhARFAemNnLQFkSctLFyDhgmFQLyyniG
YP22_YEAST|Q08968     HYPOTHETICAL 78.3 KD PROTEIN IN SSM1-GRE1 INTERGENIC REG      2034  0   641    688 KKlyLmsvNpydRtKWdvTlrpeleTKWAdlshqDdAKFMMQaScS
RPOD_ORYSA|P12093     DNA-DIRECTED RNA POLYMERASE BETA" CHAIN (EC 2.7.7.6)          2016  0   865   1513 ggsLIPLereKKdsKesKkReNWvyvQWkKILkSkEKyFvLvrPav
NUCL_HUMAN|P19338     NUCLEOLIN (PROTEIN C23) | PS00030                             2012  0   379    706 pKgkdSKKeRDARtlLAKnlpyKvtQDelKeVFEDaAeIrLvskDG
YFEH_ECOLI|P39836     HYPOTHETICAL 36.4 KD PROTEIN IN XAPB-LIG INTERGENIC REGI      2007  0    37    332 tTaaIaLLffMHgaKLsREAiiaGGghWRlHLWvmcStFvLFpilG
YDF7_SCHPO|Q10479     PUTATIVE GLUCOSYLTRANSFERASE C17C9.07 (EC 2.4.1.-)            2006  0   240    501 mKqiPqLLSRlfpfSRgLcHayWaPnFWAlysFvDrvAFaVlprfG
ACVS_EMENI|P27742     DELTA-(L-ALPHA-AMINOADIPYL)-L-CYSTEINYL-D-VALINE SYNTHET      2005  0  2061   3770 EeaLyTiLSRheaLRtfLlRdqaTGTFyqKILtTDEAKcMLiiekS
MAOC_FLAPR|P36444     MALATE OXIDOREDUCTASE, CHLOROPLAST PRECURSOR (EC 1.1.1.4      2005  0   210    647 KnPqglyiSlKdKgKvLEilKNWPQkKiqvIVvTDGerIlglGdlG
MSH5_YEAST|Q12175     MUTS PROTEIN HOMOLOG 5 | PS00486                              2005  0   295    901 KswLInPLtnKKRiEtrysiiRtlLDKqNaIIFSDlSqsIkrcPDa
GLGA_METJA|Q59001     PROBABLE GLYCOGEN SYNTHASE (EC 2.4.1.21) (STARCH [BACTER      2004  0    53    521 dikkITviyKGAKiTFdvlRtKhPtTgvDlIVFSnESvnNLnVwDp
YQHN_BACSU|P54512     HYPOTHETICAL 16.7 KD PROTEIN IN GCVT-SPOIIIAA INTERGENIC      2004  0    55    142 KyRgLvLTSKGKKigkrLvYrHelLDQflrIIgvDEeKIynDVegi
NIFK_AZOVI|P07329     NITROGENASE MOLYBDENUM-IRON PROTEIN BETA CHAIN (EC 1.18.      1998  0   401    522 KKavdaiLaAspygKnAtvYigKDLwhlRslVFTDkpdFMIgnSYG
OE66_NPVAC|Q00704     OCCLUSION-DERIVED VIRUS ENVELOPE PROTEIN E66 (ODV-E66)        1993  0   460    704 qTaiAkTdtAGAiLvyAKFAemNnLQFkSctLFyDhgmFQLyyniG
SPCB_DROME|Q00963     SPECTRIN BETA CHAIN | PS00019 | PS00020 | PS50003             1989  0  1469   2291 EKIkAPLLeRqKaLEkkKEAfqfcRDveDekLWiDEKlpvansPDy
MAON_SOLTU|P37225     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 59 KD ISOFORM      1988  0   144    601 rrPrgmyfSAKdKgEmmsmifNWPsTQvDmIVlTDGSrIlglGdlG
MAOX_POPTR|P34105     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)       1983  0   154    591 KrPqglyiSlKeKgKvLdvlKNWPQksiqvIVvTDGerIlglGdlG
PSRC_WOLSU|P31077     POLYSULFIDE REDUCTASE CHAIN C (SULPHUR REDUCTASE CHAIN C      1982  0    56    317 agaLIaPLtIGAgLlLLiFdLtrPLhFWkllIFynfSsvMtlGvla
YPB4_CAEEL|Q11107     HYPOTHETICAL ZINC FINGER PROTEIN B03B8.4 IN CHROMOSOME I      1982  0   460   2111 KseFVePdeyTiRkKLLRwkhaKTkkEnRNItdSnEKeFsYepGeS
MAOC_LYCES|P37222     MALATE OXIDOREDUCTASE, CHLOROPLAST (EC 1.1.1.4 (FRAGMENT      1980  0   138    573 KrPqglffSlKeKgKihEvlKNWPekKiqvIVvTDGerIlglGdlG
MAOM_SOLTU|P37221     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 62 KD ISOFORM      1979  0   161    626 rrPrgmyfSAedRgEmmsmvyNWPaDQvDmIVvTDGSrIlglGdlG
TYRA_HAEIN|P43902     CHORISMATE MUTASE (EC 5.4.99.5) (CM) / PREPHENATE DEHYDR      1979  0    64    377 KagisadLieDvlrRFmREsyaNenQFgFKtInSDihKIvIvGGYG
MAOM_AMAHP|P37224     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 65 KD ISOFORM      1976  0   158    623 rrPrgmyfSsDdRgEmmsmvyNWPaEQvDmIVvTDGSrIlglGdlG
HOFB_HAEIN|P44622     PROTEIN TRANSPORT PROTEIN HOFB HOMOLOG | PS00662              1975  0   170    464 anRiISrLkllAKLdisEnRLpqDGRFqFKttFSDildFrLStlpT
MAOX_VITVI|P51615     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)       1974  0   154    591 rrPqglyiSlKeKgKiLEvlKNWPeRriqvIVvTDGerIlglGdlG
TRA0_ECOLI|P15025     TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS21               1974  0    38    390 KyPEPPaRktrHKMvkLKpfMDyidmrlAenVWnsEviFaeikamG
TRA0_SHISO|P16944     TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS640              1974  0    38    315 KyPEPPaRktrHKMvkLKpfMDyidmrlAenVWnsEviFaeikamG
GYRB_ACIJO|Q44081     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177      1973  0    81    216 rLRELSfLNAGvRivWrdERiHaehvFdyegglSekSAlDIaGlpG
NRAM_INBHK|P16191     NEURAMINIDASE (EC 3.2.1.18)                                   1973  0   190    466 vgvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc
NRAM_INBBE|P27907     NEURAMINIDASE (EC 3.2.1.18)                                   1972  0   189    465 igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc
NRAM_INBLN|P16193     NEURAMINIDASE (EC 3.2.1.18)                                   1972  0   189    465 igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc
NRAM_INBMF|P16199     NEURAMINIDASE (EC 3.2.1.18)                                   1972  0   189    465 igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc
NRAM_INBOR|P16201     NEURAMINIDASE (EC 3.2.1.18)                                   1972  0   190    466 igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc
NRAM_INBSI|P16203     NEURAMINIDASE (EC 3.2.1.18)                                   1972  0   190    466 igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc
NRAM_INBUS|P16205     NEURAMINIDASE (EC 3.2.1.18)                                   1972  0   190    466 igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc
NRAM_INBVI|P16207     NEURAMINIDASE (EC 3.2.1.18)                                   1972  0   189    465 igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc
NRAM_INBYB|Q90021     NEURAMINIDASE (EC 3.2.1.18)                                   1972  0   190    466 igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc
YBDM_ECOLI|P77174     HYPOTHETICAL 23.9 KD PROTEIN IN CSTA-DSBG INTERGENIC REG      1972  0   135    209 qrIaATiRHnrARgRhqiTAMSeiVRElSqlgWdDnKigkelGmDS
YCF2_MARPO|P09975     HYPOTHETICAL 259 KD PROTEIN (ORF 2136)                        1970  0  1129   2136 KffLkSKKislKtLSFhnFkLKWnLRFfNeInykknyllNflwSDf
AST5_DROME|P10083     ACHAETE-SCUTE COMPLEX PROTEIN T5 (ACHAETE) | PS00038          1969  0    91    201 KVlhendqQKqKqLhLqqQHLHfqQQQqhqHLyawhqelQLQsPTG
EUTE_ECOLI|P77445     ETHANOLAMINE UTILIZATION PROTEIN EUTE                         1969  0   236    467 agnPPvvvdeTAdLARAaQsivKGaSFdNNIIcaDEKvlIVvdSva
GLO2_HUMAN|Q16775     HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6) (GLYOXALAS      1969  0    34    260 KVvdAarKHgvKltTvLtTHhHWDhaggNekLvklESglkVyGGDd
TRFE_RABIT|P19134     SEROTRANSFERRIN PRECURSOR (SIDEROPHILIN) (BETA-1-METAL B      1968  0   595    694 KaPnhavvSRKdKaAcvKQkLldlQvEygNtVadcsSKFcMFhSkT
YNC4_YEAST|P53970     HYPOTHETICAL 27.7 KD PROTEIN IN UME3-HDA1 INTERGENIC REG      1968  0   191    246 inPPViLmayKKRrKadKhffNKikRNfDvleiTDfSKFehylker
KINN_HUMAN|Q12840     NEURONAL KINESIN HEAVY CHAIN (NKHC) | PS00411 | PS50067       1966  0   522   1032 vatmLSLeSelqRLQevsgHqRKriaEvlNgLmkDlSeFsViVGnG
CRTI_RHOCA|P17054     PHYTOENE DEHYDROGENASE (EC 1.3.-.-) (PHYTOENE DESATURASE      1964  0   277    524 vVsnAdagHtyKRLlRnRdRwRWTdEKlDKkrWSmGlfvwYFGTkG
GYRB_ACICA|Q43947     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177      1964  0    81    216 rLRELSfLNAGvRivLrdERiNlGhvFdyegglSekSAlDIaGlpG
PARF_PARTE|P47244     PARAFUSIN | PS00710                                           1964  0    30    582 qKPgtSgLrKKvseAtqpnYLeNfVQsiFNtLrkDElKnvLFVGgd
GYRB_ACIS1|Q44272     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177      1963  0    81    216 rLRELSLLNAGvRivLrdERiNaehvFdyegglSekSAlDIaGlpG
KINN_MOUSE|P28738     NEURONAL KINESIN HEAVY CHAIN (NKHC) | PS00411 | PS50067       1963  0   522   1027 vatmLSLeSelqRLQevsgHqRKriaEvlNgLmrDlSeFsViVGnG
PPS2_BACSU|P39846     PEPTIDE SYNTHETASE 2 | PS00012 | PS00455 | PS50075            1963  0  1586   2560 ErISfmLndsGAKLlLtErgLNKPaDytghILyiDEcenNsipaDv
CYRG_MOUSE|P34902     CYTOKINE RECEPTOR COMMON GAMMA CHAIN PRECURSOR (GAMMA-C       1962  0   170    369 ELRwkSrhiKercLQyLvQYrSNrdRsWtelIvnhEprFsLpsvDe
YOUG_BACLI|Q45292     HYPOTHETICAL 17.3 KD PROTEIN IN GNTR 5'REGION                 1961  0    98    147 KcREtPihpfIpnLSFiKnkrHWGySFrFgHIeisEhdFkLiVkqm
YENR_YEREN|P54295     YENR REGULATORY PROTEIN | PS00622                             1960  0    38    244 KTPLhPTiisnypLdWvKkYKKNsyhliDpVIlTakdKvapFawDd
YFJJ_ECOLI|P52125     HYPOTHETICAL 24.6 KD PROTEIN IN ALPA-GABD INTERGENIC REG      1960  0    82    208 rKdwPdsRHsTlRyAWvREYtKNrkRhyhlILcfnqdAyyhlGdYd
ITA2_HUMAN|P17301     PLATELET MEMBRANE GLYCOPROTEIN IA PRECURSOR (GPIA) (COLL      1959  0   809   1181 qeqPfivsNqnKRLTFsvTlKNKreSayNTgIvvDfSenlfFaSfS
LEF4_NPVAC|P41477     LATE EXPRESSION FACTOR 4                                      1959  0    98    464 KLPykTLsHnlsKiikvyvYqHdkiEikFeHVyfskSdIDLFdSTm
CP4C_BLADI|P29981     CYTOCHROME P450 4C1 (EC 1.14.14.1) (CYPIVC1) | PS00086        1958  0   272    511 EdeLLgKKkRlAfLdLLLEAseNGtkmsDTdIrEevdtFMfeGhDT
YDIL_ECOLI|P76196     HYPOTHETICAL 15.0 KD PROTEIN IN LPP-AROD INTERGENIC REGI      1958  0    57    127 EqlLAmrqQRKKhLhaiiEkiNNrigNntmrfFpDltAFQrvyPDG
DHA6_YEAST|P54115     ALDEHYDE DEHYDROGENASE, CYTOSOLIC (EC 1.2.1.3) | PS00070      1957  0   267    501 KKItLeLggKsAhLvFddAniKKTLpNlvNgIFknagqIcsSGSri
DPOM_CLAPU|P22373     PROBABLE DNA POLYMERASE (EC 2.7.7.7) | PS00116                1957  0   710   1063 KikSPdnLylGllpKRtETsLifPGgaWegwyFSeElKFaVahGYe
GYRB_ACIS6|Q44277     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177      1957  0    81    216 rLRELSfLNAGvRivLrdERVNlehiydyeVglSekSAlDIaGlpG
GYRB_ACIS9|Q44276     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177      1957  0    81    216 rLRELSfLNAGvRivLrdERVNlehiydyeVglSekSAlDIaGlpG
ITA2_BOVIN|P53710     PLATELET MEMBRANE GLYCOPROTEIN IA PRECURSOR (G (FRAGMENT      1957  0   798   1170 qqqPfivsNqnKRLTFsvQlKNKkeSayNTeIvvDfSenlfFaSwS
SIN3_YEAST|P22579     PAIRED AMPHIPATHIC HELIX PROTEIN                              1957  0   884   1536 EhPaVTapvvlKRLKqkdEewRraQREWNKVwrElEqKvffkslDh
THIS_ECOLI|O32583     THIS PROTEIN                                                  1957  0    18     66 helLeqLdQRqAgaALAinqqivPREQWAqHIvqDGdqIlLFqvia
MAOX_PHAVU|P12628     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)       1956  0   152    589 rrPqglyiSlKeKgKiLEvlKNWPeksiqvIVvTDGerIlglGdlG
PH81_YEAST|P17442     PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO81 (CDK       1956  0   127   1178 KKfqkdLRNleqyVELnKTgfSKaLkKWDKrsqShdKdFyLatvvS
GSHC_SCHMA|Q00277     GLUTATHIONE PEROXIDASE (EC 1.11.1.9) (GPX) | PS00460 | P      1955  0    65    169 rilafPcnQfGgqepWAEAeiKKfVTEkygVqFdmfSKIkVnGSDa
NUCL_MOUSE|P09405     NUCLEOLIN (PROTEIN C23) | PS00030                             1955  0   381    706 pKgrdSKKvRaARtlLAKnlsfNitEDelKeVFEDameIrLvsqDG
RL17_SCHPO|O59794     60S RIBOSOMAL PROTEIN L17 | PS00464                           1955  0     5    187 aaPaLeTKcAKARgAyLRTHfKNsREvaFTIngmnlKKafIFldnv
MAOX_MESCR|P37223     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)       1954  0   148    585 rrPqglfiSlKdKgRiLEllrNWPekKiqvIVvTDGerIlglGdlG
RPOC_TREPA|O83270     DNA-DIRECTED RNA POLYMERASE BETA' CHAIN (EC 2.7.7.6) (TR      1953  0   565   1416 EiPFVneTldDKRiRkLiERVfKrQDsWlaVqmlDalKtIgytyaT
SN2L_CAEEL|P41877     POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L                 1953  0   142    971 asPhLvivpKsTlqnWAnEfKKWcPSinAvVLigDEAArNqvlrDv
YM8I_YEAST|Q03529     HYPOTHETICAL 44.9 KD PROTEIN IN URA10-NRC1 INTERGENIC RE      1953  0   330    384 hskLPPfmrKlKKyhLehhYKNyqLgFgvTswFwDEvfgtYlGPDa
EUTE_SALTY|P41793     ETHANOLAMINE UTILIZATION PROTEIN EUTE                         1951  0   236    467 agnPPvvvdeTAdLpRAaQsivKGaSFdNNIIcaDEKvlIVvdSva
GLND_MYCTU|Q10961     PROBABLE [PROTEIN-PII] URIDYLYLTRANSFERASE (EC 2.7.7.59)      1951  0    20    808 sgnhreLdpvGlRqTWLdlHeSWliDKaDeIgiaDaSgFaIvGvgG
HBB1_TRICR|P10785     HEMOGLOBIN BETA-1 CHAIN (MAJOR) | PS01033                     1951  0    63    145 aKvmhSiaeAvKhLddLKAYyadlsTihcKkLyvDpAnFkLFGGiv
MA2X_HUMAN|P49641     ALPHA-MANNOSIDASE IIX (EC 3.2.1.114) (MANNOSYL-OLIGOSACC      1951  0   195   1139 lnsmVSKLQeDpRrRFLwAeVSffakwWDNInvqkrAAvrrlVGnG
VIL1_MOUSE|Q62468     VILLIN                                                        1951  0   690    826 ETPiIvvKQgheppTFtgwfLaWDPfKWSNtksyDdlKaeLgnSgd
Y08F_MYCTU|Q11052     PROBABLE REGULATORY PROTEIN CY50.15 | PS50006                 1951  0   117    388 EKtagvhaaAagRfEqAsrHLSaaLREWRgpVldDlrdFQfvePfa
GYRB_ACIS8|Q44275     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177      1950  0    81    216 rLRELSfLNAGvRivLcdERiNlehvFdyegglSekSAlDIaGlpG
PTP1_DROME|P35992     PROTEIN-TYROSINE PHOSPHATASE 10D PRECURSOR (EC 3.1.3.48)      1950  0  1273   1630 EfeELkhvgRDqpcTFAdlpcNrPknrftNILpyDhSrFkLQpvDd
RFAB_ECOLI|P27127     LIPOPOLYSACCHARIDE 1,6-GALACTOSYLTRANSFERASE (EC 2.4.1.-      1949  0   191    369 iyvgrmKfegqKRVKdLLdgLSqakgNWklHVlgDGSdFekcqaYG
YO96_CAEEL|P41846     HYPOTHETICAL 93.9 KD PROTEIN T20B12.6 IN CHROMOSOME III       1949  0   100    843 rKhtVPKetIesKLRsyEppVKlqRSQtpKHtiSDEfAwDfDdlDn
NOD1_RHIGA|P50331     NODULATION PROTEIN D I | PS00044                              1948  0   261    310 vehPLPPLHfplaVQWpalHntdPGniWmreImfDEAsrMeasSeT
nLRFfNeInykknyllNflwSDf
AST5_DROME|P10083     ACHAETE-SCUTE COMPLEX PROTEIN T5 (ACHAETE) | PS00038          1969  0    91    201 KVlhendqQKqKqLhLqqQHLHfqQQQqhqHLyawhqelQLQsPTG
EUTE_ECOLI|P77445     ETHANOLAMINE UTILIZATION PROTEIN EUTE                         1969  0   236    467 agnPPvvvdeTAdLARAaQsivKGaSFdNNIIcaDEKvlIVvdSva
GLO2_HUMAN|Q16775     HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6) (GLYOXALAS      1969  0    blimps-3.9/examples/blimps/distribution/exampleB.blk.bli000064400001460000012000000250561062461201400237710ustar00jorjastaff00000400000027BLIMPS (BLocks IMProved Searcher)   Version 3.8  2006/04
(C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center



Block File: exampleB.blk

Target File (s) : example.pros

Records Searched:   89

Scores Done:                      89

Alignments Done:               59658

AC#                    Description                                                Score RF  AA# Length
TC1A_CAEBR|P35072     TRANSPOSABLE ELEMENT TCB1 TRANSPOSASE (TRANSPOSABLE ELEM       815  0   121    273 GGGSVMVWGCF
TC1A_CAEEL|P03934     TRANSPOSABLE ELEMENT TC1 TRANSPOSASE                           815  0   121    273 GGGSVMVWGCF
TC2A_CAEBR|Q04202     TRANSPOSABLE ELEMENT TCB2 TRANSPOSASE                          815  0   121    273 GGGSVMVWGCF
TC3A_CAEEL|P34257     TRANSPOSABLE ELEMENT TC3 TRANSPOSASE                           764  0   175    329 GGGTVMVWGAF
GLND_MYCTU|Q10961     PROBABLE [PROTEIN-PII] URIDYLYLTRANSFERASE (EC 2.7.7.59)       540  0   750    808 GaGagiVWAkv
RPOC_TREPA|O83270     DNA-DIRECTED RNA POLYMERASE BETA' CHAIN (EC 2.7.7.6) (TR       537  0    50   1416 ifGTTkeWeCF
VIL1_MOUSE|Q62468     VILLIN                                                         535  0   289    826 GGlKIfVWkgk
ACVS_EMENI|P27742     DELTA-(L-ALPHA-AMINOADIPYL)-L-CYSTEINYL-D-VALINE SYNTHET       524  0   147   3770 GGGShtVaAsI
PTP1_DROME|P35992     PROTEIN-TYROSINE PHOSPHATASE 10D PRECURSOR (EC 3.1.3.48)       512  0  1362   1630 srAiVMltrCF
GLO2_HUMAN|Q16775     HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6) (GLYOXALAS       510  0   131    260 tGdTlfVaGCg
MSH5_YEAST|Q12175     MUTS PROTEIN HOMOLOG 5 | PS00486                               510  0   613    901 iPnSTMidGgL
PH81_YEAST|P17442     PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO81 (CDK        510  0  1158   1178 GGySgiyyACe
YNC4_YEAST|P53970     HYPOTHETICAL 27.7 KD PROTEIN IN UME3-HDA1 INTERGENIC REG       509  0    86    246 GsGTglVglCv
MA2X_HUMAN|P49641     ALPHA-MANNOSIDASE IIX (EC 3.2.1.114) (MANNOSYL-OLIGOSACC       508  0   876   1139 GttSTrsWpCt
GLGA_METJA|Q59001     PROBABLE GLYCOGEN SYNTHASE (EC 2.4.1.21) (STARCH [BACTER       506  0   477    521 sPlSmMmknCy
MAOC_LYCES|P37222     MALATE OXIDOREDUCTASE, CHLOROPLAST (EC 1.1.1.4 (FRAGMENT       505  0   291    573 GtASVvlaGlM
YM8I_YEAST|Q03529     HYPOTHETICAL 44.9 KD PROTEIN IN URA10-NRC1 INTERGENIC RE       505  0   228    384 FcvgVfVWtlI
OE66_NPVAC|Q00704     OCCLUSION-DERIVED VIRUS ENVELOPE PROTEIN E66 (ODV-E66)         503  0   468    704 taGaIlVyAkF
HBB1_TRICR|P10785     HEMOGLOBIN BETA-1 CHAIN (MAJOR) | PS01033                      500  0    61    145 HGAKVMhsiAe
YPB4_CAEEL|Q11107     HYPOTHETICAL ZINC FINGER PROTEIN B03B8.4 IN CHROMOSOME I       498  0  1120   2111 GGGrVysctCs
PSRC_WOLSU|P31077     POLYSULFIDE REDUCTASE CHAIN C (SULPHUR REDUCTASE CHAIN C       497  0   253    317 GGlaslFWlgv
PPS2_BACSU|P39846     PEPTIDE SYNTHETASE 2 | PS00012 | PS00455 | PS50075             496  0  2110   2560 FnqSVMiyrAe
RFAB_ECOLI|P27127     LIPOPOLYSACCHARIDE 1,6-GALACTOSYLTRANSFERASE (EC 2.4.1.-       496  0    40    369 HiqSeMFffCr
SIN3_YEAST|P22579     PAIRED AMPHIPATHIC HELIX PROTEIN                               496  0   767   1536 sGrddMcWevL
YO96_CAEEL|P41846     HYPOTHETICAL 93.9 KD PROTEIN T20B12.6 IN CHROMOSOME III        496  0   586    843 GPASVpVqAsq
MAOC_FLAPR|P36444     MALATE OXIDOREDUCTASE, CHLOROPLAST PRECURSOR (EC 1.1.1.4       495  0   364    647 GtASVvlaGlI
MAOX_MESCR|P37223     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)        495  0   302    585 GtASVvlaGlI
LEF4_NPVAC|P41477     LATE EXPRESSION FACTOR 4                                       493  0   260    464 GrGlfMrnfCI
MAOX_PHAVU|P12628     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)        493  0   306    589 GtASVvlaGlL
KINN_HUMAN|Q12840     NEURONAL KINESIN HEAVY CHAIN (NKHC) | PS00411 | PS50067        491  0   294   1032 ncrTTMFicCs
GYRB_ACIJO|Q44081     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       489  0    55    216 tGtTVrFWpsa
GYRB_ACICA|Q43947     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       486  0    55    216 sGtTVrFWpse
GYRB_ACIS6|Q44277     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       486  0    55    216 sGtTVrFWpse
GYRB_ACIS9|Q44276     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       486  0    55    216 sGtTVrFWpse
YDF7_SCHPO|Q10479     PUTATIVE GLUCOSYLTRANSFERASE C17C9.07 (EC 2.4.1.-)             486  0   313    501 iPPaltFyiCL
DPOM_CLAPU|P22373     PROBABLE DNA POLYMERASE (EC 2.7.7.7) | PS00116                 485  0   647   1063 yGGrVeVfnpI
ITA2_BOVIN|P53710     PLATELET MEMBRANE GLYCOPROTEIN IA PRECURSOR (G (FRAGMENT       485  0   261   1170 GatKVMVvvtd
MAOX_VITVI|P51615     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)        485  0   308    591 GtASVvlaGiv
OE66_NPVOP|O10305     OCCLUSION-DERIVED VIRUS ENVELOPE PROTEIN E66 (ODV-E66)         485  0   445    682 taGaIlVhArF
ITA2_HUMAN|P17301     PLATELET MEMBRANE GLYCOPROTEIN IA PRECURSOR (GPIA) (COLL       484  0   245   1181 GGdlTntfGAI
GYRB_ACIS8|Q44275     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       483  0    55    216 tGtKVrFWpsa
NIFK_AZOVI|P07329     NITROGENASE MOLYBDENUM-IRON PROTEIN BETA CHAIN (EC 1.18.       483  0   361    522 HGkrfalWGdp
RPOD_ORYSA|P12093     DNA-DIRECTED RNA POLYMERASE BETA" CHAIN (EC 2.7.7.6)           483  0  1090   1513 riPipkFWGlF
PARF_PARTE|P47244     PARAFUSIN | PS00710                                            482  0   386    582 FfGnlMdaGlI
YFEH_ECOLI|P39836     HYPOTHETICAL 36.4 KD PROTEIN IN XAPB-LIG INTERGENIC REGI       482  0   299    332 HqiqlMVcAvL
MAOX_POPTR|P34105     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)        480  0    23    591 GGGvedVyGed
YCF2_MARPO|P09975     HYPOTHETICAL 259 KD PROTEIN (ORF 2136)                         480  0  1936   2136 FiGKrilWdpI
DHA6_YEAST|P54115     ALDEHYDE DEHYDROGENASE, CYTOSOLIC (EC 1.2.1.3) | PS00070       479  0   184    501 aPAlaMgnvCI
GYRB_ACIS1|Q44272     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       477  0     8    216 HGvgVsVvnAL
CRTI_RHOCA|P17054     PHYTOENE DEHYDROGENASE (EC 1.3.-.-) (PHYTOENE DESATURASE       473  0     6    524 GmGravViGAg
CP4C_BLADI|P29981     CYTOCHROME P450 4C1 (EC 1.14.14.1) (CYPIVC1) | PS00086         471  0    69    511 yGPlyriWAgp
KINN_MOUSE|P28738     NEURONAL KINESIN HEAVY CHAIN (NKHC) | PS00411 | PS50067        468  0   294   1027 ncrSrMFicCs
YP22_YEAST|Q08968     HYPOTHETICAL 78.3 KD PROTEIN IN SSM1-GRE1 INTERGENIC REG       466  0   317    688 nanTVahWqAy
EUTE_ECOLI|P77445     ETHANOLAMINE UTILIZATION PROTEIN EUTE                          463  0   214    467 tGGeavVeAAr
TRA0_ECOLI|P15025     TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS21                463  0   193    390 nnGKVvFnsgF
TRA0_SHISO|P16944     TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS640               463  0   193    315 nnGKVvFnsgF
MAOM_SOLTU|P37221     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 62 KD ISOFORM       462  0   314    626 GtAgVaiaGlL
NOD1_RHIGA|P50331     NODULATION PROTEIN D I | PS00044                               459  0   203    310 mkPSVeqWllL
TRFE_RABIT|P19134     SEROTRANSFERRIN PRECURSOR (SIDEROPHILIN) (BETA-1-METAL B       459  0   274    694 dGkedliWelL
TYRA_HAEIN|P43902     CHORISMATE MUTASE (EC 5.4.99.5) (CM) / PREPHENATE DEHYDR       458  0   228    377 lleqIqiWGAk
NUCL_HUMAN|P19338     NUCLEOLIN (PROTEIN C23) | PS00030                              457  0   648    706 FGGrgggrGgF
NUCL_MOUSE|P09405     NUCLEOLIN (PROTEIN C23) | PS00030                              457  0   648    706 FGGrgggrGgF
SN2L_CAEEL|P41877     POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L                  457  0   411    971 qGsrVlifsqF
NRAM_INBBE|P27907     NEURAMINIDASE (EC 3.2.1.18)                                    456  0    43    465 itApTMtldCa
NRAM_INBLN|P16193     NEURAMINIDASE (EC 3.2.1.18)                                    456  0    43    465 itApTMtldCa
NRAM_INBMF|P16199     NEURAMINIDASE (EC 3.2.1.18)                                    456  0    43    465 itApTMtldCa
NRAM_INBVI|P16207     NEURAMINIDASE (EC 3.2.1.18)                                    456  0    43    465 itApTMtldCt
SPCB_DROME|Q00963     SPECTRIN BETA CHAIN | PS00019 | PS00020 | PS50003              455  0   951   2291 HGvqTfyieCr
HOFB_HAEIN|P44622     PROTEIN TRANSPORT PROTEIN HOFB HOMOLOG | PS00662               454  0   267    464 sGkSIslytAL
MAON_SOLTU|P37225     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 59 KD ISOFORM       452  0   297    601 GtAgValaGlL
NRAM_INBUS|P16205     NEURAMINIDASE (EC 3.2.1.18)                                    452  0    44    466 rtAqTMsldCa
YENR_YEREN|P54295     YENR REGULATORY PROTEIN | PS00622                              451  0   183    244 reneIlyWAsv
EUTE_SALTY|P41793     ETHANOLAMINE UTILIZATION PROTEIN EUTE                          450  0   214    467 tGGervVdAAr
AST5_DROME|P10083     ACHAETE-SCUTE COMPLEX PROTEIN T5 (ACHAETE) | PS00038           448  0    21    201 nGPSVirrnAr
NRAM_INBHK|P16191     NEURAMINIDASE (EC 3.2.1.18)                                    448  0   438    466 HsAaTaiyclM
NRAM_INBOR|P16201     NEURAMINIDASE (EC 3.2.1.18)                                    448  0    44    466 itApTMsldCa
NRAM_INBSI|P16203     NEURAMINIDASE (EC 3.2.1.18)                                    448  0   438    466 HsAaTaiyclM
NRAM_INBYB|Q90021     NEURAMINIDASE (EC 3.2.1.18)                                    448  0   438    466 HsAaTaiyclM
RL17_SCHPO|O59794     60S RIBOSOMAL PROTEIN L17 | PS00464                            446  0    75    187 FGvTqarWpvk
MAOM_AMAHP|P37224     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 65 KD ISOFORM       443  0   198    623 GlGdlgVhGig
GSHC_SCHMA|Q00277     GLUTATHIONE PEROXIDASE (EC 1.11.1.9) (GPX) | PS00460 | P       440  0    62    169 kGlrIlafpCn
CYRG_MOUSE|P34902     CYTOKINE RECEPTOR COMMON GAMMA CHAIN PRECURSOR (GAMMA-C        430  0   302    369 yqGnfsaWsgv
Y08F_MYCTU|Q11052     PROBABLE REGULATORY PROTEIN CY50.15 | PS50006                  430  0   200    388 HPyreplWtqL
YDIL_ECOLI|P76196     HYPOTHETICAL 15.0 KD PROTEIN IN LPP-AROD INTERGENIC REGI       429  0   100    127 pdGnfidWkiy
YFJJ_ECOLI|P52125     HYPOTHETICAL 24.6 KD PROTEIN IN ALPA-GABD INTERGENIC REG       427  0   195    208 vGdgdrnfGCs
YQHN_BACSU|P54512     HYPOTHETICAL 16.7 KD PROTEIN IN GCVT-SPOIIIAA INTERGENIC       425  0    99    142 GiehhlsWnsI
THIS_ECOLI|O32583     THIS PROTEIN                                                   424  0    52     66 dGdqIllfqvI
YOUG_BACLI|Q45292     HYPOTHETICAL 17.3 KD PROTEIN IN GNTR 5'REGION                  418  0    27    147 GGfaqlchGke
YBDM_ECOLI|P77174     HYPOTHETICAL 23.9 KD PROTEIN IN CSTA-DSBG INTERGENIC REG       405  0    44    209 ePvdcvlWvkn
blimps-3.9/examples/blimps/distribution/exampleC.blk.bli000064400001460000012000000250561062461201400237720ustar00jorjastaff00000400000027BLIMPS (BLocks IMProved Searcher)   Version 3.8  2006/04
(C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center



Block File: exampleC.blk

Target File (s) : example.pros

Records Searched:   89

Scores Done:                      89

Alignments Done:               59658

AC#                    Description                                                Score RF  AA# Length
TC1A_CAEBR|P35072     TRANSPOSABLE ELEMENT TCB1 TRANSPOSASE (TRANSPOSABLE ELEM       913  0   171    273 WVFQQDNDPKH
TC1A_CAEEL|P03934     TRANSPOSABLE ELEMENT TC1 TRANSPOSASE                           899  0   171    273 FVFQQDNDPKH
TC2A_CAEBR|Q04202     TRANSPOSABLE ELEMENT TCB2 TRANSPOSASE                          899  0   171    273 FVFQQDNDPKH
TC3A_CAEEL|P34257     TRANSPOSABLE ELEMENT TC3 TRANSPOSASE                           847  0   225    329 FRFQQDNATIH
TYRA_HAEIN|P43902     CHORISMATE MUTASE (EC 5.4.99.5) (CM) / PREPHENATE DEHYDR       582  0   237    377 akiYQtNATeH
GLGA_METJA|Q59001     PROBABLE GLYCOGEN SYNTHASE (EC 2.4.1.21) (STARCH [BACTER       578  0   449    521 WTFYklNeiCm
PPS2_BACSU|P39846     PEPTIDE SYNTHETASE 2 | PS00012 | PS00455 | PS50075             570  0  2099   2560 WfFsQsleShH
LEF4_NPVAC|P41477     LATE EXPRESSION FACTOR 4                                       564  0   364    464 lRFQQffDPpl
AST5_DROME|P10083     ACHAETE-SCUTE COMPLEX PROTEIN T5 (ACHAETE) | PS00038           555  0   111    201 lhFQQqqqhqH
SPCB_DROME|Q00963     SPECTRIN BETA CHAIN | PS00019 | PS00020 | PS50003              553  0   637   2291 WqFYwDtAdee
VIL1_MOUSE|Q62468     VILLIN                                                         551  0   635    826 FdFnQDdleee
RPOD_ORYSA|P12093     DNA-DIRECTED RNA POLYMERASE BETA" CHAIN (EC 2.7.7.6)           550  0   493   1513 FsLhkDqDQmn
YP22_YEAST|Q08968     HYPOTHETICAL 78.3 KD PROTEIN IN SSM1-GRE1 INTERGENIC REG       549  0    88    688 FnLvQDqDlek
SIN3_YEAST|P22579     PAIRED AMPHIPATHIC HELIX PROTEIN                               544  0   487   1536 haqQQheAQmH
YPB4_CAEEL|Q11107     HYPOTHETICAL ZINC FINGER PROTEIN B03B8.4 IN CHROMOSOME I       544  0   514   2111 slLeQDNqSSs
GLND_MYCTU|Q10961     PROBABLE [PROTEIN-PII] URIDYLYLTRANSFERASE (EC 2.7.7.59)       538  0   326    808 iVLarDaePeH
YO96_CAEEL|P41846     HYPOTHETICAL 93.9 KD PROTEIN T20B12.6 IN CHROMOSOME III        534  0   120    843 vkLQrsqtPKH
PTP1_DROME|P35992     PROTEIN-TYROSINE PHOSPHATASE 10D PRECURSOR (EC 3.1.3.48)       532  0  1481   1630 rILQQiNtSdy
ACVS_EMENI|P27742     DELTA-(L-ALPHA-AMINOADIPYL)-L-CYSTEINYL-D-VALINE SYNTHET       531  0  2351   3770 klLrvDNDaSR
YM8I_YEAST|Q03529     HYPOTHETICAL 44.9 KD PROTEIN IN URA10-NRC1 INTERGENIC RE       531  0   166    384 FyvdQihrPrH
THIS_ECOLI|O32583     THIS PROTEIN                                                   529  0    47     66 qhivQDGDQIl
KINN_HUMAN|Q12840     NEURONAL KINESIN HEAVY CHAIN (NKHC) | PS00411 | PS50067        528  0   890   1032 rRyQQevDrIk
KINN_MOUSE|P28738     NEURONAL KINESIN HEAVY CHAIN (NKHC) | PS00411 | PS50067        528  0   890   1027 rRyQQevDrIk
PH81_YEAST|P17442     PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO81 (CDK        528  0   724   1178 ikLtQDNgiIm
YENR_YEREN|P54295     YENR REGULATORY PROTEIN | PS00622                              519  0   158    244 lgLYQsNsdKn
RPOC_TREPA|O83270     DNA-DIRECTED RNA POLYMERASE BETA' CHAIN (EC 2.7.7.6) (TR       518  0  1277   1416 FIygQqvDkyR
YCF2_MARPO|P09975     HYPOTHETICAL 259 KD PROTEIN (ORF 2136)                         518  0   459   2136 lfFkQkNskSf
OE66_NPVAC|Q00704     OCCLUSION-DERIVED VIRUS ENVELOPE PROTEIN E66 (ODV-E66)         517  0    65    704 vaFrQnNiQel
CP4C_BLADI|P29981     CYTOCHROME P450 4C1 (EC 1.14.14.1) (CYPIVC1) | PS00086         516  0    18    511 FlFrQgakraR
HOFB_HAEIN|P44622     PROTEIN TRANSPORT PROTEIN HOFB HOMOLOG | PS00662               515  0   367    464 sRLQQlGiQqy
TRA0_SHISO|P16944     TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS640               514  0   147    315 rsFhvfaAPKH
YQHN_BACSU|P54512     HYPOTHETICAL 16.7 KD PROTEIN IN GCVT-SPOIIIAA INTERGENIC       514  0   117    142 qyFeeDdArKk
GYRB_ACIS9|Q44276     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       512  0    66    216 WTFsQtifSvd
YOUG_BACLI|Q45292     HYPOTHETICAL 17.3 KD PROTEIN IN GNTR 5'REGION                  512  0   124    147 FRFghieiSeH
MA2X_HUMAN|P49641     ALPHA-MANNOSIDASE IIX (EC 3.2.1.114) (MANNOSYL-OLIGOSACC       506  0   331   1139 WRqtwDsDSSt
NUCL_MOUSE|P09405     NUCLEOLIN (PROTEIN C23) | PS00030                              502  0   420    706 rlvsQDGkSKg
DHA6_YEAST|P54115     ALDEHYDE DEHYDROGENASE, CYTOSOLIC (EC 1.2.1.3) | PS00070       501  0    33    501 FmkaQDGkTyp
MAOC_FLAPR|P36444     MALATE OXIDOREDUCTASE, CHLOROPLAST PRECURSOR (EC 1.1.1.4       501  0   408    647 eIskQtNAPle
MAOX_PHAVU|P12628     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)        501  0    81    589 sVFnQelqeKR
RFAB_ECOLI|P27127     LIPOPOLYSACCHARIDE 1,6-GALACTOSYLTRANSFERASE (EC 2.4.1.-       501  0    34    369 tTFrQqhiQSe
ITA2_BOVIN|P53710     PLATELET MEMBRANE GLYCOPROTEIN IA PRECURSOR (G (FRAGMENT       497  0    38   1170 yavQQfinPKg
ITA2_HUMAN|P17301     PLATELET MEMBRANE GLYCOPROTEIN IA PRECURSOR (GPIA) (COLL       497  0    49   1181 yavQQfinPKg
GYRB_ACICA|Q43947     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       496  0    34    216 eqeYQhGDPqy
YDIL_ECOLI|P76196     HYPOTHETICAL 15.0 KD PROTEIN IN LPP-AROD INTERGENIC REGI       496  0   107    127 WkiYQsvAael
Y08F_MYCTU|Q11052     PROBABLE REGULATORY PROTEIN CY50.15 | PS50006                  493  0   317    388 iVLdsaNvSrH
HBB1_TRICR|P10785     HEMOGLOBIN BETA-1 CHAIN (MAJOR) | PS01033                      492  0    80    145 kayYaDlsTIH
OE66_NPVOP|O10305     OCCLUSION-DERIVED VIRUS ENVELOPE PROTEIN E66 (ODV-E66)         490  0   172    682 vTivlDNtPhy
PARF_PARTE|P47244     PARAFUSIN | PS00710                                            490  0   312    582 FgaacDGDadR
NIFK_AZOVI|P07329     NITROGENASE MOLYBDENUM-IRON PROTEIN BETA CHAIN (EC 1.18.       489  0   380    522 FlLelgcePvH
CRTI_RHOCA|P17054     PHYTOENE DEHYDROGENASE (EC 1.3.-.-) (PHYTOENE DESATURASE       486  0   103    524 yTaYgDdAkvk
CYRG_MOUSE|P34902     CYTOKINE RECEPTOR COMMON GAMMA CHAIN PRECURSOR (GAMMA-C        486  0   127    369 FVvQlqdpQKp
SN2L_CAEEL|P41877     POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L                  486  0   623    971 FTvYQfegeny
TRFE_RABIT|P19134     SEROTRANSFERRIN PRECURSOR (SIDEROPHILIN) (BETA-1-METAL B       481  0   457    694 WnnlegkkSCH
RL17_SCHPO|O59794     60S RIBOSOMAL PROTEIN L17 | PS00464                            480  0    43    187 afiflDNvkeH
MAOM_AMAHP|P37224     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 65 KD ISOFORM       477  0   457    623 aIFamsNpTKn
MSH5_YEAST|Q12175     MUTS PROTEIN HOMOLOG 5 | PS00486                               477  0   136    901 WIFdyiktkCd
TRA0_ECOLI|P15025     TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS21                476  0   147    390 rRFhvfaAPKq
YFEH_ECOLI|P39836     HYPOTHETICAL 36.4 KD PROTEIN IN XAPB-LIG INTERGENIC REGI       476  0   194    332 WIaktDqtSIl
YBDM_ECOLI|P77174     HYPOTHETICAL 23.9 KD PROTEIN IN CSTA-DSBG INTERGENIC REG       475  0   184    209 lRLkQiNglqe
DPOM_CLAPU|P22373     PROBABLE DNA POLYMERASE (EC 2.7.7.7) | PS00116                 474  0   911   1063 tlyYtDtDSIv
EUTE_ECOLI|P77445     ETHANOLAMINE UTILIZATION PROTEIN EUTE                          469  0    -1    467  mnQQDieQvv
EUTE_SALTY|P41793     ETHANOLAMINE UTILIZATION PROTEIN EUTE                          469  0    -1    467  mnQQDieQvv
YFJJ_ECOLI|P52125     HYPOTHETICAL 24.6 KD PROTEIN IN ALPA-GABD INTERGENIC REG       469  0    98    208 vReYtkNrkrH
MAON_SOLTU|P37225     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 59 KD ISOFORM       465  0    65    601 isFeQqyDrfm
NRAM_INBHK|P16191     NEURAMINIDASE (EC 3.2.1.18)                                    465  0   378    466 lyvkyDGDPwt
NRAM_INBLN|P16193     NEURAMINIDASE (EC 3.2.1.18)                                    465  0   377    465 lyvkyDGDPwt
NRAM_INBMF|P16199     NEURAMINIDASE (EC 3.2.1.18)                                    465  0   377    465 lyvkyDGDPwt
NRAM_INBOR|P16201     NEURAMINIDASE (EC 3.2.1.18)                                    465  0   378    466 lyvkyDGDPwt
NRAM_INBSI|P16203     NEURAMINIDASE (EC 3.2.1.18)                                    465  0   378    466 lyvkyDGDPwt
NRAM_INBUS|P16205     NEURAMINIDASE (EC 3.2.1.18)                                    465  0   378    466 lyvkyDGDPwt
NRAM_INBVI|P16207     NEURAMINIDASE (EC 3.2.1.18)                                    465  0   377    465 lyvkyDGDPwt
NRAM_INBYB|Q90021     NEURAMINIDASE (EC 3.2.1.18)                                    465  0   378    466 lyvkyDGDPwt
MAOX_POPTR|P34105     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)        463  0   484    591 FVpgQsNnayi
NRAM_INBBE|P27907     NEURAMINIDASE (EC 3.2.1.18)                                    463  0   377    465 lyvryDGDPwt
YDF7_SCHPO|Q10479     PUTATIVE GLUCOSYLTRANSFERASE C17C9.07 (EC 2.4.1.-)             461  0   400    501 llFtlneAPIk
MAOX_MESCR|P37223     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)        460  0   377    585 eTLQQfklPwa
MAOC_LYCES|P37222     MALATE OXIDOREDUCTASE, CHLOROPLAST (EC 1.1.1.4 (FRAGMENT       458  0   272    573 FnLlakygTSH
MAOX_VITVI|P51615     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)        457  0   484    591 FVpgQaNnayi
PSRC_WOLSU|P31077     POLYSULFIDE REDUCTASE CHAIN C (SULPHUR REDUCTASE CHAIN C       457  0   234    317 gmyYQgGsTae
GYRB_ACIS8|Q44275     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       456  0   142    216 FlvegDsAggs
MAOM_SOLTU|P37221     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 62 KD ISOFORM       456  0   443    626 FskevleAlKH
NUCL_HUMAN|P19338     NUCLEOLIN (PROTEIN C23) | PS00030                              456  0   685    706 FRggrgGggdH
NOD1_RHIGA|P50331     NODULATION PROTEIN D I | PS00044                               454  0   128    310 elLplDdDPde
GLO2_HUMAN|Q16775     HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6) (GLYOXALAS       450  0   224    260 mRvrektvQqH
GYRB_ACIJO|Q44081     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       447  0    71    216 tIFnvDilarR
GYRB_ACIS1|Q44272     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       447  0    71    216 tIFnvDilarR
GYRB_ACIS6|Q44277     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       445  0    66    216 lTFsQtifSvd
GSHC_SCHMA|Q00277     GLUTATHIONE PEROXIDASE (EC 1.11.1.9) (GPX) | PS00460 | P       443  0    93    169 ygvQfDmfSKi
YNC4_YEAST|P53970     HYPOTHETICAL 27.7 KD PROTEIN IN UME3-HDA1 INTERGENIC REG       422  0    34    246 lkiceDGgeSg
blimps-3.9/examples/blimps/distribution/exampleD.blk.bli000064400001460000012000000256221062461201400237720ustar00jorjastaff00000400000027BLIMPS (BLocks IMProved Searcher)   Version 3.8  2006/04
(C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center



Block File: exampleD.blk

Target File (s) : example.pros

Records Searched:   89

Scores Done:                      89

Alignments Done:               60014

AC#                    Description                                                Score RF  AA# Length
TC1A_CAEEL|P03934     TRANSPOSABLE ELEMENT TC1 TRANSPOSASE                          1107  0   200    273 WPSQSPDLNPIEHLW
TC2A_CAEBR|Q04202     TRANSPOSABLE ELEMENT TCB2 TRANSPOSASE                         1107  0   200    273 WPSQSPDLNPIEHLW
TC1A_CAEBR|P35072     TRANSPOSABLE ELEMENT TCB1 TRANSPOSASE (TRANSPOSABLE ELEM      1100  0   200    273 WPSQSPDLNPIEHMW
TC3A_CAEEL|P34257     TRANSPOSABLE ELEMENT TC3 TRANSPOSASE                          1094  0   254    329 WPARSPDLNPIENLW
CYRG_MOUSE|P34902     CYTOKINE RECEPTOR COMMON GAMMA CHAIN PRECURSOR (GAMMA-C        686  0   282    369 WleRmPpipPIkNLe
RPOC_TREPA|O83270     DNA-DIRECTED RNA POLYMERASE BETA' CHAIN (EC 2.7.7.6) (TR       678  0   230   1416 iPviPPDLrPmvqLd
RPOD_ORYSA|P12093     DNA-DIRECTED RNA POLYMERASE BETA" CHAIN (EC 2.7.7.6)           672  0  1319   1513 aQSRiSlVNkIqkVY
MAOM_AMAHP|P37224     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 65 KD ISOFORM       667  0   276    623 WPnvivqfedIqNkW
VIL1_MOUSE|Q62468     VILLIN                                                         644  0   401    826 WriedleLvPvEskW
YDF7_SCHPO|Q10479     PUTATIVE GLUCOSYLTRANSFERASE C17C9.07 (EC 2.4.1.-)             637  0   136    501 diflSPgLlIIdHIh
LEF4_NPVAC|P41477     LATE EXPRESSION FACTOR 4                                       636  0    53    464 iPiQSacnNIIssVk
SIN3_YEAST|P22579     PAIRED AMPHIPATHIC HELIX PROTEIN                               635  0   827   1536 iQcletiVNkIENMt
EUTE_ECOLI|P77445     ETHANOLAMINE UTILIZATION PROTEIN EUTE                          634  0   132    467 tPStnPaatVInNai
EUTE_SALTY|P41793     ETHANOLAMINE UTILIZATION PROTEIN EUTE                          634  0   132    467 tPStnPaatVInNai
PH81_YEAST|P17442     PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO81 (CDK        633  0    84   1178 ylAReSDLrIkfNIl
YCF2_MARPO|P09975     HYPOTHETICAL 259 KD PROTEIN (ORF 2136)                         629  0   539   2136 nkikSSDnfrfiNLW
NRAM_INBOR|P16201     NEURAMINIDASE (EC 3.2.1.18)                                    627  0    46    466 aPtmSlDcanIsNVq
GYRB_ACICA|Q43947     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       626  0    62    216 WPSeltftqtIfNVe
PPS2_BACSU|P39846     PEPTIDE SYNTHETASE 2 | PS00012 | PS00455 | PS50075             623  0  1343   2560 hktfSSyLhdIrHLa
PTP1_DROME|P35992     PROTEIN-TYROSINE PHOSPHATASE 10D PRECURSOR (EC 3.1.3.48)       619  0   706   1630 WPSdnPgrvqtkNVs
NIFK_AZOVI|P07329     NITROGENASE MOLYBDENUM-IRON PROTEIN BETA CHAIN (EC 1.18.       617  0   307    522 WkhevPkLNIpmgLd
MAOM_SOLTU|P37221     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 62 KD ISOFORM       615  0   458    626 rPAifPmsNPtrNae
GYRB_ACIJO|Q44081     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       614  0    62    216 WPSaetfsqtIfNVd
GYRB_ACIS1|Q44272     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       614  0    62    216 WPSaetfsqtIfNVd
GYRB_ACIS8|Q44275     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       614  0    62    216 WPSaetfsqtIfNVd
SPCB_DROME|Q00963     SPECTRIN BETA CHAIN | PS00019 | PS00020 | PS50003              612  0  2006   2291 WeeRwenLqlIleVY
MAON_SOLTU|P37225     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 59 KD ISOFORM       608  0   477    601 gngkigHVNqanNMY
ITA2_BOVIN|P53710     PLATELET MEMBRANE GLYCOPROTEIN IA PRECURSOR (G (FRAGMENT       607  0   981   1170 iPqytkDkNPlmyLt
ACVS_EMENI|P27742     DELTA-(L-ALPHA-AMINOADIPYL)-L-CYSTEINYL-D-VALINE SYNTHET       606  0  2768   3770 nklRSgfrgPIyNaY
YFEH_ECOLI|P39836     HYPOTHETICAL 36.4 KD PROTEIN IN XAPB-LIG INTERGENIC REGI       606  0    23    332 fPARgdfVpffENLt
YP22_YEAST|Q08968     HYPOTHETICAL 78.3 KD PROTEIN IN SSM1-GRE1 INTERGENIC REG       606  0   630    688 dPSselDtSalkkLY
YPB4_CAEEL|Q11107     HYPOTHETICAL ZINC FINGER PROTEIN B03B8.4 IN CHROMOSOME I       606  0  1971   2111 fPAdvnqdqVIaHIl
TYRA_HAEIN|P43902     CHORISMATE MUTASE (EC 5.4.99.5) (CM) / PREPHENATE DEHYDR       605  0   309    377 imdkSenLaVIEtLk
YOUG_BACLI|Q45292     HYPOTHETICAL 17.3 KD PROTEIN IN GNTR 5'REGION                  602  0   104    147 ihPfiPnLSfIkNkr
GLND_MYCTU|Q10961     PROBABLE [PROTEIN-PII] URIDYLYLTRANSFERASE (EC 2.7.7.59)       601  0   405    808 WgrllPewePIrdLp
YO96_CAEEL|P41846     HYPOTHETICAL 93.9 KD PROTEIN T20B12.6 IN CHROMOSOME III        598  0   412    843 pQShdPmmaPsrswW
TRFE_RABIT|P19134     SEROTRANSFERRIN PRECURSOR (SIDEROPHILIN) (BETA-1-METAL B       592  0   361    694 WcAlShHerlkcdeW
YDIL_ECOLI|P76196     HYPOTHETICAL 15.0 KD PROTEIN IN LPP-AROD INTERGENIC REGI       592  0    95    127 fQrvyPDgNfIdwki
MAOC_FLAPR|P36444     MALATE OXIDOREDUCTASE, CHLOROPLAST PRECURSOR (EC 1.1.1.4       590  0    19    647 tQSQSvrLSVrrpMv
GLGA_METJA|Q59001     PROBABLE GLYCOGEN SYNTHASE (EC 2.4.1.21) (STARCH [BACTER       588  0   473    521 ydeNSPlsmmmkNcY
NRAM_INBHK|P16191     NEURAMINIDASE (EC 3.2.1.18)                                    586  0    46    466 aPtmSlDcanvsNVq
NRAM_INBSI|P16203     NEURAMINIDASE (EC 3.2.1.18)                                    586  0    46    466 aPtmSlDcanvsNVq
DPOM_CLAPU|P22373     PROBABLE DNA POLYMERASE (EC 2.7.7.7) | PS00116                 584  0   332   1063 WtringnfNtlyNLe
NOD1_RHIGA|P50331     NODULATION PROTEIN D I | PS00044                               584  0    33    310 qPAmSaaiarlrNyf
TRA0_ECOLI|P15025     TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS21                584  0   360    390 WQtvPeHhaPlwqqv
Y08F_MYCTU|Q11052     PROBABLE REGULATORY PROTEIN CY50.15 | PS50006                  584  0   130    388 feqaSrHLSaalreW
OE66_NPVAC|Q00704     OCCLUSION-DERIVED VIRUS ENVELOPE PROTEIN E66 (ODV-E66)         583  0   144    704 yQnPelayNlIngLr
PARF_PARTE|P47244     PARAFUSIN | PS00710                                            582  0   404    582 fgtgSnHirekdgIW
RL17_SCHPO|O59794     60S RIBOSOMAL PROTEIN L17 | PS00464                            581  0   138    187 ylSsPSHieIIvaee
SN2L_CAEEL|P41877     POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L                  580  0   247    971 litgtPlqNnlheLW
RFAB_ECOLI|P27127     LIPOPOLYSACCHARIDE 1,6-GALACTOSYLTRANSFERASE (EC 2.4.1.-       578  0   232    369 cQAygreLNIddrIv
MAOX_PHAVU|P12628     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)        577  0   174    589 WPekSiqViVvtdge
MAOX_POPTR|P34105     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)        576  0   176    591 WPqkSiqViVvtdge
OE66_NPVOP|O10305     OCCLUSION-DERIVED VIRUS ENVELOPE PROTEIN E66 (ODV-E66)         575  0   255    682 gnglhPDsiyIdHLd
TRA0_SHISO|P16944     TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS640               575  0    56    315 pfmdyiDmrlaENVW
ITA2_HUMAN|P17301     PLATELET MEMBRANE GLYCOPROTEIN IA PRECURSOR (GPIA) (COLL       574  0   162   1181 sPAtqPcpSlIdvVv
NRAM_INBBE|P27907     NEURAMINIDASE (EC 3.2.1.18)                                    574  0   141    465 yngtreDrNklrHLi
NRAM_INBLN|P16193     NEURAMINIDASE (EC 3.2.1.18)                                    574  0   141    465 yngtreDrNklrHLi
NRAM_INBMF|P16199     NEURAMINIDASE (EC 3.2.1.18)                                    574  0   141    465 yngtreDrNklrHLi
NRAM_INBUS|P16205     NEURAMINIDASE (EC 3.2.1.18)                                    574  0   142    466 yngtreDrNklrHLi
NRAM_INBVI|P16207     NEURAMINIDASE (EC 3.2.1.18)                                    574  0   141    465 yngtreDrNklrHLi
NRAM_INBYB|Q90021     NEURAMINIDASE (EC 3.2.1.18)                                    574  0   142    466 yngtreDrNklrHLi
MA2X_HUMAN|P49641     ALPHA-MANNOSIDASE IIX (EC 3.2.1.114) (MANNOSYL-OLIGOSACC       573  0   992   1139 stSyPSlLShltsMY
GYRB_ACIS6|Q44277     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       571  0   161    216 mQAilPlkgkIlNVe
GYRB_ACIS9|Q44276     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177       571  0   161    216 mQAilPlkgkIlNVe
YNC4_YEAST|P53970     HYPOTHETICAL 27.7 KD PROTEIN IN UME3-HDA1 INTERGENIC REG       571  0   143    246 gePlSaDfSPqEgam
CP4C_BLADI|P29981     CYTOCHROME P450 4C1 (EC 1.14.14.1) (CYPIVC1) | PS00086         570  0   126    511 WhShrkmitPtfHfk
DHA6_YEAST|P54115     ALDEHYDE DEHYDROGENASE, CYTOSOLIC (EC 1.2.1.3) | PS00070       569  0    99    501 leSQidlVSsIEaLd
MSH5_YEAST|Q12175     MUTS PROTEIN HOMOLOG 5 | PS00486                               569  0   490    901 svlmePlLdgIpNLq
KINN_HUMAN|Q12840     NEURONAL KINESIN HEAVY CHAIN (NKHC) | PS00411 | PS50067        567  0   255   1032 nkSlSalgNVIsaLa
KINN_MOUSE|P28738     NEURONAL KINESIN HEAVY CHAIN (NKHC) | PS00411 | PS50067        567  0   255   1027 nkSlSalgNVIsaLa
YQHN_BACSU|P54512     HYPOTHETICAL 16.7 KD PROTEIN IN GCVT-SPOIIIAA INTERGENIC       564  0   122    142 ddARkkDLksIqkkt
NUCL_MOUSE|P09405     NUCLEOLIN (PROTEIN C23) | PS00030                              560  0   512    706 kvPQnPHgkPkgyaf
HBB1_TRICR|P10785     HEMOGLOBIN BETA-1 CHAIN (MAJOR) | PS01033                      555  0    79    145 lkAyyaDLStIhckk
CRTI_RHOCA|P17054     PHYTOENE DEHYDROGENASE (EC 1.3.-.-) (PHYTOENE DESATURASE       552  0   132    524 WdAkaryefgyENLg
GSHC_SCHMA|Q00277     GLUTATHIONE PEROXIDASE (EC 1.11.1.9) (GPX) | PS00460 | P       552  0    25    169 lekyrgHVclIvNVa
HOFB_HAEIN|P44622     PROTEIN TRANSPORT PROTEIN HOFB HOMOLOG | PS00662               552  0   321    464 flrQdPDiimlgeIr
MAOX_VITVI|P51615     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)        550  0   575    591 kyAeScmySPvyrsY
PSRC_WOLSU|P31077     POLYSULFIDE REDUCTASE CHAIN C (SULPHUR REDUCTASE CHAIN C       549  0   123    317 degPfgfLaPlaNIa
GLO2_HUMAN|Q16775     HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6) (GLYOXALAS       542  0   122    260 ggSePPaVftgdtLf
MAOC_LYCES|P37222     MALATE OXIDOREDUCTASE, CHLOROPLAST (EC 1.1.1.4 (FRAGMENT       539  0   513    573 nfekgtHipPfsNIr
YFJJ_ECOLI|P52125     HYPOTHETICAL 24.6 KD PROTEIN IN ALPA-GABD INTERGENIC REG       539  0   174    208 eQtySdlmNrvdyMt
AST5_DROME|P10083     ACHAETE-SCUTE COMPLEX PROTEIN T5 (ACHAETE) | PS00038           536  0   151    201 atStiPgatPpnNfh
YENR_YEREN|P54295     YENR REGULATORY PROTEIN | PS00622                              536  0    36    244 nkktPlHptIIsNyp
MAOX_MESCR|P37223     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)        535  0   170    585 WPekkiqViVvtdge
YBDM_ECOLI|P77174     HYPOTHETICAL 23.9 KD PROTEIN IN CSTA-DSBG INTERGENIC REG       529  0    55    209 sQlmPnDyNPnnvap
NUCL_HUMAN|P19338     NUCLEOLIN (PROTEIN C23) | PS00030                              527  0   479    706 WsgeSktLvlsnlsY
YM8I_YEAST|Q03529     HYPOTHETICAL 44.9 KD PROTEIN IN URA10-NRC1 INTERGENIC RE       519  0   279    384 rlvmPPtLfVIlcap
THIS_ECOLI|O32583     THIS PROTEIN                                                   480  0    36     66 nQqivPreqwaqHIv
            644  0   401    826 WriedleLvPvEskW
YDF7_SCHPO|Q10479     PUTATIVE GLUCOSYLTRANSFERASE C17C9.07 (Eblimps-3.9/examples/blimps/distribution/exampleE.blk.bli000064400001460000012000000314671062461201400237770ustar00jorjastaff00000400000027BLIMPS (BLocks IMProved Searcher)   Version 3.8  2006/04
(C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center



Block File: exampleE.blk

Target File (s) : example.pros

Records Searched:   89

Scores Done:                      89

Alignments Done:               61972

AC#                    Description                                                Score RF  AA# Length
TC1A_CAEBR|P35072     TRANSPOSABLE ELEMENT TCB1 TRANSPOSASE (TRANSPOSABLE ELEM      2351  0   236    273 LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY
TC2A_CAEBR|Q04202     TRANSPOSABLE ELEMENT TCB2 TRANSPOSASE                         2348  0   236    273 LQDVWQAIPMSVIDTILDSMPRRCQTVIDAKGFPTKY
TC1A_CAEEL|P03934     TRANSPOSABLE ELEMENT TC1 TRANSPOSASE                          2338  0   236    273 LENAWKAIPMSVIHKLIDSMPRRCQAVIDANGYATKY
TC3A_CAEEL|P34257     TRANSPOSABLE ELEMENT TC3 TRANSPOSASE                          2210  0   292    329 ILDAWKSIPDNQLKSLVRSMEDRLIEIIRTQGNPINY
DPOM_CLAPU|P22373     PROBABLE DNA POLYMERASE (EC 2.7.7.7) | PS00116                1558  0   932   1063 hQtEigKLkLEHTiTqgyFIaDktyAIvnTeGeiIKr
ACVS_EMENI|P27742     DELTA-(L-ALPHA-AMINOADIPYL)-L-CYSTEINYL-D-VALINE SYNTHET      1557  0  2964   3770 LAhMkSKLPaymVpKyLcrlEgGLpvtIngKlDVrKl
HOFB_HAEIN|P44622     PROTEIN TRANSPORT PROTEIN HOFB HOMOLOG | PS00662              1548  0   275    464 tAlqWlntPDKHImTaeDpIEieLdgIIQsQiNPqig
SPCB_DROME|Q00963     SPECTRIN BETA CHAIN | PS00019 | PS00020 | PS50003             1546  0  1863   2291 IQEEsAKLqDayAgDkakeItNReQEVLhAwdNlqam
GLGA_METJA|Q59001     PROBABLE GLYCOGEN SYNTHASE (EC 2.4.1.21) (STARCH [BACTER      1539  0    92    521 nLNVWDpIkyEifaDLVitylDeVKdIdvvsGhdwmc
YP22_YEAST|Q08968     HYPOTHETICAL 78.3 KD PROTEIN IN SSM1-GRE1 INTERGENIC REG      1536  0   403    688 LElllKgelnSVdDaLektMieRVQklvelsaNeyKY
MA2X_HUMAN|P49641     ALPHA-MANNOSIDASE IIX (EC 3.2.1.114) (MANNOSYL-OLIGOSACC      1526  0   179   1139 wikTfDKyytEQTQhILnSMvskLQEDpRrrflwAev
NIFK_AZOVI|P07329     NITROGENASE MOLYBDENUM-IRON PROTEIN BETA CHAIN (EC 1.18.      1523  0   377    522 LvkflleLgcEPVHiLchngNKRwKkavDAilaAspY
Y08F_MYCTU|Q11052     PROBABLE REGULATORY PROTEIN CY50.15 | PS50006                 1519  0    55    388 ItAlWeewPPSgARasIhSyvsnLrklLggaGidprv
CRTI_RHOCA|P17054     PHYTOENE DEHYDROGENASE (EC 1.3.-.-) (PHYTOENE DESATURASE      1514  0   345    524 VQDIfiKgeLaedmSLyvhrPsvtdptaApKGDdTfY
TRFE_RABIT|P19134     SEROTRANSFERRIN PRECURSOR (SIDEROPHILIN) (BETA-1-METAL B      1511  0   626    694 VADcsSKfcMfHsKTkdllfrDdtKClvDlrGknTye
ITA2_BOVIN|P53710     PLATELET MEMBRANE GLYCOPROTEIN IA PRECURSOR (G (FRAGMENT      1507  0   642   1170 dvsVdASfTPKkItlLnknaEikLKlcfsAKfrPTNq
TYRA_HAEIN|P43902     CHORISMATE MUTASE (EC 5.4.99.5) (CM) / PREPHENATE DEHYDR      1504  0    60    377 LEAEkAgISadlIeDvLRrfmResyAnenqfGFkTin
YCF2_MARPO|P09975     HYPOTHETICAL 259 KD PROTEIN (ORF 2136)                        1504  0   458   2136 ILffkQKnSkSFnKNLVkknsKdVITnvfsKeNkIei
LEF4_NPVAC|P41477     LATE EXPRESSION FACTOR 4                                      1502  0   327    464 gvNAsyAIdPvTAiecInyMNNnVQsVtlTdtcPAie
PPS2_BACSU|P39846     PEPTIDE SYNTHETASE 2 | PS00012 | PS00455 | PS50075            1502  0   750   2560 LANEygptenSVAtTILRhlNKkeritIghpirnTKv
TRA0_SHISO|P16944     TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS640              1500  0   260    315 IADVaDKreLrQfKetpEqrsRwsrnIcsvtGYrlrY
GLND_MYCTU|Q10961     PROBABLE [PROTEIN-PII] URIDYLYLTRANSFERASE (EC 2.7.7.59)      1498  0   545    808 skATgpgvwsdwkaSLVDdlvRRCrmVMAgeslPqae
RPOD_ORYSA|P12093     DNA-DIRECTED RNA POLYMERASE BETA" CHAIN (EC 2.7.7.6)          1498  0   888   1513 VyvqWKKIlkSkeKyfVlvrPavayEmnegrnlATlF
MAOX_MESCR|P37223     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)       1496  0   396    585 LiDAvQAIkPTVLigtsgkgkqftKEVveAmaNinak
GYRB_ACICA|Q43947     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177      1490  0   138    216 LsElylvegDSaggSakqgrNRkmQAILplKGkilNv
GYRB_ACIJO|Q44081     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177      1490  0   138    216 LsElylvegDSaggSakqgrNRkmQAILplKGkilNv
GYRB_ACIS1|Q44272     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177      1490  0   138    216 LsElylvegDSaggSakqgrNRkmQAILplKGkilNv
GYRB_ACIS6|Q44277     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177      1490  0   138    216 LsElylvegDSaggSakqgrNRkmQAILplKGkilNv
GYRB_ACIS9|Q44276     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177      1490  0   138    216 LsElylvegDSaggSakqgrNRkmQAILplKGkilNv
SN2L_CAEEL|P41877     POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L                 1490  0   906    971 LksrtAmelQrrCnTLItlIERemgEVvesKpvivta
PH81_YEAST|P17442     PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO81 (CDK       1486  0   960   1178 tLkqylSsrvvPLRSLLEvIPgsaQlVIRvyfptdKe
GYRB_ACIS8|Q44275     DNA GYRASE SUBUNIT B (EC 5.99.1.3) (FRAGMENTS) | PS00177      1485  0   138    216 LsElflvegDSaggSakqgrNRkmQAILplKGkilNv
MAOX_VITVI|P51615     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)       1479  0   402    591 LLDAvKvIkPTVLigssgvgkaftKEVIeAmascnek
MAOX_POPTR|P34105     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)       1478  0   169    591 VLDVlKnwPQKsIQvIVvtdgeRilglgDlgcqgIgi
RL17_SCHPO|O59794     60S RIBOSOMAL PROTEIN L17 | PS00464                           1478  0   102    187 eAkglDmdkLiikHvqVnaaPKqrrrtyRAhGrVTaY
YPB4_CAEEL|Q11107     HYPOTHETICAL ZINC FINGER PROTEIN B03B8.4 IN CHROMOSOME I      1478  0  1079   2111 pLAnrvhIqrSHAlTLrRFqcayCIkVfvsvGeyyeh
RPOC_TREPA|O83270     DNA-DIRECTED RNA POLYMERASE BETA' CHAIN (EC 2.7.7.6) (TR      1477  0   659   1416 VvEVWSKtSeElTslmmEtlERdkdgfntiymmATsg
ITA2_HUMAN|P17301     PLATELET MEMBRANE GLYCOPROTEIN IA PRECURSOR (GPIA) (COLL      1474  0   653   1181 dvAIeASfTPEkItlvnknaqiiLKlcfsAKfrPTKq
PARF_PARTE|P47244     PARAFUSIN | PS00710                                           1471  0   341    582 IAAnanlIfkNgLlgaaRSMPtsgalDkvAakNgIKl
MSH5_YEAST|Q12175     MUTS PROTEIN HOMOLOG 5 | PS00486                              1470  0   529    901 ygDIygAISDfeIeiLfSlqEqiLrrktQltaYnIll
RFAB_ECOLI|P27127     LIPOPOLYSACCHARIDE 1,6-GALACTOSYLTRANSFERASE (EC 2.4.1.-      1470  0   333    369 IhiEheKIPaSidefyqSkyyDRLhkVIisaisrrK
YDIL_ECOLI|P76196     HYPOTHETICAL 15.0 KD PROTEIN IN LPP-AROD INTERGENIC REGI      1470  0    32    127 IAqTgDSeSwrQweNgkcaIPDRVvEqLlAmrqqrKk
MAOM_SOLTU|P37221     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 62 KD ISOFORM      1469  0    73    626 IrgllppnvMSFeQqIaRFMaDlkrlevQArdGPsdp
OE66_NPVOP|O10305     OCCLUSION-DERIVED VIRUS ENVELOPE PROTEIN E66 (ODV-E66)        1469  0   370    682 yEAdptnnTQaPLwTmtRrIwNRrarVInyNaNtvmF
MAOC_LYCES|P37222     MALATE OXIDOREDUCTASE, CHLOROPLAST (EC 1.1.1.4 (FRAGMENT      1463  0   385    573 LvNAvKSIkPTVLigssgagrtftKEVvQAmatfnek
MAOX_PHAVU|P12628     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)       1462  0   400    589 LLEAvKAIkPTVLigssgagktftKEVveTmaslnek
DHA6_YEAST|P54115     ALDEHYDE DEHYDROGENASE, CYTOSOLIC (EC 1.2.1.3) | PS00070      1461  0   379    501 VgDkgyfIrPTVfyDvnEdMrivkeEIfgpvvtVAKF
PTP1_DROME|P35992     PROTEIN-TYROSINE PHOSPHATASE 10D PRECURSOR (EC 3.1.3.48)      1460  0   748   1630 IQtTsygIlsgiTslypRtMPliqsdVvvANGekede
KINN_HUMAN|Q12840     NEURONAL KINESIN HEAVY CHAIN (NKHC) | PS00411 | PS50067       1459  0   581   1032 eEfTvArLyiSkIKSeVkSvvKRCrqlenlQvechrk
KINN_MOUSE|P28738     NEURONAL KINESIN HEAVY CHAIN (NKHC) | PS00411 | PS50067       1459  0   581   1027 eEfTvArLyiSkIKSeVkSvvKRCrqlenlQvechrk
MAOM_AMAHP|P37224     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 65 KD ISOFORM      1459  0   418    623 LvEVvrqvkPdVLlgLsaygglfsKEVLeAlkDsTst
MAOC_FLAPR|P36444     MALATE OXIDOREDUCTASE, CHLOROPLAST PRECURSOR (EC 1.1.1.4      1454  0   458    647 fLDAvKAIkPTVLigssgagqtftKEVveAmssfnek
SIN3_YEAST|P22579     PAIRED AMPHIPATHIC HELIX PROTEIN                              1454  0  1134   1536 IfNlfAntniyiffrhwttIyeRLlEIkQmNerVTKe
YFEH_ECOLI|P39836     HYPOTHETICAL 36.4 KD PROTEIN IN XAPB-LIG INTERGENIC REGI      1453  0   216    332 VngIWhKvgwgsLlfIVvvscvlLaiVIvvNvFmArr
YM8I_YEAST|Q03529     HYPOTHETICAL 44.9 KD PROTEIN IN URA10-NRC1 INTERGENIC RE      1453  0   200    384 VpvAWlpvvvyHmgvaLknMNqlfaCfLfcvGvfvwt
AST5_DROME|P10083     ACHAETE-SCUTE COMPLEX PROTEIN T5 (ACHAETE) | PS00038          1450  0    66    201 gpgAnKKLSkvsTlKmaveyiRRLQkVLheNdqqkQk
NUCL_MOUSE|P09405     NUCLEOLIN (PROTEIN C23) | PS00030                             1449  0   149    706 eEDEdDSdeDEddeeedEFePpiVKgVkpAKaaPAap
EUTE_ECOLI|P77445     ETHANOLAMINE UTILIZATION PROTEIN EUTE                         1447  0   261    467 sfDnniicaDEkVlivVDSvaDeLMrlMegQhaVklt
EUTE_SALTY|P41793     ETHANOLAMINE UTILIZATION PROTEIN EUTE                         1447  0   261    467 sfDnniicaDEkVlivVDSvaDeLMrlMegQhaVklt
YO96_CAEEL|P41846     HYPOTHETICAL 93.9 KD PROTEIN T20B12.6 IN CHROMOSOME III       1447  0   729    843 tnAVvlAkSadHIRrLqaekwDktQkIdeAKakieKl
CP4C_BLADI|P29981     CYTOCHROME P450 4C1 (EC 1.14.14.1) (CYPIVC1) | PS00086        1446  0   335    511 IQDkvyeelDhifQgsdRSttmRdlADMKylerVIKe
MAON_SOLTU|P37225     MALATE OXIDOREDUCTASE [NAD], MITOCHONDRIAL 59 KD ISOFORM      1444  0   398    601 LAEVvKKvkPhVLlgLsgvggifheEVLRAmkesdsv
NUCL_HUMAN|P19338     NUCLEOLIN (PROTEIN C23) | PS00030                             1439  0    55    706 aAtsaKKvvvSPTKKvavatPakkaAVtpgKkaAAtp
VIL1_MOUSE|Q62468     VILLIN                                                        1436  0   556    826 cgkgcSgderEmAKmvaDtIsRteKqVvvegqePANF
NOD1_RHIGA|P50331     NODULATION PROTEIN D I | PS00044                              1435  0    82    310 sviAWDpIkPaesDrrfRiIlsdfMTlIfmekvikri
NRAM_INBBE|P27907     NEURAMINIDASE (EC 3.2.1.18)                                   1435  0   352    465 hQrMaSKIgrwysRTmsktermGmelyvRydGDPwtd
NRAM_INBHK|P16191     NEURAMINIDASE (EC 3.2.1.18)                                   1432  0   353    466 hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd
NRAM_INBLN|P16193     NEURAMINIDASE (EC 3.2.1.18)                                   1432  0   352    465 hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd
NRAM_INBMF|P16199     NEURAMINIDASE (EC 3.2.1.18)                                   1432  0   352    465 hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd
NRAM_INBOR|P16201     NEURAMINIDASE (EC 3.2.1.18)                                   1432  0   353    466 hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd
NRAM_INBSI|P16203     NEURAMINIDASE (EC 3.2.1.18)                                   1432  0   353    466 hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd
NRAM_INBUS|P16205     NEURAMINIDASE (EC 3.2.1.18)                                   1432  0   353    466 hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd
NRAM_INBVI|P16207     NEURAMINIDASE (EC 3.2.1.18)                                   1432  0   352    465 hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd
NRAM_INBYB|Q90021     NEURAMINIDASE (EC 3.2.1.18)                                   1432  0   353    466 hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd
OE66_NPVAC|Q00704     OCCLUSION-DERIVED VIRUS ENVELOPE PROTEIN E66 (ODV-E66)        1429  0   393    704 yEsdptnniQaPLwTmaRrIwNRrgrIInyNaNtvsF
YDF7_SCHPO|Q10479     PUTATIVE GLUCOSYLTRANSFERASE C17C9.07 (EC 2.4.1.-)            1428  0   452    501 LfiyncfIhklVmgDkfEFlPlmLlstyAAwGifwsF
YOUG_BACLI|Q45292     HYPOTHETICAL 17.3 KD PROTEIN IN GNTR 5'REGION                 1423  0    55    147 kQNlkDdaPyqkftavgEvsdNRVykVhAgeGFspyr
GLO2_HUMAN|Q16775     HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6) (GLYOXALAS      1420  0    81    260 IgAlthKIThlsTlqvgSlnvKcLaTpchTsGhicyF
YNC4_YEAST|P53970     HYPOTHETICAL 27.7 KD PROTEIN IN UME3-HDA1 INTERGENIC REG      1420  0   112    246 VtDIdKlIPLlkrnieLDevqyeVlArelwwGePlsa
HBB1_TRICR|P10785     HEMOGLOBIN BETA-1 CHAIN (MAJOR) | PS01033                     1417  0    50    145 eAiqhnpkvaSHgaKvmhSIaeaVKhldDlKaYyAdl
CYRG_MOUSE|P34902     CYTOKINE RECEPTOR COMMON GAMMA CHAIN PRECURSOR (GAMMA-C       1416  0   144    369 kLNlqnlviPrapeNLtlSnlsesQleLRwKsrHIKe
YBDM_ECOLI|P77174     HYPOTHETICAL 23.9 KD PROTEIN IN CSTA-DSBG INTERGENIC REG      1413  0   169    209 dnkIgKeLgMdsdevLrlkqiNGLQElfAdrqYsraw
GSHC_SCHMA|Q00277     GLUTATHIONE PEROXIDASE (EC 1.11.1.9) (GPX) | PS00460 | P      1412  0    52    169 LQEMhtrLvgKgLRiLafpcNqfggqepwAeaeikKF
PSRC_WOLSU|P31077     POLYSULFIDE REDUCTASE CHAIN C (SULPHUR REDUCTASE CHAIN C      1411  0   121    317 LcDEgpfgfLaPLaNIaySMaRpLeiVtfvlaigvga
YQHN_BACSU|P54512     HYPOTHETICAL 16.7 KD PROTEIN IN GCVT-SPOIIIAA INTERGENIC      1407  0     5    142 mEDyieqIyMlieeKgyarvsDiaeAlavhpssVTKm
YENR_YEREN|P54295     YENR REGULATORY PROTEIN | PS00622                             1406  0   134    244 sfDErieInkEkIQmLLiithekmlglyQsNsDknen
YFJJ_ECOLI|P52125     HYPOTHETICAL 24.6 KD PROTEIN IN ALPA-GABD INTERGENIC REG      1406  0    41    208 piDTenmdnPfFqprvdSgaisRftsaLKAKlkHdKh
TRA0_ECOLI|P15025     TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS21               1390  0     3    390 rEDfymikqMrQqgayIvdIatqigCseRTvrrylKY
THIS_ECOLI|O32583     THIS PROTEIN                                                  1354  0     5     66 ndqAmQcaagqTVHeLLEqldqRqagaalAinqqIvp
216 LsElflvegDSaggSakqgrNRkmQAILplKGkilNv
MAOX_VITVI|P51615     MALATE OXIDOREDUCTASE (EC 1.1.1.40) (MALIC ENZYME) (ME)       1479  0   402    591 LLDAvKvIkPTVLigssgvgkaftKEVIeAmascnek
MAOX_POPTR|P3410blimps-3.9/examples/blimps/distribution/multimat.dat000064400001460000012000000000551062461201400233130ustar00jorjastaff00000400000027example 89 1000 0 0 0 0 0 1 89 0 -1 0.000000
blimps-3.9/examples/blimps/distribution/multimat.example.err000064400001460000012000000002141041506464700247750ustar00jorjastaff00000400000027Warning: Using default.qij

Warning: Using default.qij

Warning: Using default.qij

Warning: Using default.qij

Warning: Using default.qij

blimps-3.9/examples/blimps/distribution/multimat.out000064400001460000012000003226201062461201400233570ustar00jorjastaff00000400000027MULTIMAT: (C) Copyright 1991 by Fred Hutchinson Cancer Research Center
Version  6/11/00.1

Search results will be compared with example.blocks
Cannot open file none;
search results will not be compared with true positive list.

Reading exampleA.blk.bli...
89 scores read from exampleA

Reading exampleB.blk.bli...
89 scores read from exampleB

Reading exampleC.blk.bli...
89 scores read from exampleC

Reading exampleD.blk.bli...
89 scores read from exampleD

Reading exampleE.blk.bli...
89 scores read from exampleE
AC family name = example


Top 1000 sequences sorted by maximum normalized score:
(the normalized score is the Score divided by the
99.5 score in the block if available, or by the
smallest Score in the search results file for the block)

Block     Rank Frame Score      Location(aa) Sequence
1.----------------------------------------------------------------------------------
exampleA     2   0    1496       53-     98 TC1A_CAEEL|P03934    TRANSPOSABLE ELEMEN
exampleB     2   0    2012      122-    132 TC1A_CAEEL|P03934    TRANSPOSABLE ELEMEN
exampleC     2   0    2130      172-    182 TC1A_CAEEL|P03934    TRANSPOSABLE ELEMEN
exampleD     1   0    2306      201-    215 TC1A_CAEEL|P03934    TRANSPOSABLE ELEMEN
exampleE     3   0    1727      237-    273 TC1A_CAEEL|P03934    TRANSPOSABLE ELEMEN

P<2.9e-09 for exampleB exampleA exampleC exampleE in support of exampleD
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
TC1A_CAEEL|P03934    AAAAAAAAAAAA::::::BBB::::::::::CCC:::::DDDD::::::EEEEEEEEEE


exampleA              <->A    (52,155):52                                      
TC1A_CAEEL               53   KKPFISKKNRMARVAWAKAHLRWGRQEWAKHIWSDESKFNLFGSDG   
                              ||||||||||||||||||||||||||||||||||||||||||||||   
TC1A_CAEEL|P03934        53   KKPFISKKNRMARVAWAKAHLRWGRQEWAKHIWSDESKFNLFGSDG   

exampleB             A<->B    (20,24):23    
TC1A_CAEBR              122   GGGSVMVWGCF   
                              |||||||||||   
TC1A_CAEEL|P03934       122   GGGSVMVWGCF   

exampleC             B<->C    (39,40):39    
TC1A_CAEEL              172   FVFQQDNDPKH   
                              |||||||||||   
TC1A_CAEEL|P03934       172   FVFQQDNDPKH   

exampleD             C<->D    (18,18):18        
TC1A_CAEEL              201   WPSQSPDLNPIEHLW   
                              |||||||||||||||   
TC1A_CAEEL|P03934       201   WPSQSPDLNPIEHLW   

exampleE             D<->E    (17,23):21                              
TC1A_CAEEL              237   LENAWKAIPMSVIHKLIDSMPRRCQAVIDANGYATKY   
                              |||||||||||||||||||||||||||||||||||||   
TC1A_CAEEL|P03934       237   LENAWKAIPMSVIHKLIDSMPRRCQAVIDANGYATKY   

2.----------------------------------------------------------------------------------
exampleA     3   0    1478       53-     98 TC2A_CAEBR|Q04202    TRANSPOSABLE ELEMEN
exampleB     3   0    2012      122-    132 TC2A_CAEBR|Q04202    TRANSPOSABLE ELEMEN
exampleC     3   0    2130      172-    182 TC2A_CAEBR|Q04202    TRANSPOSABLE ELEMEN
exampleD     2   0    2306      201-    215 TC2A_CAEBR|Q04202    TRANSPOSABLE ELEMEN
exampleE     2   0    1734      237-    273 TC2A_CAEBR|Q04202    TRANSPOSABLE ELEMEN

P<3.2e-08 for exampleD exampleA exampleB exampleC in support of exampleE
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
TC2A_CAEBR|Q04202    A    (52,155):52                                      
TC2A_CAEBR               53   KKPSISKKNRIARVAWARAHLHWGRQDWANHVFSDESKFNLFGTDG   
                              ||||||||||||||||||||||||||||||||||||||||||||||   
TC2A_CAEBR|Q04202        53   KKPSISKKNRIARVAWARAHLHWGRQDWANHVFSDESKFNLFGTDG   

exampleB             A<->B    (20,24):23    
TC1A_CAEBR              122   GGGSVMVWGCF   
                              |||||||||||   
TC2A_CAEBR|Q04202       122   GGGSVMVWGCF   

exampleC             B<->C    (39,40):39    
TC1A_CAEEL              172   FVFQQDNDPKH   
                              |||||||||||   
TC2A_CAEBR|Q04202       172   FVFQQDNDPKH   

exampleD             C<->D    (18,18):18        
TC1A_CAEEL              201   WPSQSPDLNPIEHLW   
                              |||||||||||||||   
TC2A_CAEBR|Q04202       201   WPSQSPDLNPIEHLW   

exampleE             D<->E    (17,23):21                              
TC2A_CAEBR              237   LQDVWQAIPMSVIDTILDSMPRRCQTVIDAKGFPTKY   
                              |||||||||||||||||||||||||||||||||||||   
TC2A_CAEBR|Q04202       237   LQDVWQAIPMSVIDTILDSMPRRCQTVIDAKGFPTKY   

3.----------------------------------------------------------------------------------
exampleA     1   0    1496       53-     98 TC1A_CAEBR|P35072    TRANSPOSABLE ELEMEN
exampleB     1   0    2012      122-    132 TC1A_CAEBR|P35072    TRANSPOSABLE ELEMEN
exampleC     1   0    2164      172-    182 TC1A_CAEBR|P35072    TRANSPOSABLE ELEMEN
exampleD     3   0    2292      201-    215 TC1A_CAEBR|P35072    TRANSPOSABLE ELEMEN
exampleE     1   0    1736      237-    273 TC1A_CAEBR|P35072    TRANSPOSABLE ELEMEN

P<1.8e-09 for exampleB exampleC exampleE exampleD in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
TC1A_CAEBR|P35072    AAAAAAAAAAAA::::::BBB::::::::::CCC:::::DDDD::::::EEEEEEEEEE


exampleA              <->A    (52,155):52                                      
TC1A_CAEBR               53   KKPLVSLKNRKARVEWAKQHLSWGPREWANHIWSDESKFNMFGTDG   
                              ||||||||||||||||||||||||||||||||||||||||||||||   
TC1A_CAEBR|P35072        53   KKPLVSLKNRKARVEWAKQHLSWGPREWANHIWSDESKFNMFGTDG   

exampleB             A<->B    (20,24):23    
TC1A_CAEBR              122   GGGSVMVWGCF   
                              |||||||||||   
TC1A_CAEBR|P35072       122   GGGSVMVWGCF   

exampleC             B<->C    (39,40):39    
TC1A_CAEBR              172   WVFQQDNDPKH   
                              |||||||||||   
TC1A_CAEBR|P35072       172   WVFQQDNDPKH   

exampleD             C<->D    (18,18):18        
TC1A_CAEBR              201   WPSQSPDLNPIEHMW   
                              |||||||||||||||   
TC1A_CAEBR|P35072       201   WPSQSPDLNPIEHMW   

exampleE             D<->E    (17,23):21                              
TC1A_CAEBR              237   LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY   
                              |||||||||||||||||||||||||||||||||||||   
TC1A_CAEBR|P35072       237   LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY   

4.----------------------------------------------------------------------------------
exampleA     4   0    1371      110-    155 TC3A_CAEEL|P34257    TRANSPOSABLE ELEMEN
exampleB     4   0    1886      176-    186 TC3A_CAEEL|P34257    TRANSPOSABLE ELEMEN
exampleC     4   0    2007      226-    236 TC3A_CAEEL|P34257    TRANSPOSABLE ELEMEN
exampleD     4   0    2279      255-    269 TC3A_CAEEL|P34257    TRANSPOSABLE ELEMEN
exampleE     4   0    1632      293-    329 TC3A_CAEEL|P34257    TRANSPOSABLE ELEMEN

P<7.3e-08 for exampleB exampleC exampleD exampleE in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
TC3A_CAEEL|P34257    AAAAAAAAAAAA:::::BBB::::::::::CCC:::::DDDD::::::EEEEEEEEEE


exampleA              <->A    (52,155):109                                     
TC3A_CAEEL              110   KLRPAPLLSADHKLKRLEFAKNNMGTNWSKVVFSDEKKFNLDGPDG   
                              ||||||||||||||||||||||||||||||||||||||||||||||   
TC3A_CAEEL|P34257       110   KLRPAPLLSADHKLKRLEFAKNNMGTNWSKVVFSDEKKFNLDGPDG   

exampleB             A<->B    (20,24):20    
TC3A_CAEEL              176   GGGTVMVWGAF   
                              |||||||||||   
TC3A_CAEEL|P34257       176   GGGTVMVWGAF   

exampleC             B<->C    (39,40):39    
TC3A_CAEEL              226   FRFQQDNATIH   
                              |||||||||||   
TC3A_CAEEL|P34257       226   FRFQQDNATIH   

exampleD             C<->D    (18,18):18        
TC3A_CAEEL              255   WPARSPDLNPIENLW   
                              |||||||||||||||   
TC3A_CAEEL|P34257       255   WPARSPDLNPIENLW   

exampleE             D<->E    (17,23):23                              
TC3A_CAEEL              293   ILDAWKSIPDNQLKSLVRSMEDRLIEIIRTQGNPINY   
                              |||||||||||||||||||||||||||||||||||||   
TC3A_CAEEL|P34257       293   ILDAWKSIPDNQLKSLVRSMEDRLIEIIRTQGNPINY   

5.----------------------------------------------------------------------------------
exampleA    55   0    1007      171-    216 CYRG_MOUSE|P34902    CYTOKINE RECEPTOR C
exampleB    82   0    1062      303-    313 CYRG_MOUSE|P34902    CYTOKINE RECEPTOR C
exampleC    51   0    1152      128-    138 CYRG_MOUSE|P34902    CYTOKINE RECEPTOR C
exampleD     5   0    1429      283-    297 CYRG_MOUSE|P34902    CYTOKINE RECEPTOR C
exampleE    81   0    1046      145-    181 CYRG_MOUSE|P34902    CYTOKINE RECEPTOR C

P<  0.31 for exampleA in support of exampleD
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
CYRG_MOUSE|P34902    <::::::::AAAAAAAAAAAA::::::::::::::::::DDDD
CYRG_MOUSE|P34902                                                                                    BBB                                                                                  BBB


exampleA              <->A    (52,155):170                                     
Minos                   156   EKPLLTLRQKKKRLQWARERMSWTQRQWDTIIFSDEAKFDVSVGDT   
                              |        |   ||      |   | |   |   |  |     |    
CYRG_MOUSE|P34902       171   ELRwkSrhiKercLQyLvQYrSNrdRsWtelIvnhEprFsLpsvDe   

exampleD             A<->D    (99,104):66       
TC3A_CAEEL              255   WPARSPDLNPIENLW   
                              |  | |   || ||    
CYRG_MOUSE|P34902       283   WleRmPpipPIkNLe   

6.----------------------------------------------------------------------------------
exampleA    76   0    1003      566-    611 RPOC_TREPA|O83270    DNA-DIRECTED RNA PO
exampleB     6   0    1326       51-     61 RPOC_TREPA|O83270    DNA-DIRECTED RNA PO
exampleC    26   0    1227     1278-   1288 RPOC_TREPA|O83270    DNA-DIRECTED RNA PO
exampleD     6   0    1413      231-    245 RPOC_TREPA|O83270    DNA-DIRECTED RNA PO
exampleE    37   0    1091      660-    696 RPOC_TREPA|O83270    DNA-DIRECTED RNA PO

No P-value computed for single block hits.

exampleD              <->D    (197,305):230     
TC1A_CAEEL              201   WPSQSPDLNPIEHLW   
                               |   ||| |   |    
RPOC_TREPA|O83270       231   iPviPPDLrPmvqLd   

7.----------------------------------------------------------------------------------
exampleA     7   0    1035      866-    911 RPOD_ORYSA|P12093    DNA-DIRECTED RNA PO
exampleB    43   0    1193     1091-   1101 RPOD_ORYSA|P12093    DNA-DIRECTED RNA PO
exampleC    12   0    1303      494-    504 RPOD_ORYSA|P12093    DNA-DIRECTED RNA PO
exampleD     7   0    1400     1320-   1334 RPOD_ORYSA|P12093    DNA-DIRECTED RNA PO
exampleE    23   0    1106      889-    925 RPOD_ORYSA|P12093    DNA-DIRECTED RNA PO

No P-value computed for single block hits.

exampleA              <->A    (52,155):865                                     
TC3A_CAEEL              110   KLRPAPLLSADHKLKRLEFAKNNMGTNWSKVVFSDEKKFNLDGPDG   
                                   ||       |      |     | |   | || | |  |     
RPOD_ORYSA|P12093       866   ggsLIPLereKKdsKesKkReNWvyvQWkKILkSkEKyFvLvrPav   

8.----------------------------------------------------------------------------------
exampleA    26   0    1014      159-    204 MAOM_AMAHP|P37224    MALATE OXIDOREDUCTA
exampleB    80   0    1094      199-    209 MAOM_AMAHP|P37224    MALATE OXIDOREDUCTA
exampleC    55   0    1130      458-    468 MAOM_AMAHP|P37224    MALATE OXIDOREDUCTA
exampleD     8   0    1390      277-    291 MAOM_AMAHP|P37224    MALATE OXIDOREDUCTA
exampleE    51   0    1078      419-    455 MAOM_AMAHP|P37224    MALATE OXIDOREDUCTA

P< 0.088 for exampleA in support of exampleD
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
MAOM_AMAHP|P37224    <:::::::AAAAAAAAAAAA:::::::::::::::::::DDDD
MAOM_AMAHP|P37224                                                        BBB                                                       EEEEEEEEEE CCC                                                      BBB                                                       EEEEEEEEEE CCC


exampleA              <->A    (52,155):158                                     
HB1                      98   KVPLPSPRHIKARLSLAKTYLNWPVSKWRNILWTDGSKIMLFGGTG   
                                |         |        |||      |  |||| |   |  |   
MAOM_AMAHP|P37224       159   rrPrgmyfSsDdRgEmmsmvyNWPaEQvDmIVvTDGSrIlglGdlG   

exampleD             A<->D    (99,104):72       
Minos                   304   WPSNSPDLSPIENIW   
                              ||        | | |   
MAOM_AMAHP|P37224       277   WPnvivqfedIqNkW   

9.----------------------------------------------------------------------------------
exampleA    25   0    1016       65-    110 TYRA_HAEIN|P43902    CHORISMATE MUTASE (
exampleB    60   0    1131      229-    239 TYRA_HAEIN|P43902    CHORISMATE MUTASE (
exampleC     5   0    1379      238-    248 TYRA_HAEIN|P43902    CHORISMATE MUTASE (
exampleD    33   0    1260      310-    324 TYRA_HAEIN|P43902    CHORISMATE MUTASE (
exampleE    17   0    1111       61-     97 TYRA_HAEIN|P43902    CHORISMATE MUTASE (

P<   0.1 for exampleA in support of exampleC
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
TYRA_HAEIN|P43902    <::::::::::::::::::::::::::::::CCC
TYRA_HAEIN|P43902                                                                BBB                  DDDD                                                              BBB                  DDDD


exampleA              <->A    (52,155):64                                      
TC3A_CAEEL              110   KLRPAPLLSADHKLKRLEFAKNNMGTNWSKVVFSDEKKFNLDGPDG   
                              |      |  |           |      |   ||  |    |  |   
TYRA_HAEIN|P43902        65   KagisadLieDvlrRFmREsyaNenQFgFKtInSDihKIvIvGGYG   

exampleC             A<->C    (70,75):127   
TC3A_CAEEL              226   FRFQQDNATIH   
                                  | ||| |   
TYRA_HAEIN|P43902       238   akiYQtNATeH   

10.----------------------------------------------------------------------------------
exampleA    14   0    1029       54-     99 GLGA_METJA|Q59001    PROBABLE GLYCOGEN S
exampleB    15   0    1249      478-    488 GLGA_METJA|Q59001    PROBABLE GLYCOGEN S
exampleC     6   0    1370      450-    460 GLGA_METJA|Q59001    PROBABLE GLYCOGEN S
exampleD    40   0    1225      474-    488 GLGA_METJA|Q59001    PROBABLE GLYCOGEN S
exampleE     9   0    1137       93-    129 GLGA_METJA|Q59001    PROBABLE GLYCOGEN S

P< 0.032 for exampleD in support of exampleC
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
GLGA_METJA|Q59001    <::::::::::::::::::::::::::::::CCC:::DDDD
GLGA_METJA|Q59001                                                                                                                                  BBB                                                                                                                                BBB


exampleC              <->C    (168,276):449 
HB1                     218   WTFQQDNDQKR   
                              |||   |       
GLGA_METJA|Q59001       450   WTFYklNeiCm   

exampleD             C<->D    (18,18):13        
Minos                   304   WPSNSPDLSPIENIW   
                                 |||      |     
GLGA_METJA|Q59001       474   ydeNSPlsmmmkNcY   

11.----------------------------------------------------------------------------------
exampleA    54   0    1008     1587-   1632 PPS2_BACSU|P39846    PEPTIDE SYNTHETASE 
exampleB    22   0    1225     2111-   2121 PPS2_BACSU|P39846    PEPTIDE SYNTHETASE 
exampleC     7   0    1351     2100-   2110 PPS2_BACSU|P39846    PEPTIDE SYNTHETASE 
exampleD    19   0    1298     1344-   1358 PPS2_BACSU|P39846    PEPTIDE SYNTHETASE 
exampleE    20   0    1109      751-    787 PPS2_BACSU|P39846    PEPTIDE SYNTHETASE 

No P-value computed for single block hits.

exampleC              <->C    (168,276):2099
Minos                   275   FTFQQDGASSH   
                                | |   | |   
PPS2_BACSU|P39846      2100   WfFsQsleShH   

12.----------------------------------------------------------------------------------
exampleA    83   0    1002      691-    736 VIL1_MOUSE|Q62468    VILLIN             
exampleB     7   0    1321      290-    300 VIL1_MOUSE|Q62468    VILLIN             
exampleC    11   0    1306      636-    646 VIL1_MOUSE|Q62468    VILLIN             
exampleD     9   0    1342      402-    416 VIL1_MOUSE|Q62468    VILLIN             
exampleE    64   0    1061      557-    593 VIL1_MOUSE|Q62468    VILLIN             

P< 0.016 for exampleD in support of exampleB
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
VIL1_MOUSE|Q62468    <:::::::::::::::::BBB:::::::::::::::::::::::::::DDDD
VIL1_MOUSE|Q62468                                                                                                                                                       EEEEEEEEEE           CCC            AAAAAAAAAAAA                                                                                                                                                     EEEEEEEEEE           CCC            AAAAAAAAAAAA


exampleB              <->B    (118,225):289 
HB1                     168   GGPKIMVWACF   
                              || || ||      
VIL1_MOUSE|Q62468       290   GGlKIfVWkgk   

exampleD             B<->D    (68,69):101       
Minos                   304   WPSNSPDLSPIENIW   
                              |      | | |  |   
VIL1_MOUSE|Q62468       402   WriedleLvPvEskW   

13.----------------------------------------------------------------------------------
exampleA    60   0    1006       99-    144 LEF4_NPVAC|P41477    LATE EXPRESSION FAC
exampleB    28   0    1217      261-    271 LEF4_NPVAC|P41477    LATE EXPRESSION FAC
exampleC     8   0    1336      365-    375 LEF4_NPVAC|P41477    LATE EXPRESSION FAC
exampleD    11   0    1325       54-     68 LEF4_NPVAC|P41477    LATE EXPRESSION FAC
exampleE    19   0    1109      328-    364 LEF4_NPVAC|P41477    LATE EXPRESSION FAC

No P-value computed for single block hits.

exampleC              <->C    (168,276):364 
TC1A_CAEBR              172   WVFQQDNDPKH   
                                |||  ||     
LEF4_NPVAC|P41477       365   lRFQQffDPpl   

14.----------------------------------------------------------------------------------
exampleA    80   0    1002       21-     66 GLND_MYCTU|Q10961    PROBABLE [PROTEIN-P
exampleB     5   0    1333      751-    761 GLND_MYCTU|Q10961    PROBABLE [PROTEIN-P
exampleC    16   0    1275      327-    337 GLND_MYCTU|Q10961    PROBABLE [PROTEIN-P
exampleD    35   0    1252      406-    420 GLND_MYCTU|Q10961    PROBABLE [PROTEIN-P
exampleE    22   0    1106      546-    582 GLND_MYCTU|Q10961    PROBABLE [PROTEIN-P

No P-value computed for single block hits.

exampleB              <->B    (118,225):750 
HB1                     168   GGPKIMVWACF   
                              |     |||     
GLND_MYCTU|Q10961       751   GaGagiVWAkv   

15.----------------------------------------------------------------------------------
exampleA    10   0    1030      241-    286 YDF7_SCHPO|Q10479    PUTATIVE GLUCOSYLTR
exampleB    35   0    1200      314-    324 YDF7_SCHPO|Q10479    PUTATIVE GLUCOSYLTR
exampleC    75   0    1092      401-    411 YDF7_SCHPO|Q10479    PUTATIVE GLUCOSYLTR
exampleD    10   0    1327      137-    151 YDF7_SCHPO|Q10479    PUTATIVE GLUCOSYLTR
exampleE    76   0    1055      453-    489 YDF7_SCHPO|Q10479    PUTATIVE GLUCOSYLTR

P<0.0033 for exampleB exampleC exampleE in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
YDF7_SCHPO|Q10479    AAAAAAAAAAAA:::::::BBB::::::::::::::::::::CCC:::::::::::EEEE>


exampleA              <->A    (52,155):240                                     
TC1A_CAEBR               53   KKPLVSLKNRKARVEWAKQHLSWGPREWANHIWSDESKFNMFGTDG   
                               |    |  |         |  | |  ||     |   |      |   
YDF7_SCHPO|Q10479       241   mKqiPqLLSRlfpfSRgLcHayWaPnFWAlysFvDrvAFaVlprfG   

exampleB             A<->B    (20,24):27    
Bari-1                  187   GGGTVMFWGCL   
                                    |  ||   
YDF7_SCHPO|Q10479       314   iPPaltFyiCL   

exampleC             B<->C    (39,40):76    
TC3A_CAEEL              226   FRFQQDNATIH   
                                |    | |    
YDF7_SCHPO|Q10479       401   llFtlneAPIk   

exampleE             C<->E    (50,56):41                              
TC1A_CAEBR              237   LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY   
                              |      |   |     |  |        | |        
YDF7_SCHPO|Q10479       453   LfiyncfIhklVmgDkfEFlPlmLlstyAAwGifwsF   

16.----------------------------------------------------------------------------------
exampleA    68   0    1005      885-    930 SIN3_YEAST|P22579    PAIRED AMPHIPATHIC 
exampleB    24   0    1225      768-    778 SIN3_YEAST|P22579    PAIRED AMPHIPATHIC 
exampleC    14   0    1289      488-    498 SIN3_YEAST|P22579    PAIRED AMPHIPATHIC 
exampleD    12   0    1323      828-    842 SIN3_YEAST|P22579    PAIRED AMPHIPATHIC 
exampleE    53   0    1074     1135-   1171 SIN3_YEAST|P22579    PAIRED AMPHIPATHIC 

P< 0.022 for exampleB in support of exampleD
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
SIN3_YEAST|P22579    <::::::::::::::::::::::BBB:::::::::::::DDDD
SIN3_YEAST|P22579                                                                                                                                                                                                                                               AAAAAAAAAAAA                                                      EEEEEEEEEE                                                                                                                                                                                                                                             AAAAAAAAAAAA                                                      EEEEEEEEEE


exampleB              <->B    (118,225):767 
Bari-1                  187   GGGTVMFWGCL   
                               |   | |  |   
SIN3_YEAST|P22579       768   sGrddMcWevL   

exampleD             B<->D    (68,69):49        
HB1                     247   WQAPPSHLNPIENLY   
                               |      | |||     
SIN3_YEAST|P22579       828   iQcletiVNkIENMt   

17.----------------------------------------------------------------------------------
exampleA    44   0    1011      237-    282 EUTE_ECOLI|P77445    ETHANOLAMINE UTILIZ
exampleB    54   0    1143      215-    225 EUTE_ECOLI|P77445    ETHANOLAMINE UTILIZ
exampleC    61   0    1111        0-     10 EUTE_ECOLI|P77445    ETHANOLAMINE UTILIZ
exampleD    13   0    1321      133-    147 EUTE_ECOLI|P77445    ETHANOLAMINE UTILIZ
exampleE    58   0    1069      262-    298 EUTE_ECOLI|P77445    ETHANOLAMINE UTILIZ

No P-value computed for single block hits.

exampleD              <->D    (197,305):132     
Uhu                     229   XPAQSPDVNVIXNLW   
                               |   |   || |     
EUTE_ECOLI|P77445       133   tPStnPaatVInNai   

18.----------------------------------------------------------------------------------
exampleA    79   0    1002      237-    282 EUTE_SALTY|P41793    ETHANOLAMINE UTILIZ
exampleB    73   0    1111      215-    225 EUTE_SALTY|P41793    ETHANOLAMINE UTILIZ
exampleC    62   0    1111        0-     10 EUTE_SALTY|P41793    ETHANOLAMINE UTILIZ
exampleD    14   0    1321      133-    147 EUTE_SALTY|P41793    ETHANOLAMINE UTILIZ
exampleE    59   0    1069      262-    298 EUTE_SALTY|P41793    ETHANOLAMINE UTILIZ

No P-value computed for single block hits.

exampleD              <->D    (197,305):132     
Uhu                     229   XPAQSPDVNVIXNLW   
                               |   |   || |     
EUTE_SALTY|P41793       133   tPStnPaatVInNai   

19.----------------------------------------------------------------------------------
exampleA    71   0    1004      128-    173 PH81_YEAST|P17442    PHOSPHATE SYSTEM PO
exampleB    12   0    1259     1159-   1169 PH81_YEAST|P17442    PHOSPHATE SYSTEM PO
exampleC    24   0    1251      725-    735 PH81_YEAST|P17442    PHOSPHATE SYSTEM PO
exampleD    15   0    1319       85-     99 PH81_YEAST|P17442    PHOSPHATE SYSTEM PO
exampleE    31   0    1097      961-    997 PH81_YEAST|P17442    PHOSPHATE SYSTEM PO

No P-value computed for single block hits.

exampleB              <->B    (118,225):1158
HB1                     168   GGPKIMVWACF   
                              ||      ||    
PH81_YEAST|P17442      1159   GGySgiyyACe   

20.----------------------------------------------------------------------------------
exampleA    43   0    1011       92-    137 AST5_DROME|P10083    ACHAETE-SCUTE COMPL
exampleB    74   0    1106       22-     32 AST5_DROME|P10083    ACHAETE-SCUTE COMPL
exampleC     9   0    1315      112-    122 AST5_DROME|P10083    ACHAETE-SCUTE COMPL
exampleD    83   0    1117      152-    166 AST5_DROME|P10083    ACHAETE-SCUTE COMPL
exampleE    56   0    1071       67-    103 AST5_DROME|P10083    ACHAETE-SCUTE COMPL

P< 0.058 for exampleB exampleD in support of exampleC
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
AST5_DROME|P10083     
AST5_DROME|P10083                      EEEEEEEEEEAAAAAAAA                    EEEEEEEEEEAAAAAAAA


exampleB              <->B    (118,225):21  
TC1A_CAEBR              122   GGGSVMVWGCF   
                               | ||         
AST5_DROME|P10083        22   nGPSVirrnAr   

exampleC             B<->C    (39,40):79    
TC3A_CAEEL              226   FRFQQDNATIH   
                                |||     |   
AST5_DROME|P10083       112   lhFQQqqqhqH   

exampleD             C<->D    (18,18):29        
Minos                   304   WPSNSPDLSPIENIW   
                                |  |   |  |     
AST5_DROME|P10083       152   atStiPgatPpnNfh   

21.----------------------------------------------------------------------------------
exampleA    18   0    1021     1470-   1515 SPCB_DROME|Q00963    SPECTRIN BETA CHAIN
exampleB    68   0    1123      952-    962 SPCB_DROME|Q00963    SPECTRIN BETA CHAIN
exampleC    10   0    1310      638-    648 SPCB_DROME|Q00963    SPECTRIN BETA CHAIN
exampleD    26   0    1275     2007-   2021 SPCB_DROME|Q00963    SPECTRIN BETA CHAIN
exampleE     8   0    1142     1864-   1900 SPCB_DROME|Q00963    SPECTRIN BETA CHAIN

No P-value computed for single block hits.

exampleE              <->E    (229,343):1863                          
Bari-1                  303   IAEIWSKLTLEFAQTLVRSIPKRLQAVIDAKGGVTKY   
                              | |   ||    |      |  | | |  |          
SPCB_DROME|Q00963      1864   IQEEsAKLqDayAgDkakeItNReQEVLhAwdNlqam   

22.----------------------------------------------------------------------------------
exampleA    42   0    1011     1130-   1175 YCF2_MARPO|P09975    HYPOTHETICAL 259 KD
exampleB    47   0    1185     1937-   1947 YCF2_MARPO|P09975    HYPOTHETICAL 259 KD
exampleC    27   0    1227      460-    470 YCF2_MARPO|P09975    HYPOTHETICAL 259 KD
exampleD    16   0    1310      540-    554 YCF2_MARPO|P09975    HYPOTHETICAL 259 KD
exampleE    18   0    1111      459-    495 YCF2_MARPO|P09975    HYPOTHETICAL 259 KD

No P-value computed for single block hits.

exampleD              <->D    (197,305):539     
Uhu                     229   XPAQSPDVNVIXNLW   
                                  | |     |||   
YCF2_MARPO|P09975       540   nkikSSDnfrfiNLW   

23.----------------------------------------------------------------------------------
exampleA    36   0    1012      191-    236 NRAM_INBOR|P16201    NEURAMINIDASE (EC 3
exampleB    76   0    1106       45-     55 NRAM_INBOR|P16201    NEURAMINIDASE (EC 3
exampleC    68   0    1102      379-    389 NRAM_INBOR|P16201    NEURAMINIDASE (EC 3
exampleD    17   0    1306       47-     61 NRAM_INBOR|P16201    NEURAMINIDASE (EC 3
exampleE    70   0    1058      354-    390 NRAM_INBOR|P16201    NEURAMINIDASE (EC 3

No P-value computed for single block hits.

exampleD              <->D    (197,305):46      
Bari-1                  267   WPPQSPDLNIIENVW   
                               |  | |   | ||    
NRAM_INBOR|P16201        47   aPtmSlDcanIsNVq   

24.----------------------------------------------------------------------------------
exampleA    50   0    1008       82-    127 GYRB_ACICA|Q43947    DNA GYRASE SUBUNIT 
exampleB    32   0    1200       56-     66 GYRB_ACICA|Q43947    DNA GYRASE SUBUNIT 
exampleC    43   0    1175       35-     45 GYRB_ACICA|Q43947    DNA GYRASE SUBUNIT 
exampleD    18   0    1304       63-     77 GYRB_ACICA|Q43947    DNA GYRASE SUBUNIT 
exampleE    25   0    1100      139-    175 GYRB_ACICA|Q43947    DNA GYRASE SUBUNIT 

P< 0.083 for exampleC in support of exampleD
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
GYRB_ACICA|Q43947                          
GYRB_ACICA|Q43947                                        BBB    AAAAAAAAAAAA   EEEEEEEEEE                                      BBB    AAAAAAAAAAAA   EEEEEEEEEE


exampleC              <->C    (168,276):34  
TC1A_CAEBR              172   WVFQQDNDPKH   
                                  |  ||     
GYRB_ACICA|Q43947        35   eqeYQhGDPqy   

exampleD             C<->D    (18,18):17        
Minos                   304   WPSNSPDLSPIENIW   
                              |||       | |     
GYRB_ACICA|Q43947        63   WPSeltftqtIfNVe   

25.----------------------------------------------------------------------------------
exampleA     6   0    1044      642-    687 YP22_YEAST|Q08968    HYPOTHETICAL 78.3 K
exampleB    53   0    1151      318-    328 YP22_YEAST|Q08968    HYPOTHETICAL 78.3 K
exampleC    13   0    1301       89-     99 YP22_YEAST|Q08968    HYPOTHETICAL 78.3 K
exampleD    31   0    1263      631-    645 YP22_YEAST|Q08968    HYPOTHETICAL 78.3 K
exampleE    10   0    1134      404-    440 YP22_YEAST|Q08968    HYPOTHETICAL 78.3 K

No P-value computed for single block hits.

exampleA              <->A    (52,155):641                                     
TC1A_CAEBR               53   KKPLVSLKNRKARVEWAKQHLSWGPREWANHIWSDESKFNMFGTDG   
                              ||      |   |  |           ||     |  || |        
YP22_YEAST|Q08968       642   KKlyLmsvNpydRtKWdvTlrpeleTKWAdlshqDdAKFMMQaScS   

26.----------------------------------------------------------------------------------
exampleA    11   0    1029     2062-   2107 ACVS_EMENI|P27742    DELTA-(L-ALPHA-AMIN
exampleB     8   0    1294      148-    158 ACVS_EMENI|P27742    DELTA-(L-ALPHA-AMIN
exampleC    19   0    1258     2352-   2362 ACVS_EMENI|P27742    DELTA-(L-ALPHA-AMIN
exampleD    29   0    1263     2769-   2783 ACVS_EMENI|P27742    DELTA-(L-ALPHA-AMIN
exampleE     6   0    1150     2965-   3001 ACVS_EMENI|P27742    DELTA-(L-ALPHA-AMIN

No P-value computed for single block hits.

exampleE              <->E    (229,343):2964                          
Bari-1                  303   IAEIWSKLTLEFAQTLVRSIPKRLQAVIDAKGGVTKY   
                               |   |||               |   |  |  | |    
ACVS_EMENI|P27742      2965   LAhMkSKLPaymVpKyLcrlEgGLpvtIngKlDVrKl   

27.----------------------------------------------------------------------------------
exampleA    86   0    1001     1274-   1319 PTP1_DROME|P35992    PROTEIN-TYROSINE PH
exampleB     9   0    1264     1363-   1373 PTP1_DROME|P35992    PROTEIN-TYROSINE PH
exampleC    18   0    1261     1482-   1492 PTP1_DROME|P35992    PROTEIN-TYROSINE PH
exampleD    20   0    1290      707-    721 PTP1_DROME|P35992    PROTEIN-TYROSINE PH
exampleE    48   0    1078      749-    785 PTP1_DROME|P35992    PROTEIN-TYROSINE PH

P< 0.029 for exampleA in support of exampleB
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
PTP1_DROME|P35992    AAAAAAA:::::::::::BBB
PTP1_DROME|P35992                                                                                                                                                                                                                                                                                                                                                                                                              CCC                                                                                                                                                                                                                                                                                                                                                                                                            CCC


exampleA              <->A    (52,155):1273                                    
Bari-1                  120   KTIEITPTNKTKRLRFALEYVKKPLDFWFNILWTDESAFQYQGSYS   
                                 |           ||      |     |||  | | |  |       
PTP1_DROME|P35992      1274   EfeELkhvgRDqpcTFAdlpcNrPknrftNILpyDhSrFkLQpvDd   

exampleB             A<->B    (20,24):43    
TC1A_CAEBR              122   GGGSVMVWGCF   
                                  ||   ||   
PTP1_DROME|P35992      1363   srAiVMltrCF   

28.----------------------------------------------------------------------------------
exampleA    22   0    1017      461-    506 YPB4_CAEEL|Q11107    HYPOTHETICAL ZINC F
exampleB    20   0    1230     1121-   1131 YPB4_CAEEL|Q11107    HYPOTHETICAL ZINC F
exampleC    15   0    1289      515-    525 YPB4_CAEEL|Q11107    HYPOTHETICAL ZINC F
exampleD    32   0    1263     1972-   1986 YPB4_CAEEL|Q11107    HYPOTHETICAL ZINC F
exampleE    36   0    1092     1080-   1116 YPB4_CAEEL|Q11107    HYPOTHETICAL ZINC F

No P-value computed for single block hits.

exampleC              <->C    (168,276):514 
Minos                   275   FTFQQDGASSH   
                                  ||  ||    
YPB4_CAEEL|Q11107       515   slLeQDNqSSs   

29.----------------------------------------------------------------------------------
exampleA    16   0    1026      402-    447 NIFK_AZOVI|P07329    NITROGENASE MOLYBDE
exampleB    42   0    1193      362-    372 NIFK_AZOVI|P07329    NITROGENASE MOLYBDE
exampleC    49   0    1159      381-    391 NIFK_AZOVI|P07329    NITROGENASE MOLYBDE
exampleD    21   0    1285      308-    322 NIFK_AZOVI|P07329    NITROGENASE MOLYBDE
exampleE    12   0    1125      378-    414 NIFK_AZOVI|P07329    NITROGENASE MOLYBDE

No P-value computed for single block hits.

exampleE              <->E    (229,343):377                           
TC1A_CAEBR              237   LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY   
                              |           |  |      | |   ||      |   
NIFK_AZOVI|P07329       378   LvkflleLgcEPVHiLchngNKRwKkavDAilaAspY   

30.----------------------------------------------------------------------------------
exampleA    24   0    1016      162-    207 MAOM_SOLTU|P37221    MALATE OXIDOREDUCTA
exampleB    57   0    1141      315-    325 MAOM_SOLTU|P37221    MALATE OXIDOREDUCTA
exampleC    81   0    1081      444-    454 MAOM_SOLTU|P37221    MALATE OXIDOREDUCTA
exampleD    22   0    1281      459-    473 MAOM_SOLTU|P37221    MALATE OXIDOREDUCTA
exampleE    43   0    1085       74-    110 MAOM_SOLTU|P37221    MALATE OXIDOREDUCTA

P< 0.054 for exampleC in support of exampleD
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
MAOM_SOLTU|P37221    <::::::::::::::::::::::::::::::::::CCC:DDDD


exampleC              <->C    (168,276):443 
TC3A_CAEEL              226   FRFQQDNATIH   
                              |      |  |   
MAOM_SOLTU|P37221       444   FskevleAlKH   

exampleD             C<->D    (18,18):4         
TC3A_CAEEL              255   WPARSPDLNPIENLW   
                               ||  |  ||  |     
MAOM_SOLTU|P37221       459   rPAifPmsNPtrNae   

31.----------------------------------------------------------------------------------
exampleA    31   0    1013       82-    127 GYRB_ACIJO|Q44081    DNA GYRASE SUBUNIT 
exampleB    31   0    1207       56-     66 GYRB_ACIJO|Q44081    DNA GYRASE SUBUNIT 
exampleC    85   0    1059       72-     82 GYRB_ACIJO|Q44081    DNA GYRASE SUBUNIT 
exampleD    23   0    1279       63-     77 GYRB_ACIJO|Q44081    DNA GYRASE SUBUNIT 
exampleE    26   0    1100      139-    175 GYRB_ACIJO|Q44081    DNA GYRASE SUBUNIT 

No P-value computed for single block hits.

exampleD              <->D    (197,305):62      
Minos                   304   WPSNSPDLSPIENIW   
                              |||       | |     
GYRB_ACIJO|Q44081        63   WPSaetfsqtIfNVd   

32.----------------------------------------------------------------------------------
exampleA    52   0    1008       82-    127 GYRB_ACIS1|Q44272    DNA GYRASE SUBUNIT 
exampleB    49   0    1178        9-     19 GYRB_ACIS1|Q44272    DNA GYRASE SUBUNIT 
exampleC    86   0    1059       72-     82 GYRB_ACIS1|Q44272    DNA GYRASE SUBUNIT 
exampleD    24   0    1279       63-     77 GYRB_ACIS1|Q44272    DNA GYRASE SUBUNIT 
exampleE    27   0    1100      139-    175 GYRB_ACIS1|Q44272    DNA GYRASE SUBUNIT 

P<  0.16 for exampleB in support of exampleD
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
GYRB_ACIS1|Q44272                           
GYRB_ACIS1|Q44272                                             CCCAAAAAAAAAAAA   EEEEEEEEEE                                           CCCAAAAAAAAAAAA   EEEEEEEEEE


exampleB              <->B    (118,225):8   
TC3A_CAEEL              176   GGGTVMVWGAF   
                               |  | |  |    
GYRB_ACIS1|Q44272         9   HGvgVsVvnAL   

exampleD             B<->D    (68,69):43        
Minos                   304   WPSNSPDLSPIENIW   
                              |||       | |     
GYRB_ACIS1|Q44272        63   WPSaetfsqtIfNVd   

33.----------------------------------------------------------------------------------
exampleA    85   0    1001       82-    127 GYRB_ACIS8|Q44275    DNA GYRASE SUBUNIT 
exampleB    41   0    1193       56-     66 GYRB_ACIS8|Q44275    DNA GYRASE SUBUNIT 
exampleC    80   0    1081      143-    153 GYRB_ACIS8|Q44275    DNA GYRASE SUBUNIT 
exampleD    25   0    1279       63-     77 GYRB_ACIS8|Q44275    DNA GYRASE SUBUNIT 
exampleE    32   0    1097      139-    175 GYRB_ACIS8|Q44275    DNA GYRASE SUBUNIT 

No P-value computed for single block hits.

exampleD              <->D    (197,305):62      
Minos                   304   WPSNSPDLSPIENIW   
                              |||       | |     
GYRB_ACIS8|Q44275        63   WPSaetfsqtIfNVd   

34.----------------------------------------------------------------------------------
exampleA    19   0    1021      145-    190 MAON_SOLTU|P37225    MALATE OXIDOREDUCTA
exampleB    70   0    1116      298-    308 MAON_SOLTU|P37225    MALATE OXIDOREDUCTA
exampleC    64   0    1102       66-     76 MAON_SOLTU|P37225    MALATE OXIDOREDUCTA
exampleD    27   0    1267      478-    492 MAON_SOLTU|P37225    MALATE OXIDOREDUCTA
exampleE    62   0    1066      399-    435 MAON_SOLTU|P37225    MALATE OXIDOREDUCTA

P<  0.29 for exampleE in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
MAON_SOLTU|P37225    AAAAAAAAAAAA::::::::::::::::::::::::::::::::::::::::::::::::>
MAON_SOLTU|P37225                                                                                  BBB                                             DDDD                                                                                BBB                                             DDDD


exampleA              <->A    (52,155):144                                     
HB1                      98   KVPLPSPRHIKARLSLAKTYLNWPVSKWRNILWTDGSKIMLFGGTG   
                                |       |          |||      |  |||| |   |  |   
MAON_SOLTU|P37225       145   rrPrgmyfSAKdKgEmmsmifNWPsTQvDmIVlTDGSrIlglGdlG   

exampleE             A<->E    (131,142):208                           
TC1A_CAEBR              237   LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY   
                              |    |     |   |          |  |          
MAON_SOLTU|P37225       399   LAEVvKKvkPhVLlgLsgvggifheEVLRAmkesdsv   

35.----------------------------------------------------------------------------------
exampleA    67   0    1005      799-    844 ITA2_BOVIN|P53710    PLATELET MEMBRANE G
exampleB    37   0    1198      262-    272 ITA2_BOVIN|P53710    PLATELET MEMBRANE G
exampleC    41   0    1178       39-     49 ITA2_BOVIN|P53710    PLATELET MEMBRANE G
exampleD    28   0    1265      982-    996 ITA2_BOVIN|P53710    PLATELET MEMBRANE G
exampleE    16   0    1113      643-    679 ITA2_BOVIN|P53710    PLATELET MEMBRANE G

No P-value computed for single block hits.

exampleE              <->E    (229,343):642                           
TC1A_CAEBR              237   LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY   
                                    |        |        |    ||  ||     
ITA2_BOVIN|P53710       643   dvsVdASfTPKkItlLnknaEikLKlcfsAKfrPTNq   

36.----------------------------------------------------------------------------------
exampleA    88   0    1001      101-    146 YO96_CAEEL|P41846    HYPOTHETICAL 93.9 K
exampleB    25   0    1225      587-    597 YO96_CAEEL|P41846    HYPOTHETICAL 93.9 K
exampleC    17   0    1265      121-    131 YO96_CAEEL|P41846    HYPOTHETICAL 93.9 K
exampleD    36   0    1246      413-    427 YO96_CAEEL|P41846    HYPOTHETICAL 93.9 K
exampleE    60   0    1069      730-    766 YO96_CAEEL|P41846    HYPOTHETICAL 93.9 K

No P-value computed for single block hits.

exampleC              <->C    (168,276):120 
TC1A_CAEBR              172   WVFQQDNDPKH   
                                 |    |||   
YO96_CAEEL|P41846       121   vkLQrsqtPKH   

37.----------------------------------------------------------------------------------
exampleA     9   0    1030       38-     83 YFEH_ECOLI|P39836    HYPOTHETICAL 36.4 K
exampleB    45   0    1190      300-    310 YFEH_ECOLI|P39836    HYPOTHETICAL 36.4 K
exampleC    58   0    1128      195-    205 YFEH_ECOLI|P39836    HYPOTHETICAL 36.4 K
exampleD    30   0    1263       24-     38 YFEH_ECOLI|P39836    HYPOTHETICAL 36.4 K
exampleE    54   0    1073      217-    253 YFEH_ECOLI|P39836    HYPOTHETICAL 36.4 K

P<  0.45 for exampleE in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
YFEH_ECOLI|P39836    AAAAAAAAAAAA:::::::::::::::::::::::::::::::::::EEEEEEEEEE
YFEH_ECOLI|P39836                                                       CCC                         BBB                                                     CCC                         BBB


exampleA              <->A    (52,155):37                                      
TC1A_CAEEL               53   KKPFISKKNRMARVAWAKAHLRWGRQEWAKHIWSDESKFNLFGSDG   
                                  |     |            |   |  | |   | | ||   |   
YFEH_ECOLI|P39836        38   tTaaIaLLffMHgaKLsREAiiaGGghWRlHLWvmcStFvLFpilG   

exampleE             A<->E    (131,142):133                           
Bari-1                  303   IAEIWSKLTLEFAQTLVRSIPKRLQAVIDAKGGVTKY   
                                 || |         |      |  ||            
YFEH_ECOLI|P39836       217   VngIWhKvgwgsLlfIVvvscvlLaiVIvvNvFmArr   

38.----------------------------------------------------------------------------------
exampleA    45   0    1011       35-     80 GLO2_HUMAN|Q16775    HYDROXYACYLGLUTATHI
exampleB    10   0    1259      132-    142 GLO2_HUMAN|Q16775    HYDROXYACYLGLUTATHI
exampleC    84   0    1066      225-    235 GLO2_HUMAN|Q16775    HYDROXYACYLGLUTATHI
exampleD    80   0    1129      123-    137 GLO2_HUMAN|Q16775    HYDROXYACYLGLUTATHI
exampleE    78   0    1049       82-    118 GLO2_HUMAN|Q16775    HYDROXYACYLGLUTATHI

No P-value computed for single block hits.

exampleB              <->B    (118,225):131 
TC1A_CAEBR              122   GGGSVMVWGCF   
                               |    | ||    
GLO2_HUMAN|Q16775       132   tGdTlfVaGCg   

39.----------------------------------------------------------------------------------
exampleA    13   0    1029      296-    341 MSH5_YEAST|Q12175    MUTS PROTEIN HOMOLO
exampleB    11   0    1259      614-    624 MSH5_YEAST|Q12175    MUTS PROTEIN HOMOLO
exampleC    56   0    1130      137-    147 MSH5_YEAST|Q12175    MUTS PROTEIN HOMOLO
exampleD    69   0    1185      491-    505 MSH5_YEAST|Q12175    MUTS PROTEIN HOMOLO
exampleE    40   0    1086      530-    566 MSH5_YEAST|Q12175    MUTS PROTEIN HOMOLO

No P-value computed for single block hits.

exampleB              <->B    (118,225):613 
Minos                   224   FPASTMVWGCM   
                               | |||  |     
MSH5_YEAST|Q12175       614   iPnSTMidGgL   

40.----------------------------------------------------------------------------------
exampleA    78   0    1003      331-    376 YM8I_YEAST|Q03529    HYPOTHETICAL 44.9 K
exampleB    17   0    1247      229-    239 YM8I_YEAST|Q03529    HYPOTHETICAL 44.9 K
exampleC    20   0    1258      167-    177 YM8I_YEAST|Q03529    HYPOTHETICAL 44.9 K
exampleD    88   0    1081      280-    294 YM8I_YEAST|Q03529    HYPOTHETICAL 44.9 K
exampleE    55   0    1073      201-    237 YM8I_YEAST|Q03529    HYPOTHETICAL 44.9 K

P<  0.33 for exampleD in support of exampleB
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
YM8I_YEAST|Q03529    <:::::::::::::::::BBB:::::::::::DDDD
YM8I_YEAST|Q03529                                                                                           AAAAAAAAAAAA                                                                                         AAAAAAAAAAAA


exampleB              <->B    (118,225):228 
Uhu                     150   HGGSVMVWACI   
                                  | ||  |   
YM8I_YEAST|Q03529       229   FcvgVfVWtlI   

exampleD             B<->D    (68,69):40        
HB1                     247   WQAPPSHLNPIENLY   
                                  |  |  |       
YM8I_YEAST|Q03529       280   rlvmPPtLfVIlcap   

41.----------------------------------------------------------------------------------
exampleA    47   0    1010      192-    237 YNC4_YEAST|P53970    HYPOTHETICAL 27.7 K
exampleB    13   0    1257       87-     97 YNC4_YEAST|P53970    HYPOTHETICAL 27.7 K
exampleC    89   0    1000       35-     45 YNC4_YEAST|P53970    HYPOTHETICAL 27.7 K
exampleD    66   0    1190      144-    158 YNC4_YEAST|P53970    HYPOTHETICAL 27.7 K
exampleE    79   0    1049      113-    149 YNC4_YEAST|P53970    HYPOTHETICAL 27.7 K

P<  0.39 for exampleD in support of exampleB
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
YNC4_YEAST|P53970    <:::::::::::::::::BBB::::::::::::DDDD
YNC4_YEAST|P53970                                 EEEEEEEEEE           AAAAAAAAAAAA                               EEEEEEEEEE           AAAAAAAAAAAA


exampleB              <->B    (118,225):86  
TC1A_CAEBR              122   GGGSVMVWGCF   
                              | |   |  |    
YNC4_YEAST|P53970        87   GsGTglVglCv   

exampleD             B<->D    (68,69):46        
Minos                   304   WPSNSPDLSPIENIW   
                                  | | || |      
YNC4_YEAST|P53970       144   gePlSaDfSPqEgam   

42.----------------------------------------------------------------------------------
exampleA    82   0    1002      196-    241 MA2X_HUMAN|P49641    ALPHA-MANNOSIDASE I
exampleB    14   0    1254      877-    887 MA2X_HUMAN|P49641    ALPHA-MANNOSIDASE I
exampleC    35   0    1199      332-    342 MA2X_HUMAN|P49641    ALPHA-MANNOSIDASE I
exampleD    63   0    1194      993-   1007 MA2X_HUMAN|P49641    ALPHA-MANNOSIDASE I
exampleE    11   0    1127      180-    216 MA2X_HUMAN|P49641    ALPHA-MANNOSIDASE I

No P-value computed for single block hits.

exampleE              <->E    (229,343):179                           
Uhu                     261   LLDEWSKISPETTRKLVSSMNNRLMEDIKAKGYHTKY   
                                    |   | |     ||   | ||             
MA2X_HUMAN|P49641       180   wikTfDKyytEQTQhILnSMvskLQEDpRrrflwAev   

43.----------------------------------------------------------------------------------
exampleA    69   0    1005       19-     64 THIS_ECOLI|O32583    THIS PROTEIN       
exampleB    87   0    1047       53-     63 THIS_ECOLI|O32583    THIS PROTEIN       
exampleC    21   0    1254       48-     58 THIS_ECOLI|O32583    THIS PROTEIN       
exampleD    89   0    1000       37-     51 THIS_ECOLI|O32583    THIS PROTEIN       
exampleE    89   0    1000        6-     42 THIS_ECOLI|O32583    THIS PROTEIN       

No P-value computed for single block hits.

exampleC              <->C    (168,276):47  
HB1                     218   WTFQQDNDQKR   
                                  || ||     
THIS_ECOLI|O32583        48   qhivQDGDQIl   

44.----------------------------------------------------------------------------------
exampleA    56   0    1007       99-    144 YOUG_BACLI|Q45292    HYPOTHETICAL 17.3 K
exampleB    88   0    1032       28-     38 YOUG_BACLI|Q45292    HYPOTHETICAL 17.3 K
exampleC    34   0    1213      125-    135 YOUG_BACLI|Q45292    HYPOTHETICAL 17.3 K
exampleD    34   0    1254      105-    119 YOUG_BACLI|Q45292    HYPOTHETICAL 17.3 K
exampleE    77   0    1051       56-     92 YOUG_BACLI|Q45292    HYPOTHETICAL 17.3 K

No P-value computed for single block hits.

exampleC              <->C    (168,276):124 
TC3A_CAEEL              226   FRFQQDNATIH   
                              |||       |   
YOUG_BACLI|Q45292       125   FRFghieiSeH   

45.----------------------------------------------------------------------------------
exampleA    48   0    1009      523-    568 KINN_HUMAN|Q12840    NEURONAL KINESIN HE
exampleB    30   0    1212      295-    305 KINN_HUMAN|Q12840    NEURONAL KINESIN HE
exampleC    22   0    1251      891-    901 KINN_HUMAN|Q12840    NEURONAL KINESIN HE
exampleD    70   0    1181      256-    270 KINN_HUMAN|Q12840    NEURONAL KINESIN HE
exampleE    49   0    1078      582-    618 KINN_HUMAN|Q12840    NEURONAL KINESIN HE

No P-value computed for single block hits.

exampleC              <->C    (168,276):890 
TC3A_CAEEL              226   FRFQQDNATIH   
                               | ||    |    
KINN_HUMAN|Q12840       891   rRyQQevDrIk   

46.----------------------------------------------------------------------------------
exampleA    53   0    1008      523-    568 KINN_MOUSE|P28738    NEURONAL KINESIN HE
exampleB    52   0    1156      295-    305 KINN_MOUSE|P28738    NEURONAL KINESIN HE
exampleC    23   0    1251      891-    901 KINN_MOUSE|P28738    NEURONAL KINESIN HE
exampleD    71   0    1181      256-    270 KINN_MOUSE|P28738    NEURONAL KINESIN HE
exampleE    50   0    1078      582-    618 KINN_MOUSE|P28738    NEURONAL KINESIN HE

No P-value computed for single block hits.

exampleC              <->C    (168,276):890 
TC3A_CAEEL              226   FRFQQDNATIH   
                               | ||    |    
KINN_MOUSE|P28738       891   rRyQQevDrIk   

47.----------------------------------------------------------------------------------
exampleA    23   0    1016      139-    184 MAOC_LYCES|P37222    MALATE OXIDOREDUCTA
exampleB    16   0    1247      292-    302 MAOC_LYCES|P37222    MALATE OXIDOREDUCTA
exampleC    77   0    1085      273-    283 MAOC_LYCES|P37222    MALATE OXIDOREDUCTA
exampleD    81   0    1123      514-    528 MAOC_LYCES|P37222    MALATE OXIDOREDUCTA
exampleE    45   0    1081      386-    422 MAOC_LYCES|P37222    MALATE OXIDOREDUCTA

P<  0.17 for exampleE in support of exampleB
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
MAOC_LYCES|P37222    <:::::::::::::::::BBB::::::::::::::::::::::EEEEEEEEEE
MAOC_LYCES|P37222                                                                                                                                            DDDD                                                                                                                                          DDDD


exampleB              <->B    (118,225):291 
Minos                   224   FPASTMVWGCM   
                                ||    | |   
MAOC_LYCES|P37222       292   GtASVvlaGlM   

exampleE             B<->E    (100,107):83                            
TC1A_CAEBR              237   LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY   
                              |  | |||  ||            | |  |          
MAOC_LYCES|P37222       386   LvNAvKSIkPTVLigssgagrtftKEVvQAmatfnek   

48.----------------------------------------------------------------------------------
exampleA    17   0    1023      461-    506 OE66_NPVAC|Q00704    OCCLUSION-DERIVED V
exampleB    18   0    1242      469-    479 OE66_NPVAC|Q00704    OCCLUSION-DERIVED V
exampleC    28   0    1225       66-     76 OE66_NPVAC|Q00704    OCCLUSION-DERIVED V
exampleD    47   0    1215      145-    159 OE66_NPVAC|Q00704    OCCLUSION-DERIVED V
exampleE    75   0    1055      394-    430 OE66_NPVAC|Q00704    OCCLUSION-DERIVED V

No P-value computed for single block hits.

exampleA              <->A    (52,155):460                                     
TC3A_CAEEL              110   KLRPAPLLSADHKLKRLEFAKNNMGTNWSKVVFSDEKKFNLDGPDG   
                                  |    |   |    ||  |     |   | |   | |    |   
OE66_NPVAC|Q00704       461   qTaiAkTdtAGAiLvyAKFAemNnLQFkSctLFyDhgmFQLyyniG   

49.----------------------------------------------------------------------------------
exampleA    81   0    1002       64-    109 HBB1_TRICR|P10785    HEMOGLOBIN BETA-1 C
exampleB    19   0    1235       62-     72 HBB1_TRICR|P10785    HEMOGLOBIN BETA-1 C
exampleC    46   0    1166       81-     91 HBB1_TRICR|P10785    HEMOGLOBIN BETA-1 C
exampleD    74   0    1156       80-     94 HBB1_TRICR|P10785    HEMOGLOBIN BETA-1 C
exampleE    80   0    1047       51-     87 HBB1_TRICR|P10785    HEMOGLOBIN BETA-1 C

P<  0.26 for exampleC in support of exampleB
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
HBB1_TRICR|P10785      
HBB1_TRICR|P10785                      AAAAAAAAAAAA                    AAAAAAAAAAAA
HBB1_TRICR|P10785                          DDDD                        DDDD


exampleB              <->B    (118,225):61  
TC3A_CAEEL              176   GGGTVMVWGAF   
                               |  ||   |    
HBB1_TRICR|P10785        62   HGAKVMhsiAe   

exampleC             B<->C    (39,40):8     
TC3A_CAEEL              226   FRFQQDNATIH   
                                   |  |||   
HBB1_TRICR|P10785        81   kayYaDlsTIH   

50.----------------------------------------------------------------------------------
exampleA    46   0    1010      596-    641 TRFE_RABIT|P19134    SEROTRANSFERRIN PRE
exampleB    59   0    1133      275-    285 TRFE_RABIT|P19134    SEROTRANSFERRIN PRE
exampleC    53   0    1140      458-    468 TRFE_RABIT|P19134    SEROTRANSFERRIN PRE
exampleD    37   0    1233      362-    376 TRFE_RABIT|P19134    SEROTRANSFERRIN PRE
exampleE    15   0    1116      627-    663 TRFE_RABIT|P19134    SEROTRANSFERRIN PRE

No P-value computed for single block hits.

exampleE              <->E    (229,343):626                           
Bari-1                  303   IAEIWSKLTLEFAQTLVRSIPKRLQAVIDAKGGVTKY   
                               |   ||       |             |  |  |     
TRFE_RABIT|P19134       627   VADcsSKfcMfHsKTkdllfrDdtKClvDlrGknTye   

51.----------------------------------------------------------------------------------
exampleA    62   0    1005       58-    103 YDIL_ECOLI|P76196    HYPOTHETICAL 15.0 K
exampleB    84   0    1059      101-    111 YDIL_ECOLI|P76196    HYPOTHETICAL 15.0 K
exampleC    44   0    1175      108-    118 YDIL_ECOLI|P76196    HYPOTHETICAL 15.0 K
exampleD    38   0    1233       96-    110 YDIL_ECOLI|P76196    HYPOTHETICAL 15.0 K
exampleE    42   0    1086       33-     69 YDIL_ECOLI|P76196    HYPOTHETICAL 15.0 K

No P-value computed for single block hits.

exampleD              <->D    (197,305):95      
Uhu                     229   XPAQSPDVNVIXNLW   
                                   || | |       
YDIL_ECOLI|P76196        96   fQrvyPDgNfIdwki   

52.----------------------------------------------------------------------------------
exampleA    57   0    1006       39-     84 YENR_YEREN|P54295    YENR REGULATORY PRO
exampleB    72   0    1114      184-    194 YENR_YEREN|P54295    YENR REGULATORY PRO
exampleC    25   0    1230      159-    169 YENR_YEREN|P54295    YENR REGULATORY PRO
exampleD    84   0    1117       37-     51 YENR_YEREN|P54295    YENR REGULATORY PRO
exampleE    86   0    1038      135-    171 YENR_YEREN|P54295    YENR REGULATORY PRO

P<  0.37 for exampleA in support of exampleC
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
YENR_YEREN|P54295    AAAAAAAAAAA::::::::::::::::::::CCC
YENR_YEREN|P54295                                       EEEEEEEEEE   BBB                                     EEEEEEEEEE   BBB


exampleA              <->A    (52,155):38                                      
TC1A_CAEBR               53   KKPLVSLKNRKARVEWAKQHLSWGPREWANHIWSDESKFNMFGTDG   
                              | ||           | |             |     |   |  |    
YENR_YEREN|P54295        39   KTPLhPTiisnypLdWvKkYKKNsyhliDpVIlTakdKvapFawDd   

exampleC             A<->C    (70,75):74    
Uhu                     200   FRFYQDNDQKH   
                                 || |  |    
YENR_YEREN|P54295       159   lgLYQsNsdKn   

53.----------------------------------------------------------------------------------
exampleA    12   0    1029      211-    256 MAOC_FLAPR|P36444    MALATE OXIDOREDUCTA
exampleB    26   0    1222      365-    375 MAOC_FLAPR|P36444    MALATE OXIDOREDUCTA
exampleC    38   0    1187      409-    419 MAOC_FLAPR|P36444    MALATE OXIDOREDUCTA
exampleD    39   0    1229       20-     34 MAOC_FLAPR|P36444    MALATE OXIDOREDUCTA
exampleE    52   0    1074      459-    495 MAOC_FLAPR|P36444    MALATE OXIDOREDUCTA

P<  0.22 for exampleE in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
MAOC_FLAPR|P36444    AAAAAAAAAAAA::::::::::::::::::::::::::::::::::::::::::::::::>
MAOC_FLAPR|P36444                                                                                                    BBB         CCC                                                                                                  BBB         CCC


exampleA              <->A    (52,155):210                                     
HB1                      98   KVPLPSPRHIKARLSLAKTYLNWPVSKWRNILWTDGSKIMLFGGTG   
                              | |       |          |||  |   |  |||  |   |  |   
MAOC_FLAPR|P36444       211   KnPqglyiSlKdKgKvLEilKNWPQkKiqvIVvTDGerIlglGdlG   

exampleE             A<->E    (131,142):202                           
TC1A_CAEBR              237   LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY   
                                 | | |  ||            | |  |          
MAOC_FLAPR|P36444       459   fLDAvKAIkPTVLigssgagqtftKEVveAmssfnek   

54.----------------------------------------------------------------------------------
exampleA    21   0    1017       57-    102 PSRC_WOLSU|P31077    POLYSULFIDE REDUCTA
exampleB    21   0    1227      254-    264 PSRC_WOLSU|P31077    POLYSULFIDE REDUCTA
exampleC    79   0    1083      235-    245 PSRC_WOLSU|P31077    POLYSULFIDE REDUCTA
exampleD    79   0    1144      124-    138 PSRC_WOLSU|P31077    POLYSULFIDE REDUCTA
exampleE    84   0    1042      122-    158 PSRC_WOLSU|P31077    POLYSULFIDE REDUCTA

P<  0.52 for exampleD in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
PSRC_WOLSU|P31077    AAAAAAAAAAAA::::::DDDD
PSRC_WOLSU|P31077                                   EEEEEEEEEE                    CCC  BBB                                 EEEEEEEEEE                    CCC  BBB


exampleA              <->A    (52,155):56                                      
HB1                      98   KVPLPSPRHIKARLSLAKTYLNWPVSKWRNILWTDGSKIMLFGGTG   
                                 |  |  | | | |    |  |   |        |  |  |      
PSRC_WOLSU|P31077        57   agaLIaPLtIGAgLlLLiFdLtrPLhFWkllIFynfSsvMtlGvla   

exampleD             A<->D    (99,104):21       
HB1                     247   WQAPPSHLNPIENLY   
                                 |   | |  |     
PSRC_WOLSU|P31077       124   degPfgfLaPlaNIa   

55.----------------------------------------------------------------------------------
exampleA    87   0    1001      192-    237 RFAB_ECOLI|P27127    LIPOPOLYSACCHARIDE 
exampleB    23   0    1225       41-     51 RFAB_ECOLI|P27127    LIPOPOLYSACCHARIDE 
exampleC    40   0    1187       35-     45 RFAB_ECOLI|P27127    LIPOPOLYSACCHARIDE 
exampleD    51   0    1204      233-    247 RFAB_ECOLI|P27127    LIPOPOLYSACCHARIDE 
exampleE    41   0    1086      334-    369 RFAB_ECOLI|P27127    LIPOPOLYSACCHARIDE 

No P-value computed for single block hits.

exampleB              <->B    (118,225):40  
Uhu                     150   HGGSVMVWACI   
                              |  | |   |    
RFAB_ECOLI|P27127        41   HiqSeMFffCr   

56.----------------------------------------------------------------------------------
exampleA    61   0    1005      273-    318 CP4C_BLADI|P29981    CYTOCHROME P450 4C1
exampleB    51   0    1163       70-     80 CP4C_BLADI|P29981    CYTOCHROME P450 4C1
exampleC    29   0    1223       19-     29 CP4C_BLADI|P29981    CYTOCHROME P450 4C1
exampleD    67   0    1188      127-    141 CP4C_BLADI|P29981    CYTOCHROME P450 4C1
exampleE    61   0    1068      336-    372 CP4C_BLADI|P29981    CYTOCHROME P450 4C1

No P-value computed for single block hits.

exampleC              <->C    (168,276):18  
TC3A_CAEEL              226   FRFQQDNATIH   
                              | | |         
CP4C_BLADI|P29981        19   FlFrQgakraR   

57.----------------------------------------------------------------------------------
exampleA    75   0    1003      149-    194 MAOX_MESCR|P37223    MALATE OXIDOREDUCTA
exampleB    27   0    1222      303-    313 MAOX_MESCR|P37223    MALATE OXIDOREDUCTA
exampleC    76   0    1090      378-    388 MAOX_MESCR|P37223    MALATE OXIDOREDUCTA
exampleD    85   0    1115      171-    185 MAOX_MESCR|P37223    MALATE OXIDOREDUCTA
exampleE    24   0    1105      397-    433 MAOX_MESCR|P37223    MALATE OXIDOREDUCTA

P< 0.098 for exampleB in support of exampleE
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
MAOX_MESCR|P37223    <::::::::::::::::::::::::BBB::::::::::::::::::::::EEEEEEEEEE
MAOX_MESCR|P37223                                                                                                        CCC                                                                                                      CCC


exampleB              <->B    (118,225):302 
TC1A_CAEBR              122   GGGSVMVWGCF   
                              |  ||   |     
MAOX_MESCR|P37223       303   GtASVvlaGlI   

exampleE             B<->E    (100,107):83                            
TC1A_CAEBR              237   LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY   
                              |  |   |  ||            | |  |          
MAOX_MESCR|P37223       397   LiDAvQAIkPTVLigtsgkgkqftKEVveAmaNinak   

58.----------------------------------------------------------------------------------
exampleA    32   0    1013      191-    236 NRAM_INBHK|P16191    NEURAMINIDASE (EC 3
exampleB    75   0    1106      439-    449 NRAM_INBHK|P16191    NEURAMINIDASE (EC 3
exampleC    65   0    1102      379-    389 NRAM_INBHK|P16191    NEURAMINIDASE (EC 3
exampleD    41   0    1221       47-     61 NRAM_INBHK|P16191    NEURAMINIDASE (EC 3
exampleE    67   0    1058      354-    390 NRAM_INBHK|P16191    NEURAMINIDASE (EC 3

P<  0.37 for exampleE in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
NRAM_INBHK|P16191    AAAAAAAAAAAA:::::::::::::::::::::::::::::::EEEEEEEEEE
NRAM_INBHK|P16191                                                                                                        CCC             BBB                                                                                                      CCC             BBB


exampleA              <->A    (52,155):190                                     
Bari-1                  120   KTIEITPTNKTKRLRFALEYVKKPLDFWFNILWTDESAFQYQGSYS   
                                      |          |         ||| | |||    |      
NRAM_INBHK|P16191       191   vgvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc   

exampleE             A<->E    (131,142):117                           
HB1                     283   VQDTWAKIPPKPCXDLVDFMPRGCKAVLANKGYPAKY   
                               |    ||              |        | |      
NRAM_INBHK|P16191       354   hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd   

59.----------------------------------------------------------------------------------
exampleA    37   0    1012      191-    236 NRAM_INBSI|P16203    NEURAMINIDASE (EC 3
exampleB    77   0    1106      439-    449 NRAM_INBSI|P16203    NEURAMINIDASE (EC 3
exampleC    69   0    1102      379-    389 NRAM_INBSI|P16203    NEURAMINIDASE (EC 3
exampleD    42   0    1221       47-     61 NRAM_INBSI|P16203    NEURAMINIDASE (EC 3
exampleE    71   0    1058      354-    390 NRAM_INBSI|P16203    NEURAMINIDASE (EC 3

P<   0.4 for exampleE in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
NRAM_INBSI|P16203    AAAAAAAAAAAA:::::::::::::::::::::::::::::::EEEEEEEEEE
NRAM_INBSI|P16203                                                                                                        CCC             BBB                                                                                                      CCC             BBB


exampleA              <->A    (52,155):190                                     
Bari-1                  120   KTIEITPTNKTKRLRFALEYVKKPLDFWFNILWTDESAFQYQGSYS   
                                      |          |         ||| | |||    |      
NRAM_INBSI|P16203       191   igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc   

exampleE             A<->E    (131,142):117                           
HB1                     283   VQDTWAKIPPKPCXDLVDFMPRGCKAVLANKGYPAKY   
                               |    ||              |        | |      
NRAM_INBSI|P16203       354   hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd   

60.----------------------------------------------------------------------------------
exampleA    27   0    1014      171-    216 HOFB_HAEIN|P44622    PROTEIN TRANSPORT P
exampleB    69   0    1121      268-    278 HOFB_HAEIN|P44622    PROTEIN TRANSPORT P
exampleC    30   0    1220      368-    378 HOFB_HAEIN|P44622    PROTEIN TRANSPORT P
exampleD    77   0    1150      322-    336 HOFB_HAEIN|P44622    PROTEIN TRANSPORT P
exampleE     7   0    1143      276-    312 HOFB_HAEIN|P44622    PROTEIN TRANSPORT P

P<  0.16 for exampleA in support of exampleE
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
HOFB_HAEIN|P44622    <:::::::::::::::::::::AAAAAAAAAAAA::::::::::::::::EEEEEEEEEE
HOFB_HAEIN|P44622                                                                          BBB            DDDD        CCC                                                                        BBB            DDDD        CCC


exampleA              <->A    (52,155):170                                     
TC3A_CAEEL              110   KLRPAPLLSADHKLKRLEFAKNNMGTNWSKVVFSDEKKFNLDGPDG   
                                |    |    ||   |      |    |  |||   | |        
HOFB_HAEIN|P44622       171   anRiISrLkllAKLdisEnRLpqDGRFqFKttFSDildFrLStlpT   

exampleE             A<->E    (131,142):59                            
TC3A_CAEEL              293   ILDAWKSIPDNQLKSLVRSMEDRLIEIIRTQGNPINY   
                                  |   ||          |  |  ||  | ||      
HOFB_HAEIN|P44622       276   tAlqWlntPDKHImTaeDpIEieLdgIIQsQiNPqig   

61.----------------------------------------------------------------------------------
exampleA    30   0    1013       39-     84 TRA0_SHISO|P16944    TRANSPOSASE FOR INS
exampleB    56   0    1143      194-    204 TRA0_SHISO|P16944    TRANSPOSASE FOR INS
exampleC    31   0    1218      148-    158 TRA0_SHISO|P16944    TRANSPOSASE FOR INS
exampleD    55   0    1198       57-     71 TRA0_SHISO|P16944    TRANSPOSASE FOR INS
exampleE    21   0    1108      261-    297 TRA0_SHISO|P16944    TRANSPOSASE FOR INS

P<  0.27 for exampleA in support of exampleE
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
TRA0_SHISO|P16944    AAA:::::::::::::::::::::::::::::::::::::::::::::::EEEEEEEEEE
TRA0_SHISO|P16944                  DDDD                    CCC         BBB                DDDD                    CCC         BBB


exampleA              <->A    (52,155):38                                      
TC3A_CAEEL              110   KLRPAPLLSADHKLKRLEFAKNNMGTNWSKVVFSDEKKFNLDGPDG   
                              |    |     ||   |              |   |  |      |   
TRA0_SHISO|P16944        39   KyPEPPaRktrHKMvkLKpfMDyidmrlAenVWnsEviFaeikamG   

exampleE             A<->E    (131,142):176                           
TC3A_CAEEL              293   ILDAWKSIPDNQLKSLVRSMEDRLIEIIRTQGNPINY   
                              | |        | |            |    |    |   
TRA0_SHISO|P16944       261   IADVaDKreLrQfKetpEqrsRwsrnIcsvtGYrlrY   

62.----------------------------------------------------------------------------------
exampleA    15   0    1029       56-    101 YQHN_BACSU|P54512    HYPOTHETICAL 16.7 K
exampleB    86   0    1049      100-    110 YQHN_BACSU|P54512    HYPOTHETICAL 16.7 K
exampleC    32   0    1218      118-    128 YQHN_BACSU|P54512    HYPOTHETICAL 16.7 K
exampleD    72   0    1175      123-    137 YQHN_BACSU|P54512    HYPOTHETICAL 16.7 K
exampleE    85   0    1039        6-     42 YQHN_BACSU|P54512    HYPOTHETICAL 16.7 K

P<  0.03 for exampleC exampleB in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
YQHN_BACSU|P54512    AAAAAAAAAAAABBB::CCC
YQHN_BACSU|P54512                                    DDDD                                  DDDD


exampleA              <->A    (52,155):55                                      
Bari-1                  120   KTIEITPTNKTKRLRFALEYVKKPLDFWFNILWTDESAFQYQGSYS   
                              |      | | |     | |    ||    |   ||             
YQHN_BACSU|P54512        56   KyRgLvLTSKGKKigkrLvYrHelLDQflrIIgvDEeKIynDVegi   

exampleB             A<->B    (20,24):-2    
HB1                     168   GGPKIMVWACF   
                              |      |      
YQHN_BACSU|P54512       100   GiehhlsWnsI   

exampleC             B<->C    (39,40):7     
TC3A_CAEEL              226   FRFQQDNATIH   
                                |  | |      
YQHN_BACSU|P54512       118   qyFeeDdArKk   

63.----------------------------------------------------------------------------------
exampleA    64   0    1005      711-    756 DPOM_CLAPU|P22373    PROBABLE DNA POLYME
exampleB    36   0    1198      648-    658 DPOM_CLAPU|P22373    PROBABLE DNA POLYME
exampleC    60   0    1123      912-    922 DPOM_CLAPU|P22373    PROBABLE DNA POLYME
exampleD    43   0    1217      333-    347 DPOM_CLAPU|P22373    PROBABLE DNA POLYME
exampleE     5   0    1151      933-    969 DPOM_CLAPU|P22373    PROBABLE DNA POLYME

P<  0.17 for exampleA in support of exampleE
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
DPOM_CLAPU|P22373    AAA:::::::::::::::::::::::::::::::::::::::::::::::EEEEEEEEEE
DPOM_CLAPU|P22373                                                                                                                                                                                                                                                      CCC                                                                                                                                                                                                                                                    CCC


exampleA              <->A    (52,155):710                                     
TC3A_CAEEL              110   KLRPAPLLSADHKLKRLEFAKNNMGTNWSKVVFSDEKKFNLDGPDG   
                              |      |      || |      |  |    || | ||          
DPOM_CLAPU|P22373       711   KikSPdnLylGllpKRtETsLifPGgaWegwyFSeElKFaVahGYe   

exampleE             A<->E    (131,142):176                           
Bari-1                  303   IAEIWSKLTLEFAQTLVRSIPKRLQAVIDAKGGVTKY   
                                    || ||   |    |     |     |   |    
DPOM_CLAPU|P22373       933   hQtEigKLkLEHTiTqgyFIaDktyAIvnTeGeiIKr   

64.----------------------------------------------------------------------------------
exampleA    70   0    1004      153-    198 MAOX_PHAVU|P12628    MALATE OXIDOREDUCTA
exampleB    29   0    1217      307-    317 MAOX_PHAVU|P12628    MALATE OXIDOREDUCTA
exampleC    39   0    1187       82-     92 MAOX_PHAVU|P12628    MALATE OXIDOREDUCTA
exampleD    52   0    1202      175-    189 MAOX_PHAVU|P12628    MALATE OXIDOREDUCTA
exampleE    46   0    1080      401-    437 MAOX_PHAVU|P12628    MALATE OXIDOREDUCTA

P<  0.17 for exampleE in support of exampleB
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
MAOX_PHAVU|P12628    <:::::::::::::::::BBB::::::::::::::::::::::EEEEEEEEEE


exampleB              <->B    (118,225):306 
TC1A_CAEBR              122   GGGSVMVWGCF   
                              |  ||   |     
MAOX_PHAVU|P12628       307   GtASVvlaGlL   

exampleE             B<->E    (100,107):83                            
TC1A_CAEBR              237   LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY   
                              |  | | |  ||            | |             
MAOX_PHAVU|P12628       401   LLEAvKAIkPTVLigssgagktftKEVveTmaslnek   

65.----------------------------------------------------------------------------------
exampleA    89   0    1000      262-    307 NOD1_RHIGA|P50331    NODULATION PROTEIN 
exampleB    58   0    1133      204-    214 NOD1_RHIGA|P50331    NODULATION PROTEIN 
exampleC    83   0    1076      129-    139 NOD1_RHIGA|P50331    NODULATION PROTEIN 
exampleD    44   0    1217       34-     48 NOD1_RHIGA|P50331    NODULATION PROTEIN 
exampleE    65   0    1060       83-    119 NOD1_RHIGA|P50331    NODULATION PROTEIN 

P<  0.11 for exampleE in support of exampleD
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
NOD1_RHIGA|P50331                                  
NOD1_RHIGA|P50331                                                                   CCC                 BBB             AAAAAAAAAAAA                                                                 CCC                 BBB             AAAAAAAAAAAA


exampleD              <->D    (197,305):33      
Uhu                     229   XPAQSPDVNVIXNLW   
                               || |       |     
NOD1_RHIGA|P50331        34   qPAmSaaiarlrNyf   

exampleE             D<->E    (17,23):34                              
TC2A_CAEBR              237   LQDVWQAIPMSVIDTILDSMPRRCQTVIDAKGFPTKY   
                                  |  |     |           | |            
NOD1_RHIGA|P50331        83   sviAWDpIkPaesDrrfRiIlsdfMTlIfmekvikri   

66.----------------------------------------------------------------------------------
exampleA    29   0    1013       39-     84 TRA0_ECOLI|P15025    TRANSPOSASE FOR INS
exampleB    55   0    1143      194-    204 TRA0_ECOLI|P15025    TRANSPOSASE FOR INS
exampleC    57   0    1128      148-    158 TRA0_ECOLI|P15025    TRANSPOSASE FOR INS
exampleD    45   0    1217      361-    375 TRA0_ECOLI|P15025    TRANSPOSASE FOR INS
exampleE    88   0    1027        4-     40 TRA0_ECOLI|P15025    TRANSPOSASE FOR INS

P<  0.23 for exampleC in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
TRA0_ECOLI|P15025    AAAAAAAAAAAA:::::::::::::::::CCC
TRA0_ECOLI|P15025                                                      BBB                                          DDDD                                                    BBB                                          DDDD


exampleA              <->A    (52,155):38                                      
TC3A_CAEEL              110   KLRPAPLLSADHKLKRLEFAKNNMGTNWSKVVFSDEKKFNLDGPDG   
                              |    |     ||   |              |   |  |      |   
TRA0_ECOLI|P15025        39   KyPEPPaRktrHKMvkLKpfMDyidmrlAenVWnsEviFaeikamG   

exampleC             A<->C    (70,75):63    
TC3A_CAEEL              226   FRFQQDNATIH   
                               ||    |      
TRA0_ECOLI|P15025       148   rRFhvfaAPKq   

67.----------------------------------------------------------------------------------
exampleA    84   0    1002      118-    163 Y08F_MYCTU|Q11052    PROBABLE REGULATORY
exampleB    83   0    1062      201-    211 Y08F_MYCTU|Q11052    PROBABLE REGULATORY
exampleC    45   0    1168      318-    328 Y08F_MYCTU|Q11052    PROBABLE REGULATORY
exampleD    46   0    1217      131-    145 Y08F_MYCTU|Q11052    PROBABLE REGULATORY
exampleE    13   0    1122       56-     92 Y08F_MYCTU|Q11052    PROBABLE REGULATORY

No P-value computed for single block hits.

exampleE              <->E    (229,343):55                            
TC1A_CAEEL              237   LENAWKAIPMSVIHKLIDSMPRRCQAVIDANGYATKY   
                                  |   | |     | |            |        
Y08F_MYCTU|Q11052        56   ItAlWeewPPSgARasIhSyvsnLrklLggaGidprv   

68.----------------------------------------------------------------------------------
exampleA    66   0    1005       82-    127 GYRB_ACIS9|Q44276    DNA GYRASE SUBUNIT 
exampleB    34   0    1200       56-     66 GYRB_ACIS9|Q44276    DNA GYRASE SUBUNIT 
exampleC    33   0    1213       67-     77 GYRB_ACIS9|Q44276    DNA GYRASE SUBUNIT 
exampleD    65   0    1190      162-    176 GYRB_ACIS9|Q44276    DNA GYRASE SUBUNIT 
exampleE    29   0    1100      139-    175 GYRB_ACIS9|Q44276    DNA GYRASE SUBUNIT 

P< 0.041 for exampleC exampleB in support of exampleE
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
GYRB_ACIS9|Q44276                 
GYRB_ACIS9|Q44276                                      AAAAAAAAAAAA         DDDD                                    AAAAAAAAAAAA         DDDD


exampleB              <->B    (118,225):55  
Bari-1                  187   GGGTVMFWGCL   
                               | || ||      
GYRB_ACIS9|Q44276        56   sGtTVrFWpse   

exampleC             B<->C    (39,40):0     
Minos                   275   FTFQQDGASSH   
                               || |   |     
GYRB_ACIS9|Q44276        67   WTFsQtifSvd   

exampleE             C<->E    (50,56):61                              
TC1A_CAEEL              237   LENAWKAIPMSVIHKLIDSMPRRCQAVIDANGYATKY   
                              |         |          |  ||     |        
GYRB_ACIS9|Q44276       139   LsElylvegDSaggSakqgrNRkmQAILplKGkilNv   

69.----------------------------------------------------------------------------------
exampleA    51   0    1008       31-     76 PARF_PARTE|P47244    PARAFUSIN | PS00710
exampleB    44   0    1190      387-    397 PARF_PARTE|P47244    PARAFUSIN | PS00710
exampleC    48   0    1161      313-    323 PARF_PARTE|P47244    PARAFUSIN | PS00710
exampleD    48   0    1213      405-    419 PARF_PARTE|P47244    PARAFUSIN | PS00710
exampleE    39   0    1086      342-    378 PARF_PARTE|P47244    PARAFUSIN | PS00710

P< 0.091 for exampleC in support of exampleE
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
PARF_PARTE|P47244    <:::::::::::::::::::::::::::::::::::::::::CCC:::::EEEEEEEEEE
PARF_PARTE|P47244                                                                                                          BBB  DDDD                                                                                                        BBB  DDDD


exampleC              <->C    (168,276):312 
Minos                   275   FTFQQDGASSH   
                              |    ||       
PARF_PARTE|P47244       313   FgaacDGDadR   

exampleE             C<->E    (50,56):18                              
TC3A_CAEEL              293   ILDAWKSIPDNQLKSLVRSMEDRLIEIIRTQGNPINY   
                              |      |  | |    |||            | |     
PARF_PARTE|P47244       342   IAAnanlIfkNgLlgaaRSMPtsgalDkvAakNgIKl   

70.----------------------------------------------------------------------------------
exampleA    74   0    1004        6-     51 RL17_SCHPO|O59794    60S RIBOSOMAL PROTE
exampleB    79   0    1101       76-     86 RL17_SCHPO|O59794    60S RIBOSOMAL PROTE
exampleC    54   0    1137       44-     54 RL17_SCHPO|O59794    60S RIBOSOMAL PROTE
exampleD    49   0    1210      139-    153 RL17_SCHPO|O59794    60S RIBOSOMAL PROTE
exampleE    35   0    1092      103-    139 RL17_SCHPO|O59794    60S RIBOSOMAL PROTE

P<  0.32 for exampleC in support of exampleE
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
RL17_SCHPO|O59794                           
RL17_SCHPO|O59794                         AAAAAAAAAAAA         BBB              DDDD                       AAAAAAAAAAAA         BBB              DDDD


exampleC              <->C    (168,276):43  
TC3A_CAEEL              226   FRFQQDNATIH   
                                   ||   |   
RL17_SCHPO|O59794        44   afiflDNvkeH   

exampleE             C<->E    (50,56):48                              
Bari-1                  303   IAEIWSKLTLEFAQTLVRSIPKRLQAVIDAKGGVTKY   
                               |       |      |   ||       | | || |   
RL17_SCHPO|O59794       103   eAkglDmdkLiikHvqVnaaPKqrrrtyRAhGrVTaY   

71.----------------------------------------------------------------------------------
exampleA    77   0    1003      143-    188 SN2L_CAEEL|P41877    POSSIBLE GLOBAL TRA
exampleB    63   0    1128      412-    422 SN2L_CAEEL|P41877    POSSIBLE GLOBAL TRA
exampleC    52   0    1152      624-    634 SN2L_CAEEL|P41877    POSSIBLE GLOBAL TRA
exampleD    50   0    1208      248-    262 SN2L_CAEEL|P41877    POSSIBLE GLOBAL TRA
exampleE    30   0    1100      907-    943 SN2L_CAEEL|P41877    POSSIBLE GLOBAL TRA

No P-value computed for single block hits.

exampleE              <->E    (229,343):906                           
TC1A_CAEBR              237   LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY   
                              |             ||     |    |   |         
SN2L_CAEEL|P41877       907   LksrtAmelQrrCnTLItlIERemgEVvesKpvivta   

72.----------------------------------------------------------------------------------
exampleA    65   0    1005       82-    127 GYRB_ACIS6|Q44277    DNA GYRASE SUBUNIT 
exampleB    33   0    1200       56-     66 GYRB_ACIS6|Q44277    DNA GYRASE SUBUNIT 
exampleC    87   0    1055       67-     77 GYRB_ACIS6|Q44277    DNA GYRASE SUBUNIT 
exampleD    64   0    1190      162-    176 GYRB_ACIS6|Q44277    DNA GYRASE SUBUNIT 
exampleE    28   0    1100      139-    175 GYRB_ACIS6|Q44277    DNA GYRASE SUBUNIT 

P<  0.11 for exampleB exampleC in support of exampleE
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
GYRB_ACIS6|Q44277                 
GYRB_ACIS6|Q44277                                      AAAAAAAAAAAA         DDDD                                    AAAAAAAAAAAA         DDDD


exampleB              <->B    (118,225):55  
Bari-1                  187   GGGTVMFWGCL   
                               | || ||      
GYRB_ACIS6|Q44277        56   sGtTVrFWpse   

exampleC             B<->C    (39,40):0     
Minos                   275   FTFQQDGASSH   
                               || |   |     
GYRB_ACIS6|Q44277        67   lTFsQtifSvd   

exampleE             C<->E    (50,56):61                              
TC1A_CAEEL              237   LENAWKAIPMSVIHKLIDSMPRRCQAVIDANGYATKY   
                              |         |          |  ||     |        
GYRB_ACIS6|Q44277       139   LsElylvegDSaggSakqgrNRkmQAILplKGkilNv   

73.----------------------------------------------------------------------------------
exampleA    20   0    1018      155-    200 MAOX_POPTR|P34105    MALATE OXIDOREDUCTA
exampleB    46   0    1185       24-     34 MAOX_POPTR|P34105    MALATE OXIDOREDUCTA
exampleC    73   0    1097      485-    495 MAOX_POPTR|P34105    MALATE OXIDOREDUCTA
exampleD    53   0    1200      177-    191 MAOX_POPTR|P34105    MALATE OXIDOREDUCTA
exampleE    34   0    1092      170-    206 MAOX_POPTR|P34105    MALATE OXIDOREDUCTA

No P-value computed for single block hits.

exampleA              <->A    (52,155):154                                     
HB1                      98   KVPLPSPRHIKARLSLAKTYLNWPVSKWRNILWTDGSKIMLFGGTG   
                              | |       |          |||      |  |||  |   |  |   
MAOX_POPTR|P34105       155   KrPqglyiSlKeKgKvLdvlKNWPQksiqvIVvTDGerIlglGdlG   

74.----------------------------------------------------------------------------------
exampleA    28   0    1013      155-    200 MAOX_VITVI|P51615    MALATE OXIDOREDUCTA
exampleB    38   0    1198      309-    319 MAOX_VITVI|P51615    MALATE OXIDOREDUCTA
exampleC    78   0    1083      485-    495 MAOX_VITVI|P51615    MALATE OXIDOREDUCTA
exampleD    78   0    1146      576-    590 MAOX_VITVI|P51615    MALATE OXIDOREDUCTA
exampleE    33   0    1092      403-    439 MAOX_VITVI|P51615    MALATE OXIDOREDUCTA

P<  0.16 for exampleE in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
MAOX_VITVI|P51615    AAAAAAAAAAAA::::::::::::::::::::::::::::::::::::::::::::::::>
MAOX_VITVI|P51615                                                                                     BBB                                            CCC                     DDDD                                                                                   BBB                                            CCC                     DDDD


exampleA              <->A    (52,155):154                                     
HB1                      98   KVPLPSPRHIKARLSLAKTYLNWPVSKWRNILWTDGSKIMLFGGTG   
                                |       |          |||      |  |||  |   |  |   
MAOX_VITVI|P51615       155   rrPqglyiSlKeKgKiLEvlKNWPeRriqvIVvTDGerIlglGdlG   

exampleE             A<->E    (131,142):202                           
TC1A_CAEBR              237   LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY   
                              |  | | |  ||            | || |          
MAOX_VITVI|P51615       403   LLDAvKvIkPTVLigssgvgkaftKEVIeAmascnek   

75.----------------------------------------------------------------------------------
exampleA     5   0    1055      438-    483 OE66_NPVOP|O10305    OCCLUSION-DERIVED V
exampleB    39   0    1198      446-    456 OE66_NPVOP|O10305    OCCLUSION-DERIVED V
exampleC    47   0    1161      173-    183 OE66_NPVOP|O10305    OCCLUSION-DERIVED V
exampleD    54   0    1198      256-    270 OE66_NPVOP|O10305    OCCLUSION-DERIVED V
exampleE    44   0    1085      371-    407 OE66_NPVOP|O10305    OCCLUSION-DERIVED V

No P-value computed for single block hits.

exampleA              <->A    (52,155):437                                     
TC3A_CAEEL              110   KLRPAPLLSADHKLKRLEFAKNNMGTNWSKVVFSDEKKFNLDGPDG   
                              |   |    |   |    ||  |     |   | |   | |    |   
OE66_NPVOP|O10305       438   KTaLAkTRtAGAiLvhARFAemNnLQFkSctLFyDhgmFQLyyniG   

76.----------------------------------------------------------------------------------
exampleA    59   0    1006      810-    855 ITA2_HUMAN|P17301    PLATELET MEMBRANE G
exampleB    40   0    1195      246-    256 ITA2_HUMAN|P17301    PLATELET MEMBRANE G
exampleC    42   0    1178       50-     60 ITA2_HUMAN|P17301    PLATELET MEMBRANE G
exampleD    56   0    1196      163-    177 ITA2_HUMAN|P17301    PLATELET MEMBRANE G
exampleE    38   0    1089      654-    690 ITA2_HUMAN|P17301    PLATELET MEMBRANE G

No P-value computed for single block hits.

exampleE              <->E    (229,343):653                           
TC1A_CAEBR              237   LEAAWKSIPMTVVQTLLESMPRRCKAVIDAKGYPTKY   
                                |   |                 |    ||  |||    
ITA2_HUMAN|P17301       654   dvAIeASfTPEkItlvnknaqiiLKlcfsAKfrPTKq   

77.----------------------------------------------------------------------------------
exampleA    33   0    1012      190-    235 NRAM_INBBE|P27907    NEURAMINIDASE (EC 3
exampleB    64   0    1126       44-     54 NRAM_INBBE|P27907    NEURAMINIDASE (EC 3
exampleC    74   0    1097      378-    388 NRAM_INBBE|P27907    NEURAMINIDASE (EC 3
exampleD    57   0    1196      142-    156 NRAM_INBBE|P27907    NEURAMINIDASE (EC 3
exampleE    66   0    1060      353-    389 NRAM_INBBE|P27907    NEURAMINIDASE (EC 3

P<  0.37 for exampleE in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
NRAM_INBBE|P27907    AAAAAAAAAAAA:::::::::::::::::::::::::::::::EEEEEEEEEE
NRAM_INBBE|P27907                                                                                                        CCC                                                                                                      CCC


exampleA              <->A    (52,155):189                                     
Bari-1                  120   KTIEITPTNKTKRLRFALEYVKKPLDFWFNILWTDESAFQYQGSYS   
                                      |          |         ||| | |||    |      
NRAM_INBBE|P27907       190   igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc   

exampleE             A<->E    (131,142):117                           
HB1                     283   VQDTWAKIPPKPCXDLVDFMPRGCKAVLANKGYPAKY   
                               |    ||              |        | |      
NRAM_INBBE|P27907       353   hQrMaSKIgrwysRTmsktermGmelyvRydGDPwtd   

78.----------------------------------------------------------------------------------
exampleA    34   0    1012      190-    235 NRAM_INBLN|P16193    NEURAMINIDASE (EC 3
exampleB    65   0    1126       44-     54 NRAM_INBLN|P16193    NEURAMINIDASE (EC 3
exampleC    66   0    1102      378-    388 NRAM_INBLN|P16193    NEURAMINIDASE (EC 3
exampleD    58   0    1196      142-    156 NRAM_INBLN|P16193    NEURAMINIDASE (EC 3
exampleE    68   0    1058      353-    389 NRAM_INBLN|P16193    NEURAMINIDASE (EC 3

P<  0.38 for exampleE in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
NRAM_INBLN|P16193    AAAAAAAAAAAA:::::::::::::::::::::::::::::::EEEEEEEEEE
NRAM_INBLN|P16193                                                                                                        CCC                                                                                                      CCC


exampleA              <->A    (52,155):189                                     
Bari-1                  120   KTIEITPTNKTKRLRFALEYVKKPLDFWFNILWTDESAFQYQGSYS   
                                      |          |         ||| | |||    |      
NRAM_INBLN|P16193       190   igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc   

exampleE             A<->E    (131,142):117                           
HB1                     283   VQDTWAKIPPKPCXDLVDFMPRGCKAVLANKGYPAKY   
                               |    ||              |        | |      
NRAM_INBLN|P16193       353   hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd   

79.----------------------------------------------------------------------------------
exampleA    35   0    1012      190-    235 NRAM_INBMF|P16199    NEURAMINIDASE (EC 3
exampleB    66   0    1126       44-     54 NRAM_INBMF|P16199    NEURAMINIDASE (EC 3
exampleC    67   0    1102      378-    388 NRAM_INBMF|P16199    NEURAMINIDASE (EC 3
exampleD    59   0    1196      142-    156 NRAM_INBMF|P16199    NEURAMINIDASE (EC 3
exampleE    69   0    1058      353-    389 NRAM_INBMF|P16199    NEURAMINIDASE (EC 3

P<  0.39 for exampleE in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
NRAM_INBMF|P16199    AAAAAAAAAAAA:::::::::::::::::::::::::::::::EEEEEEEEEE
NRAM_INBMF|P16199                                                                                                        CCC                                                                                                      CCC


exampleA              <->A    (52,155):189                                     
Bari-1                  120   KTIEITPTNKTKRLRFALEYVKKPLDFWFNILWTDESAFQYQGSYS   
                                      |          |         ||| | |||    |      
NRAM_INBMF|P16199       190   igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc   

exampleE             A<->E    (131,142):117                           
HB1                     283   VQDTWAKIPPKPCXDLVDFMPRGCKAVLANKGYPAKY   
                               |    ||              |        | |      
NRAM_INBMF|P16199       353   hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd   

80.----------------------------------------------------------------------------------
exampleA    38   0    1012      191-    236 NRAM_INBUS|P16205    NEURAMINIDASE (EC 3
exampleB    71   0    1116       45-     55 NRAM_INBUS|P16205    NEURAMINIDASE (EC 3
exampleC    70   0    1102      379-    389 NRAM_INBUS|P16205    NEURAMINIDASE (EC 3
exampleD    60   0    1196      143-    157 NRAM_INBUS|P16205    NEURAMINIDASE (EC 3
exampleE    72   0    1058      354-    390 NRAM_INBUS|P16205    NEURAMINIDASE (EC 3

P<   0.4 for exampleE in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
NRAM_INBUS|P16205    AAAAAAAAAAAA:::::::::::::::::::::::::::::::EEEEEEEEEE
NRAM_INBUS|P16205                                                                                                        CCC                                                                                                      CCC


exampleA              <->A    (52,155):190                                     
Bari-1                  120   KTIEITPTNKTKRLRFALEYVKKPLDFWFNILWTDESAFQYQGSYS   
                                      |          |         ||| | |||    |      
NRAM_INBUS|P16205       191   igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc   

exampleE             A<->E    (131,142):117                           
HB1                     283   VQDTWAKIPPKPCXDLVDFMPRGCKAVLANKGYPAKY   
                               |    ||              |        | |      
NRAM_INBUS|P16205       354   hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd   

81.----------------------------------------------------------------------------------
exampleA    39   0    1012      190-    235 NRAM_INBVI|P16207    NEURAMINIDASE (EC 3
exampleB    67   0    1126       44-     54 NRAM_INBVI|P16207    NEURAMINIDASE (EC 3
exampleC    71   0    1102      378-    388 NRAM_INBVI|P16207    NEURAMINIDASE (EC 3
exampleD    61   0    1196      142-    156 NRAM_INBVI|P16207    NEURAMINIDASE (EC 3
exampleE    73   0    1058      353-    389 NRAM_INBVI|P16207    NEURAMINIDASE (EC 3

P<  0.41 for exampleE in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
NRAM_INBVI|P16207    AAAAAAAAAAAA:::::::::::::::::::::::::::::::EEEEEEEEEE
NRAM_INBVI|P16207                                                                                                        CCC                                                                                                      CCC


exampleA              <->A    (52,155):189                                     
Bari-1                  120   KTIEITPTNKTKRLRFALEYVKKPLDFWFNILWTDESAFQYQGSYS   
                                      |          |         ||| | |||    |      
NRAM_INBVI|P16207       190   igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc   

exampleE             A<->E    (131,142):117                           
HB1                     283   VQDTWAKIPPKPCXDLVDFMPRGCKAVLANKGYPAKY   
                               |    ||              |        | |      
NRAM_INBVI|P16207       353   hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd   

82.----------------------------------------------------------------------------------
exampleA    40   0    1012      191-    236 NRAM_INBYB|Q90021    NEURAMINIDASE (EC 3
exampleB    78   0    1106      439-    449 NRAM_INBYB|Q90021    NEURAMINIDASE (EC 3
exampleC    72   0    1102      379-    389 NRAM_INBYB|Q90021    NEURAMINIDASE (EC 3
exampleD    62   0    1196      143-    157 NRAM_INBYB|Q90021    NEURAMINIDASE (EC 3
exampleE    74   0    1058      354-    390 NRAM_INBYB|Q90021    NEURAMINIDASE (EC 3

P<  0.41 for exampleE in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
NRAM_INBYB|Q90021    AAAAAAAAAAAA:::::::::::::::::::::::::::::::EEEEEEEEEE
NRAM_INBYB|Q90021                                                                                                        CCC             BBB                                                                                                      CCC             BBB


exampleA              <->A    (52,155):190                                     
Bari-1                  120   KTIEITPTNKTKRLRFALEYVKKPLDFWFNILWTDESAFQYQGSYS   
                                      |          |         ||| | |||    |      
NRAM_INBYB|Q90021       191   igvdgPdsNAliKiKygEAYtDtyhSyaNNILrTqESAcNciGGDc   

exampleE             A<->E    (131,142):117                           
HB1                     283   VQDTWAKIPPKPCXDLVDFMPRGCKAVLANKGYPAKY   
                               |    ||              |        | |      
NRAM_INBYB|Q90021       354   hQrMaSKIgrwysRTmsktermGmelyvKydGDPwtd   

83.----------------------------------------------------------------------------------
exampleA    73   0    1004      382-    427 NUCL_MOUSE|P09405    NUCLEOLIN (PROTEIN 
exampleB    62   0    1128      649-    659 NUCL_MOUSE|P09405    NUCLEOLIN (PROTEIN 
exampleC    36   0    1190      421-    431 NUCL_MOUSE|P09405    NUCLEOLIN (PROTEIN 
exampleD    73   0    1167      513-    527 NUCL_MOUSE|P09405    NUCLEOLIN (PROTEIN 
exampleE    57   0    1070      150-    186 NUCL_MOUSE|P09405    NUCLEOLIN (PROTEIN 

No P-value computed for single block hits.

exampleC              <->C    (168,276):420 
Minos                   275   FTFQQDGASSH   
                                  ||| |     
NUCL_MOUSE|P09405       421   rlvsQDGkSKg   

84.----------------------------------------------------------------------------------
exampleA    63   0    1005      268-    313 DHA6_YEAST|P54115    ALDEHYDE DEHYDROGEN
exampleB    48   0    1183      185-    195 DHA6_YEAST|P54115    ALDEHYDE DEHYDROGEN
exampleC    37   0    1187       34-     44 DHA6_YEAST|P54115    ALDEHYDE DEHYDROGEN
exampleD    68   0    1185      100-    114 DHA6_YEAST|P54115    ALDEHYDE DEHYDROGEN
exampleE    47   0    1079      380-    416 DHA6_YEAST|P54115    ALDEHYDE DEHYDROGEN

No P-value computed for single block hits.

exampleC              <->C    (168,276):33  
TC3A_CAEEL              226   FRFQQDNATIH   
                              |   ||  |     
DHA6_YEAST|P54115        34   FmkaQDGkTyp   

85.----------------------------------------------------------------------------------
exampleA    49   0    1008      278-    323 CRTI_RHOCA|P17054    PHYTOENE DEHYDROGEN
exampleB    50   0    1168        7-     17 CRTI_RHOCA|P17054    PHYTOENE DEHYDROGEN
exampleC    50   0    1152      104-    114 CRTI_RHOCA|P17054    PHYTOENE DEHYDROGEN
exampleD    75   0    1150      133-    147 CRTI_RHOCA|P17054    PHYTOENE DEHYDROGEN
exampleE    14   0    1118      346-    382 CRTI_RHOCA|P17054    PHYTOENE DEHYDROGEN

No P-value computed for single block hits.

exampleE              <->E    (229,343):345                           
HB1                     283   VQDTWAKIPPKPCXDLVDFMPRGCKAVLANKGYPAKY   
                              |||   |        |    |       | ||    |   
CRTI_RHOCA|P17054       346   VQDIfiKgeLaedmSLyvhrPsvtdptaApKGDdTfY   

86.----------------------------------------------------------------------------------
exampleA    72   0    1004       66-    111 GSHC_SCHMA|Q00277    GLUTATHIONE PEROXID
exampleB    81   0    1086       63-     73 GSHC_SCHMA|Q00277    GLUTATHIONE PEROXID
exampleC    88   0    1050       94-    104 GSHC_SCHMA|Q00277    GLUTATHIONE PEROXID
exampleD    76   0    1150       26-     40 GSHC_SCHMA|Q00277    GLUTATHIONE PEROXID
exampleE    83   0    1043       53-     89 GSHC_SCHMA|Q00277    GLUTATHIONE PEROXID

No P-value computed for single block hits.

exampleA              <->A    (52,155):65                                      
Uhu                      82   KKPFISTKNKGTRMTFAKTHLDKDLEFWNTIIFEDESKFIIFGSDG   
                                        |     |     |         |   ||    |||    
GSHC_SCHMA|Q00277        66   rilafPcnQfGgqepWAEAeiKKfVTEkygVqFdmfSKIkVnGSDa   

87.----------------------------------------------------------------------------------
exampleA     8   0    1033      380-    425 NUCL_HUMAN|P19338    NUCLEOLIN (PROTEIN 
exampleB    61   0    1128      649-    659 NUCL_HUMAN|P19338    NUCLEOLIN (PROTEIN 
exampleC    82   0    1081      686-    696 NUCL_HUMAN|P19338    NUCLEOLIN (PROTEIN 
exampleD    87   0    1098      480-    494 NUCL_HUMAN|P19338    NUCLEOLIN (PROTEIN 
exampleE    63   0    1063       56-     92 NUCL_HUMAN|P19338    NUCLEOLIN (PROTEIN 

P<  0.26 for exampleD in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
NUCL_HUMAN|P19338    AAAAAAAAAAAA::::::::::::::DDDD
NUCL_HUMAN|P19338                                                                                                                                                                                BBB       CCC                                                                                                                                                                              BBB       CCC


exampleA              <->A    (52,155):379                                     
TC2A_CAEBR               53   KKPSISKKNRIARVAWARAHLHWGRQDWANHVFSDESKFNLFGTDG   
                               |   ||| | ||   |        ||    || |     |   ||   
NUCL_HUMAN|P19338       380   pKgkdSKKeRDARtlLAKnlpyKvtQDelKeVFEDaAeIrLvskDG   

exampleD             A<->D    (99,104):54       
HB1                     247   WQAPPSHLNPIENLY   
                              |      |      |   
NUCL_HUMAN|P19338       480   WsgeSktLvlsnlsY   

88.----------------------------------------------------------------------------------
exampleA    41   0    1012      136-    181 YBDM_ECOLI|P77174    HYPOTHETICAL 23.9 K
exampleB    89   0    1000       45-     55 YBDM_ECOLI|P77174    HYPOTHETICAL 23.9 K
exampleC    59   0    1126      185-    195 YBDM_ECOLI|P77174    HYPOTHETICAL 23.9 K
exampleD    86   0    1102       56-     70 YBDM_ECOLI|P77174    HYPOTHETICAL 23.9 K
exampleE    82   0    1044      170-    206 YBDM_ECOLI|P77174    HYPOTHETICAL 23.9 K

No P-value computed for single block hits.

exampleA              <->A    (52,155):135                                     
TC1A_CAEBR               53   KKPLVSLKNRKARVEWAKQHLSWGPREWANHIWSDESKFNMFGTDG   
                                         ||        |   ||     | |       | |    
YBDM_ECOLI|P77174       136   qrIaATiRHnrARgRhqiTAMSeiVRElSqlgWdDnKigkelGmDS   

89.----------------------------------------------------------------------------------
exampleA    58   0    1006       83-    128 YFJJ_ECOLI|P52125    HYPOTHETICAL 24.6 K
exampleB    85   0    1054      196-    206 YFJJ_ECOLI|P52125    HYPOTHETICAL 24.6 K
exampleC    63   0    1111       99-    109 YFJJ_ECOLI|P52125    HYPOTHETICAL 24.6 K
exampleD    82   0    1123      175-    189 YFJJ_ECOLI|P52125    HYPOTHETICAL 24.6 K
exampleE    87   0    1038       42-     78 YFJJ_ECOLI|P52125    HYPOTHETICAL 24.6 K

P<  0.36 for exampleD in support of exampleA
                         |-----   94 residues----|
example              AAAAAAAAAAAA:::::.BBB::::::::::CCC:::::DDDD:::::..EEEEEEEEEE
YFJJ_ECOLI|P52125    AAAAAAAAAAAA::::::::::::DDDD
YFJJ_ECOLI|P52125                             CCC                       BBB                           CCC                       BBB


exampleA              <->A    (52,155):82                                      
Bari-1                  120   KTIEITPTNKTKRLRFALEYVKKPLDFWFNILWTDESAFQYQGSYS   
                                        | |     || |        ||     |    | |    
YFJJ_ECOLI|P52125        83   rKdwPdsRHsTlRyAWvREYtKNrkRhyhlILcfnqdAyyhlGdYd   

exampleD             A<->D    (99,104):46       
TC1A_CAEBR              201   WPSQSPDLNPIEHMW   
                                  |   |    |    
YFJJ_ECOLI|P52125       175   eQtySdlmNrvdyMt   

   190-    235 NRAM_INBVI|P16207    NEURAMINIDASE (EC 3
exampleB    67   0    1126       44-     54 NRAM_INBVI|Pblimps-3.9/examples/cobbler/000075500001460000012000000000001041506316600163765ustar00jorjastaff00000400000027blimps-3.9/examples/cobbler/README000064400001460000012000000011151041506322100172440ustar00jorjastaff00000400000027	Sample configuration files for cobbler (*.cf)

S. Henikoff and J.G. Henikoff, "Embedding strategies for effective use 
of information from multiple sequence alignments", Protein Science (1997) 
6:698-705.

http://blocks.fhcrc.org/help/about_cobbler.html

The cobbler program is available from the NCBI repository:
	ftp://ncbi.nlm.nih.gov/repository/blocks/unix/blimps/

The swat searching program is available from Phil Green:
	phg@u.washington.edu

The psi-blast (blastpgp) searching program is available from NCBI:
	ftp://ncbi.nlm.nih.gov/blast/

To test the installation: cobbler.csh

blimps-3.9/examples/cobbler/blosum55.iij000064400001460000012000000025560533155213300205540ustar00jorjastaff00000400000027#  BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 55
#  Entropy =   0.5637, Expected =  -0.4179
 A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V  B   Z   X
  5 
 -2   8 
 -2  -1   8 
 -2  -2   2   8 
  0  -4  -3  -4  13 
 -1   1   0   0  -4   7 
 -1   0   0   2  -4   2   7 
  0  -3   0  -2  -3  -2  -3   8 
 -2   0   1  -1  -4   1  -1  -2  11 
 -2  -4  -4  -4  -2  -4  -4  -5  -4   6 
 -2  -3  -4  -5  -2  -3  -4  -5  -3   2   6 
 -1   3   0  -1  -4   2   1  -2   0  -4  -3   6 
 -1  -2  -3  -4  -2   0  -3  -3  -2   2   3  -2   8 
 -3  -3  -4  -5  -3  -4  -4  -4  -1   0   1  -4   0   9 
 -1  -3  -2  -2  -3  -1  -1  -3  -3  -3  -4  -1  -3  -5  10 
  2  -1   1   0  -1   0   0   0  -1  -3  -3   0  -2  -3  -1   5 
  0  -1   0  -1  -1  -1  -1  -2  -2  -1  -2  -1  -1  -3  -1   2   6 
 -4  -3  -5  -5  -4  -2  -3  -3  -3  -3  -3  -4  -2   2  -5  -4  -3  15 
 -2  -2  -2  -3  -3  -1  -2  -4   2  -1  -1  -2  -1   4  -4  -2  -2   3   9 
  0  -3  -4  -4  -1  -3  -3  -4  -4   4   1  -3   1  -1  -3  -2   0  -4  -2   5 
 -2  -1   4   5  -4   0   1  -1   0  -4  -4   0  -3  -5  -2   0  -1  -5  -3  -4   5 
 -1   0   0   1  -4   4   5  -3   0  -4  -3   1  -2  -4  -1   0  -1  -3  -2  -3   0   5 
 -1  -1  -1  -2  -2  -1  -1  -2  -1  -1  -1  -1  -1  -2  -2  -1  -1  -3  -1  -1  -1  -1  -1 
blimps-3.9/examples/cobbler/blosum55.qij000064400001460000012000000033300533155213300205530ustar00jorjastaff00000400000027#  BLOSUM Clustered Target Frequencies=qij
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 55
   A      R      N      D      C      Q      E      G      H      I      L      K      M      F      P      S      T      W      Y      V   
0.0198 
0.0025 0.0157 
0.0022 0.0019 0.0116 
0.0024 0.0018 0.0035 0.0177 
0.0016 0.0005 0.0005 0.0005 0.0100 
0.0020 0.0025 0.0015 0.0016 0.0003 0.0064 
0.0032 0.0028 0.0023 0.0048 0.0005 0.0034 0.0150 
0.0059 0.0019 0.0030 0.0026 0.0008 0.0015 0.0021 0.0341 
0.0011 0.0013 0.0014 0.0010 0.0003 0.0011 0.0012 0.0010 0.0074 
0.0034 0.0014 0.0012 0.0013 0.0010 0.0010 0.0014 0.0017 0.0006 0.0158 
0.0045 0.0026 0.0016 0.0017 0.0014 0.0018 0.0023 0.0024 0.0011 0.0105 0.0328 
0.0033 0.0062 0.0025 0.0026 0.0005 0.0030 0.0044 0.0027 0.0013 0.0016 0.0025 0.0142 
0.0015 0.0008 0.0006 0.0005 0.0004 0.0008 0.0007 0.0008 0.0004 0.0023 0.0045 0.0009 0.0036 
0.0019 0.0011 0.0008 0.0007 0.0006 0.0006 0.0010 0.0013 0.0008 0.0031 0.0057 0.0011 0.0013 0.0163 
0.0022 0.0010 0.0010 0.0014 0.0004 0.0010 0.0017 0.0016 0.0006 0.0012 0.0016 0.0018 0.0005 0.0006 0.0184 
0.0064 0.0024 0.0031 0.0028 0.0011 0.0020 0.0030 0.0042 0.0011 0.0020 0.0027 0.0032 0.0009 0.0014 0.0018 0.0122 
0.0040 0.0020 0.0025 0.0021 0.0011 0.0015 0.0023 0.0025 0.0008 0.0029 0.0035 0.0025 0.0011 0.0013 0.0016 0.0049 0.0115 
0.0004 0.0003 0.0002 0.0002 0.0001 0.0003 0.0004 0.0005 0.0002 0.0004 0.0007 0.0003 0.0002 0.0009 0.0002 0.0003 0.0003 0.0063 
0.0015 0.0011 0.0008 0.0008 0.0004 0.0008 0.0011 0.0010 0.0013 0.0016 0.0026 0.0011 0.0007 0.0040 0.0006 0.0012 0.0011 0.0010 0.0086 
0.0054 0.0018 0.0013 0.0016 0.0014 0.0013 0.0019 0.0021 0.0007 0.0115 0.0092 0.0021 0.0022 0.0028 0.0015 0.0027 0.0039 0.0004 0.0017 0.0181 
blimps-3.9/examples/cobbler/default.amino.frq000064400001460000012000000024630665366177700216700ustar00jorjastaff000004000000270.0		-- [ 0] gap score = -
.07587		-- [ 1] Alanine       (Ala, A)
0.0		-- [21] ambiguity code B = D or N
.01666		-- [ 5] Cysteine      (Cys, C)
.05287		-- [ 4] Aspartic acid (Asp, D)
.06377		-- [ 7] Glutamic acid (Glu, E)
.04096		-- [14] Phenylalanine (Phe, F)
.06847		-- [ 8] Glycine       (Gly, G)
.02246		-- [ 9] Histidine     (His, H)
.05817		-- [10] Isoleucine    (Ile, I)
0.0		-- [25] no code J, 0, U
.05957		-- [12] Lysine        (Lys, K)
.09427		-- [11] Leucine       (Leu, L)
.02376		-- [13] Methionine    (Met, M)
.04456		-- [ 3] Asparagine    (Asn, N)
0.0		-- [25] no code J, 0, U
.04906		-- [15] Proline       (Pro, P)
.03976		-- [ 6] Glutamine     (Gln, Q)
.05166		-- [ 2] Arginine      (Arg, R)
.07127		-- [16] Serine        (Ser, S)
.05677		-- [17] Threonine     (Thr, T)
0.0		-- [25] no code J, 0, U
.06587		-- [20] Valine        (Val, V)
.01236		-- [18] Tryptophan    (Trp, W)
0.0		-- [23] ambiguity code X = any amino acid
.03186		-- [19] Tyrosine      (Tyr, Y)
0.0		-- [22] ambiguity code Z = E or Q
0.0		-- [24] stop codon translation score = *
-- Created from SwissProt 37

------------------------------------------------------------------------
BLIMPS (BLocks IMProved Searcher)
(C) Copyright 1999, Fred Hutchinson Cancer Research Center

default.amino.frq -- The default amino acid frequency file access.
 
blimps-3.9/examples/cobbler/default.codon.frq000064400001460000012000000020430544044452600216410ustar00jorjastaff000004000000270.0		-- [ 0] gap score = -
.0625		-- [ 1] Alanine       (Ala, A)
0.0		-- [21] ambiguity code B = D or N
.03125		-- [ 5] Cysteine      (Cys, C)
.03125		-- [ 4] Aspartic acid (Asp, D)
.03125		-- [ 7] Glutamic acid (Glu, E)
.03125		-- [14] Phenylalanine (Phe, F)
.0625		-- [ 8] Glycine       (Gly, G)
.03125		-- [ 9] Histidine     (His, H)
.04688		-- [10] Isoleucine    (Ile, I)
0.0		-- [25] no code J, 0, U
.03125		-- [12] Lysine        (Lys, K)
.09375		-- [11] Leucine       (Leu, L)
.01563		-- [13] Methionine    (Met, M)
.03125		-- [ 3] Asparagine    (Asn, N)
0.0		-- [25] no code J, 0, U
.0625		-- [15] Proline       (Pro, P)
.03125		-- [ 6] Glutamine     (Gln, Q)
.09375		-- [ 2] Arginine      (Arg, R)
.09375		-- [16] Serine        (Ser, S)
.0625		-- [17] Threonine     (Thr, T)
0.0		-- [25] no code J, 0, U
.0625		-- [20] Valine        (Val, V)
.0156		-- [18] Tryptophan    (Trp, W)
0.0		-- [23] ambiguity code X = any amino acid
.03125		-- [19] Tyrosine      (Tyr, Y)
0.0		-- [22] ambiguity code Z = E or Q
0.0		-- [24] stop codon translation score = *
blimps-3.9/examples/cobbler/default.iij000064400001460000012000000025560533154633300205320ustar00jorjastaff00000400000027#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 62
#  Entropy =   0.6979, Expected =  -0.5209
 A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V  B   Z   X
  4 
 -1   5 
 -2   0   6 
 -2  -2   1   6 
  0  -3  -3  -3   9 
 -1   1   0   0  -3   5 
 -1   0   0   2  -4   2   5 
  0  -2   0  -1  -3  -2  -2   6 
 -2   0   1  -1  -3   0   0  -2   8 
 -1  -3  -3  -3  -1  -3  -3  -4  -3   4 
 -1  -2  -3  -4  -1  -2  -3  -4  -3   2   4 
 -1   2   0  -1  -3   1   1  -2  -1  -3  -2   5 
 -1  -1  -2  -3  -1   0  -2  -3  -2   1   2  -1   5 
 -2  -3  -3  -3  -2  -3  -3  -3  -1   0   0  -3   0   6 
 -1  -2  -2  -1  -3  -1  -1  -2  -2  -3  -3  -1  -2  -4   7 
  1  -1   1   0  -1   0   0   0  -1  -2  -2   0  -1  -2  -1   4 
  0  -1   0  -1  -1  -1  -1  -2  -2  -1  -1  -1  -1  -2  -1   1   5 
 -3  -3  -4  -4  -2  -2  -3  -2  -2  -3  -2  -3  -1   1  -4  -3  -2  11 
 -2  -2  -2  -3  -2  -1  -2  -3   2  -1  -1  -2  -1   3  -3  -2  -2   2   7 
  0  -3  -3  -3  -1  -2  -2  -3  -3   3   1  -2   1  -1  -2  -2   0  -3  -1   4 
 -2  -1   3   4  -3   0   1  -1   0  -3  -4   0  -3  -3  -2   0  -1  -4  -3  -3   4 
 -1   0   0   1  -3   3   4  -2   0  -3  -3   1  -1  -3  -1   0  -1  -3  -2  -2   0   4 
  0  -1  -1  -1  -2  -1  -1  -1  -1  -1  -1  -1  -1  -1  -2   0   0  -2  -1  -1  -1  -1  -1 
blimps-3.9/examples/cobbler/default.qij000064400001460000012000000033300533154633300205310ustar00jorjastaff00000400000027#  BLOSUM Clustered Target Frequencies=qij
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 62
   A      R      N      D      C      Q      E      G      H      I      L      K      M      F      P      S      T      W      Y      V   
0.0215 
0.0023 0.0178 
0.0019 0.0020 0.0141 
0.0022 0.0016 0.0037 0.0213 
0.0016 0.0004 0.0004 0.0004 0.0119 
0.0019 0.0025 0.0015 0.0016 0.0003 0.0073 
0.0030 0.0027 0.0022 0.0049 0.0004 0.0035 0.0161 
0.0058 0.0017 0.0029 0.0025 0.0008 0.0014 0.0019 0.0378 
0.0011 0.0012 0.0014 0.0010 0.0002 0.0010 0.0014 0.0010 0.0093 
0.0032 0.0012 0.0010 0.0012 0.0011 0.0009 0.0012 0.0014 0.0006 0.0184 
0.0044 0.0024 0.0014 0.0015 0.0016 0.0016 0.0020 0.0021 0.0010 0.0114 0.0371 
0.0033 0.0062 0.0024 0.0024 0.0005 0.0031 0.0041 0.0025 0.0012 0.0016 0.0025 0.0161 
0.0013 0.0008 0.0005 0.0005 0.0004 0.0007 0.0007 0.0007 0.0004 0.0025 0.0049 0.0009 0.0040 
0.0016 0.0009 0.0008 0.0008 0.0005 0.0005 0.0009 0.0012 0.0008 0.0030 0.0054 0.0009 0.0012 0.0183 
0.0022 0.0010 0.0009 0.0012 0.0004 0.0008 0.0014 0.0014 0.0005 0.0010 0.0014 0.0016 0.0004 0.0005 0.0191 
0.0063 0.0023 0.0031 0.0028 0.0010 0.0019 0.0030 0.0038 0.0011 0.0017 0.0024 0.0031 0.0009 0.0012 0.0017 0.0126 
0.0037 0.0018 0.0022 0.0019 0.0009 0.0014 0.0020 0.0022 0.0007 0.0027 0.0033 0.0023 0.0010 0.0012 0.0014 0.0047 0.0125 
0.0004 0.0003 0.0002 0.0002 0.0001 0.0002 0.0003 0.0004 0.0002 0.0004 0.0007 0.0003 0.0002 0.0008 0.0001 0.0003 0.0003 0.0065 
0.0013 0.0009 0.0007 0.0006 0.0003 0.0007 0.0009 0.0008 0.0015 0.0014 0.0022 0.0010 0.0006 0.0042 0.0005 0.0010 0.0009 0.0009 0.0102 
0.0051 0.0016 0.0012 0.0013 0.0014 0.0012 0.0017 0.0018 0.0006 0.0120 0.0095 0.0019 0.0023 0.0026 0.0012 0.0024 0.0036 0.0004 0.0015 0.0196 
blimps-3.9/examples/cobbler/psi-blast.cf000064400001460000012000000016130677645663700206370ustar00jorjastaff00000400000027#	cobbler config file for PSI-BLAST checkpoint file output
#		Make a PSSM for each block (BL, FR, QM)
#		Select consensus residue based on highest PSSM value
#			(TY 4)
#		Embed the PSSM in the closest sequence from test.blks,
#			which is assumed to be in test.pros with the
#			same name and position (DB test.pros)
#		Trim the embbed PSSM to within 10 aas before the first
#			block and after the last block (TR 10)
#		Print a profile using the PSSM inside the blocks and 
#			and single55.psi outside them (MA, PF)
#	MA line triggers profile output, PF line specifies profile format
#	psi-blast.pro contains the embedded sequence (OU)
#	psi-blast.pro.prf contains the embedded pssm (OU)
#
#	Execute psi-blast:   
#	 blastpgp -i psi-blast.pro -R psi-blast.pro.prf -j  -d 
#
TY	4
BL	test.blks
FR	default.amino.frq
QM	blosum55.qij
TR	10
DB	test.pros
MA	single55.psi
PF	PSI
OU	psi-blast.cob
blimps-3.9/examples/cobbler/psi-blast.sq.cf000064400001460000012000000014540677645676600212670ustar00jorjastaff00000400000027#	cobbler config file for PSI-BLAST checkpoint file output
#		Make a PSSM for each block (BL, FR, QM)
#		Select consensus residue based on highest PSSM value
#			(TY 4)
#		Embed the PSSM in the sequence in test.pro (SQ)
#		Trim the embbed PSSM to within 10 aas before the first
#			block and after the last block (TR 10)
#		Print a profile using the PSSM inside the blocks and 
#			and single55.psi outside them (MA, PF)
#	MA line triggers profile output, PF line specifies profile format
#	psi-blast.sq.cob contains the embedded sequence
#	psi-blast.sq.cob.prf contains the embedded pssm
#
#	Execute psi-blast:   
# blastpgp -i psi-blast.sq.pro -R psi-blast.sq.pro.prf -j  -d 
#
TY	4
BL	test.blks
FR	default.amino.frq
QM	blosum55.qij
TR	10
SQ	test.pro
MA	single55.psi
PF	PSI
OU	psi-blast.sq.cob
blimps-3.9/examples/cobbler/single55.mat000064400001460000012000000121420615121313500205270ustar00jorjastaff00000400000027ID   SINGLE55; MATRIX
AC   SINGLE55; distance from previous block=(0,0)
DE   Single sequence PSSM using blosum55  rows are -ARNDCQEGHILKMFPSTWYVBZX*
MA   xxx width=25 seqs=1
  A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z   *   -
 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000  0.0000 0.0000 0.0000  0.0000
 6.9886 -2.7871 -0.0436 -2.9541 -2.4626 -2.7678 -0.3452 -2.6547 -1.6537 -1.9970 -2.6464 -1.5005 -2.5888 -3.1441 -2.5911 -2.7675  0.0191 -1.1867 -0.3786 -4.6933  0.0000 -2.8632 -2.5129  0.0000  0.0000
-2.7835 -2.1229 -3.4477 -2.5691 -1.4104 -3.5032 -3.6193 -0.3016 -3.8639  2.3625 -3.3906 -2.5910 -1.5933 -4.9266  0.0048  9.0014 -2.5959 -2.5567 -3.5034 -4.3083  0.0000 -2.5754 -0.8561  0.0000  0.0000
-2.5977  4.8661 -2.7087  1.0480 -1.5227 -4.1424 -0.9033  0.7582 -3.7921 -0.8295 -4.7528 -3.0971  9.3980 -4.1875 -1.4670 -1.5861 -0.7492 -0.8518 -4.1727 -5.3242  0.0000 -3.2147 -1.5009  0.0000  0.0000
-2.9602  5.5346 -3.4477  9.3121  0.9224 -5.4594 -2.2618 -1.4371 -4.1847 -1.3988 -5.2295 -4.6253  1.0508 -3.4703 -1.9268 -2.5592 -1.9288 -2.3455 -4.0131 -6.0632  0.0000 -3.9537 -0.1935  0.0000  0.0000
-1.2925 -4.3513  14.6022 -4.6905 -5.4441 -2.7040 -3.9405 -3.2254 -1.8976 -5.1117 -2.6472 -2.1685 -3.9487 -5.4698 -5.7493 -4.6806 -2.5500 -1.7216 -1.1685 -5.6406  0.0000 -3.5312 -5.5636  0.0000  0.0000
-1.9944 -1.1125 -3.9037 -1.3240  1.1848 -4.3717 -2.8875  0.7303 -3.5653  0.9754 -3.2272 -0.8362 -0.8615 -3.1717  8.9874  0.6175 -1.6302 -2.0469 -3.1569 -2.5534  0.0000 -2.1989  4.2408  0.0000  0.0000
-2.0304  0.2439 -3.7631  1.3607  7.9359 -4.2310 -3.5015 -0.9634 -4.1793  0.5628 -4.2365 -3.4843 -1.0817 -2.9453  1.0203 -0.9623 -1.9455 -2.2671 -3.5847 -3.3786  0.0000 -2.8908  5.2273  0.0000  0.0000
-0.6101 -1.8980 -2.9564 -2.5204 -4.1984 -4.3230  8.8898 -2.9800 -4.5665 -2.7783 -5.2799 -4.1339 -1.1593 -4.4352 -3.7490 -3.8681 -1.7168 -3.1338 -4.3791 -3.6403  0.0000 -4.5308 -4.0224  0.0000  0.0000
-3.1482 -0.9194 -2.4700 -1.9245 -1.8890 -1.6929 -3.2087  12.6273 -4.3425 -1.2102 -3.9250 -2.4025  0.2736 -3.9489 -0.3599 -0.7791 -2.7840 -3.3339 -4.4025 -2.8746  0.0000  1.3362 -1.2901  0.0000  0.0000
-2.5114 -4.8555 -1.5065 -5.0363 -5.4691 -0.0776 -5.1594 -4.7067  8.1920 -4.5588  1.5921  0.9209 -4.6409 -5.1962 -5.0197 -4.7057 -4.4438 -2.0072  3.4646 -4.1219  0.0000 -2.0125 -5.2931  0.0000  0.0000
-2.9130 -5.2707 -1.6649 -5.4899 -4.9352  0.9438 -5.2816 -3.6981  2.1833 -4.2420  6.8968  2.2111 -5.0105 -5.5658 -4.0904 -3.6411 -4.7596 -2.8080  0.8841 -3.3146  0.0000 -1.5259 -4.6044  0.0000  0.0000
-2.0730 -1.2071 -3.9388 -1.4686  0.0547 -3.9943 -2.5895 -0.7927 -3.7771  8.0357 -4.0514 -2.5724 -0.8966 -2.8737  0.3028  2.3025 -1.8419 -2.0820 -3.3273 -4.7994  0.0000 -3.0665  0.1519  0.0000  0.0000
-1.8058 -4.2245 -1.2249 -4.9245 -4.2218  0.4084 -4.1745 -2.2143  1.4733 -2.8018  2.1723  10.8460 -3.3936 -4.7380 -1.7382 -2.8804 -3.6525 -1.9556  0.5537 -2.8746  0.0000 -1.3431 -3.2491  0.0000  0.0000
-3.5947 -5.6767 -2.2820 -6.2802 -5.4901  10.5221 -4.8852 -2.0263 -0.0468 -4.7452  0.3834 -0.1131 -4.9605 -6.7609 -5.7953 -4.3141 -4.5522 -4.0445 -1.2145  0.8231  0.0000  3.3886 -5.6096  0.0000  0.0000
-2.3098 -2.9565 -3.3865 -2.6298 -2.5431 -5.0996 -3.3360 -2.6210 -3.5041 -1.9633 -4.4649 -3.5982 -3.3442  10.2908 -2.9340 -4.0762 -2.8140 -2.4954 -3.2654 -5.0362  0.0000 -4.1718 -2.6962  0.0000  0.0000
 0.6756 -0.7254 -0.6445 -1.2661 -1.7211 -3.0687 -0.7954 -1.6339 -2.9295 -1.1094 -3.8365 -2.6905 -0.0837 -2.9918 -1.5703 -1.9234  6.7750  0.7124 -2.3577 -4.9176  0.0000 -2.8081 -1.6620  0.0000  0.0000
-0.8977 -1.3661 -0.1836 -2.0503 -2.4102 -2.9286 -2.5799 -2.5513 -0.8605 -1.7170 -2.2524 -1.3612 -0.5539 -3.0408 -2.3545 -2.2516  0.3449  7.7085 -0.3053 -4.4567  0.0000 -2.7239 -2.3884  0.0000  0.0000
-4.9438 -5.9684 -4.6422 -6.3076 -4.0612  1.3996 -3.6260 -2.6316 -3.5147 -4.9739 -3.2985 -2.8197 -5.5657 -6.1211 -3.4006 -4.5428 -5.8247 -4.9963 -4.2418  16.1932  0.0000  2.7833 -3.8024  0.0000  0.0000
-3.0597 -3.8050 -2.4788 -4.1442 -3.5195  4.0190 -4.4626  1.6331 -1.3513 -3.1871 -1.4558 -1.2343 -3.4023 -5.2027 -2.9921 -2.7560 -3.6612 -3.2094 -1.8160  2.8373  0.0000  10.7248 -3.3129  0.0000  0.0000
-0.9874 -4.6876 -0.5285 -4.6159 -4.6257 -0.9964 -4.7231 -4.5179  3.7135 -3.8602  0.5418  0.2503 -4.7727 -4.7087 -4.3625 -4.0962 -3.6232 -1.2032  7.5252 -4.6002  0.0000 -2.2284 -4.5226  0.0000  0.0000
-2.9602  5.5346 -3.4477  9.3121  0.9224 -5.4594 -2.2618 -1.4371 -4.1847 -1.3988 -5.2295 -4.6253  1.0508 -3.4703 -1.9268 -2.5592 -1.9288 -2.3455 -4.0131 -6.0632  0.0000 -3.9537 -0.1935  0.0000  0.0000
-2.0304  0.2439 -3.7631  1.3607  7.9359 -4.2310 -3.5015 -0.9634 -4.1793  0.5628 -4.2365 -3.4843 -1.0817 -2.9453  1.0203 -0.9623 -1.9455 -2.2671 -3.5847 -3.3786  0.0000 -2.8908  5.2273  0.0000  0.0000
 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000  0.0000 0.0000 0.0000  0.0000
 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000  0.0000 0.0000 0.0000  0.0000
//
blimps-3.9/examples/cobbler/single55.psi000064400001460000012000000121440674004056700205560ustar00jorjastaff00000400000027ID   SINGLE; MATRIX
AC   SINGLE; distance from previous block=(3,1095)
DE   Single sequence
MA   xxx width=25 seqs=1
  A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z   *   -
 0.0678  0.0483  0.0339  0.0510  0.0552  0.0500  0.0630  0.0331  0.0578  0.0566  0.0829  0.0264  0.0452  0.0444  0.0375  0.0516  0.0566  0.0515  0.0645  0.0309  0.0512  0.0400  0.0484  0.0000  0.0264
 0.3861  0.0256  0.0177  0.0266  0.0355  0.0211  0.0654  0.0122  0.0377  0.0366  0.0499  0.0166  0.0244  0.0244  0.0222  0.0277  0.0709  0.0443  0.0598  0.0044  0.0611  0.0166  0.0304  0.0000  0.0044
 0.0404  0.0298  0.0081  0.0291  0.0452  0.0178  0.0307  0.0210  0.0226  0.1001  0.0420  0.0129  0.0307  0.0161  0.0404  0.4202  0.0388  0.0323  0.0291  0.0048  0.0532  0.0178  0.0434  0.0000  0.0048
 0.0421  0.2142  0.0096  0.0670  0.0441  0.0153  0.0575  0.0268  0.0230  0.0479  0.0307  0.0115  0.3889  0.0192  0.0287  0.0364  0.0594  0.0479  0.0249  0.0038  0.0510  0.0153  0.0382  0.0000  0.0038
 0.0388  0.2714  0.0081  0.4525  0.0775  0.0113  0.0420  0.0161  0.0210  0.0420  0.0275  0.0081  0.0565  0.0226  0.0258  0.0291  0.0452  0.0339  0.0258  0.0032  0.0539  0.0129  0.0577  0.0000  0.0032
 0.0570  0.0178  0.5228  0.0178  0.0178  0.0214  0.0285  0.0107  0.0356  0.0178  0.0499  0.0142  0.0178  0.0142  0.0107  0.0178  0.0392  0.0392  0.0499  0.0036  0.0347  0.0142  0.0151  0.0000  0.0036
 0.0484  0.0377  0.0073  0.0388  0.0824  0.0145  0.0363  0.0266  0.0242  0.0727  0.0436  0.0194  0.0363  0.0242  0.3217  0.0606  0.0484  0.0363  0.0315  0.0073  0.0500  0.0194  0.1743  0.0000  0.0073
 0.0480  0.0549  0.0075  0.0721  0.3919  0.0150  0.0315  0.0180  0.0210  0.0661  0.0345  0.0105  0.0345  0.0255  0.0511  0.0420  0.0450  0.0345  0.0285  0.0060  0.0572  0.0165  0.2610  0.0000  0.0060
 0.0667  0.0315  0.0090  0.0294  0.0237  0.0147  0.5522  0.0113  0.0192  0.0305  0.0271  0.0090  0.0339  0.0181  0.0170  0.0215  0.0475  0.0283  0.0237  0.0057  0.0623  0.0113  0.0211  0.0000  0.0057
 0.0371  0.0399  0.0101  0.0337  0.0405  0.0270  0.0337  0.4163  0.0202  0.0439  0.0371  0.0135  0.0472  0.0202  0.0371  0.0439  0.0371  0.0270  0.0236  0.0067  0.0402  0.0439  0.0392  0.0000  0.0067
 0.0430  0.0159  0.0126  0.0164  0.0177  0.0392  0.0215  0.0076  0.3665  0.0202  0.1328  0.0291  0.0152  0.0152  0.0126  0.0177  0.0253  0.0367  0.1454  0.0051  0.0519  0.0202  0.0158  0.0000  0.0051
 0.0392  0.0144  0.0122  0.0148  0.0200  0.0496  0.0209  0.0096  0.0914  0.0218  0.4523  0.0392  0.0139  0.0139  0.0157  0.0226  0.0235  0.0305  0.0801  0.0061  0.0664  0.0226  0.0184  0.0000  0.0061
 0.0476  0.0368  0.0072  0.0375  0.0634  0.0159  0.0389  0.0187  0.0231  0.3714  0.0360  0.0130  0.0360  0.0260  0.0433  0.0894  0.0461  0.0360  0.0303  0.0043  0.0558  0.0159  0.0557  0.0000  0.0043
 0.0506  0.0184  0.0135  0.0169  0.0236  0.0439  0.0270  0.0135  0.0776  0.0304  0.1518  0.2881  0.0202  0.0169  0.0270  0.0270  0.0304  0.0371  0.0742  0.0067  0.0472  0.0236  0.0249  0.0000  0.0067
 0.0335  0.0131  0.0106  0.0123  0.0176  0.4538  0.0229  0.0141  0.0546  0.0194  0.1004  0.0229  0.0141  0.0106  0.0106  0.0194  0.0247  0.0229  0.0493  0.0159  0.0474  0.0705  0.0149  0.0000  0.0106
 0.0450  0.0249  0.0082  0.0287  0.0348  0.0123  0.0328  0.0123  0.0246  0.0369  0.0328  0.0102  0.0205  0.5434  0.0205  0.0205  0.0369  0.0328  0.0307  0.0041  0.0516  0.0123  0.0293  0.0000  0.0041
 0.0898  0.0412  0.0154  0.0393  0.0421  0.0196  0.0589  0.0154  0.0281  0.0449  0.0379  0.0126  0.0435  0.0253  0.0281  0.0337  0.3378  0.0687  0.0379  0.0042  0.0598  0.0168  0.0367  0.0000  0.0042
 0.0624  0.0356  0.0172  0.0328  0.0359  0.0203  0.0390  0.0125  0.0453  0.0390  0.0546  0.0172  0.0390  0.0250  0.0234  0.0312  0.0765  0.3461  0.0609  0.0047  0.0546  0.0172  0.0311  0.0000  0.0047
 0.0245  0.0123  0.0061  0.0123  0.0245  0.0551  0.0306  0.0123  0.0245  0.0184  0.0429  0.0123  0.0123  0.0123  0.0184  0.0184  0.0184  0.0184  0.0245  0.5527  0.0296  0.0613  0.0222  0.0000  0.0061
 0.0379  0.0202  0.0101  0.0202  0.0278  0.1010  0.0253  0.0328  0.0404  0.0278  0.0657  0.0177  0.0202  0.0152  0.0202  0.0278  0.0303  0.0278  0.0429  0.0253  0.0433  0.3838  0.0249  0.0000  0.0101
 0.0611  0.0166  0.0159  0.0181  0.0215  0.0317  0.0238  0.0079  0.1302  0.0238  0.1042  0.0249  0.0147  0.0170  0.0147  0.0204  0.0306  0.0442  0.3716  0.0045  0.0382  0.0192  0.0189  0.0000  0.0045
 0.0388  0.2714  0.0081  0.4525  0.0775  0.0113  0.0420  0.0161  0.0210  0.0420  0.0275  0.0081  0.0565  0.0226  0.0258  0.0291  0.0452  0.0339  0.0258  0.0032  0.0539  0.0129  0.0577  0.0000  0.0032
 0.0480  0.0549  0.0075  0.0721  0.3919  0.0150  0.0315  0.0180  0.0210  0.0661  0.0345  0.0105  0.0345  0.0255  0.0511  0.0420  0.0450  0.0345  0.0285  0.0060  0.0572  0.0165  0.2610  0.0000  0.0060
 0.0678  0.0483  0.0339  0.0510  0.0552  0.0500  0.0630  0.0331  0.0578  0.0566  0.0829  0.0264  0.0452  0.0444  0.0375  0.0516  0.0566  0.0515  0.0645  0.0309  0.0512  0.0400  0.0484  0.0000  0.0264
 0.0678  0.0483  0.0339  0.0510  0.0552  0.0500  0.0630  0.0331  0.0578  0.0566  0.0829  0.0264  0.0452  0.0444  0.0375  0.0516  0.0566  0.0515  0.0645  0.0309  0.0512  0.0400  0.0484  0.0000  0.0264
//
blimps-3.9/examples/cobbler/single62.mat000064400001460000012000000121460674202440100205330ustar00jorjastaff00000400000027ID   SINGLE; MATRIX
AC   SINGLE; distance from previous block=(3,1095)
DE   Single sequence
MA   xxx width=25 seqs=1
  A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z   *   -
-0.3872  0.0344  2.2084 -0.0297 -0.4651  0.5879 -0.2819  1.3273  0.0158 -0.1489 -0.3558  0.3251  0.1105 -0.3466 -0.1876 -0.0002 -0.7393 -0.4124 -0.1240  2.7194 -0.0631  0.6885 -0.3585 -0.7393 -0.7393
 4.8572 -2.1589  0.2222 -2.1911 -1.8370 -2.3734 -0.1400 -1.7209 -1.3856 -1.3654 -1.8598 -1.4012 -2.1207 -1.9752 -1.7918 -1.9960 -0.0170 -0.8964 -0.3994 -2.9164 -0.9023 -2.2476 -1.8196 -2.9164 -2.9164
-2.0607 -1.5456 -2.7336 -2.0657 -1.0968 -2.9894 -2.6368 -0.4256 -3.1714  1.4984 -2.5645 -1.7579 -0.9285 -3.2060  0.0443  6.2720 -1.8803 -1.9312 -2.7001 -2.7022 -1.2944 -2.2645 -0.6586 -3.2060 -3.2060
-2.1849  3.4172 -2.3065  0.7803 -1.2606 -2.9021 -0.6687  0.4463 -3.2704 -0.8129 -3.6926 -2.6869  6.5458 -3.0829 -1.0025 -0.9279 -0.5919 -0.9251 -3.1030 -3.4450 -1.2148 -2.5625 -1.1615 -3.6926 -3.6926
-2.2987  3.8481 -2.8433  6.4702  0.5131 -3.4390 -1.6338 -1.0614 -3.2812 -1.3498 -4.0304 -3.2237  0.7369 -2.7897 -1.3532 -2.1086 -1.4224 -1.8849 -3.4089 -3.9819 -1.4886 -3.5441 -0.2036 -4.0304 -4.0304
-0.9704 -3.7026  10.1919 -3.9283 -4.4691 -2.5480 -2.6743 -3.4581 -1.2851 -3.6287 -1.5970 -1.6205 -3.4349 -3.7125 -3.9361 -3.8615 -2.1461 -1.7938 -0.9479 -3.7347 -2.3388 -3.2970 -4.2644 -4.4691 -4.4691
-1.4083 -0.7215 -2.3600 -0.8620  0.8557 -3.4817 -1.9934  0.2520 -2.7978  0.7021 -2.5307 -0.9395 -0.5549 -2.6462  6.2393  0.4925 -1.2279 -1.4527 -2.3265 -2.6685 -0.9333 -1.7859  2.9232 -3.4817 -3.4817
-1.4413  0.1855 -2.8808  1.0165  5.3956 -3.1366 -2.4631 -0.1280 -3.3186  0.1580 -3.2377 -2.2903 -0.8006 -2.3824  0.8680 -0.6363 -1.2608 -1.7744 -2.6723 -2.8494 -1.0563 -2.4116  3.6568 -3.3186 -3.3186
-0.4361 -1.4007 -1.7778 -1.8222 -3.1549 -3.2035  6.2230 -1.9959 -3.7709 -2.1665 -3.9940 -3.1874 -0.9006 -3.2794 -2.6729 -2.8682 -1.4758 -2.3964 -3.4044 -2.9164 -1.7598 -3.6485 -2.9698 -3.9940 -3.9940
-2.2334 -0.7966 -2.7780 -1.4662 -1.0362 -1.3736 -2.2123  8.7278 -3.2158 -1.2844 -3.1349 -1.8023 -0.0020 -3.2504 -0.6440 -0.8734 -2.0529 -2.7008 -3.5745 -1.9166 -1.4895  1.1651 -0.8856 -3.2504 -3.2504
-1.9000 -3.7028 -0.6068 -3.6879 -4.2287 -0.3075 -3.9891 -3.2177  5.5086 -3.2021  1.1393  0.7378 -3.7205 -3.9981 -3.6957 -3.6211 -3.5446 -1.5534  2.3216 -2.6642 -1.8487 -1.7817 -4.0240 -4.2287 -4.2287
-2.0633 -3.9916 -0.6079 -4.1262 -3.8370  0.3063 -3.9014 -2.8260  1.4501 -2.9966  4.6939  1.5973 -3.8319 -4.1095 -3.1177 -2.7033 -3.6318 -2.0566  0.5654 -2.1317 -1.6489 -1.5597 -3.5608 -4.1262 -4.1262
-1.3515 -1.0025 -2.4221 -1.2282 -0.2238 -3.3218 -1.8564 -0.7580 -2.6737  5.4830 -2.7791 -1.7504 -0.7348 -2.1823  0.3326  1.5771 -1.3514 -1.5563 -2.5366 -3.0346 -0.9751 -2.2928 -0.0102 -3.3218 -3.3218
-1.6045 -3.0937 -0.6311 -3.3194 -2.8894 -0.0569 -3.0946 -1.4931  1.0488 -1.9677  1.5975  7.3219 -2.8260 -3.7475 -1.5263 -1.8965 -2.4851 -1.5248  0.4495 -1.7697 -1.2678 -1.3319 -2.3659 -3.7475 -3.7475
-2.8568 -3.5890 -1.8387 -3.8146 -4.0157  7.1555 -3.3908 -1.3445 -0.2765 -3.8191  0.0264 -0.3369 -3.3212 -4.9550 -4.3485 -3.4080 -3.5064 -2.8501 -1.0481  0.3789 -1.9931  2.4314 -4.1435 -4.9550 -4.9550
-1.3589 -2.2197 -1.9035 -2.0657 -2.1618 -3.8553 -2.3670 -2.1216 -2.8674 -1.5799 -3.2896 -2.9278 -2.4024  7.1167 -2.4134 -2.5250 -1.9224 -1.8263 -2.7001 -5.0421 -1.7772 -3.1304 -2.2584 -5.0421 -5.0421
 0.5444 -0.3934 -0.3921 -0.7533 -1.0951 -2.4616 -0.6182 -0.9790 -2.4688 -0.8039 -2.8668 -1.7204  0.0338 -1.9773 -1.0499 -1.2541  4.5913  0.5358 -1.8325 -3.0046 -0.6963 -2.2628 -1.0778 -3.0046 -3.0046
-0.6382 -1.1000 -0.3430 -1.5191 -1.9119 -2.1085 -1.8421 -1.9300 -0.7808 -1.3121 -1.5948 -1.0633 -0.6027 -2.1844 -1.5780 -1.6083  0.2325  5.4252 -0.3094 -2.6515 -0.8700 -2.2137 -1.7837 -2.6515 -2.6515
-3.1742 -3.9064 -2.7999 -4.1320 -3.5030  0.6044 -2.8781 -1.6619 -2.4077 -3.3064 -2.1860 -1.8242 -3.6386 -5.9162 -3.3098 -2.8953 -3.8238 -3.1675 -2.7664  11.0897 -2.5210  1.6692 -3.4288 -5.9162 -5.9162
-2.3374 -3.0971 -2.1941 -3.5262 -2.8971  2.8250 -3.4422  1.5878 -1.3571 -2.3965 -1.4459 -1.2184 -2.5880 -3.8365 -2.2591 -2.2895 -2.9139 -2.5616 -1.5167  1.8373 -1.6588  7.5188 -2.6521 -3.8365 -3.8365
-0.7601 -3.5419 -0.1160 -3.6619 -3.4287 -0.9255 -3.4690 -3.4227  2.4753 -2.9112  0.4082  0.2921 -3.3995 -3.6771 -3.0706 -2.9960 -2.7546 -0.9283  5.1369 -2.8693 -1.7583 -1.7876 -3.2912 -3.6771 -3.6771
-2.2987  3.8481 -2.8433  6.4702  0.5131 -3.4390 -1.6338 -1.0614 -3.2812 -1.3498 -4.0304 -3.2237  0.7369 -2.7897 -1.3532 -2.1086 -1.4224 -1.8849 -3.4089 -3.9819 -1.4886 -3.5441 -0.2036 -4.0304 -4.0304
-1.4413  0.1855 -2.8808  1.0165  5.3956 -3.1366 -2.4631 -0.1280 -3.3186  0.1580 -3.2377 -2.2903 -0.8006 -2.3824  0.8680 -0.6363 -1.2608 -1.7744 -2.6723 -2.8494 -1.0563 -2.4116  3.6568 -3.3186 -3.3186
-0.3872  0.0344  2.2084 -0.0297 -0.4651  0.5879 -0.2819  1.3273  0.0158 -0.1489 -0.3558  0.3251  0.1105 -0.3466 -0.1876 -0.0002 -0.7393 -0.4124 -0.1240  2.7194 -0.0631  0.6885 -0.3585 -0.7393 -0.7393
-0.3872  0.0344  2.2084 -0.0297 -0.4651  0.5879 -0.2819  1.3273  0.0158 -0.1489 -0.3558  0.3251  0.1105 -0.3466 -0.1876 -0.0002 -0.7393 -0.4124 -0.1240  2.7194 -0.0631  0.6885 -0.3585 -0.7393 -0.7393
//
blimps-3.9/examples/cobbler/single62.psi000064400001460000012000000121440674174043500205560ustar00jorjastaff00000400000027ID   SINGLE; MATRIX
AC   SINGLE; distance from previous block=(3,1095)
DE   Single sequence
MA   xxx width=25 seqs=1
  A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z   *   -
 0.0663  0.0496  0.0358  0.0523  0.0543  0.0502  0.0621  0.0356  0.0585  0.0566  0.0833  0.0266  0.0463  0.0435  0.0373  0.0517  0.0552  0.0492  0.0631  0.0317  0.0510  0.0404  0.0477  0.0000  0.0266
 0.4085  0.0232  0.0180  0.0247  0.0337  0.0180  0.0652  0.0124  0.0360  0.0371  0.0495  0.0146  0.0214  0.0247  0.0214  0.0259  0.0709  0.0416  0.0574  0.0045  0.0618  0.0146  0.0290  0.0000  0.0045
 0.0371  0.0288  0.0065  0.0258  0.0436  0.0145  0.0275  0.0194  0.0194  0.1001  0.0388  0.0129  0.0323  0.0161  0.0404  0.4541  0.0371  0.0291  0.0258  0.0048  0.0532  0.0145  0.0424  0.0000  0.0048
 0.0356  0.2346  0.0075  0.0693  0.0412  0.0150  0.0543  0.0262  0.0187  0.0449  0.0262  0.0094  0.4307  0.0169  0.0281  0.0375  0.0581  0.0412  0.0225  0.0037  0.0505  0.0131  0.0362  0.0000  0.0037
 0.0342  0.2965  0.0062  0.4978  0.0762  0.0124  0.0389  0.0155  0.0187  0.0373  0.0233  0.0078  0.0575  0.0187  0.0249  0.0249  0.0435  0.0295  0.0202  0.0031  0.0540  0.0093  0.0565  0.0000  0.0031
 0.0542  0.0136  0.5698  0.0136  0.0136  0.0169  0.0271  0.0068  0.0373  0.0169  0.0542  0.0136  0.0136  0.0136  0.0102  0.0136  0.0339  0.0305  0.0474  0.0034  0.0334  0.0102  0.0122  0.0000  0.0034
 0.0466  0.0381  0.0074  0.0392  0.0858  0.0123  0.0343  0.0245  0.0221  0.0760  0.0392  0.0172  0.0368  0.0196  0.3456  0.0613  0.0466  0.0343  0.0294  0.0049  0.0499  0.0172  0.1856  0.0000  0.0049
 0.0460  0.0562  0.0061  0.0752  0.4138  0.0138  0.0292  0.0215  0.0184  0.0629  0.0307  0.0107  0.0338  0.0215  0.0537  0.0414  0.0460  0.0307  0.0261  0.0046  0.0573  0.0138  0.2755  0.0000  0.0046
 0.0652  0.0302  0.0090  0.0281  0.0214  0.0135  0.5918  0.0112  0.0157  0.0281  0.0236  0.0079  0.0326  0.0157  0.0157  0.0191  0.0427  0.0247  0.0202  0.0045  0.0629  0.0090  0.0192  0.0000  0.0045
 0.0350  0.0376  0.0064  0.0318  0.0445  0.0254  0.0318  0.4625  0.0191  0.0382  0.0318  0.0127  0.0445  0.0159  0.0318  0.0382  0.0350  0.0223  0.0191  0.0064  0.0389  0.0477  0.0396  0.0000  0.0064
 0.0393  0.0136  0.0135  0.0147  0.0147  0.0368  0.0172  0.0074  0.3925  0.0196  0.1399  0.0307  0.0123  0.0123  0.0110  0.0147  0.0209  0.0331  0.1473  0.0049  0.0520  0.0172  0.0133  0.0000  0.0049
 0.0371  0.0123  0.0135  0.0127  0.0169  0.0455  0.0177  0.0084  0.0962  0.0211  0.4796  0.0413  0.0118  0.0118  0.0135  0.0202  0.0202  0.0278  0.0801  0.0059  0.0675  0.0186  0.0156  0.0000  0.0059
 0.0475  0.0345  0.0072  0.0345  0.0590  0.0130  0.0360  0.0173  0.0230  0.3984  0.0360  0.0130  0.0345  0.0230  0.0446  0.0892  0.0446  0.0331  0.0273  0.0043  0.0561  0.0144  0.0535  0.0000  0.0043
 0.0435  0.0167  0.0134  0.0167  0.0234  0.0402  0.0234  0.0134  0.0837  0.0301  0.1640  0.3005  0.0167  0.0134  0.0234  0.0268  0.0301  0.0335  0.0770  0.0067  0.0472  0.0201  0.0234  0.0000  0.0067
 0.0282  0.0141  0.0088  0.0141  0.0159  0.4891  0.0211  0.0141  0.0529  0.0159  0.0951  0.0211  0.0141  0.0088  0.0088  0.0159  0.0211  0.0211  0.0458  0.0141  0.0468  0.0740  0.0131  0.0000  0.0088
 0.0474  0.0229  0.0086  0.0258  0.0301  0.0108  0.0301  0.0108  0.0215  0.0345  0.0301  0.0086  0.0194  0.5780  0.0172  0.0215  0.0366  0.0301  0.0258  0.0022  0.0518  0.0108  0.0252  0.0000  0.0022
 0.0916  0.0427  0.0145  0.0407  0.0436  0.0175  0.0553  0.0160  0.0247  0.0451  0.0349  0.0131  0.0451  0.0247  0.0276  0.0334  0.3499  0.0684  0.0349  0.0044  0.0601  0.0145  0.0375  0.0000  0.0044
 0.0608  0.0335  0.0148  0.0312  0.0329  0.0197  0.0362  0.0115  0.0444  0.0378  0.0542  0.0164  0.0362  0.0230  0.0230  0.0296  0.0773  0.3721  0.0592  0.0049  0.0548  0.0148  0.0291  0.0000  0.0049
 0.0253  0.0126  0.0063  0.0126  0.0189  0.0505  0.0253  0.0126  0.0253  0.0189  0.0442  0.0126  0.0126  0.0063  0.0126  0.0189  0.0189  0.0189  0.0253  0.5770  0.0288  0.0568  0.0165  0.0000  0.0063
 0.0337  0.0168  0.0078  0.0156  0.0234  0.1090  0.0208  0.0389  0.0363  0.0260  0.0571  0.0156  0.0182  0.0130  0.0182  0.0234  0.0260  0.0234  0.0389  0.0234  0.0418  0.4315  0.0214  0.0000  0.0078
 0.0583  0.0143  0.0160  0.0149  0.0194  0.0297  0.0206  0.0069  0.1372  0.0217  0.1086  0.0263  0.0137  0.0137  0.0137  0.0183  0.0274  0.0412  0.3907  0.0046  0.0373  0.0171  0.0172  0.0000  0.0046
 0.0342  0.2965  0.0062  0.4978  0.0762  0.0124  0.0389  0.0155  0.0187  0.0373  0.0233  0.0078  0.0575  0.0187  0.0249  0.0249  0.0435  0.0295  0.0202  0.0031  0.0540  0.0093  0.0565  0.0000  0.0031
 0.0460  0.0562  0.0061  0.0752  0.4138  0.0138  0.0292  0.0215  0.0184  0.0629  0.0307  0.0107  0.0338  0.0215  0.0537  0.0414  0.0460  0.0307  0.0261  0.0046  0.0573  0.0138  0.2755  0.0000  0.0046
 0.0663  0.0496  0.0358  0.0523  0.0543  0.0502  0.0621  0.0356  0.0585  0.0566  0.0833  0.0266  0.0463  0.0435  0.0373  0.0517  0.0552  0.0492  0.0631  0.0317  0.0510  0.0404  0.0477  0.0000  0.0266
 0.0663  0.0496  0.0358  0.0523  0.0543  0.0502  0.0621  0.0356  0.0585  0.0566  0.0833  0.0266  0.0463  0.0435  0.0373  0.0517  0.0552  0.0492  0.0631  0.0317  0.0510  0.0404  0.0477  0.0000  0.0266
//
blimps-3.9/examples/cobbler/swat.cf000064400001460000012000000015420677645606300177110ustar00jorjastaff00000400000027#	cobbler config file for SWAT profile output
#		Make a PSSM for each block (BL, FR, QM)
#		Select consensus residue based on pairwise scores
#			from blosum55.iij (TY 2, SU)
#		Embed the PSSM in the closest sequence from test.blks,
#			which is assumed to be in test.pros with the
#			same name and position (DB test.pros)
#		Trim the embbed PSSM to within 10 aas before the first
#			block and after the last block (TR 10)
#		Print a profile using the PSSM inside the blocks and 
#			and single55.mat outside them (MA, PF)
#	MA line triggers profile output, PF line specifies profile format
#	swat.cob contains the embedded sequence
#	swat.cob.prf contains the embedded pssm
#
#	Execute swat:   swat swat.cob  -M swat.cob.prf
#
TY	2
SU	blosum55.iij
BL	test.blks
FR	default.amino.frq
QM	blosum55.qij
TR	10
DB	test.pros
MA	single55.mat
PF	SWAT
OU	swat.cob
blimps-3.9/examples/cobbler/swat.sq.cf000064400001460000012000000014160677645612600203330ustar00jorjastaff00000400000027#	cobbler config file for SWAT profile output
#		Make a PSSM for each block (BL, FR, QM)
#		Select consensus residue based on pairwise scores
#			from blosum55.iij (TY 2, SU)
#		Embed the PSSM in the sequence in test.pro (SQ)
#		Trim the embbed PSSM to within 10 aas before the first
#			block and after the last block (TR 10)
#		Print a profile using the PSSM inside the blocks and 
#			and single55.mat outside them (MA, PF)
#	MA line triggers profile output, PF line specifies profile format
#	swat.sq.cob contains the embedded sequence
#	swat.sq.cob.prf contains the embedded pssm
#
#	Execute swat:   swat swat.sq.cob  -M swat.sq.cob.prf
#
TY	2
SU	blosum55.iij
BL	test.blks
FR	default.amino.frq
QM	blosum55.qij
TR	10
SQ	test.pro
MA	single55.mat
PF	SWAT
OU	swat.sq.cob
blimps-3.9/examples/cobbler/test.blks000064400001460000012000000210650616560221000202320ustar00jorjastaff00000400000027ID   C5_MTASE_1; BLOCK
AC   PS00094A; distance from previous block=(3,1095)
DE   C-5 cytosine-specific DNA methylases active site.
BL   LFG motif=[22,0,17] motomat=[1,80,-10] width=18 seqs=36
MTA1_ARTLU (  11) VDLFAGIGGFHAALAATG  33

MTB1_BREEP (   4) LSLFSGCGGMDLGLEGGF  31

MTD2_HERAU (   6) IDLFCGVGGLTHGLILEG  45

MTDM_ARATH (1096) LDIFAGCGGLSHGLKKAG  29

MTG1_HAEGA (   8) LSLFSSAGIGEYFLSRVG 100

MTH2_HAEPA (  35) IDLFAGIGGFRIAMQNLG  40

MTS3_STAAU (   7) VELFAGVGGFRLGLENTK  31

MTS9_STAAU ( 102) FETFAGAGGLALGLESAG  38

MTSB_LACLC (   5) FEAFAGYGSQRLALIKAN  58

MTSI_SPISQ (  14) FEAFAGIGAQRKALEKVR  42

 DCM_ECOLI (  90) IDLFAGIGGIRRGFESIG  22
MTBA_BACAR (   6) VDLFAGIGGIRIGFERAA  26
MTBF_BACSU ( 104) IDLFAGIGGIRLGFEDKY  30
MTC1_HERAU (   5) IDLFAGIGGMRLGFEQAM  20
MTD1_DESDN (   4) IDLFAGCGGFSHGFKMAG  23
MTD1_HERAU (   4) IDLFAGCGGMSLGFMQAG  21
MTE2_ECOLI (  99) IDLFAGIGGIRKGFETIG  22
MTNX_NEILA (   5) IDLFAGIGGIRLGFEQAF  16
MTS2_SHISO (  75) IDLFAGIGGTRLGFHQTN  21
MTSA_LACLC (  82) IDLFAGIGGTRLGFHQTE  24

MTB1_BACSH (  61) LSLFCGAGGLDLGFELAG  24
MTBR_BACSU (  62) LSLFSGCGGLDLGFELAG  16
MTF1_FUSNU (   4) LSLFSGAGGLDLGFERAG  16
MTH3_HAEAE (   4) ISLFSGAGGLDLGFQKAG  17
MTHT_METTF (   6) ASFFSGAGGLDLGFTKAG  34
MTNG_NEIGO (   4) ISLFSGCGGLDLGFEKAG  15
MTSI_SALIN (  78) LSFFSGAMGLDLGIEQAG  62

MTB1_HERAU (   7) IDLFAGIGGFRLGLEAVG  14
MTC2_HERAU (   7) IDLFAGIGGFRLGLEAVG  14
MTE1_HERAU (   7) IDLFAGIGGFRLGLEAVG  14
MTH1_HAEHA (  15) IDLFAGLGGFRLALESCG  30

MTBP_BPPHT (   7) MSLFSGIGAFEAALRNIG  27
MTBR_BPRH1 (   7) MSLFSGIGAFEAALRNIG  27
MTBS_BPSPR (   7) MSLFSGIGAFEAALRNIG  27

MTDM_HUMAN (1021) LDVFSGCGGLSEGFHQAG  24
MTDM_MOUSE (1027) LDVFSGCGGLSEGFHQAG  24
//
ID   C5_MTASE_1; BLOCK
AC   PS00094B; distance from previous block=(40,101)
DE   C-5 cytosine-specific DNA methylases active site.
BL   PCS motif=[22,0,17] motomat=[1,80,-10] width=26 seqs=36
MTA1_ARTLU (  76) DVLTGGFPCQPFSKSGAQHGMAETRG  31

MTB1_BREEP ( 107) DVVTGGFPCQDFSFAGKRKGFDSHKD  37

MTBF_BACSU ( 162) DVLLAGFPCQPFSNIGKREGFAHERR  42

MTBP_BPPHT (  70) DLLTSGFPCPTFSVAGGRDGMEYKCS  53

MTD1_DESDN (  68) DGIIGGPPCQGFSLSGNRDQKDPRNS  39

MTD1_HERAU (  67) ELIIGGPPCQDFSSAGKRDEGLGRAN  41

MTD2_HERAU (  71) KILVGCAPCQDFSQYTKKSRTGTKWQ 100

MTDM_ARATH (1190) DFINGGPPCQGFSGMNRFNQSSWSKV  50

MTG1_HAEGA (  75) DFLIASPPCQGMSVAGKNRDVSNMAN  54

MTHT_METTF (  65) VGFIGGPPCQSWSLAGSMCGADDPRG  47

MTS3_STAAU (  77) DMIVGGFPCQDYSVARSLNGELGIQG  57

MTS9_STAAU ( 166) DILSGGYPCQTFSYAGKRNGFADTRG  31

MTSB_LACLC ( 119) DFFTYSFPCQDISVAGYQNGLVADSG  60

MTSI_SALIN ( 146) DLIMGGPPCQAFSTAGKRLGLEDERG  30

MTSI_SPISQ ( 133) DLLTYSFPCQDLSQQGIQKGMKRGSG  59

 DCM_ECOLI ( 169) DVLLAGFPCQPFSLAGVSKKNSLGRA  31
MTE2_ECOLI ( 178) DVLLAGFPCQPFSLAGVSKKNSLGRA  31

MTB1_BACSH ( 148) NLVIGGFPCPGFSEAGPRLVDDERNF  43
MTBR_BACSU ( 149) NLILGGFPCPGFSEAGPRLIDDDRNF  39

MTB1_HERAU (  67) DVLVGGVPCQPWSIAGKNQAFDDPRG  22
MTC2_HERAU (  67) DLVVGGVPCQPWSIAGKNQAFDDPRG  25
MTE1_HERAU (  67) DVLVGGVPCQPWSIAGKNQAFDDPRG  22

MTBA_BACAR (  68) DFLLAGFPCQPFSYAGKQQGFGDTRG  20
MTC1_HERAU (  67) DFLLAGFPCQPFSYAGKQKGFGDTRG  19
MTH1_HAEHA (  73) DILCAGFPCQAFSISGKQKGFEDSRG  21
MTH2_HAEPA (  95) DILCAGFPCQAFSIAGKRGGFEDTRG  22
MTNX_NEILA (  66) DILSAGFPCQPFSQAGLKKGFADTRG  22
MTS2_SHISO ( 134) EILVGGFPCVAFSQAGLKKGFNDTRG  39
MTSA_LACLC ( 141) DILVGGFPCQAFSQAGKKLGFDDTRG  18

MTBR_BPRH1 (  70) DLLVGGSPCQSFSVAGYRKGFEDTRG  21
MTBS_BPSPR (  70) DLLVGGSPCQSFSVAGHRKGFEDTRG  23

MTDM_HUMAN (1097) EMLCGGPPCQGFSGMNRFNSRTYSKF  40
MTDM_MOUSE (1103) EMLCGGPPCQGFSGMNRFNSRTYSKF  40

MTF1_FUSNU (  63) DGIIGGPPCQSWSEAGSLRGINDPRG  24
MTH3_HAEAE (  63) DGIIGGPPCQSWSEGGSLRGIDDPRG  29
MTNG_NEIGO (  65) DGIIGGPPCQSWSEAGALRGIDDARG  27
//
ID   C5_MTASE_1; BLOCK
AC   PS00094C; distance from previous block=(13,47)
DE   C-5 cytosine-specific DNA methylases active site.
BL   PFN motif=[22,0,17] motomat=[1,80,-10] width=12 seqs=36
MTA1_ARTLU ( 116) PTVLILENVRNL  45

MTD1_HERAU ( 106) PAWVIMENVERA  88

MTD2_HERAU ( 110) PDIISMENVPEV 100

MTG1_HAEGA ( 119) PAYILIENVPFL  61

MTH1_HAEHA ( 113) PKVVFMENVKNF  49

 DCM_ECOLI ( 218) PAMFVLENVKNL  31
MTB1_BACSH ( 187) PEIFVAENVKGM  34
MTB1_BREEP ( 162) PKVFIAENVKGL  27
MTB1_HERAU ( 107) PKAFIFENVKGL  26
MTBA_BACAR ( 108) PKAFLLENVRGL  22
MTBF_BACSU ( 202) PKMFLLENVKGL  27
MTBP_BPPHT ( 143) PKFVILENVKGL  31
MTBR_BACSU ( 188) PEIFVAENVKGM  34
MTBR_BPRH1 ( 110) PRYFVFENVKGL  28
MTBS_BPSPR ( 110) PKFFVFENVKGL  26
MTC1_HERAU ( 107) PKGFLLENVRGL  35
MTC2_HERAU ( 107) PKAFIFENVKGL  26
MTD1_DESDN ( 107) PKFFVMENVLGI  48
MTE1_HERAU ( 107) PKAFIFENVKGL  26
MTE2_ECOLI ( 227) PAIFVLENVKNL  28
MTF1_FUSNU ( 103) PKFFLAENVKGM  26
MTH2_HAEPA ( 135) PKAFFLENVKGL  30
MTH3_HAEAE ( 103) PIFFLAENVKGM  37
MTHT_METTF ( 105) PLFFLAENVPGI  47
MTNG_NEIGO ( 105) PKFFLAENVSGM  40
MTNX_NEILA ( 106) PQAFLLENVKQL  46
MTS2_SHISO ( 174) PHAFLLENVKNL  33
MTS9_STAAU ( 206) PKAFIAENVRGL  25
MTSA_LACLC ( 181) PKAFLLENVKNL  22
MTSI_SALIN ( 186) PKYIVIENVRGL  43

MTDM_ARATH (1232) PRYFLLENVRTF  43
MTDM_HUMAN (1139) PRFFLLENVRNF  30
MTDM_MOUSE (1145) PRFFLLENVRNF  30

MTS3_STAAU ( 120) PKYLLLENVDRL  48
MTSB_LACLC ( 162) PKYLMMENVKNL  49
MTSI_SPISQ ( 180) PKYLLMENVGAL  58
//
ID   C5_MTASE_1; BLOCK
AC   PS00094D; distance from previous block=(16,40)
DE   C-5 cytosine-specific DNA methylases active site.
BL   AQR motif=[22,0,17] motomat=[1,80,-10] width=27 seqs=36
MTA1_ARTLU ( 154) PAIFSPHLLPAWMGGTPQVRERVFITA 100

MTB1_BREEP ( 194) YVVLDAQVLNAKNYGVAQNRERVIFIG  52

MTBA_BACAR ( 139) GYGVSYLLLNSSTFGVPQNRVRIYILG  43

MTBF_BACSU ( 233) GYSVFYEVMDAQNFGLPQRRERIVIVG  43

MTC1_HERAU ( 137) LNYGVYLILNSSNFQVPQNRLRVYIVG  76

MTD1_DESDN ( 141) GYKVCVIILNACDYGVPQSRQRVFFIG  53

MTD1_HERAU ( 134) GYSLAQVVLDASLCGVPQLRKRTFVIG  83

MTD2_HERAU ( 141) GYHVSHSVVHCPDYGIPQQRDRLVLFA  85

MTDM_ARATH (1263) GYQVRFGILEAGAYGVSQSRKRAFIWA  66

MTG1_HAEGA ( 155) EYHIHFDILDAADYGTPQRRKRAIIRL  64

MTH1_HAEHA ( 144) DYSFHAKVLNALDYGIPQKRERIYMIC  48

MTH2_HAEPA ( 168) YFVPEPAIVNAKNFGVPQNRERIYIVG  49

MTHT_METTF ( 136) GYNVEYKVLNAKDYGVPQDRKRVFIVG  23

MTNG_NEIGO ( 136) GYDVTLTMANAKDYGVAQERKRVFYIG  57

MTNX_NEILA ( 137) GYKVYTEVLKARDFGIPQNRERIYLVG  33

MTS2_SHISO ( 205) NYTVYYNIFAAKDFGVPQNRERIYIVG  44

MTS3_STAAU ( 154) GYNVEWRVINAADYGNAQRRRRVFIFG  47

MTS9_STAAU ( 237) GYEVYWNILNSWNYDVAQKRERIVIIG  46

MTSA_LACLC ( 212) DYEVHTALFKARDFGLPQNRERIYIVG  40

MTSB_LACLC ( 193) GYTNYWDILNARDFGIPQNRERVFCIS  46

MTSI_SALIN ( 238) GYSVSFNLYNSANFGVPQIRERVIIIC  42

MTSI_SPISQ ( 211) GYQNSIEVLNAADFGSSQARRRVFMIS  63

 DCM_ECOLI ( 257) DNGPDDPKIIDGKHFLPQHRERIVLVG  80
MTE2_ECOLI ( 266) EMGKNDPKVIDGKHFLPQHRERIVLVG  94

MTB1_BACSH ( 218) GYRVEARLLNARDYGVPQIRERVIIVG  27
MTBR_BACSU ( 219) GYRVQFKLLNARDYGVPQLRERVIIEG  36

MTB1_HERAU ( 138) GYSVFYKLLNSFDFGVAQNRDRVFIVG  25
MTC2_HERAU ( 138) GYNVYYKLLNSFDYGVAQNRDRVFIIG  25
MTE1_HERAU ( 138) GYSVFYKLLNSFDFGVAQNRDRVFIVG  25

MTBP_BPPHT ( 174) GYRIDLELLNSKFFNVPQNRERVYIIG  30
MTBR_BPRH1 ( 141) GYRIDLELLNSKFFNVPQNRERIYIIG  30
MTBS_BPSPR ( 141) GYRIDLELLNSKFFNVPQNRERLYIIG  36

MTDM_HUMAN (1170) GYQCTFGVLQAGQYGVAQTRRRAIILA  45
MTDM_MOUSE (1176) GYQCTFGVLQAGQYGVAQTRRRAIILA  45

MTF1_FUSNU ( 134) GYNVFIKLLNAFDYGVAQDRERVFYVG  27
MTH3_HAEAE ( 134) GYDVHIILLNANDYGVAQDRKRVFYIG  35
//
ID   C5_MTASE_1; BLOCK
AC   PS00094E; distance from previous block=(70,274)
DE   C-5 cytosine-specific DNA methylases active site.
BL   RQP motif=[22,0,17] motomat=[1,80,-10] width=16 seqs=36
MTA1_ARTLU ( 437) RRLSPRETARLQGLPE  18

MTBF_BACSU ( 349) RLFSELELKRLMGFPV  30

MTD1_HERAU ( 244) RPLTTKERSLIQTFPL  30

MTD2_HERAU ( 287) RAISLREAALLQTFPR  27

MTG1_HAEGA ( 305) RVLSVLELMRLTGLPD  31

MTH1_HAEHA ( 272) RKLHPRECARVMGYPD  28

MTS3_STAAU ( 349) RTLTPIEAERLNGFPD  29

MTSB_LACLC ( 290) RQLVSGKVRPDGKYPA 100

MTSI_SALIN ( 382) RPLSVQEYKVIQQFPE  36

MTSI_SPISQ ( 332) RKMNSDETFLYIGFDS  53

 DCM_ECOLI ( 400) RRLTPRECARLMGFEA  18
MTB1_BACSH ( 345) RRLSVKEIKRIQTFPD  14
MTB1_BREEP ( 339) RRLTVRECALIQSFPP  17
MTB1_HERAU ( 378) RKITVSEAARLQGFPG  15
MTBA_BACAR ( 364) RRITPRECARLQGFPD   8
MTBR_BACSU ( 346) RRLSVKEIARVQTFPD  14
MTC1_HERAU ( 364) RRITPREMPRLQGFPD  17
MTC2_HERAU ( 378) RPITVNEAARIQGFPA  15
MTD1_DESDN ( 312) RNFTAREGARIQSFPD  26
MTDM_ARATH (1474) RILTVRECARSQGFPD  14
MTDM_HUMAN (1425) RVVSVRECARSQGFPD  15
MTDM_MOUSE (1430) RVVSVRECARSQGFPD  15
MTE1_HERAU ( 378) RPITVSEAARLQGFPS  12
MTE2_ECOLI ( 409) RRLTPRECARLMGFEK  21
MTF1_FUSNU ( 276) RRLSIRECARIQGFPD  10
MTH2_HAEPA ( 303) RKMTPREWARLQGFPD  14
MTH3_HAEAE ( 273) RRLTVRECARVQGFPD   9
MTHT_METTF ( 274) RRLSVRECARIQGFPD   8
MTNG_NEIGO ( 277) RRMTVREVARIQGFPD  12
MTNX_NEILA ( 255) RKITPPEAARLQGFPD  13
MTS2_SHISO ( 327) RKITPREASRLQGFPS  12
MTS9_STAAU ( 376) RPFSIREYARIQSFPD  18
MTSA_LACLC ( 334) RKITPREAARLQGFPE   9

MTBP_BPPHT ( 382) RKLSPLECWRLQAFDD  16
MTBR_BPRH1 ( 442) RKLTPLECWRLQAFDE  17
MTBS_BPSPR ( 378) RRLTPLECFRLQAFDD  16
//
blimps-3.9/examples/cobbler/test.pro000064400001460000012000000007550654673000400201100ustar00jorjastaff00000400000027>DCM_ECOLI 472
MQENISVTDSYSTGNAAQAMLEKLLQIYDVKTLVAQLNGVGENHWSAAILKRALANDSAWHRLSEKEFAHLQTLLPKPPA
HHPHYAFRFIDLFAGIGGIRRGFESIGGQCVFTSEWNKHAVRTYKANHYCDPATHHFNEDIRDITLSHKEGVSDEAAAEH
IRQHIPEHDVLLAGFPCQPFSLAGVSKKNSLGRAHGFACDTQGTLFFDVVRIIDARRPAMFVLENVKNLKSHDQGKTFRI
IMQTLDELGYDVADAEDNGPDDPKIIDGKHFLPQHRERIVLVGFRRDLNLKADFTLRDISECFPAQRVTLAQLLDPMVEA
KYILTPVLWKYLYRYAKKHQARGNGFGYGMVYPNNPQSVTRTLSARYYKDGAEILIDRGWDMATGEKDFDDPLNQQHRPR
RLTPRECARLMGFEAPGEAKFRIPVSDTQAYRQFGNSVVVPVFAAVAKLLEPKIKQAVALRQQEAQHGRRSR
blimps-3.9/examples/cobbler/test.pros000064400001460000012000000477340605720404600203020ustar00jorjastaff00000400000027>DCM_ECOLI 472
MQENISVTDSYSTGNAAQAMLEKLLQIYDVKTLVAQLNGVGENHWSAAILKRALANDSAWHRLSEKEFAHLQTLLPKPPA
HHPHYAFRFIDLFAGIGGIRRGFESIGGQCVFTSEWNKHAVRTYKANHYCDPATHHFNEDIRDITLSHKEGVSDEAAAEH
IRQHIPEHDVLLAGFPCQPFSLAGVSKKNSLGRAHGFACDTQGTLFFDVVRIIDARRPAMFVLENVKNLKSHDQGKTFRI
IMQTLDELGYDVADAEDNGPDDPKIIDGKHFLPQHRERIVLVGFRRDLNLKADFTLRDISECFPAQRVTLAQLLDPMVEA
KYILTPVLWKYLYRYAKKHQARGNGFGYGMVYPNNPQSVTRTLSARYYKDGAEILIDRGWDMATGEKDFDDPLNQQHRPR
RLTPRECARLMGFEAPGEAKFRIPVSDTQAYRQFGNSVVVPVFAAVAKLLEPKIKQAVALRQQEAQHGRRSR
>MTA1_ARTLU 521
MSKANAKYSFVDLFAGIGGFHAALAATGGVCEYAVEIDREAAAVYERNWNKPALGDITDDANDEGVTLRGYDGPIDVLTG
GFPCQPFSKSGAQHGMAETRGTLFWNIARIIEEREPTVLILENVRNLVGPRHRHEWLTIIETLRFFGYEVSGAPAIFSPH
LLPAWMGGTPQVRERVFITATLVPERMRDERIPRTETGEIDAEAIGPKPVATMNDRFPIKKGGTELFHPGDRKSGWNLLT
SGIIREGDPEPSNVDLRLTETETLWIDAWDDLESTIRRATGRPLEGFPYWADSWTDFRELSRLVVIRGFQAPEREVVGDR
KRYVARTDMPEGFVPASVTRPAIDETLPAWKQSHLRRNYDFFERHFAEVVAWAYRWGVYTDLFPASRRKLEWQAQDAPRL
WDTVMHFRPSGIRAKRPTYLPALVAITQTSIVGPLERRLSPRETARLQGLPEWFDFGEQRAAATYKQMGNGVNVGVVRHI
LREHVRRDRALLKLTPAGQRIINAVLADEPDATVGALGAAE
>MTAA_SYNP2 248 MINIMUM
MEKKLISLFSGAGGMDIGFHAAGFSTAVAVEQDPSCCNTLRLNMPDTPVIEGDITSITTQVILEAAKVNPLEIDLVIGGP
PCQSFSLAGKRMGMDDPRGMLVLEFLRVVREALPKCFVMENVKGMINWSKGKALEAIMTEASQPIKYAGKEYKYAVSYHV
LNAADFGVPQFRERVFIVGNRLGKTFQFPEPTHGPSNQARQIDLFGKQLKPYKTVQDAISTLPPATPPSAMALRVSQTIK
DRIKNHGY
>MTB1_BACSH 424
MAIKINEKGRGKFKPAPTYEKEEVRQLLMEKINEEMEAVATATSDISNDEIQYKSDKFNVLSLFCGAGGLDLGFELAGLE
QSLGTDKALEAFKDRDVYNAIRHESVFHTVYANDIFSEALQTYEKNMPNHVFIHEKDIRKIKEFPSANLVIGGFPCPGFS
EAGPRLVDDERNFLYIHFIRCLMQVQPEIFVAENVKGMMTLGGGEVFRQIVEDFGAAGYRVEARLLNARDYGVPQIRERV
IIVGVRNDIDFNYEYPEITHGNEEGLKPYVTLEEAIGDLSLDPGPYFTGSYSTIFMSRNRKKKWTDQSFTIQASGRQAPI
HLGGLPMEKVDKNKWIFPDGEENHRRLSVKEIKRIQTFPDWYEFSDGGNMKVSVNNRLDKQYKQIGNAVPVFLTRAVAKS
IAQFAADYLKDNHPHEAPQMKLFI
>MTB1_BREEP 403
MKVLSLFSGCGGMDLGLEGGFLAHRSSINSDLYASYISDHDENYVYLKKTGFETVFANDILPFAKLAWCNFFKNRVNQPE
NIFHLESIVDVVNNIENKQFSFPNDIDVVTGGFPCQDFSFAGKRKGFDSHKDHNGIIYNEPTEATRGQLYLWLKKVVEIT
KPKVFIAENVKGLVTLGDVKDIIQKDFRNIDDGYVVLDAQVLNAKNYGVAQNRERVIFIGISKRYANKKILDELISLQEK
SEVYPYPPYTHGTDPELKPYATLNQILAHLPEPELASTDKSQQSYSKAKLFKKTQGNIEVNMNGQAPTIRAEHHGNIEFR
RLSKENGGTNLSELHLPQRRLTVRECALIQSFPPDYEFVFNYGKANSVSASAAYKIIGNAVPPLLGFAIGRHLSQIWDKL
FKT
>MTB1_HERAU 437
MQQFRFIDLFAGIGGFRLGLEAVGGVCVASAEIDQQAIKVYRQNWPTDGVDHNLGDITAIQQLPAHDVLVGGVPCQPWSI
AGKNQAFDDPRGQLWADVIRLVQINQPKAFIFENVKGLVDPRNRLCLEIILDSFKDLGYSVFYKLLNSFDFGVAQNRDRV
FIVGIQQKLDLNGFSFPEYTESEQRLYHILDNLEVPETKLESIPIQRNLFGERIDVGYNKLTPRGAFNDFFILNDIRNGP
TSIHSWEIYPTTEREKQICMIIMRNRRNSRYGDCDGNPMSYQDIAELVAGLAEKELQTLVEKRILRQYPDGKYEFFNRRL
SGGIDGTYRIFLPNARFFGTLTARGMHDEIAEISVSGANAEEYKHNFIQQVLIPKRYRKITVSEAARLQGFPGSFQFHSN
QSANFRLIGNSVAPPVIVALGKALQCVKLFEQELCEV
>MTBA_BACAR 428
MKIKFVDLFAGIGGIRIGFERAAKRFELETECVLSSEIDKKACETYALNFKEEPQGDIHEITSFPEFDFLLAGFPCQPFS
YAGKQQGFGDTRGTLFFEVERVLRDNRPKAFLLENVRGLVTHDKGRTLKTIISKLEELGYGVSYLLLNSSTFGVPQNRVR
IYILGILGSKPKLTLTSNVGAADSHKYKNEQISLFDESYATVKDILEDSPSEKYRCSDEFIGQLSKVVGNNFELLHGYRL
IDYRGGNSIHSWELGIKGDCTKEEIEFLNQLIANRRKKIYGTHQDGKALTLEQIRTFYNHDQLEVIIKSLLQKGYLREEE
NKFNPVCGNMSFEVFKFLDPDSISITLTSSDAHKLGVVQNNVPRRITPRECARLQGFPDDFILHSNDNFAYKQLGNSVTV
KVVEKVIEDLFQNNVNELFGQMKLANVV
>MTBF_BACSU 409
MRGGNRLGAGRKVIPESEKKKRKSVYITDKLYTRIMDTDIENCNNFSQKCMALIELAMENLNKNNQEHSVKRNNILMVRD
TKSTYNKTNNNFEKQNRGIKLTFIDLFAGIGGIRLGFEDKYTKCVFSSEWDKYAAQTYEANYGEKPHGDITKINENDIPD
QDVLLAGFPCQPFSNIGKREGFAHERRNIIFDVLRILKKKQPKMFLLENVKGLLTNDNGNTFRVILDNLKSLGYSVFYEV
MDAQNFGLPQRRERIVIVGFHPDLGINDFSFPKGNPDNKVPINAILEHNPTGYSISKRLQESYLFKKDDGKPQIVDFRCT
YQVNTLVASYHKIQRLTGTFVKDGETGLRLFSELELKRLMGFPVDFKVPVSRTQMYRQFGNSVAVPMIKAVAGAMKERLL
LAEMQVLKK
>MTBP_BPPHT 443
MSKLRVMSLFSGIGAFEAALRNIGVDYELIGFSEIDKYAIKSYCAIHNVSETLNVGDISKAKKDNIPYFDLLTSGFPCPT
FSVAGGRDGMEYKCSNCSHEHLITYEDYKKGVKCPKCEAVSKAKDERGTLFFETALLAEEKKPKFVILENVKGLINSGNG
QVLRIISETMNNIGYRIDLELLNSKFFNVPQNRERVYIIGIREDLVENEQWVVGQKRNDVLSKGKKRLQEINIKSFNFKW
PLQDTVTKRLREILEDFVDEKYYLNEEKTKKLVEQLGTAPLQKQEVREPLMVGHVDLKGHDAIKRVYSPEGLSPTLTTMG
GGHREPKIAEKQKEVRAVLTPEREEKRQNGRRFKENGEPAFTVNTIDRHGVAIGEYPKYKIRKLSPLECWRLQAFDDEDF
EKAFAAGISNSQLYKQAGNSITVSVLESIFQELIHTYVNKESE
>MTBR_BACSU 436
MTLKIDIKGRGKYKPASDYSIDDVKNVLMEKIFEESSRIINSDDDLEIIEKVDFRTDKINVLSLFSGCGGLDLGFELAGL
AAVIGEQAAMEAFKDKDRFNELRNKSIFHTIYTNDLFKEANQTYKTNFPGHVIQHEKDIRQVKYFPKCNLILGGFPCPGF
SEAGPRLIDDDRNFLYLHFIRSLIQAQPEIFVAENVKGMMTLGKGEVLNQIIEDFASAGYRVQFKLLNARDYGVPQLRER
VIIEGVRKDISFNYKYPSPTHGEETGLKPFKTLRDSIGDLVTDPGPYFTGSYSSIYMSRNRKKSWDEQSFTIQASGRQAP
LHPGGLSMKKIGKDKWVFPDGEENHRRLSVKEIARVQTFPDWFQFSQGTNSQTSINNRLDKQYKQIGNAVPVLLAKAVAS
PIANWAINYLESSPNNKIKNRERKLSIRTFLRIKTS
>MTBR_BPRH1 503
LSKLRVMSLFSGIGAFEAALRNIGVEYELVGFSEIDKYAIKSYCAIHNADEQLNFGDVSKIDKKKLPEFDLLVGGSPCQS
FSVAGYRKGFEDTRGTLFFQYIDTLKEKQPRYFVFENVKGLINHDKGNTLNIMAESFSEVGYRIDLELLNSKFFNVPQNR
ERIYIIGVREDLIENDEWVVEKGRNDVLSKGKKRLKELNIKSFNFKWSAQDIVGRRLREILEEYVDEKYYLSEEKTSKLI
EQIEKPKEKDVVFVGGINVGKRWLNNGKTYSRNFKQGNRVYDSNGIATTLTSQSVGGLGGQTSLYKVEDPIMIGHIDLKG
HDAIKRVYSPDGVSPTLTTMGEGHREPKIAVEYVGNINPSGKGMNDQVYNSNGLSPTLTTNKGEGVKISVPNPEIRPVLT
PEREEKRQNGRRFKEDDEPAFTVNTIDRHGVAIGEYPKYRIRKLTPLECWRLQAFDEEDFEKALSVGISNSQLYKQAGNS
ITVTVLESIFKELIHTYVNEESE
>MTBS_BPSPR 439
MGKLRVMSLFSGIGAFEAALRNIGVGYELVGFSEIDKYAVKSFCAIHNVDEQLNFGDVSKIDKKKLPEFDLLVGGSPCQS
FSVAGHRKGFEDTRGTLFFQYVETLKEKQPKFFVFENVKGLINHDKGNTLNVMAEAFSEVGYRIDLELLNSKFFNVPQNR
ERLYIIGIREDLIKNEEWSLDFKRKDILQKGKQRLVELDIKSFNFRWTAQSAATKRLKDLLEEYVDEKYYLNEDKTNSLI
KELSTSRLNENLTVEQVGNINPSGNGMNGNVYNSSGLSPTITTNKGEGLKIAVEYSRKSGLGRELAVSHTLSASDWRGLN
RNQKQNAVVEVRPVLTPERGEKRQNGRRFKDDGEPAFTVNTIDRHGVAVGEYPKYRIRRLTPLECFRLQAFDDEDFEKAF
AAGISNSQLYKQTGNSITVTVLESIFKELIHTYINKESE
>MTC1_CHVI3 367
MSFRTLELFAGIAGISHGLRGISTPVAFVEINEDAQKFLKTKFSDASVFNDVTKFTKSDFPEDIDMITAGFPCTGFSIAG
SRTGFEHKESGLFADVVRITEEYKPKIVFLENSHMLSHTYNLDVVVKKMDEIGYFCKWVTCRASIIGAHHQRHRWFCLAI
RKDYEPEEIIVSVNATKFDWENNEPPCQVDNKSYENSTLVRLAGYSVVPDQIRYAFTGLFTGDFESSWKTTLTPGTIIGT
EHKKMKGTYDKVINGYYENDVYYSFSRKEVHRAPLNISVKPRDIPEKHNGKTLVDREMIKKYWCTPCASYGTATAGCNVL
TDRQSHALPTQVRFSYRGVCGRHLSGIWCAWLMGYDQEYLGYLVQYD
>MTC1_HERAU 420
MLKFIDLFAGIGGMRLGFEQAMHELGIETACVLSSEIDKHAQTTYAMNFHEQSQGDITQIQDFPSFDFLLAGFPCQPFSY
AGKQKGFGDTRGTLFFEIERILKAYRPKGFLLENVRGLTTHDKGRTFKTILQKLHELNYGVYLILNSSNFQVPQNRLRVY
IVGLDQSQPELTITSHIGATDSHKFKQLSNQASLFDTNKIMLVRDILEDHPLDKYNCSTDFVNKLLAFIGHPIKLNGKRL
IDYRNGNSIHSWELGIKGECTSDEIQFMNALIANRRKKHFGAHQDGKKLTIEQIKTFFEHDDLDSIMQSLITKGYLQEVN
GRFNPVAGNMSFEVFKFLDPDSVSITLVSSDAHKIGVVHQNRIRRITPREMPRLQGFPDSFQFHPKDSLAYRQFGNSVSV
PVVKAVILDLFKSADLASCF
>MTC2_HERAU 437
MKQFRFIDLFAGIGGFRLGLEAVGGICVGSAEIDQQAIKVYRQNWPTDRSEHNLGDITTLQQLPAHDLVVGGVPCQPWSI
AGKNQAFDDPRGQLWADVIRLVRINQPKAFIFENVKGLIDPRNRLCLESILDSFKAEGYNVYYKLLNSFDYGVAQNRDRV
FIIGIQQKLGVPDFSFPEYSESEQRLYDILDNLQTPSIIPESLPIQRNLFGERIEVGFNKLTPRGAFNDFFILNDIRNGP
TSIHSWEIYATTEREKQICTTIMRNRGNPRYGDCDGNPMSYQDIADLVVDLAESELQVLIQKRILRQYEDGKYEFFNRRL
SGGIDGTYRIFLPHARFFGRLTARGMHDEIAEISVSGATAEAYKQNFIQQILIPKRHRPITVNEAARIQGFPATFKFHSN
QSANFRLIGNSVAPPVIMALGKALPNDHLFEPELCEV
>MTD1_DESDN 415
MNIIDLFAGCGGFSHGFKMAGYNSILAIEKDLWASQTYSFNNPNVSVITEDITTLDPGDLKISVSDVDGIIGGPPCQGFS
LSGNRDQKDPRNSLFVDFVRFVKFFSPKFFVMENVLGILSMKTKSRQYVKDIIAEEFSNVGYKVCVIILNACDYGVPQSR
QRVFFIGLKSDRPLNQQILTPPSKVIESEYTSLEEAISDLPVIEAGEGGEVQDYPVAPRNKYQENMRKGSTCVYNHVAMR
HTQRLVDRFAAIKFGQSVKHVSEEHSQRKRGDANSISGKVFSQNNMRPYPYKPCPTVAASFQSNFIHPFYNRNFTAREGA
RIQSFPDTYIFQGKRTTMSWEKHLSQYQQIGNAVPPLLAQALAERISWYFENINLINDSNVSIKRMVQRSFMSQLNLENN
VNVRQDDNYDKVHSF
>MTD1_HERAU 309
MKTIDLFAGCGGMSLGFMQAGFEIVAAVDNWRPAINTYQQNFTHPIHELDLAQIDAAVSLIKTHSPELIIGGPPCQDFSS
AGKRDEGLGRANLTLDFAKIVLAIQPAWVIMENVERARLSKIHQQACSMLGDEGYSLAQVVLDASLCGVPQLRKRTFVIG
HRHGSIADLANVLQQRLAKQSLTVRDYFGESLDTDYYYRHPRTYERRAIFSVNEPSPTIRGVNRPIPATYRMHPKDAGDV
SLARPLTTKERSLIQTFPLDFKFVGTKSEQEQMIGNAVPVNLAFFLATSLQAYLNQPRMQQLSLLPSFF
>MTD2_HERAU 354
MVGAVIDLFCGVGGLTHGLILEGFGVLAGIDNDPSCKYAYEQNNRTRFIEKSISEVDGRELNALYPNNQHKILVGCAPCQ
DFSQYTKKSRTGTKWQLLTEFSRLIREIEPDIISMENVPEVRTFNRGEVFNNFIQSLEQLGYHVSHSVVHCPDYGIPQQR
DRLVLFAAKQGVIKIIPPTHTPENYRTVRDVIGSLATNYSGGHWEGDSMHAASRLEDINLRRIQHSVPGGTWADWPEELI
AECHKKESGESYGSVYGRMEWDKVAPTITTQCNGYGNGRFGHPEQDRAISLREAALLQTFPRSYQFAPEGQLKFKTVSRQ
IGNAVPVALGRVIAKSIKRFLEGLHERQRVRIII
>MTDM_ARATH 1534 MAXIMUM
MVENGAKAAKRKKRPLPEIQEVEDVPRTRRPRRAAACTSFKEKSIRVCEKSATIEVKKQQIVEEEFLALRLTALETDVED
RPTRRLNDFVLFDSDGVPQPLEMLEIHDIFVSGAILPSDVCTDKEKEKGVRCTSFGRVEHWSISGYEDGSPVIWISTELA
DYDCRKPAASYRKVYDYFYEKARASVAVYKKLSKSSGGDPDIGLEELLAAVVRSMSSGSKYFSSGAAIIDFVISQGDFIY
NQLAGLDETAKKHESSYVEIPVLVALREKSSKIDKPLQRERNPSNGVRIKEVSQVAESEALTSDQLVDGTDDDRRYAILL
QDEENRKSMQQPRKNSSSGSASNMFYIKINEDEIANDYPLPSYYKTSEEETDELILYDASYEVQSEHLPHRMLHNWALYN
SDLRFISLELLPMKQCDDIDVNIFGSGVVTDDNGSWISLNDPDSGSQSHDPDGMCIFLSQIKEWMIEFGSDDIISISIRT
DVAWYRLGKPSKLYAPWWKPVLKTARVGISILTFLRVESRVARLSFADVTKRLSGLQANDKAYISSDPLAVERYLVVHGQ
IILQLFAVYPDDNVKRCPFVVGLASKLEDRHHTKWIIKKKKISLKELNLNPRAGMAPVASKRKAMQATTTRLVNRIWGEF
YSNYSPEDPLQATAAENGEDEVEEEGGNGEEEVEEEGENGLTEDTVPEPVEVQKPHTPKKIRGSSGKREIKWDGESLGKT
SAGEPLYQQALVGGEMVAVGGAVTLEVDDPDEMPAIYFVEYMFESTDHCKMLHGRFLQRGSMTVLGNAANERELFLTNEC
MTTQLKDIKGVASFEIRSRPWGHQYRKKNITADKLDWARALERKVKDLPTEYYCKSLYSPERGGFFSLPLSDIGRSSGFC
TSCKIREDEEKRSTIKLNVSKTGFFINGIEYSVEDFVYVNPDSIGGLKEGSKTSFKSGRNIGLRAYVVCQLLEIVPKESR
KADLGSFDVKVRRFYRPEDVSAEKAYASDIQELYFSQDTVVLPPGALEGKCEVRKKSDMPLSREYPISDHIFFCDLFFDT
SKGSLKQLPANMKPKFSTIKDDTLLRKKKGKGVESEIESEIVKPVEPPKEIRLATLDIFAGCGGLSHGLKKAGVSDAKWA
IEYEEPAGQAFKQNHPESTVFVDNCNVILRAIMEKGGDQDDCVSTTEANELAAKLTEEQKSTLPLPGQVDFINGGPPCQG
FSGMNRFNQSSWSKVQCEMILAFLSFADYFRPRYFLLENVRTFVSFNKGQTFQLTLASLLEMGYQVRFGILEAGAYGVSQ
SRKRAFIWAAAPEEVLPEWPEPMHVFGVPKLKISLSQGLHYAAVRSTALGAPFRPITVRDTIGDLPSVENGDSRTNKEYK
EVAVSWFQKEIRGNTIALTDHICKAMNELNLIRCKLIPTRPGADWHDLPKRKVTLSDGRVEEMIPFCLPNTAERHNGWKG
LYGRLDWQGNFPTSVTDPQPMGKVGMCFHPEQHRILTVRECARSQGFPDSYEFAGNINHKHRQIGNAVPPPLAFALGRKL
KEALHLKKSPQHQP
>MTDM_HUMAN 1495
MADANSPPKPLSKPRTPRRSKSDGEAKPEPSPSPRITRKSTRQTTITSHFAKGPAKRKPQEESERAKSDESIKEEDKDQD
EKRRRVTSRERVARPLPAEEPERAKSGTRTEKEEERDEKEEKRLRSQTKEPTPKQKLKEEPDREARAGVQADEDEDGDEK
DEKKHRSQPKDLAAKRRPEEKEPEKVNPQISDEKDEDEKEEKRRKTTPKEPTEKKMARAKTVMNSKTHPPKCIQCGQYLD
DPDLKYGQHPPDAVDEPQMLTNEKLSIFDANESGFESYEALPQHKLTCFSVYCKHGHLCPIDTGLIEKNIELFFSGSAKP
IYDDDPSLEGGVNGKNLGPINEWWITGFDGGEKALIGFSTSFAEYILMDPSPEYAPIFGLMQEKIYISKIVVEFLQSNSD
STYEDLINKIETTVPPSGLNLNRFTEDSLLRHAQFVVEQVESYDEAGDSDEQPIFLTPCMRDLIKLAGVTLGQRRAQARR
QTIRHSTREKDRGPTKATTTKLVYQIFDTFFAEQIEKDDREDKENAFKRRRCGVCEVCQQPECGKCKACKDMVKFGGSGR
SKQACQERRCPNMAMKEADDDEEVDDNIPEMPSPKKMHQGKKKKQNKNRISWVGEAVKTDGKKSYYKKVCIDAETLEVGD
CVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVKVIYKAPSE
NWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFESPPKTQPTEDNKFKFCVSCARLAEMRQKEIPRVLEQLEDLDSRV
LYYSATKNGILYRVGDGVYLPPEAFTFNIKLSSPVKRPRKEPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFC
PKKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGGPN
RFYFLEAYNAKSKSFEDPPNHARSPGNKGKGKGKGKGKPKSQACEPSEPEIEIKLPKLRTLDVFSGCGGLSEGFHQAGIS
DTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYS
KFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPG
EKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALEISYNGEPQSWFQRQLR
GAQYQPILRDHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEA
GKACDPAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPD
TYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKLCMLAKARESASAKIKEEEAAKD
>MTDM_MOUSE 1502
MADSNRSPRSRPKPRGPRRSKSDSDTLFETSPSSVATRRTTRQTTITAHFTKGPTKRKPKEESEEGNSAESAAEERDQDK
KRRVVDTESGAAAAVEKLEEVTAGTQLGPEEPCEQEDDNRSLRRHTRELSLRRKSKEDPDREARPETHLDEDEDGKKDKR
SSRPRSQPRDPAAKRRPKEVRARAGSSRDSEDRDEDEREEKRRKTTRKKLESHTVPVQSRSERKAAQSKSVIPKINSPKC
PECGQHLDDPNLKYQQHPEDAVDEPQMLTSEKLSIYDSTSTWFDTYEDSPMHRFTSFSVYCSRGHLCPVDTGLIEKNVEL
YFSGCAKAIHDENPSMEGGINGKNLGPINQWWLSGFDGGEKVLIGFSTAFAEYILMEPSKEYEPIFGLMQEKIYISKIVV
EFLQNNPDAVYEDLINKIETTVPPSTINVNRFTEDSLLRHAQFVVSQVESYDEAKDDDETPIFLSPCMRALIHLAGVSLG
QRRATRRVMGATKEKDKAPTKATTTKLVYQIFDTFFSEQIEKYDKEDKENAMKRRRCGVCEVCQQPECGKCKACKDMVKF
GGTGRSKQACLKRRCPNLAVKEADDDEEADDDVSEMPSPKKLHQGKKKKQNKDRISWLGQPMKIEENRTYYQKVSIDEEM
LEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWFCAGTDTVLGATSDPLELFLVGECENMQLSYIHSKVKVIY
KAPSENWAMEGGTDPETTLPGAEDGKTYFFQLWYNQEYARFESPPKTQPTEDNKHKFCLSCIRLAELRQKEMPKVLEQIE
EVDGRVYCSSITKNGVCYRLGDSVYLPREAFTFNIKVASPVKRPKKDPVKENPVPRDTYRKYSDYIKGRNLDAPEPYRIG
RIKEIHCGKKKGKVNEADIKLRLYKFYRPENTHRSYNGSYHTDINMLCWSDEEAVVNFSDVQGRCTVEYREDLLESIQDY
SQGGPDRFYFLEAYNSKTKNFEDPPNHARSPGNKGKGKGKGKGKGKHQVSEPKEPEAAIKLPKLRTLDVFSGCGGLSEGF
HQAGISETLWAIEMWDPAAQAFRLNNPGTTVFTEDCNVLLKLVMAGEVTNSLGQRLPQKGDVEMLCGGPPCQGFSGMNRF
NSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSYRRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAII
LAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITERDTMSDLPEIQNGASNSEIPYNWRATVQ
VPEAAARITLPAHPQGPYLQGHEPTGGCPHAHIPLFPGSDWRDLPNIQVRLGDGVIADKLQYTFHDVKNGYSSTGALRGV
CSCAEGKACDPESRQFSTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARS
QGFPDSYRFFGNILDRHRQVGNAVPPPLAKAIGLEIKLCLLSSARESASAAVKAKEEAATKD
>MTE1_HERAU 437
MQQFRFIDLFAGIGGFRLGLEAVGGVCVASAEIDQQAIKVYWQNWPTDGVDHNLGDITQIQQLPAHDVLVGGVPCQPWSI
AGKNQAFDDPRGQLWADVIRLVQINQPKAFIFENVKGLVDPRNRLCLEIILDSFKDLGYSVFYKLLNSFDFGVAQNRDRV
FIVGIQQKLDLNGFSFPEYAESDQRLYHILDNLEAPETKLESIPIQRNLFGERIEVGYNKLTPRGAFNDFFILNDIRNGP
TSIHSWEIYPTTEREKHICMIIMRNRRNSRYGNCDGNPMSYSDIAELVVDLAENELQILVKKRILRQYPDGKYEFFNRRL
SGGIDGTYRIFMPNARFFGTLTARGMHDEIAEINVSGANAAEYKYNFIQQVLIPKRYRPITVSEAARLQGFPSTFKFHSN
QSANFRLIGNSVAPPVIVALGKRLQCVKLFEQELCEV
>MTE2_ECOLI 477
MSEFELLAQDLLEKAEAEEQLRQENDKKLLGQVLEIYDQKYVAELLRKVGKNEWSRETLNRWINGKCSPKTLTLAEEELL
RKMLPEAPAHHPDYAFRFIDLFAGIGGIRKGFETIGGQCVFTSEWNKEAVRTYKANWFNDAQEHTFNLDIREVTLSDKPE
VPENDAYAYINEHVPDHDVLLAGFPCQPFSLAGVSKKNSLGRAHGFECEAQGTLFFDVARIIRAKKPAIFVLENVKNLKS
HDKGKTFKVIMDTLDELGYEVADAAEMGKNDPKVIDGKHFLPQHRERIVLVGFRRDLNIHQGFTLRDISRFYPEQRPSFG
ELLEPVVDSKYILTPKLWEYLYNYAKKHAAKGNGFGFGLVNPENKESIARTLSARYHKDGSEILIDRGWDMATGETDFAN
EENQAHRPRRLTPRECARLMGFEKVDGRPFRIPVSDTQSYRQFGNSVVVPVFEAVAKLLEPYILKAVNADSCKVERI
>MTF1_FUSNU 344
MKLLSLFSGAGGLDLGFERAGFEIIVANEYDKTIWETYEKNHKAKLIKKDIREILSEELPKSDGIIGGPPCQSWSEAGSL
RGINDPRGKLFYEYIRILKDIQPKFFLAENVKGMLSKRNTEAVKDIIKEFEEAGYNVFIKLLNAFDYGVAQDRERVFYVG
FRKDLNISNFEFPYPISEKERKYLKDSIWDLKDNALPGKDKNKTNADDCIVENHEYLTGSYSTIFMSRNRVRQWEQPAFT
VQASGRQCQLHPQAPTMIKIDKNMYKFVAGKENLYRRLSIRECARIQGFPDTFKFYYTSLEDGYKMVGNAVPVDLAYIIA
KRIKETLTDKEKIKKEIRQKTLFD
>MTG1_HAEGA 357
MKKNIMGLSLFSSAGIGEYFLSRVGIDIIVANELIKKRADLYQKIYPNHKMVIGDIRDQRIFNKVLNIALTNQVDFLIAS
PPCQGMSVAGKNRDVSNMANDNRNYLIMYVIAMIKKLKPAYILIENVPFLLKLELYIDNKLTPIKNILEDEFGSEYHIHF
DILDAADYGTPQRRKRAIIRLNKKGTIWNLPLKQNIVSVEQAIGNLPSIESGKHSGLKWHYGRGHTEQQIEWMKHTPTGK
SAFENLVHYPRKANGEKVKGYHSSYRRIRWDEPAPTITIRNDAISSQRNVHPGRPLLDGTYSDARVLSVLELMRLTGLPD
NWEIPDDTPEILIRQIIGECIPPLLIENITREIFNEN
>MTG2_HAEGA 358
MKINAMSLFSSAGIGELDLHKGNLNFVVANELLKKRADTYQFFYPETKMFQGDISDEKLKREILLSAQQNNVKFLLATPP
CQGLSSVGKNKHQDHFIKDNRNFLIFEVFEFIDVLNLDFILIENVPRFIEMYFPYNGQLLLLEEILKIKYASKYQIDIVI
LNAKDYGICQSRPRAIIKMYKYGITWKLPTIQAEISLQRAIGHLPPLEPGEVSSIKWHSAPNVKPSIIEAIRHTKPGTSA
ISNPIFYPKKDNGERIKGFHNTYKRMEWDKPAPARTTYSGSISSHNNIHPGRLQLDGTYSDPRVLSLLETFIVSSIDENI
EFPPGSSETYIRTIIGEAIPPKLLSAICFPDGENINVK
>MTH1_HAEHA 327
MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGFP
CQAFSISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIP
QKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGQGER
IYSTRGIAITLSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYKQFGNSVVINVLQYIAYNIGS
SLNFKPY
>MTH2_HAEPA 358
MKDVLDDNLLEEPAAQYSLFEPESNPNLREKFTFIDLFAGIGGFRIAMQNLGGKCIFSSEWDEQAQKTYEANFGDLPYGD
ITLEETKAFIPEKFDILCAGFPCQAFSIAGKRGGFEDTRGTLFFDVAEIIRRHQPKAFFLENVKGLKNHDKGRTLKTILN
VLREDLGYFVPEPAIVNAKNFGVPQNRERIYIVGFHKSTGVNSFSYPEPLDKIVTFADIREEKTVPTKYYLSTQYIDTLR
KHKERHESKGNGFGYEIIPDDGIANAIVVGGMGRERNLVIDHRITDFTPTTNIKGEVNREGIRKMTPREWARLQGFPDSY
VIPVSDASAYKQFGNSVAVPAIQATGKKILEKLGNLYD
>MTH3_HAEAE 330
MNLISLFSGAGGLDLGFQKAGFRIICANEYDKSIWKTYESNHSAKLIKGDISKISSDEFPKCDGIIGGPPCQSWSEGGSL
RGIDDPRGKLFYEYIRILKQKKPIFFLAENVKGMMAQRHNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIG
FRKELNINYLPPIPHLIKPTFKDVIWDLKDNPIPALDKNKTNGNKCIYPNHEYFIGSYSTIFMSRNRVRQWNEPAFTVQA
SGRQCQLHPQAPVMLKVSKNLNKFVEGKEHLYRRLTVRECARVQGFPDDFIFHYESLNDGYKMIGNAVPVNLAYEIAKTI
KSALEICKGN
>MTHT_METTF 330
MNMDIASFFSGAGGLDLGFTKAGFNIVFANDNWKGCWKTFEKNHGIKINKKPIEWLKPSEIPDVVGFIGGPPCQSWSLAG
SMCGADDPRGKTFYAYVDLVKEKDPLFFLAENVPGIVSRTHLPEFKRLVNSFIDIGYNVEYKVLNAKDYGVPQDRKRVFI
VGYREDLNLKFEFPKPLNKKVTLRDAIGDLPEPKPALEKNRSNGENLEVPNHEYMTGTFSSRYMSRNRVRSWDEVSFTIQ
AGGRHAPCHPQANKMIKVGPDKFIFDPESPKPYRRLSVRECARIQGFPDDFIFYYKNVADGYTMVGNAVPVKLAEELAKK
IKKDLEGVLN
>MTM1_MORSP 418
MKPEILKLIRSKLDLTQKQASEIIEVSDKTWQQWESGKTEMHPAYYSFLQEKLKDKINFEELSAQKTLQKKIFDKYNQNQ
ITKNAEELAEITHIEERKDAYSSDFKFIDLFSGIGGIRQSFEVNGGKCVFSSEIDPFAKFTYYTNFGVVPFGDITKVEAT
TIPQHDILCAGFPCQPFSHIGKREGFEHPTQGTMFHEIVRIIETKKTPVLFLENVPGLINHDDGNTLKVIIETLEDMGYK
VHHTVLDASHFGIPQKRKRFYLVAFLNQNIHFEFPKPPMISKDIGEVLESDVTGYSISEHLQKSYLFKKDDGKPSLIDKN
TTGAVKTLVSTYHKIQRLTGTFVKDGETGIRLLTTNECKAIMGFPKDFVIPVSRTQMYRQMGNSVVVPVVTKIAEQISLA
LKTVNQQSPQENFELELV
>MTNG_NEIGO 330
MKIISLFSGCGGLDLGFEKAGFEIPAANEYDKTIWATFKANHPKTHLIEGDIRKIKEEDFPEEIDGIIGGPPCQSWSEAG
ALRGIDDARGQLFFDYIRILKSKQPKFFLAENVSGMLANRHNGAVQNLLKMFDGCGYDVTLTMANAKDYGVAQERKRVFY
IGFRKDLEIKFSFPKGSTVEDKDKITLKDVIWDLQDTAVPSAPQNKTNPDAVNNNEYFTGSFSPIFMSRNRVKAWDEQGF
TVQASGRQCQLHPQAPKMEKHGANDYRFAAGKETLYRRMTVREVARIQGFPDNFKFIYQNVNDAYKMIGNAVPVNLAYEI
AAAIKKTLER
>MTNM_NEIGO 312
MQFTSLEICAGAGGQALGLERAGFSHVALIEIEPSACQTLRLNRPDWNVIEGDVRLFQGEGYDGIDLLAGGVPCPPFSKA
GKQLGKDDERDLFPEAIRLAKETDPKAIMLENVRGLLDPKFENYRNHITEQFAKLGYLGQWKLLYAADYGVSQLRPRVLF
VALKNEYTNFFKWPEPNSEQPKTVGELLFDLMSENNWQGAHNWRLKAAQIAPTLVAVQKNTAVLTWDLHDPNAHGRSWVW
MVQVCGIVRRLKTFTGMPRLTVRMTARIQGFPDDWQFFGKKTPMYRQIGNAFPPPVAEAVGRQIIKALKKEN
>MTNX_NEILA 313
MFKIIDLFAGIGGIRLGFEQAFDDVRCVFSSEIDKYAVQTYQANHGGETVCGDITQTDVADIPDHDILSAGFPCQPFSQA
GLKKGFADTRGTLFFDIERILLAKKPQAFLLENVKQLKGHDKGRTLQVILAHLQQAGYKVYTEVLKARDFGIPQNRERIY
LVGFLNHDVDFRFPQPIGQATAVGDILEAYPDEKYTISDKLWQGYQRRKAENRAAGKGFGYGLFNAESAYTNTISARYYK
DGSEILIEQPGKNPRKITPPEAARLQGFPDSFQIPVSDAQAYRQFGNSVCVPVIRAIAEQMKAALSAVSDRKV
>MTS2_SHISO 379
MTDNIAATIKEKRERLHMTQKEFADALGLSKYGDRTIRRWERGETKPTGAELKAVIDFPDTPPYPNNENGRYRMIDLFAG
IGGTRLGFHQTNAVNVVFSSEWDKFAQKTYHANYGDFPDGDITKIDEKDIPDHEILVGGFPCVAFSQAGLKKGFNDTRGT
LFFDIARIIKEKKPHAFLLENVKNLLGHDKGRTFSIIKNTLEELNYTVYYNIFAAKDFGVPQNRERIYIVGFNKEKVRNH
EHFTFPTPLKTKTRVGDILEKSVDNKYTLSDALWNGHQRRKLVNAAAGKGFGYGLFNENSPYTNTISARYYKDGSEILIE
QKGSNPRKITPREASRLQGFPSDFIIPVSDTQAYKQFGNSVAVPVINAIAEKIISTLDS
>MTS3_STAAU 412
MNKIKVVELFAGVGGFRLGLENTKNGIFDITWANQWEPSRKIQHAFDCYSKRFKNGIHSNKDIAQVSDEEMANTEADMIV
GGFPCQDYSVARSLNGELGIQGKKGVLFWQIIRYIQNTFPKYLLLENVDRLLKSPSSQRGRDFAVMLSTLNELGYNVEWR
VINAADYGNAQRRRRVFIFGYKQDLNYSKAMEESPLDKIIYHNGLFAEAFPIEDYANKNRVNRTHITHDIVDISDNFSFQ
FYNSGIMKNGEILTIDTIPKYEKSVTLGEIIESNVDDGFSLNQDQIDKFKYLRGPKKIKRTTKDGHEYYFSEGGMSETDS
LELPARTMLTSESSINRSTHFLNVDGVYRTLTPIEAERLNGFPDNWTEGMPIKMRYFCMGNALVVPLITRIGNQIEKIDS
ITNDEFSQLRLF
>MTS9_STAAU 430
MRLNKGSIIEKMKNQNIKTQTELAEKIDISKSQLSFMFSDEYEPLKKNVIKLADVLKVSPNDIILDEEDQMPINSDFNRY
DYKLDEFIDVSNVRKNKDYNVFETFAGAGGLALGLESAGLSTYGAVEIDKNAAETLRINRPKWKVIENDIEFIADNLDEF
IDEEIDILSGGYPCQTFSYAGKRNGFADTRGTLFYPYSKILSKLKPKAFIAENVRGLVNHDDGKTLEVMLKVFIKEGYEV
YWNILNSWNYDVAQKRERIVIIGIREDLVKEQKYPFRFPLAQVYKPVLKDVLKDVPKSKVTAYSDKKREVMKLVPPGGCW
VDLPEQIAKDYMGKSWYSGGGKRGMARRISWDEPCLTLTTSPSQKQTERCHPDETRPFSIREYARIQSFPDEWEFSGGVG
AQYRQIGNAVPVNLAKYIGKSLVHYLNQFN
>MTSA_LACLC 389
MTTISRNTGTEISIMIKEKRLRLNMTQKELADAVGMSKNGDRTIRRWENGETCPSQLEISAILRFPEIAPFENRKTAKYK
MIDLFAGIGGTRLGFHQTEKVKSVFSSEIDKFAIKTYKANFGDEPHGDITKIDEKDIPDHDILVGGFPCQAFSQAGKKLG
FDDTRGTLFFEIARIIKEKRPKAFLLENVKNLKTHDKGRTFKTILNTLEELDYEVHTALFKARDFGLPQNRERIYIVGFD
RKSISNYSDFQMPTPLQEKTRVGNILESVVDDKYTISDKLWDGHQRRKTENKKNGKGFGYTLFNQDSEYTNTLSARYYKD
GSEILIEQKNKNPRKITPREAARLQGFPENFIIPVSDTQAYKEFGNSVAVPTIHAIAEKMLEVLEKSKK
>MTSB_LACLC 360
MLRVFEAFAGYGSQRLALIKANIPHEIVGISEIEGDVLLSYSAIHENLLEERNKNIKLTDDEMRDYLKNINIPLDYKTFE
NRADKLGGQKLKDMYIANKLNKNFGDIRSIDPKKLPDFDFFTYSFPCQDISVAGYQNGLVADSGTRSSLLWECCKIIEHK
KPKYLMMENVKNLVGKNHKVNFNKFLLYLESLGYTNYWDILNARDFGIPQNRERVFCISILNPNEDFTFPQKQNLTLSMN
DLLEENVSEKFYLKNNQVSDEPILQDYIYCLDSNYWKGTFLKDFLSKKRRQLVSGKVRPDGKYPARRLTPRETWRFMGVE
DTNFDKASILVSNTSLYKQSGNSIVVPVLESLFKELFKSQ
>MTSI_SALIN 461
MIMNDIITVTEAAQLLELTPQRVRTMCKQGSIDAYQSGRTWLIKSSSVEKLMLVNSLSDAQNSYSMLASEPKNKPKALSF
FSGAMGLDLGIEQAGFETLLASEIDKAARDTILSNRPNMALIGDIRDYTTEDILKLAGVSSGNEIDLIMGGPPCQAFSTA
GKRLGLEDERGNVFIKYLDVALDIRPKYIVIENVRGLLSAPMKHRPHNERGEGLPPLKSEEQPGGVLHYIIRIIKSAGYS
VSFNLYNSANFGVPQIRERVIIICSRDGSRVPFLQPTHSEKGEYGLPKWITLRETITNLKNITHEHVLFPEKRLKYYRLL
KEGQYWKHLPEDLQKEALGKSFFLGGGKTGFLRRVAWDRPSPTLVTHPAMPATDLAHPDELRPLSVQEYKVIQQFPEEWV
IKGKLLDKYRQLGNAVPIGLGLAVGKNILDHMNGRKIESFPNFRYSRYKNTSDLDIFGELV
>MTSI_SPISQ 386
MSKVENKTKKLRVFEAFAGIGAQRKALEKVRKDEYEIVGLAEWYVPAIVMYQAIHNNFHTKLEYKSVSREEMIDYLENKT
LSWNSKNPVSNGYWKRKKDDELKIIYNAIKLSEKEGNIFDIRDLYKRTLKNIDLLTYSFPCQDLSQQGIQKGMKRGSGTR
SGLLWEIERALDSTEKNDLPKYLLMENVGALLHKKNEEELNQWKQKLESLGYQNSIEVLNAADFGSSQARRRVFMISTLN
EFVELPKGDKKPKSIKKVLNKIVSEKDILNNLLKYNLTEFKKTKSNINKASLIGYSKFNSEGYVYDPEFTGPTLTASGAN
SRIKIKDGSNIRKMNSDETFLYIGFDSQDGKRVNEIEFLTENQKIFVCGNSISVEVLEAIIDKIGG
GDDGKTYFYQLWYDQDYARFESPPKTQPTEDNKFKFblimps-3.9/examples/cobbler/distribution/000075500001460000012000000000001041506306700211155ustar00jorjastaff00000400000027blimps-3.9/examples/cobbler/distribution/psi-blast.cob000064400001460000012000000005461041506274700235110ustar00jorjastaff00000400000027>PS00094 MTSA_LACLC from 72 to 359 with embedded consensus blocks
enrktakykmIDLFAGCGGFRLGFEQAGkvksvfsseidkfaiktykanfgdephgditkidekdipdhDMLCGGFPCQD
FSQAGKRNGFDDTRGtlffeiariikekrPKYFLMENVKGLkthdkgrtfktilntleelGYHVHWHVLNAWDYGVPQNR
ERVFIIGfdrksisnysdfqmptplqektrvgnilesvvddkytisdklwdghqrrktenkkngkgfgytlfnqdseytn
tlsaryykdgseilieqknknpRRLTPRECARLQGFPDnfiipvsdtq
blimps-3.9/examples/cobbler/distribution/psi-blast.sq.cob000064400001460000012000000006401041506274700241260ustar00jorjastaff00000400000027>PS00094 DCM_ECOLI from 80 to 425 with embedded consensus blocks
ahhphyafrfIDLFAGCGGFRLGFEQAGgqcvftsewnkhavrtykanhycdpathhfnedirditlshkegvsdeaaae
hirqhipehDMLCGGFPCQDFSQAGKRNGFDDTRGhgfacdtqgtlffdvvriidarrPKYFLMENVKGLkshdqgktfr
iimqtldelgydvadaeGYHVHWHVLNAWDYGVPQNRERVFIIGfrrdlnlkadftlrdisecfpaqrvtlaqlldpmve
akyiltpvlwkylyryakkhqargngfgygmvypnnpqsvtrtlsaryykdgaeilidrgwdmatgekdfddplnqqhrp
RRLTPRECARLQGFPDpgeakfripv
blimps-3.9/examples/cobbler/distribution/swat.cob000064400001460000012000000007131041506274700225650ustar00jorjastaff00000400000027>PS00094 MTBA_BACAR from 1 to 389 with embedded consensus blocks
mkikfIDLFAGIGGFRLGFEQAGkrfeletecvlsseidkkacetyalnfkeepqgdiheitsfpefDLLIGGFPCQDFS
xAGKRNGFDDTRGtlffevervlrdnrPKYFLMENVKGLvthdkgrtlktiiskleelGYQVSYEILNAKDYGVPQNRER
VFIIGilgskpkltltsnvgaadshkykneqislfdesyatvkdiledspsekyrcsdefigqlskvvgnnfellhgyrl
idyrggnsihswelgikgdctkeeieflnqlianrrkkiygthqdgkaltleqirtfynhdqleviiksllqkgylreee
nkfnpvcgnmsfevfkfldpdsisitltssdahklgvvqnnvpRRLTPRECARLQGFPDdfilhsndnf
blimps-3.9/examples/cobbler/distribution/swat.sq.cob000064400001460000012000000006401041506274700232060ustar00jorjastaff00000400000027>PS00094 DCM_ECOLI from 80 to 425 with embedded consensus blocks
ahhphyafrfIDLFAGIGGFRLGFEQAGgqcvftsewnkhavrtykanhycdpathhfnedirditlshkegvsdeaaae
hirqhipehDLLIGGFPCQDFSxAGKRNGFDDTRGhgfacdtqgtlffdvvriidarrPKYFLMENVKGLkshdqgktfr
iimqtldelgydvadaeGYQVSYEILNAKDYGVPQNRERVFIIGfrrdlnlkadftlrdisecfpaqrvtlaqlldpmve
akyiltpvlwkylyryakkhqargngfgygmvypnnpqsvtrtlsaryykdgaeilidrgwdmatgekdfddplnqqhrp
RRLTPRECARLQGFPDpgeakfripv
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#
        A    R    N    D    C    Q    E    G    H    I    L    K    M    F    P    S    T    W    Y    V  
m      -2   -3   -3   -5   -1   -2   -4   -4   -2    1    2   -3   11    0   -5   -4   -2   -3   -1    1 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
I      -2   -7   -7   -8   -4   -7   -8   -7   -6    7    4   -7    4    4   -8   -7   -5   -5   -3    2 
D      -6   -6   -4    9   -6   -6    4   -6   -6   -8   -9   -6   -8   -9   -8    6   -5   -9   -8   -8 
L       0   -6   -7   -8   -4   -7   -7   -7   -6    0    7   -7   -1    3   -8   -6   -2   -5   -4    0 
F     -12  -13  -13  -15  -10  -14  -14  -13  -10   -9   -8  -13   -8   13  -15  -13  -12   -7   -5  -10 
A       8   -7   -6   -7    6   -7   -7   -5   -7   -7   -8   -6   -7   -8   -8    6   -5   -9   -7   -6 
G      -6   -9   -7   -8   -8   -9  -10   11   -9  -10  -11   -9  -10  -10  -10    1   -8   -9  -10  -10 
I       4   -6   -6   -7    9   -7   -7   -6   -6    7   -1   -6   -3   -3   -7   -5   -4   -6    2    2 
G      -6  -10   -7   -8   -8   -9  -10   11   -9  -10  -10   -9    3  -10  -10   -8   -9   -9  -10  -10 
G       2   -7   -5   -6   -6   -7   -8    9   -7    1   -7   -6   -7   -7   -8   -1   -6   -7   -8   -6 
F      -5   -5   -6   -7   -4    2   -6    1   -5    2    4   -6    4    7   -7   -6   -1   -4   -2   -2 
R      -2    7   -3    5   -5   -3    3   -5    1   -6   -6   -2   -5   -6   -6    1   -1   -6   -5   -5 
L       1   -2   -5   -6   -3   -4   -2   -6    5    1    6    0   -1   -2   -7   -5   -4   -4    3   -2 
G       5   -8   -6   -7   -6   -8   -8    9   -7   -8   -8   -7   -7    3   -9   -6   -7   -7   -7   -7 
F      -7   -8   -9   -9   -5   -8   -9   -9   -7    1    7   -8    2    9   -9   -8   -7   -5   -3   -3 
E      -2    1   -3   -2   -4    1    6   -4    4    1   -4    0   -1   -5   -5    0   -1   -5   -4   -3 
Q       0    3    4   -1   -4    5   -2   -1   -2   -4   -1    4    0   -5   -5    0   -2   -5   -4   -4 
A       6   -5   -5   -5    2   -5   -2   -1   -5    2   -1   -2   -3   -4   -5   -3    2   -6   -4    3 
G      -2   -1    2   -4   -4   -5   -3    9   -4   -6   -6   -2   -1    0   -6   -4   -4   -5   -1   -5 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
c      -1   -5   -4   -5   15   -6   -5   -4   -3   -2   -3   -5   -2   -3   -5   -3   -2   -6   -4   -1 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
c      -1   -5   -4   -5   15   -6   -5   -4   -3   -2   -3   -5   -2   -3   -5   -3   -2   -6   -4   -1 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
D      -6   -5    2   10   -6   -4    3   -5   -4   -7   -8    1   -7   -8   -6   -5   -5   -8   -7   -2 
L      -5   -6   -7   -7   -4   -7   -8    2   -6    4    4   -7    5    5   -8   -7   -5   -5   -3    3 
L      -6   -8   -9   -9   -5   -8   -9   -9   -7    6    7   -8   -2    3   -9   -8   -6   -6   -5    2 
I      -3   -5   -1   -6    6   -6   -6   -6   -5    5    2   -5    1   -3   -6   -2    4   -6   -4    5 
G       3   -7   -5   -6   -5   -7   -7    9   -6   -7   -8   -6   -7   -6   -8   -2   -6   -6    4   -7 
G      -5   -8   -6   -7    6   -8   -8   10   -7   -9   -9   -7   -8   -9   -9    2   -7   -8   -9   -8 
F       0   -6   -7   -7   -5   -7   -7   -6   -5   -4   -4   -6   -4    9    7   -3   -5   -3    1   -1 
P     -11  -12  -12  -11  -11  -11  -11  -12  -11  -12  -13  -10  -12  -14   13  -11  -11  -13  -12  -12 
C     -10  -13  -12  -13   17  -14  -14  -12  -12  -10  -11  -14  -11  -11  -14  -11  -10  -14  -12  -10 
Q      -6   -4   -6   -6   -8   12   -4   -7   -4   -8   -8   -4   -6   -9    3   -6   -6   -7   -7   -3 
D       1   -6   -3    6   -4   -5   -4    5   -5   -6   -7   -5   -6   -7    5    2    0   -7   -6   -6 
F      -6   -7   -8   -9   -5   -7   -8   -7   -5    0   -1   -7    2   11   -9   -7   -6   10    3   -4 
S      -8  -10   -8  -10   -9  -10  -10   -9  -10  -11  -12  -10  -11  -11  -11   11   -7  -13  -11  -11 
x      -3   -3   -1   -3   -3    4    2    1   -3    2    1   -2   -2    0   -5   -2   -2   -4    1    3 
A       7   -5   -5   -5   -3    0   -5   -2   -4   -1   -4   -4    4   -4   -6    0   -3   -5    3   -3 
G      -4   -1    3   -6   -6   -7   -7   10   -6   -8   -9   -6   -7   -8   -8   -5    1   -7   -8   -8 
K      -1    3   -1   -3   -3   -2   -3   -1    0   -1   -2    6   -3   -3    1    1   -3   -4    2   -1 
R      -4    6    2   -4   -5    4   -3   -5   -3   -4    0    3    1    3   -6   -1   -4   -5   -3   -4 
N      -3    2    5    2    3    1   -1   -2    1   -4   -1    4   -3   -5   -5    0   -3   -6   -4   -4 
G       0    1   -3   -1   -4    1   -2    8   -4   -2   -6    0   -5   -5   -5   -1   -4   -5   -5   -2 
F      -2    0    0    0   -3   -4   -1   -2   -3    1    0   -2    4    6   -6   -2    0   -3   -1    0 
D       1   -4    1    5   -3   -3    2    2   -3   -4   -1   -1   -4   -5   -5    1    0   -6   -5   -1 
D      -1    0    1    6   -3   -3    0    0    1   -4   -2   -3   -4   -3   -1   -2    0    4    3   -4 
T      -2    3   -2    0   -3   -3    0    1    1   -1   -4    2    1   -5    3    1    3   -5   -4   -3 
R       0    8    2   -4    3    1   -3   -4   -3   -6   -6    3   -4   -5   -6    0   -4    7   -4   -5 
G      -1   -1    1   -1   -4    1   -5    7   -4   -5   -5   -4   -4    3   -6    0   -4   -4   -4   -2 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
P     -11  -12  -12  -11  -11  -11  -11  -12  -11  -12  -13  -10  -12  -14   13  -11  -11  -13  -12  -12 
K       2    3   -3    1   -4    0    0   -4    1   -2   -3    7   -4   -5   -5   -3   -1   -6   -4   -4 
Y       2   -5   -6   -7   -3   -6   -6   -3   -3    3   -2   -6    2    6   -7   -5   -4    6    7    1 
F      -7   -8   -9   -9   -5   -9   -9   -8   -6    4    2   -8   -3   10  -10   -8   -7   -4   -2    2 
L      -5   -6   -7   -7   -4   -7   -7   -7   -6    5    6   -7    2    2   -8   -1   -4   -6   -4    4 
M       3   -6   -7   -8   -4   -6   -7   -6   -6    2    5   -7    9    3   -8   -6   -5   -6   -4   -2 
E     -10   -9   -9   -7  -12   -7   12  -12   -9  -13  -13   -8  -12  -13  -11  -10  -10  -11  -11  -12 
N     -11  -10   13   -7  -11  -10  -10   -9   -8  -12  -13   -9  -11  -13  -12   -9   -9  -13  -11  -13 
V      -9  -12  -13  -13   -9  -13  -13  -13  -13   -5   -8  -12   -8   -9  -13  -12   -9  -13  -10   11 
K      -4    5   -3   -1   -5   -2    0   -1   -3   -6   -3    7   -5   -6    4   -2   -4   -6   -5   -5 
G      -1    2    5   -3   -4   -1    0    7   -3   -6   -6   -3   -5    0   -6   -4   -2   -5   -5   -6 
L      -1   -6   -7   -8   -4   -6   -7   -7   -6    2    7   -7    6    4   -8   -7   -5   -5   -3    1 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
G      -3   -5   -1    2   -5   -5    1    8   -4   -6   -3   -5   -6   -5    0   -4   -5   -5    1   -6 
Y      -1   -5    2   -6   -4   -5   -6   -6   -2   -4   -4   -6    2    2   -7   -6   -5    0   12   -2 
Q      -3    2    1    0   -3    3    0    2    4    0   -4    0   -3   -4   -5    2    0   -4    1   -1 
V      -3   -5    0   -5    4   -5   -6   -2   -5    3    0   -1   -2    2    1   -5   -3   -5   -3    6 
S      -1   -1    1    3    2   -1    1   -3    5   -3   -4   -3   -3    2   -5    2    1   -3    4   -1 
Y      -1   -4   -4    1   -3    0   -4   -5    2    1    0   -4   -2    5    1   -4   -1    7    6   -1 
E      -1    0    1    1   -3    0    2    1    3   -1   -1    2   -3   -4    2   -1   -1   -5   -3   -1 
I      -5   -6   -7   -8   -4   -7   -7   -8   -7    6    4    1    2   -3   -8   -7   -5   -7   -5    6 
L      -2   -6   -7   -8   -3   -6   -7   -7   -6    2    7   -6    2    2   -7   -7   -5   -5    0    3 
N      -3   -3    9    3   -4    1   -1   -3    3    1   -5   -1   -4   -5    0   -3   -3   -6   -4   -4 
A       8   -6   -5    2    4   -6   -6   -4   -6   -6   -7   -6   -6   -7   -7    4   -4   -8   -7   -5 
K       1    2   -1   -4    2   -1   -3    3   -3   -4   -3    3   -4    1    0    1   -3    7   -3   -4 
D      -2   -3    5    8   -4    1   -2   -4   -3   -4   -2    1    2    0   -5   -4   -2   -6   -4   -4 
Y      -6   -6   -6   -7    4   -7   -7   -1    6   -4   -4   -7   -4    8   -8   -7   -6   -1   10   -5 
G      -4   -6    1   -2   -6    0   -7    9   -5   -7   -7   -6   -6    3   -7   -5   -6   -6   -6   -7 
V      -4   -6   -2   -7   -3   -6   -7   -7   -6    3    2   -6   -2   -4   -7   -2    2   -7   -5    8 
P       4   -8   -7   -7   -6   -7   -7   -7   -7   -8   -9   -7   -7   -9   11    0   -6   -9   -8   -7 
Q     -10   -8   -9  -10  -12   14   -7  -11   -8  -12  -12   -7   -9  -13  -11  -10  -10  -11  -10  -12 
N      -1    2    6    1   -3    0   -1   -3    5   -1   -1    0   -3   -4   -5    0    0   -5   -3   -1 
R     -11   12  -10  -11  -11   -8  -10  -12   -9  -12  -12   -6  -11  -12  -13  -11  -11  -12  -11  -12 
E      -4    3   -3    2   -5    0    7   -5   -3   -6   -3    4   -5   -6   -5   -4   -4   -6   -5   -3 
R     -11   12  -10  -11  -11   -8  -10  -12   -9  -12  -12   -6  -11  -12  -13  -11  -11  -12  -11  -12 
V       2   -7   -7   -7   -4   -7   -8   -7   -7    6    0   -7   -3   -4   -8   -6    0   -7   -5    7 
F      -6   -7   -8   -9   -5   -8   -9   -8   -5    4   -3   -8   -4    9   -9   -8   -6   -3    8    4 
I      -5   -6   -7   -7    2   -7   -7   -7   -6    8    3   -7    3    2   -7   -7   -4   -5    2    2 
I      -4   -2   -6   -6   -3   -6   -4   -6   -6    6    1   -6   -2    2   -7   -6    0    4   -3    6 
G       3   -7   -5   -6    4   -6   -7    9   -6   -6   -3   -6   -6   -7   -7    0   -5   -7   -7   -6 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
c      -1   -5   -4   -5   15   -6   -5   -4   -3   -2   -3   -5   -2   -3   -5   -3   -2   -6   -4   -1 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
w      -5   -5   -6   -6   -5   -3   -4   -4   -3   -4   -3   -5   -3    1   -6   -6   -5   16    3   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
c      -1   -5   -4   -5   15   -6   -5   -4   -3   -2   -3   -5   -2   -3   -5   -3   -2   -6   -4   -1 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
c      -1   -5   -4   -5   15   -6   -5   -4   -3   -2   -3   -5   -2   -3   -5   -3   -2   -6   -4   -1 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
m      -2   -3   -3   -5   -1   -2   -4   -4   -2    1    2   -3   11    0   -5   -4   -2   -3   -1    1 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
R     -11   12  -10  -11  -11   -8  -10  -12   -9  -12  -12   -6  -11  -12  -13  -11  -11  -12  -11  -12 
R      -2    5   -1   -4   -4    3   -3   -4   -3   -2   -2    4   -3   -5    4   -4   -1   -6   -4    0 
L      -6   -7   -8   -8   -4   -7   -8   -8   -7    4    7   -7    5    4   -8   -8   -6   -6   -4    0 
T      -3   -5    2   -5   -3   -5   -5   -5    2   -4   -6   -5   -5   -6   -6    5    7   -7   -5    2 
P      -1   -5   -5   -5   -3   -5   -2   -5   -5    0   -2   -4   -3   -5    7    3   -1   -6   -5    5 
R      -4    7   -1    1   -4    1   -3    2   -3   -1    1    2   -3   -4   -3   -2   -4   -5   -4   -4 
E      -8   -6   -7   -5   -9   -5   11   -9   -7  -10  -10    3   -9  -10   -9   -8   -8   -9   -9   -9 
C       2   -1   -5   -5   11   -5   -5   -2   -4    0    0   -4    0   -2   -6   -3    1    1    2    2 
A       6    3   -4   -4   -3   -3   -1   -3   -4   -4   -4    2    1    2   -2    0   -3    4   -3   -3 
R      -6   10   -6   -7   -6   -5   -6   -7   -5   -5    2   -3   -5   -6    4   -7   -6   -8   -6   -1 
L      -5   -6   -6    3   -4   -6   -6   -7   -5    5    5   -6   -2   -2   -7   -1   -5   -5    2    1 
Q      -4   -3    0   -5   -5   10   -3    2   -3    0   -4   -3    6   -6   -6   -5   -1   -5   -5   -4 
G       0   -4   -4   -5   -5    0   -5    8   -5   -6   -7    2   -6   -7   -6    0    2   -6   -6   -6 
F      -8   -8   -9  -10   -6  -10  -10   -9   -6   -5   -1   -9   -5   12  -11   -9   -8   -3    7   -6 
P      -7   -8   -7    3   -8   -7   -1   -8   -7   -8   -9   -6   -8  -10   11   -7   -7   -9   -9   -8 
D       2   -1   -2    7   -3   -3    2   -2   -3   -4   -3   -1   -4   -5   -2    1   -3   -6   -5   -2 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
-3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
i      -3  blimps-3.9/examples/cobbler/distribution/swat.sq.cob.prf000064400001460000012000001077471041506274700240140ustar00jorjastaff00000400000027#COBBLER Profile for PS00094 DCM_ECOLI from 80 to 425
#
        A    R    N    D    C    Q    E    G    H    I    L    K    M    F    P    S    T    W    Y    V  
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
I      -2   -7   -7   -8   -4   -7   -8   -7   -6    7    4   -7    4    4   -8   -7   -5   -5   -3    2 
D      -6   -6   -4    9   -6   -6    4   -6   -6   -8   -9   -6   -8   -9   -8    6   -5   -9   -8   -8 
L       0   -6   -7   -8   -4   -7   -7   -7   -6    0    7   -7   -1    3   -8   -6   -2   -5   -4    0 
F     -12  -13  -13  -15  -10  -14  -14  -13  -10   -9   -8  -13   -8   13  -15  -13  -12   -7   -5  -10 
A       8   -7   -6   -7    6   -7   -7   -5   -7   -7   -8   -6   -7   -8   -8    6   -5   -9   -7   -6 
G      -6   -9   -7   -8   -8   -9  -10   11   -9  -10  -11   -9  -10  -10  -10    1   -8   -9  -10  -10 
I       4   -6   -6   -7    9   -7   -7   -6   -6    7   -1   -6   -3   -3   -7   -5   -4   -6    2    2 
G      -6  -10   -7   -8   -8   -9  -10   11   -9  -10  -10   -9    3  -10  -10   -8   -9   -9  -10  -10 
G       2   -7   -5   -6   -6   -7   -8    9   -7    1   -7   -6   -7   -7   -8   -1   -6   -7   -8   -6 
F      -5   -5   -6   -7   -4    2   -6    1   -5    2    4   -6    4    7   -7   -6   -1   -4   -2   -2 
R      -2    7   -3    5   -5   -3    3   -5    1   -6   -6   -2   -5   -6   -6    1   -1   -6   -5   -5 
L       1   -2   -5   -6   -3   -4   -2   -6    5    1    6    0   -1   -2   -7   -5   -4   -4    3   -2 
G       5   -8   -6   -7   -6   -8   -8    9   -7   -8   -8   -7   -7    3   -9   -6   -7   -7   -7   -7 
F      -7   -8   -9   -9   -5   -8   -9   -9   -7    1    7   -8    2    9   -9   -8   -7   -5   -3   -3 
E      -2    1   -3   -2   -4    1    6   -4    4    1   -4    0   -1   -5   -5    0   -1   -5   -4   -3 
Q       0    3    4   -1   -4    5   -2   -1   -2   -4   -1    4    0   -5   -5    0   -2   -5   -4   -4 
A       6   -5   -5   -5    2   -5   -2   -1   -5    2   -1   -2   -3   -4   -5   -3    2   -6   -4    3 
G      -2   -1    2   -4   -4   -5   -3    9   -4   -6   -6   -2   -1    0   -6   -4   -4   -5   -1   -5 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
c      -1   -5   -4   -5   15   -6   -5   -4   -3   -2   -3   -5   -2   -3   -5   -3   -2   -6   -4   -1 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
w      -5   -5   -6   -6   -5   -3   -4   -4   -3   -4   -3   -5   -3    1   -6   -6   -5   16    3   -4 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
c      -1   -5   -4   -5   15   -6   -5   -4   -3   -2   -3   -5   -2   -3   -5   -3   -2   -6   -4   -1 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
D      -6   -5    2   10   -6   -4    3   -5   -4   -7   -8    1   -7   -8   -6   -5   -5   -8   -7   -2 
L      -5   -6   -7   -7   -4   -7   -8    2   -6    4    4   -7    5    5   -8   -7   -5   -5   -3    3 
L      -6   -8   -9   -9   -5   -8   -9   -9   -7    6    7   -8   -2    3   -9   -8   -6   -6   -5    2 
I      -3   -5   -1   -6    6   -6   -6   -6   -5    5    2   -5    1   -3   -6   -2    4   -6   -4    5 
G       3   -7   -5   -6   -5   -7   -7    9   -6   -7   -8   -6   -7   -6   -8   -2   -6   -6    4   -7 
G      -5   -8   -6   -7    6   -8   -8   10   -7   -9   -9   -7   -8   -9   -9    2   -7   -8   -9   -8 
F       0   -6   -7   -7   -5   -7   -7   -6   -5   -4   -4   -6   -4    9    7   -3   -5   -3    1   -1 
P     -11  -12  -12  -11  -11  -11  -11  -12  -11  -12  -13  -10  -12  -14   13  -11  -11  -13  -12  -12 
C     -10  -13  -12  -13   17  -14  -14  -12  -12  -10  -11  -14  -11  -11  -14  -11  -10  -14  -12  -10 
Q      -6   -4   -6   -6   -8   12   -4   -7   -4   -8   -8   -4   -6   -9    3   -6   -6   -7   -7   -3 
D       1   -6   -3    6   -4   -5   -4    5   -5   -6   -7   -5   -6   -7    5    2    0   -7   -6   -6 
F      -6   -7   -8   -9   -5   -7   -8   -7   -5    0   -1   -7    2   11   -9   -7   -6   10    3   -4 
S      -8  -10   -8  -10   -9  -10  -10   -9  -10  -11  -12  -10  -11  -11  -11   11   -7  -13  -11  -11 
x      -3   -3   -1   -3   -3    4    2    1   -3    2    1   -2   -2    0   -5   -2   -2   -4    1    3 
A       7   -5   -5   -5   -3    0   -5   -2   -4   -1   -4   -4    4   -4   -6    0   -3   -5    3   -3 
G      -4   -1    3   -6   -6   -7   -7   10   -6   -8   -9   -6   -7   -8   -8   -5    1   -7   -8   -8 
K      -1    3   -1   -3   -3   -2   -3   -1    0   -1   -2    6   -3   -3    1    1   -3   -4    2   -1 
R      -4    6    2   -4   -5    4   -3   -5   -3   -4    0    3    1    3   -6   -1   -4   -5   -3   -4 
N      -3    2    5    2    3    1   -1   -2    1   -4   -1    4   -3   -5   -5    0   -3   -6   -4   -4 
G       0    1   -3   -1   -4    1   -2    8   -4   -2   -6    0   -5   -5   -5   -1   -4   -5   -5   -2 
F      -2    0    0    0   -3   -4   -1   -2   -3    1    0   -2    4    6   -6   -2    0   -3   -1    0 
D       1   -4    1    5   -3   -3    2    2   -3   -4   -1   -1   -4   -5   -5    1    0   -6   -5   -1 
D      -1    0    1    6   -3   -3    0    0    1   -4   -2   -3   -4   -3   -1   -2    0    4    3   -4 
T      -2    3   -2    0   -3   -3    0    1    1   -1   -4    2    1   -5    3    1    3   -5   -4   -3 
R       0    8    2   -4    3    1   -3   -4   -3   -6   -6    3   -4   -5   -6    0   -4    7   -4   -5 
G      -1   -1    1   -1   -4    1   -5    7   -4   -5   -5   -4   -4    3   -6    0   -4   -4   -4   -2 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
c      -1   -5   -4   -5   15   -6   -5   -4   -3   -2   -3   -5   -2   -3   -5   -3   -2   -6   -4   -1 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
P     -11  -12  -12  -11  -11  -11  -11  -12  -11  -12  -13  -10  -12  -14   13  -11  -11  -13  -12  -12 
K       2    3   -3    1   -4    0    0   -4    1   -2   -3    7   -4   -5   -5   -3   -1   -6   -4   -4 
Y       2   -5   -6   -7   -3   -6   -6   -3   -3    3   -2   -6    2    6   -7   -5   -4    6    7    1 
F      -7   -8   -9   -9   -5   -9   -9   -8   -6    4    2   -8   -3   10  -10   -8   -7   -4   -2    2 
L      -5   -6   -7   -7   -4   -7   -7   -7   -6    5    6   -7    2    2   -8   -1   -4   -6   -4    4 
M       3   -6   -7   -8   -4   -6   -7   -6   -6    2    5   -7    9    3   -8   -6   -5   -6   -4   -2 
E     -10   -9   -9   -7  -12   -7   12  -12   -9  -13  -13   -8  -12  -13  -11  -10  -10  -11  -11  -12 
N     -11  -10   13   -7  -11  -10  -10   -9   -8  -12  -13   -9  -11  -13  -12   -9   -9  -13  -11  -13 
V      -9  -12  -13  -13   -9  -13  -13  -13  -13   -5   -8  -12   -8   -9  -13  -12   -9  -13  -10   11 
K      -4    5   -3   -1   -5   -2    0   -1   -3   -6   -3    7   -5   -6    4   -2   -4   -6   -5   -5 
G      -1    2    5   -3   -4   -1    0    7   -3   -6   -6   -3   -5    0   -6   -4   -2   -5   -5   -6 
L      -1   -6   -7   -8   -4   -6   -7   -7   -6    2    7   -7    6    4   -8   -7   -5   -5   -3    1 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
m      -2   -3   -3   -5   -1   -2   -4   -4   -2    1    2   -3   11    0   -5   -4   -2   -3   -1    1 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
G      -3   -5   -1    2   -5   -5    1    8   -4   -6   -3   -5   -6   -5    0   -4   -5   -5    1   -6 
Y      -1   -5    2   -6   -4   -5   -6   -6   -2   -4   -4   -6    2    2   -7   -6   -5    0   12   -2 
Q      -3    2    1    0   -3    3    0    2    4    0   -4    0   -3   -4   -5    2    0   -4    1   -1 
V      -3   -5    0   -5    4   -5   -6   -2   -5    3    0   -1   -2    2    1   -5   -3   -5   -3    6 
S      -1   -1    1    3    2   -1    1   -3    5   -3   -4   -3   -3    2   -5    2    1   -3    4   -1 
Y      -1   -4   -4    1   -3    0   -4   -5    2    1    0   -4   -2    5    1   -4   -1    7    6   -1 
E      -1    0    1    1   -3    0    2    1    3   -1   -1    2   -3   -4    2   -1   -1   -5   -3   -1 
I      -5   -6   -7   -8   -4   -7   -7   -8   -7    6    4    1    2   -3   -8   -7   -5   -7   -5    6 
L      -2   -6   -7   -8   -3   -6   -7   -7   -6    2    7   -6    2    2   -7   -7   -5   -5    0    3 
N      -3   -3    9    3   -4    1   -1   -3    3    1   -5   -1   -4   -5    0   -3   -3   -6   -4   -4 
A       8   -6   -5    2    4   -6   -6   -4   -6   -6   -7   -6   -6   -7   -7    4   -4   -8   -7   -5 
K       1    2   -1   -4    2   -1   -3    3   -3   -4   -3    3   -4    1    0    1   -3    7   -3   -4 
D      -2   -3    5    8   -4    1   -2   -4   -3   -4   -2    1    2    0   -5   -4   -2   -6   -4   -4 
Y      -6   -6   -6   -7    4   -7   -7   -1    6   -4   -4   -7   -4    8   -8   -7   -6   -1   10   -5 
G      -4   -6    1   -2   -6    0   -7    9   -5   -7   -7   -6   -6    3   -7   -5   -6   -6   -6   -7 
V      -4   -6   -2   -7   -3   -6   -7   -7   -6    3    2   -6   -2   -4   -7   -2    2   -7   -5    8 
P       4   -8   -7   -7   -6   -7   -7   -7   -7   -8   -9   -7   -7   -9   11    0   -6   -9   -8   -7 
Q     -10   -8   -9  -10  -12   14   -7  -11   -8  -12  -12   -7   -9  -13  -11  -10  -10  -11  -10  -12 
N      -1    2    6    1   -3    0   -1   -3    5   -1   -1    0   -3   -4   -5    0    0   -5   -3   -1 
R     -11   12  -10  -11  -11   -8  -10  -12   -9  -12  -12   -6  -11  -12  -13  -11  -11  -12  -11  -12 
E      -4    3   -3    2   -5    0    7   -5   -3   -6   -3    4   -5   -6   -5   -4   -4   -6   -5   -3 
R     -11   12  -10  -11  -11   -8  -10  -12   -9  -12  -12   -6  -11  -12  -13  -11  -11  -12  -11  -12 
V       2   -7   -7   -7   -4   -7   -8   -7   -7    6    0   -7   -3   -4   -8   -6    0   -7   -5    7 
F      -6   -7   -8   -9   -5   -8   -9   -8   -5    4   -3   -8   -4    9   -9   -8   -6   -3    8    4 
I      -5   -6   -7   -7    2   -7   -7   -7   -6    8    3   -7    3    2   -7   -7   -4   -5    2    2 
I      -4   -2   -6   -6   -3   -6   -4   -6   -6    6    1   -6   -2    2   -7   -6    0    4   -3    6 
G       3   -7   -5   -6    4   -6   -7    9   -6   -6   -3   -6   -6   -7   -7    0   -5   -7   -7   -6 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
c      -1   -5   -4   -5   15   -6   -5   -4   -3   -2   -3   -5   -2   -3   -5   -3   -2   -6   -4   -1 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
m      -2   -3   -3   -5   -1   -2   -4   -4   -2    1    2   -3   11    0   -5   -4   -2   -3   -1    1 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
w      -5   -5   -6   -6   -5   -3   -4   -4   -3   -4   -3   -5   -3    1   -6   -6   -5   16    3   -4 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
m      -2   -3   -3   -5   -1   -2   -4   -4   -2    1    2   -3   11    0   -5   -4   -2   -3   -1    1 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
s       1   -2    0   -1   -1   -2   -2   -1   -2   -3   -4   -1   -3   -3   -3    7    1   -5   -3   -2 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
y      -3   -3   -3   -4   -2   -3   -4   -4    2   -1   -1   -3   -1    4   -5   -4   -3    3   11   -2 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
w      -5   -5   -6   -6   -5   -3   -4   -4   -3   -4   -3   -5   -3    1   -6   -6   -5   16    3   -4 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
m      -2   -3   -3   -5   -1   -2   -4   -4   -2    1    2   -3   11    0   -5   -4   -2   -3   -1    1 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
t      -1   -2   -1   -2    0   -2   -2   -3   -3   -1   -2   -2   -1   -3   -3    0    8   -4   -3    0 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
d      -3   -3    1    9   -3   -2    1   -2   -1   -4   -5   -1   -5   -5   -3   -2   -2   -6   -4   -4 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
l      -3   -4   -5   -5   -2   -4   -5   -5   -4    2    7   -4    2    1   -6   -5   -3   -3   -2    1 
n      -3   -2    9    1   -3   -1   -2   -1    1   -4   -5   -1   -3   -4   -4   -1   -1   -5   -3   -4 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
q      -2    1   -1   -1   -4    9    1   -3    1   -4   -3    1   -1   -4   -3   -2   -2   -3   -2   -3 
h      -3   -1    0   -2   -2    0   -2   -3   13   -4   -4   -1   -2   -2   -4   -3   -3   -3    1   -4 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
R     -11   12  -10  -11  -11   -8  -10  -12   -9  -12  -12   -6  -11  -12  -13  -11  -11  -12  -11  -12 
R      -2    5   -1   -4   -4    3   -3   -4   -3   -2   -2    4   -3   -5    4   -4   -1   -6   -4    0 
L      -6   -7   -8   -8   -4   -7   -8   -8   -7    4    7   -7    5    4   -8   -8   -6   -6   -4    0 
T      -3   -5    2   -5   -3   -5   -5   -5    2   -4   -6   -5   -5   -6   -6    5    7   -7   -5    2 
P      -1   -5   -5   -5   -3   -5   -2   -5   -5    0   -2   -4   -3   -5    7    3   -1   -6   -5    5 
R      -4    7   -1    1   -4    1   -3    2   -3   -1    1    2   -3   -4   -3   -2   -4   -5   -4   -4 
E      -8   -6   -7   -5   -9   -5   11   -9   -7  -10  -10    3   -9  -10   -9   -8   -8   -9   -9   -9 
C       2   -1   -5   -5   11   -5   -5   -2   -4    0    0   -4    0   -2   -6   -3    1    1    2    2 
A       6    3   -4   -4   -3   -3   -1   -3   -4   -4   -4    2    1    2   -2    0   -3    4   -3   -3 
R      -6   10   -6   -7   -6   -5   -6   -7   -5   -5    2   -3   -5   -6    4   -7   -6   -8   -6   -1 
L      -5   -6   -6    3   -4   -6   -6   -7   -5    5    5   -6   -2   -2   -7   -1   -5   -5    2    1 
Q      -4   -3    0   -5   -5   10   -3    2   -3    0   -4   -3    6   -6   -6   -5   -1   -5   -5   -4 
G       0   -4   -4   -5   -5    0   -5    8   -5   -6   -7    2   -6   -7   -6    0    2   -6   -6   -6 
F      -8   -8   -9  -10   -6  -10  -10   -9   -6   -5   -1   -9   -5   12  -11   -9   -8   -3    7   -6 
P      -7   -8   -7    3   -8   -7   -1   -8   -7   -8   -9   -6   -8  -10   11   -7   -7   -9   -9   -8 
D       2   -1   -2    7   -3   -3    2   -2   -3   -4   -3   -1   -4   -5   -2    1   -3   -6   -5   -2 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
g      -1   -4   -1   -3   -3   -4   -4    9   -3   -5   -5   -3   -4   -4   -4   -2   -3   -4   -5   -4 
e      -2   -1   -1    1   -4    1    8   -4   -1   -4   -4    1   -3   -4   -3   -2   -2   -3   -3   -4 
a       7   -3   -3   -3    0   -3   -2    0   -3   -2   -3   -2   -2   -3   -3    0   -1   -5   -3    0 
k      -2    2   -1   -1   -4    0    0   -3   -1   -4   -4    8   -3   -4   -3   -2   -2   -5   -3   -3 
f      -4   -4   -5   -6   -2   -6   -5   -5   -2    0    0   -5    0   11   -7   -5   -4    1    3   -1 
r      -3    9   -2   -3   -3    0   -1   -4    0   -4   -3    2   -3   -4   -5   -3   -3   -4   -3   -4 
i      -3   -5   -5   -5   -2   -5   -5   -5   -5    8    2   -5    1    0   -5   -4   -2   -4   -2    3 
p      -2   -4   -3   -3   -3   -3   -3   -3   -3   -4   -4   -2   -4   -5   10   -3   -2   -5   -4   -3 
v      -1   -4   -5   -5   -1   -4   -5   -5   -5    4    1   -4    0   -1   -5   -4   -1   -5   -2    8 
-4   -3   -4   -3   -5   blimps-3.9/examples/cobbler/cobbler.csh000075500001460000012000000004531041506323700205110ustar00jorjastaff00000400000027#!/bin/csh

#	Test cobbler installation

setenv BLIMPS_DIR ../..

set cfs = (*.cf)
foreach cf ($cfs)
echo "Running $cf..."
	$BLIMPS_DIR/bin/cobbler $cf
echo ""
end

set files = (distribution/*.*)
foreach file ($files)
	set test = $file:t
echo "Checking $test..."
	diff $test $file
echo ""
end
exit

blimps-3.9/examples/codehop/000075500001460000012000000000001041506354100164045ustar00jorjastaff00000400000027blimps-3.9/examples/codehop/README000064400001460000012000000011430733525405500172740ustar00jorjastaff00000400000027	Sample files for codehop


T.M. Rose, E.R. Schultz, J.G. Henikoff, C.M. McCallum & S. Henikoff, 
"Consensus-degenerate hybrid oligonucleotide primers for amplification 
of distantly-related sequences", Nucl. Acids Res.  26:1628-1635 (1998). 

http://blocks.fhcrc.org/blocks/help/CODEHOP/CODEHOP_help.html


The codehop program is available from the NCBI repository:
	ftp://ncbi.nlm.nih.gov/repository/blocks/unix/blimps/


To test the installation:

	codehop.csh euk.blks euk.out
	Compare euk.out with distribution/euk.out

To create codon usage files for more organisms:

	coduse.csh (see instructions there)
blimps-3.9/examples/codehop/codehop.csh000075500001460000012000000014201041506340200205200ustar00jorjastaff00000400000027#!/bin/csh
#      codehop.csh  
#
#  Make codehops from a set of blocks
#
unalias rm
unalias mv
#echo "codehop.csh"
#echo $1
#echo $2
#echo $3
#
#
setenv BLIMPS_DIR ../..
set bin = $BLIMPS_DIR/bin
#	See coduse.csh to create the codon usage files
set docs = $BLIMPS_DIR/docs
#
#	Type "$bin/codehop" to see parameter options
if ( -e $1 ) then
#	These are the WWW defaults
#  $bin/codehop $1 -O3 >& $2
#	Use an alternative codon usage file
   $bin/codehop $1 -C$docs/arab.codon.use -O3 >& $2
#	Use most common codons (many people prefer this option)
#  $bin/codehop $1 -O3 -M >& $2
#  
else
   echo "Cannot open blocks file $1."
endif
#

set files = (distribution/*.*)
foreach file ($files)
	set test = $file:t
echo "Checking $test..."
	diff $test $file
echo ""
end
exit(0)
blimps-3.9/examples/codehop/coduse.csh000075500001460000012000000170701001025330400203620ustar00jorjastaff00000400000027#!/bin/csh
#		coduse.csh
#   How to create codon usage files for codehop
#
#   First get the CUTG codon usage files:
#	mkdir GB138 (or whatever the GenBank release number is)
# 	ftp://ftp.kazusa.or.jp/pub/codon/current/	
#	mget gb*.spsum

set bin = ../../bin

$bin/coduse GB138/gbpln.spsum "Arabidopsis thaliana" arab.codon.use
$bin/coduse GB138/gbpln.spsum "Amanita muscaria" amanita.codon.use
$bin/coduse GB138/gbpln.spsum "Brassica oleracea" broc.codon.use
$bin/coduse GB138/gbpln.spsum "Brassica napus" napus.codon.use
$bin/coduse GB138/gbpln.spsum "Oryza sativa" rice.codon.use
$bin/coduse GB138/gbpln.spsum "Nicotiana tabacum" tobacco.codon.use
$bin/coduse GB138/gbpln.spsum "Zea mays" zea.codon.use
$bin/coduse GB138/gbpln.spsum "Hordeum vulgare" barley.codon.use
$bin/coduse GB138/gbpln.spsum "Laccaria bicolor" laccaria.codon.use
$bin/coduse GB138/gbpln.spsum "Lycopersicon esculentum" tomato.codon.use
$bin/coduse GB138/gbpln.spsum "Mesembryanthemum crystallinum" iceplant.codon.use
$bin/coduse GB138/gbpln.spsum "Neurospora crassa" neur.codon.use
$bin/coduse GB138/gbpln.spsum "Porphyra pulchra" porph.codon.use
$bin/coduse GB138/gbpln.spsum "Chlamydomonas reinhardtii" chlamy.codon.use
$bin/coduse GB138/gbpln.spsum "Schizosaccharomyces pombe" pombe.codon.use
$bin/coduse GB138/gbpln.spsum "Saccharomyces cerevisiae" yeast.codon.use
$bin/coduse GB138/gbpln.spsum "Physcomitrella patens" moss.codon.use
$bin/coduse GB138/gbpln.spsum "Prunus persica" peach.codon.use
$bin/coduse GB138/gbpln.spsum "Ustilago maydis" ustilago.codon.use
$bin/coduse GB138/gbpln.spsum "Malus domestica" apple.codon.use
$bin/coduse GB138/gbpln.spsum "Solanum tuberosum" potato.codon.use
$bin/coduse GB138/gbpln.spsum "Gonyaulax polyedra" gony.codon.use
$bin/coduse GB138/gbpln.spsum "Pisum sativum" pea.codon.use
$bin/coduse GB138/gbpln.spsum "Euglena gracilis" euglena.codon.use
$bin/coduse GB138/gbpln.spsum "Gossypium hirsutum" gossy.codon.use
$bin/coduse GB138/gbpln.spsum "Clarkia breweri" clarkiab.codon.use
$bin/coduse GB138/gbpln.spsum "Clarkia concinna" clarkiac.codon.use
$bin/coduse GB138/gbpln.spsum "Dunaliella salina" dunal.codon.use
$bin/coduse GB138/gbpln.spsum "Marchantia polymorpha" marchan.codon.use
$bin/coduse GB138/gbpln.spsum "Chara corallina" chara.codon.use
$bin/coduse GB138/gbpln.spsum "Mucor racemosus" mucor.codon.use
$bin/coduse GB138/gbpln.spsum "Ceratopteris richardii" fern.codon.use
$bin/coduse GB138/gbpln.spsum "Antirrhinum majus" snapdragon.codon.use
#	NOTE:  mucorc.codon.use is a custom table from a user


$bin/coduse GB138/gbbct.spsum "Acholeplasma laidlawii" achole.codon.use
$bin/coduse GB138/gbbct.spsum "Chlorobium vibrioforme" chlvib.codon.use
$bin/coduse GB138/gbbct.spsum "Chlorobium tepidum" chltep.codon.use
$bin/coduse GB138/gbbct.spsum "Chlorobium limicola" chllim.codon.use
$bin/coduse GB138/gbbct.spsum "Haemophilus influenzae" haemophilus.codon.use
$bin/coduse GB138/gbbct.spsum "Escherichia coli" ecoli.codon.use
$bin/coduse GB138/gbbct.spsum "Ralstonia eutropha" ralston.codon.use
$bin/coduse GB138/gbbct.spsum "Rhodobacter sphaeroides" rhodo.codon.use
$bin/coduse GB138/gbbct.spsum "Streptomyces coelicolor" strep.codon.use
$bin/coduse GB138/gbbct.spsum "Lactobacillus casei" lacto.codon.use
$bin/coduse GB138/gbbct.spsum "Staphylococcus aureus" staph.codon.use
$bin/coduse GB138/gbbct.spsum "Bartonella bacilliformis" bartb.codon.use
$bin/coduse GB138/gbbct.spsum "Bartonella henselae" barth.codon.use
$bin/coduse GB138/gbbct.spsum "Brucella abortus" brucella.codon.use
$bin/coduse GB138/gbbct.spsum "Ehrlichia chaffeensis" ehrl.codon.use
$bin/coduse GB138/gbbct.spsum "Bacillus subtilis" bacsub.codon.use
$bin/coduse GB138/gbbct.spsum "Bacillus thuringiensis" bact.codon.use
$bin/coduse GB138/gbbct.spsum "Agrobacterium tumefaciens" agro.codon.use
$bin/coduse GB138/gbbct.spsum "Chlamydia trachomatis" chlam.codon.use
$bin/coduse GB138/gbbct.spsum "Paracoccus denitrificans" paraco.codon.use
$bin/coduse GB138/gbbct.spsum "Pseudomonas syringae pv. glycinea" pseudo.codon.use
$bin/coduse GB138/gbbct.spsum "Synechococcus sp." synecho.codon.use
$bin/coduse GB138/gbbct.spsum "Leptospira interrogans" lepto.codon.use
$bin/coduse GB138/gbbct.spsum "Chlorobium vibrioforme" greenv.codon.use

$bin/coduse GB138/gbinv.spsum "Giardia intestinalis" giardia.codon.use
$bin/coduse GB138/gbinv.spsum "Musca domestica" musca.codon.use
$bin/coduse GB138/gbinv.spsum "Tetrahymena thermophila" tetra.codon.use
$bin/coduse GB138/gbinv.spsum "Tetrahymena pyriformis" tetrapyr.codon.use
$bin/coduse GB138/gbinv.spsum "Trypanosoma brucei" tryp.codon.use
$bin/coduse GB138/gbinv.spsum "Leishmania major" leishm.codon.use
$bin/coduse GB138/gbinv.spsum "Leishmania tarentolae" leish.codon.use
$bin/coduse GB138/gbinv.spsum "Plasmodium falciparum" plasmo.codon.use
$bin/coduse GB138/gbinv.spsum "Schistosoma mansoni" schis.codon.use
$bin/coduse GB138/gbinv.spsum "Bombyx mori" bombyx.codon.use
$bin/coduse GB138/gbinv.spsum "Caenorhabditis elegans" worm.codon.use
$bin/coduse GB138/gbinv.spsum "Drosophila melanogaster" fly.codon.use
$bin/coduse GB138/gbinv.spsum "Hydra vulgaris" hydra.codon.use
$bin/coduse GB138/gbinv.spsum "Brugia malayi" brugia.codon.use
$bin/coduse GB138/gbinv.spsum "Onchocerca volvulus" onch.codon.use
$bin/coduse GB138/gbinv.spsum "Ascaris suum" ascaris.codon.use
$bin/coduse GB138/gbinv.spsum "Trichinella spiralis" trich.codon.use
$bin/coduse GB138/gbinv.spsum "Haemonchus contortus" haem.codon.use
$bin/coduse GB138/gbinv.spsum "Ancylostoma caninum" ancyl.codon.use
$bin/coduse GB138/gbinv.spsum "Lymnaea stagnalis" lymn.codon.use
$bin/coduse GB138/gbinv.spsum "Placopecten magellanicus" placo.codon.use
$bin/coduse GB138/gbinv.spsum "Strongylocentrotus purpuratus" strongy.codon.use
$bin/coduse GB138/gbinv.spsum "Hirudo medicinalis" hirudo.codon.use
$bin/coduse GB138/gbinv.spsum "Myzus persicae" myzus.codon.use
$bin/coduse GB138/gbinv.spsum "Heliothis virescens" helio.codon.use
$bin/coduse GB138/gbinv.spsum "Helicoverpa armigera" helicov.codon.use
$bin/coduse GB138/gbinv.spsum "Lucilia cuprina" luci.codon.use
$bin/coduse GB138/gbinv.spsum "Entamoeba histolytica" entam.codon.use
$bin/coduse GB138/gbinv.spsum "Geodia cydonium" geodia.codon.use
$bin/coduse GB138/gbinv.spsum "Suberites domuncula" suberites.codon.use
$bin/coduse GB138/gbinv.spsum "Heterodera glycines" soycyst.codon.use

$bin/coduse GB138/gbvrt.spsum "Danio rerio" zebra.codon.use
$bin/coduse GB138/gbvrt.spsum "Myxine glutinosa" ahagfish.codon.use
$bin/coduse GB138/gbvrt.spsum "Eptatretus stouti" phagfish.codon.use
#src/coduse GB121/gbvrt.spsum "Fugu rubripes" fugu.codon.use
$bin/coduse GB138/gbvrt.spsum "Takifugu rubripes" fugu.codon.use
$bin/coduse GB138/gbvrt.spsum "Xenopus laevis" frog.codon.use
$bin/coduse GB138/gbvrt.spsum "Ambystoma mexicanum" amby.codon.use
$bin/coduse GB138/gbvrt.spsum "Gallus gallus" chicken.codon.use
$bin/coduse GB138/gbvrt.spsum "Anas platyrhynchos" anas.codon.use
$bin/coduse GB138/gbvrt.spsum "Cairina moschata" duck.codon.use
$bin/coduse GB138/gbvrt.spsum "Anser anser" goose.codon.use

$bin/coduse GB138/gbrod.spsum "Cavia porcellus" cavia.codon.use
$bin/coduse GB138/gbrod.spsum "Mus musculus" mouse.codon.use
$bin/coduse GB138/gbrod.spsum "Rattus norvegicus" rat.codon.use

$bin/coduse GB138/gbmam.spsum "Bos taurus" cow.codon.use
$bin/coduse GB138/gbmam.spsum "Oryctolagus cuniculus" rabbit.codon.use
$bin/coduse GB138/gbmam.spsum "Ovis aries" sheep.codon.use
$bin/coduse GB138/gbmam.spsum "Sus scrofa" pig.codon.use

$bin/coduse GB138/gbpri.spsum "Homo sapiens" human.codon.use

$bin/coduse GB138/gbvrl.spsum "Chilo iridescent virus" civ.codon.use
$bin/coduse GB138/gbvrl.spsum "Human herpesvirus 4" herpes4.codon.use

unalias mv
mv *.codon.use ../../docs

exit
blimps-3.9/examples/codehop/euk.blks000064400001460000012000000115320637163715200200620ustar00jorjastaff00000400000027ID   Methylases Eukaryotes; BLOCK
AC   MethylaA; distance from previous block=(227,1136)
DE   MTCH_ARATH Chromomethylase Arabidopsis coding, tra... family
BL   GWP motif=[8,0,17] motomat=[1,1,-10] width=29 seqs=8
MTCH_ARAAR ( 221) LDLYSGCGAMSTGFCMGASIAGVKLITKW  94
MTCH_ARATH ( 229) LDLYSGCGAMSTGFCMGASISGVKLITKW  94
MTDM_ARATH (1092) LDIFAGCGGLSHGLKKAGVSDAKWAIEYE 100
MTDM_CHICK (1057) LDVFSGCGGLSEGFHQAGVSETLWAIEMW  52
MTDM_HUMAN (1021) LDVFSGCGGLSEGFHQAGISDTLWAIEMW  52
MTDM_MOUSE (1027) LDVFSGCGGLSEGFHQAGISETLWAIEMW  50
MTDM_PARLI (1134) LDVFAGCGGLSEGFHQAGICESSWAIEKE  69
MTDM_XENLA (1017) LDVFSGCGGLSEGFHQAGISETNWAIEMW  53
//
ID   Methylases Eukaryotes; BLOCK
AC   MethylaB; distance from previous block=(227,1136)
DE   MTCH_ARATH Chromomethylase Arabidopsis coding, tra... family
BL   GWP motif=[8,0,17] motomat=[1,1,-10] width=29 seqs=8
MTCH_ARAAR ( 254) KFACDSFRHNHPETEVRNEAAEDFLILLK  97
MTCH_ARATH ( 262) KFACDSLKLNHPETEVRNEAAEDFLALLK 100
MTDM_ARATH (1125) EPAGQAFKQNHPESTVFVDNCNVILRAIM  97
MTDM_CHICK (1086) EPAAQAFRLNNPGTTVFTEDCNVLLKLVM  48
MTDM_HUMAN (1050) DPAAQAFRLNNPGSTVFTEDCNILLKLVM  52
MTDM_MOUSE (1056) DPAAQAFRLNNPGTTVFTEDCNVLLKLVM  50
MTDM_PARLI (1163) EPAAQAYRLNNPGSTVFSDDCNELLRLVM  66
MTDM_XENLA (1046) EPAAQAFRLNNPGTTVFTEDCNILLKLVM  49
//
ID   Methylases Eukaryotes; BLOCK
AC   MethylaC; distance from previous block=(11,111)
DE   MTCH_ARATH Chromomethylase Arabidopsis coding, tra... family
BL   CSR motif=[8,0,17] motomat=[1,1,-10] width=26 seqs=8
MTCH_ARAAR ( 394) LPLPGTVYSVCGGPPCQGISGYNRFR  90
MTCH_ARATH ( 402) LPLPGTVYTVCGGPPCQGISGYNRYR 100
MTDM_ARATH (1183) LPLPGQVDFINGGPPCQGFSGMNRFN 100
MTDM_CHICK (1126) LPQKGDVEMLCGGPPCQGFSGMNRFN  64
MTDM_HUMAN (1090) LPQKGDVEMLCGGPPCQGFSGMNRFN  64
MTDM_MOUSE (1096) LPQKGDVEMLCGGPPCQGFSGMNRFN  64
MTDM_PARLI (1203) LPQKGDVELLCGGPPCQGFSGMNRFN  68
MTDM_XENLA (1086) LPQKGDVEMLCGGPPCQGFSGMNRFN  64
//
ID   Methylases Eukaryotes; BLOCK
AC   MethylaD; distance from previous block=(49,51)
DE   MTCH_ARATH Chromomethylase Arabidopsis coding, tra... family
BL   AAH motif=[8,0,17] motomat=[1,1,-10] width=48 seqs=8
MTCH_ARAAR ( 471) SFVAMNYQTRLGMMTAGSYGLPQVRNRVFLWAAQPTEKLPPYPLPTHE  94
MTCH_ARATH ( 479) SFVAMNYQTRLGMMAAGSYGLPQLRNRVFLWAAQPSEKLPPYPLPTHE  94
MTDM_ARATH (1258) SLLEMGYQVRFGILEAGAYGVSQSRKRAFIWAAAPEEVLPEWPEPMHV 100
MTDM_CHICK (1201) CLVRMGYQCTFGVLQAGQYGVAQTRRRAIVLAAAPGEKLPMFPEPLHV  58
MTDM_HUMAN (1165) CLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHV  57
MTDM_MOUSE (1171) CLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHV  57
MTDM_PARLI (1278) CLIRMGYQCTFGILQAGQYGVPQTRRRAIILAAAPGEKLPFYPEPLHV  63
MTDM_XENLA (1161) CLVRMGYQCTFGVLQAGQYGVAQTRRRAIVLAAAPGEKLPMFPEPLHV  58
//
ID   Methylases Eukaryotes; BLOCK
AC   MethylaE; distance from previous block=(26,28)
DE   MTCH_ARATH Chromomethylase Arabidopsis coding, tra... family
BL   DDN motif=[8,0,17] motomat=[1,1,-10] width=28 seqs=8
MTCH_ARAAR ( 545) DNALTLADAISDLPPVTNSEANDVRNYN  94
MTCH_ARATH ( 553) DNALTLADAISDLPPVTNYVANDVMDYN  94
MTDM_ARATH (1333) FRPITVRDTIGDLPSVENGDSRTNKEYK 100
MTDM_CHICK (1277) FRTITVRDTMSDLPEIRNGASALEISYN  48
MTDM_HUMAN (1241) FRTITVRDTMSDLPEVRNGASALEISYN  48
MTDM_MOUSE (1247) FRTITERDTMSDLPEIQNGASNSEIPYN  63
MTDM_PARLI (1354) YRTITVRDTMSDLPTINNGAQKLEISYD  75
MTDM_XENLA (1237) FRTITVRDTMSDLPEIRNGASALEISYN  48
//
ID   Methylases Eukaryotes; BLOCK
AC   MethylaF; distance from previous block=(19,33)
DE   MTCH_ARATH Chromomethylase Arabidopsis coding, tra... family
BL   GDP motif=[8,0,17] motomat=[1,1,-10] width=54 seqs=8
MTCH_ARAAR ( 606) DHHPLELRDDDLERISYIPKKKGANFRDMPGVLVHNNKAQLNLRVKRAKLKSGK 100
MTCH_ARATH ( 614) DHQPLVLGDDDLERVSYIPKQKGANYRDMPGVLVHNNKAEINPRFRAKLKSGKN  89
MTDM_ARATH (1380) DHICKAMNELNLIRCKLIPTRPGADWHDLPKRKVTLSDGRVEEMIPFCLPNTAE  97
MTDM_CHICK (1326) DHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTSTRKLRYTHHEKKN  44
MTDM_HUMAN (1290) DHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTMARKLRYTHHDRKN  43
MTDM_MOUSE (1296) GPYLQGHEPTGGCPHAHIPLFPGSDWRDLPNIQVRLGDGVIADKLQYTFHDVKN  94
MTDM_PARLI (1403) DHICKDMSSLVAARMKHIPLAPGSDWRDLPNIPVTLKDGTTCRKLRYTHKDKKN  48
MTDM_XENLA (1286) DHVCKDMSALVAARMRHIPLAPGSDWRDLPNMEVRLSDGTTSRKLRYTHHDKKN  45
//
ID   Methylases Eukaryotes; BLOCK
AC   MethylaG; distance from previous block=(27,68)
DE   MTCH_ARATH Chromomethylase Arabidopsis coding, tra... family
BL   AIA motif=[8,0,17] motomat=[1,1,-10] width=57 seqs=8
MTCH_ARAAR ( 695) EPHNQCVIHPMQERVLSVRENARLQGFPDCYKLCGSIKEKYIQVGNAVAVPVGVALG  96
MTCH_ARATH ( 702) EPHNQCVIHPMQNRVLSVRENARLQGFPDCYKLCGTIKEKYIQVGNAVAVPVGVALG  98
MTDM_ARATH (1461) MGKVGMCFHPEQHRILTVRECARSQGFPDSYEFAGNINHKHRQIGNAVPPPLAFALG 100
MTDM_CHICK (1447) MGKQGRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIG  60
MTDM_HUMAN (1412) MGKQGRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIG  60
MTDM_MOUSE (1417) MGKQGRVLHPEQHRVVSVRECARSQGFPDSYRFFGNILDRHRQVGNAVPPPLAKAIG  66
MTDM_PARLI (1524) MGKQGRVLHPEQHRVVSVRECARSQGFPDTYRFFGSILDKHRQIGNAVPPPMAAAIG  68
MTDM_XENLA (1407) MGKQGRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLSRAIG  64
//
HGLKKAGVSDAKWAIEYE 100
MTDM_CHICK (1057) LDVFSGCGGLSEGFHQAGVSETLWAIEMW  52
MTDM_HUMAN (1021) LDVFSGCGGLSEGFHQAGISDTLWAIEMW  52
MTDM_MOUSE (1027) LDVFSGCGGLSEGFHQAGISEblimps-3.9/examples/codehop/distribution/000075500001460000012000000000001041506353500211265ustar00jorjastaff00000400000027blimps-3.9/examples/codehop/distribution/euk.out000064400001460000012000000176161041506342600224550ustar00jorjastaff00000400000027CODEHOP Version 10/14/04.1
COPYRIGHT 1997-2004, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

Parameters:
 Amino acids PSSM calculated with odds ratios normalized to 100
 and back-translated with Standard genetic code
 and codon usage table "../../docs/arab.codon.use"
 Maximum core degeneracy 128    Core strictness 0.00
 Clamp strictness 1.00   Target clamp temperature 60.00 C
 DNA Concentration 50.00 nM   Salt Concentration 50.00 mM
 Codon boundary 0   Most common codon 0
 Verbose 0   Output 3
 Begin 1   PolyX 5
Suggested CODEHOPS: The degenerate region (core) is printed in lower case,
the non-degenerate region (clamp) is printed in upper case.

Processing Block MethylaA
L  D  V  F  S  G  C  G  G  M  S  H  G  F  H  M  A  G  I  S  E  T  V  W  A  I  E  M  W  
CTGGATGTCTTTTCnggntgyggng -3'  Core: degen=128 len=11  Clamp: score=69, len=14 temp= 35.8 *** CLAMP NEEDS EXTENSION

Processing Complement of Block MethylaA
L  D  V  F  S  G  C  G  G  M  S  H  G  F  H  M  A  G  I  S  E  T  V  W  A  I  E  M  W  
               ccnacrccncsATACAGAGTACCTAAAGTATTCCGA -5'  Core: degen=64 len=11  Clamp: score=66, len=25 temp= 60.2

Processing Block MethylaB
E  P  A  C  Q  A  F  R  H  N  H  P  E  T  T  V  F  N  E  D  C  N  D  F  L  K  L  V  M  
   CCTGCTTGTCAAGCTTTTAGACAnaaymayccng -3'  Core: degen=128 len=11  Clamp: score=69, len=23 temp= 60.9
GAACCTGCTTGTCAAGCTTTTAGAywnaaymaycc -3'  Core: degen=128 len=11  Clamp: score=67, len=24 temp= 61.2

Processing Complement of Block MethylaB
E  P  A  C  Q  A  F  R  H  N  H  P  E  T  T  V  F  N  E  D  C  N  D  F  L  K  L  V  M  
                           ttrktrggncyTTGATGTCAAAAATTACTTCTAACATTACAAAA -5'  Core: degen=64 len=11  Clamp: score=67, len=33 temp= 60.5

Processing Block MethylaC
L  P  Q  P  G  D  V  Y  M  L  C  G  G  P  P  C  Q  G  F  S  G  M  N  R  F  N  
                          GGTTTGTGGAGGACCTCCTtgycarggnwt -3'  Core: degen=32 len=11  Clamp: score=77, len=19 temp= 63.1
                         TGGTTTGTGGAGGACCTccntgycargg -3'  Core: degen=16 len=11  Clamp: score=76, len=17 temp= 60.9
                   TTGATATGGTTTGTGGAGGAccnccntgyca -3'  Core: degen=32 len=11  Clamp: score=74, len=20 temp= 61.0

Processing Complement of Block MethylaC
L  P  Q  P  G  D  V  Y  M  L  C  G  G  P  P  C  Q  G  F  S  G  M  N  R  F  N  
                                       ggnggnacrgtTCCTAAAAGACCTTACTTATCTAA -5'  Core: degen=32 len=11  Clamp: score=74, len=24 temp= 60.1
                                          ggnacrgtyccTAAAAGACCTTACTTATCTAAATTA -5'  Core: degen=16 len=11  Clamp: score=71, len=25 temp= 58.5 *** CLAMP NEEDS EXTENSION
                                             acrgtyccnwaAAGACCTTACTTATCTAAATTA -5'  Core: degen=32 len=11  Clamp: score=72, len=22 temp= 52.0 *** CLAMP NEEDS EXTENSION

Processing Block MethylaD
C  F  V  R  M  G  Y  Q  C  R  F  G  M  M  Q  A  G  Q  Y  G  V  P  Q  T  R  R  R  A  F  I  W  A  A  A  P  G  E  K  L  P  M  Y  P  E  P  M  H  V  
TGTTTTGTTGGAatgrrntayca -3'  Core: degen=32 len=11  Clamp: score=60, len=12 temp= 42.3 *** CLAMP NEEDS EXTENSION
TGTTTTGTTGGnatgrrntayc -3'  Core: degen=128 len=11  Clamp: score=63, len=11 temp= 25.6 *** CLAMP NEEDS EXTENSION

Processing Complement of Block MethylaD
C  F  V  R  M  G  Y  Q  C  R  F  G  M  M  Q  A  G  Q  Y  G  V  P  Q  T  R  R  R  A  F  I  W  A  A  A  P  G  E  K  L  P  M  Y  P  E  P  M  H  V  
            tacyynatrgtTACATCTAAACCTTACTACGTT -5'  Core: degen=32 len=11  Clamp: score=71, len=22 temp= 61.1

Processing Block MethylaE
F  R  T  I  T  V  R  D  T  M  S  D  L  P  P  V  T  N  G  A  S  N  D  E  I  S  Y  N  
No suggested primers found.

Processing Complement of Block MethylaE
F  R  T  I  T  V  R  D  T  M  S  D  L  P  P  V  T  N  G  A  S  N  D  E  I  S  Y  N  
No suggested primers found.

Processing Block MethylaF
D  H  H  C  K  D  M  S  D  D  D  L  C  R  M  S  H  I  P  K  F  P  G  S  D  W  R  D  M  P  N  I  Q  V  H  N  N  D  G  T  I  N  R  K  L  R  Y  C  H  H  D  K  K  N  
No suggested primers found.

Processing Complement of Block MethylaF
D  H  H  C  K  D  M  S  D  D  D  L  C  R  M  S  H  I  P  K  F  P  G  S  D  W  R  D  M  P  N  I  Q  V  H  N  N  D  G  T  I  N  R  K  L  R  Y  C  H  H  D  K  K  N  
No suggested primers found.

Processing Block MethylaG
M  G  H  Q  G  C  V  I  H  P  M  Q  H  R  V  V  S  V  R  E  C  A  R  S  Q  G  F  P  D  C  Y  R  F  C  G  N  I  L  D  K  H  R  Q  V  G  N  A  V  P  P  P  L  A  K  A  I  G  
                                                                                                               AAGGATAAGCATAGACAAGTTGGAaaygcngtnsc -3'  Core: degen=64 len=11  Clamp: score=73, len=24 temp= 60.7
                                                                                                        AAATATTAAGGATAAGCATAGACAAGTTggnaaygcngt -3'  Core: degen=32 len=11  Clamp: score=71, len=28 temp= 60.6
                                                                                                    GTGGAAATATTAAGGATAAGCATAGACAArtnggnaaygc -3'  Core: degen=64 len=11  Clamp: score=72, len=29 temp= 60.3
                                                                                                   TGTGGAAATATTAAGGATAAGCATAGAcarrtnggnaa -3'  Core: degen=64 len=11  Clamp: score=69, len=27 temp= 61.4
                                                  TGTTAGAGAATGTGCTAGATCTCAAggnttyccnga -3'  Core: degen=32 len=11  Clamp: score=72, len=25 temp= 61.4
                                              TTTCTGTTAGAGAATGTGCTAGATCTCArggnttyccng -3'  Core: degen=64 len=11  Clamp: score=73, len=28 temp= 61.1
                                              TTTCTGTTAGAGAATGTGCTAGATCTcarggnttycc -3'  Core: degen=16 len=11  Clamp: score=69, len=26 temp= 61.1
                                           TTGTTTCTGTTAGAGAATGTGCTAGATCncarggnttyc -3'  Core: degen=64 len=11  Clamp: score=71, len=28 temp= 60.5
                               TGCAACATAGAGTTGTTTCTGTTAGAgarwrygcnmg -3'  Core: degen=128 len=11  Clamp: score=70, len=26 temp= 61.8
                           CCTATGCAACATAGAGTTGTTTCTGTTmgngarwrygc -3'  Core: degen=128 len=11  Clamp: score=71, len=27 temp= 61.1
   GGTCATCAAGGATGTGTTTTTcayccnrwrca -3'  Core: degen=64 len=11  Clamp: score=56, len=21 temp= 61.1

Processing Complement of Block MethylaG
M  G  H  Q  G  C  V  I  H  P  M  Q  H  R  V  V  S  V  R  E  C  A  R  S  Q  G  F  P  D  C  Y  R  F  C  G  N  I  L  D  K  H  R  Q  V  G  N  A  V  P  P  P  L  A  K  A  I  G  
                        gtrggnywygtTGTATCTCAACAAAGACAATCTCTTAC -5'  Core: degen=64 len=11  Clamp: score=71, len=27 temp= 60.1
                                                         ctywyrcgnkcTAGAGTTCCTAAAGGACTAACAATA -5'  Core: degen=128 len=11  Clamp: score=74, len=25 temp= 60.1
                                                                        gtyccnaarggACTAACAATATCTAAAACACCTTTATA -5'  Core: degen=16 len=11  Clamp: score=72, len=27 temp= 60.1
                                                                         tyccnaarggncTAACAATATCTAAAACACCTTTATAATTCC -5'  Core: degen=64 len=12  Clamp: score=72, len=30 temp= 60.1
                                                                           ccnaarggnctAACAATATCTAAAACACCTTTATAATTCC -5'  Core: degen=32 len=11  Clamp: score=70, len=29 temp= 60.1
                                                                              aarggnctrwsAATATCTAAAACACCTTTATAATTCCTATTCG -5'  Core: degen=64 len=11  Clamp: score=70, len=32 temp= 60.7
                                                                                                                              gtyyanccnttACGACAAGGAGGAGGACAC -5'  Core: degen=64 len=11  Clamp: score=74, len=19 temp= 61.6
                                                                                                                                    ccnttrcgncaAGGAGGAGGACACCGATAAC -5'  Core: degen=32 len=11  Clamp: score=66, len=20 temp= 62.2
                                                                                                                                       ttrcgncansgAGGAGGACACCGATAACGATAA -5'  Core: degen=64 len=11  Clamp: score=64, len=22 temp= 61.0
blimps-3.9/examples/processor/000075500001460000012000000000001062461220100167755ustar00jorjastaff00000400000027blimps-3.9/examples/processor/calibrate.csh000075500001460000012000000011221026224543200214270ustar00jorjastaff00000400000027#!/bin/csh
#	Calibrate blocks for searching with blimps

#		calibrate.csh blks-in blks-out
#
set BLIMPS_DIR = ../../
set bin = $BLIMPS_DIR/bin
set frq = $BLIMPS_DIR/docs/default.amino.frq

unalias rm
unalias mv

#	Parameters for theoretical calibration
set NSEQ = 80000
set NRES = 29085965

#       Make matrices and observed frequency files
$bin/blk2pssm $1 $1.mats B 3 >& /dev/null
$bin/blk2pssm $1 $1.obsf B 21 >& /dev/null
#               writes $1.dat
$bin/pssmdist $1.mats $1.obsf $frq $NSEQ $NRES $1 >& /dev/null
$bin/pssmBL $1.dat $1 $2 >& /dev/null

rm $1.dat $1.mats $1.obsf

exit(0)
blimps-3.9/examples/processor/clustal.in000064400001460000012000000047701026224527300210150ustar00jorjastaff00000400000027CLUSTAL

MTCH_ARATH      ---------DGFKSHL----LPLPGTVYTVCGGPPCQGISGYNRYRNNEAPLEDQKNQQL
MTCH_ARAAR      ---------DGFKSHL----LPLPGTVYSVCGGPPCQGISGYNRFRNKQAPLEDKKNQQL
MTDM_ARATH      VSTTEANELAAKLTEEQKSTLPLPGQVDFINGGPPCQGFSGMNRFNQ--SSWSKVQCEMI
MET2_ARATH      VSTVEAAELAAKLDENQKSTLPLPGQVDFINGGPPCQGFSGMNRFSH--GSWSKVQCEMI
MTDM_PISAT      ISTAEAAELASKLDDKDLNSLPLPGQVDFINGGPPCQGFSGMNRFNT--STWSKVQCEMI
MTDM_MOUSE      -------EVTNSLGQR----LPQKGDVEMLCGGPPCQGFSGMNRFNS--RTYSKFKNSLV
MTDM_HUMAN      -------ETTNSRGQR----LPQKGDVEMLCGGPPCQGFSGMNRFNS--RTYSKFKNSLV
MTDM_XENLA      -------EKTNSLGQR----LPQKGDVEMLCGGPPCQGFSGMNRFNS--RTYSKFKNSLV
MTDM_PARLI      -------EKTSRTGQK----LPQKGDVELLCGGPPCQGFSGMNRFNS--REYSKFKNSLI
MTDM_CHICK      -------EKTNSLGQK----LPQKGDVEMLCGGPPCQGFSGMNRFNS--RTYSKFKNSLV
                                    **  * *  . ******* ** **.          .   .

MTCH_ARATH      LVFLDIIDFLKPNYVLMENVVDLLRFSKGFLARHAVASFVAMNYQTRLGMMAAGSYGLPQ
MTCH_ARAAR      LVFLDIIDFLKPSYVLMENVVDLLRFSKGYLARHAVASFVAMNYQTRLGMMTAGSYGLPQ
MTDM_ARATH      LAFLSFADYFRPRYFLLENVRTFVSFNKGQTFQLTLASLLEMGYQVRFGILEAGAYGVSQ
MET2_ARATH      LAFLSFADYFRPKYFLLENVKKFVTYNKGRTFQLTMASLLEMGYQVRFGILEAGTYGVSQ
MTDM_PISAT      LAFLSFADYFRPRYFLLENVRNFVSFNKGQTFRLTLASLLEMGYQVRFGILEAGAFGVSQ
MTDM_MOUSE      VSFLSYCDYYRPRFFLLENVRNFVSYRRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQ
MTDM_HUMAN      VSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQ
MTDM_XENLA      VSYLSYCDYYRPKYFLLENVRNFVSFKKSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQ
MTDM_PARLI      SSYLSYCDYYRPRFFLLENVRNFVSYKKNMVLKLALRCLIRMGYQCTFGILQAGQYGVPQ
MTDM_CHICK      VSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQ
                  .*   *. .* . *.***   . . .    . .. . . *.**   *.. ** .*. *

MTCH_ARATH      LRNRVFLWAAQPSEKLPPYPLPTHEVAKKFNTPKEFKDLQ--VGRIQMEFLKLDNALTLA
MTCH_ARAAR      VRNRVFLWAAQPTEKLPPYPLPTHEVEKKYNTPKEFEDLQ--VGLIQKELLQLDNALTLA
MTDM_ARATH      SRKRAFIWAAAPEEVLPEWPEPMHVFGVPKLKISLSQGLHYAAVRSTALG-APFRPITVR
MET2_ARATH      PRKRVIIWAASPEEVLPEWPEPMHVFDNPGSKISLPRGLRYDAGCNTKFG-APFRSITVR
MTDM_PISAT      SRKRAFIWAASPEDVLPEWPEPMHVFSAPELKITLAENVQYAAVCSTANG-APLRAITVR
MTDM_MOUSE      TRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITER
MTDM_HUMAN      TRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVR
MTDM_XENLA      TRRRAIVLAAAPGEKLPMFPEPLHVFAPRACTLSVVVDEKKYVSNTTRTNSSLFRTITVR
MTDM_PARLI      TRRRAIILAAAPGEKLPFYPEPLHVFSSRACSLSVMIGEKKIESNNQWCLSAPYRTITVR
MTDM_CHICK      TRRRAIVLAAAPGEKLPMFPEPLHVFAPRACQLSVVVDDKKFVSNITRTYSGPFRTITVR
                 * *  . ** * . **  * * *               .                .*  
blimps-3.9/examples/processor/fasta.in000064400001460000012000000021251026224526500204350ustar00jorjastaff00000400000027>BBP_PIEBR
-------NVYHDGACPE-----VKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCG--WAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDS---KIGKIYHKLTYGGVTKENVFN-----VLSTDNKNYIIGYYCKY-DEDKKGHQDFVWVLSRSKV-LTGEAKTAVENYLIG-SPVVDSQKLVYSDFSEAACKVN-----------
>ICYA_MANSE
------GDIFYPGYCPD-----VKPVNDFDLSAFAGAWHEIAKLPLENENQGKCT--IAEYKYDGKKASVYNSFVSNGVKEYMEGDLEIAPDAKYTKQGKYVMTFKFGQRVVNLVPW-----VLATDYKNYAINYNCDY-HPDKKAHSIHAWILSKSKV-LEGNTKEVVDNVLKTFSHLIDASKFISNDFSEAACQYSTTYSLTGPDRH
>LACB_BOVIN
---MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAE---KT-KIPAVFKIDALNENKVL------VLDTDYKKYLL--FCME-NSAEPEQSLACQCLVRTPE-VDDEALEKFDKALKA-LPMHIRLSFNPTQL-EEQCHI------------
>MUP2_MOUSE
MKMLLLLCLGLTLVCVH-AEEASSTGRNFNVEKINGEWHTIILASDKREKIEDNGN-FRLFLEQIHVLEKSLVLKFHTVRDEECSELSMVADK---TEKAGEYSVTYDGFNTFTIP--------KTDYDNFLMAHLINE-KDGETFQ--LMGLYGREPD-LSSDIKERFAKLCEE--HGILRENIIDLSN-ANRCLQARE---------
>RETB_BOVIN
-----------ERDCRVSS---FRVKENFDKARFAGTWYAMAKKDPEGLFLQDNIVAEFSVDENGHMSATAKGRVRLLNNWDVCADMVGTFTD---TEDPAKFKMKYWGVASFLQKGNDDHWIIDTDYETFAVQYSCRLLNLDGTCADSYSFVFARDPSGFSPEVQKIVRQRQEE-LCLARQYRLIPHNG---YCDGKSERNIL-----
blimps-3.9/examples/processor/msf.in000064400001460000012000000213451026224531100201210ustar00jorjastaff00000400000027
            1                                                   50
P09254-1    .....KRQED AGYDICVPYN LYLKR..... NEFIKIVLPI IRDWDLQHPS
A37470-1    .TFAPKRDED AGYDIAMPYT AVL....... APGENLHVRL PVAYAADAHA
Q00030-2    DYFAPKRDED AGYDISAQTN ATI....... EPDESYFVEL PIVFSSSNPA
P28892-1    .....KRVED AGYDISAPED ATI....... DPDESHFVDL PIVFANSNPA
P10234-1    .....KREED AGFDIVVRRP VTV.P..... ANGTTVVQPS LRMLHADAGP
P11365-6    .......... HKVDLRAASD FLL.M..... PQMSIQPVPV EPIPSLPLGT
P06968-1    ....YATSGS AGLDLRACLN DAVEL..... APGDTTLVPT GLAIHIADPS
P43792-1    ....YATEGS AGLDLRALID ESFEI..... QPGETKLIPT GLSIYIADPN
S44300-1    ....YATTGS AGLDLRACLD EPLKI..... EPDETCLIST GLAIYLGHSN
P31625-2    .....ATRGS AGLDLCATSY TVL.T..... PEMGVQTLAT GVFGPLPPGT
P07570-2    ....RATPGS AGLDLCSTSH TVL.T..... PEMGPQALST GIYGPLPPNT
P10271-1    .....GTPGS AGLDLSSQKD LIL.S..... LEDGVSLVPT LVKGTLPEGT
P21407-2    ....RATAGS AGLDLCTTTD TIL.T..... TQNSPLTLPV GIYGPLPPQT
P10265-1    .....TTSGS AAVDLCTIQA VSL.L..... PGEPPQKIPT GVYGPLPEGT
P11204-4    .QIKEKRDED AGFDLCVPYD IMI....... PVSDTKIIPT DVKIQVPPNS
P16088-4    ...LDKRSED AGYDLLAAKE IHL....... LPGEVKVIPT GVKLMLPKGY
JQ1162-4    ..IVKKRAED AGYDLICPQE VSI....... PAGQVKKIPI DLRINLRKNQ
P16901-4    ..ILPKRAED AGYDLICPQE VCI....... PAGQVRKIPI NLRINLKEDQ
P23427-4    ..ILQKRAED AGYDLICPQE ISI....... PAGQVKRIAI DLKINLKKDQ
P03370-4    ..ILQKRAED AGYDLICPQE ISI....... PAGQVKRIAI DLKINLKKDQ
P23426-4    ..ILQKRAED AGYDLICPQE ISI....... PAGQVKRIAI DLKINLKKDQ
P35956-4    ..ILQKRAED AGYDLICPQE ISI....... PAGQVKRIAI DLKINLKKDQ
P33459-4    ..ILPKREED AGYDLICPEE VTI....... EPGQVKCIPI ELRLNLKKSQ
P32208-1    .....SMSGS AGYDLYSAYS YTV....... KPYNRILVRT DICLMIPDKC
P32518-1    .....ASSLA AGYDLSSAAE TKV....... PARGKALVPT DLSIAVPQGT
P33317-1    .....GSATA AGYDIYASQD ITI....... PAMGQGMVST DISFTVPVGT
P43058-1    .....GSALA AGYDLYSAEA ATI....... PAHGQGLVST DISIIVPIGT
P33316-1    .....GSARA AGYDLYSAYD YTI....... PPMEKAVVKT DIQIALPSGC
P14597-1    .....GSPGA AGLDLCSAYD CVI....... PSHCSRVVFT DLLIKPPSGC
P21035-1    .....QSPGA AGYDLYSAYD YTI....... PPGERQLIKT DISMSMPKIC
S26429-1    .....ATHGA AGYDLFSAYD IKV....... PARGRALVPT DLVFQFPPGC
P28893-1    .....SSPGS AGFDLSVLED REF....... IRGCHYRLPT GLAIAVPRGY
Q00030-1    .....ARAEA DGRLLVLINN HTVELSAGLG SAGEFYSVLT DVGVRVACSS

            51                                                 100
P09254-1    I.NAYIFGRS SKSRSGI... .......... ........IV CPTAWPAGEH
A37470-1    A.APYVFGRS SCNLRGL... .......... ........IV LPTAWPPGEP
Q00030-2    V.TPCIFGRS SMNRRGL... .......... ........IV LPTRWVTGRT
P28892-1    V.TPCIFGRS SMNRRGL... .......... ........IV LPTRWVAGRT
P10234-1    A.ACYVLGRS SLNARGL... .......... ........LV VPTRWLPGHV
P11365-6    M..GLILGRG SASTLQG... .......... ...LVVHPEL WIVNIPQKYQ
P06968-1    L.AAMMLPRS GLGHKHG... .......... .IVLGNLVGL IDSDYQGQLM
P43792-1    L.AAVILPRS GLGHKHG... .......... .IVLGNLVGL IDSDYQGPLM
S44300-1    V.AATILPRS GLGHKHG... .......... .IVLGNLVGL IDSDYQGPLM
P31625-2    V..GLLLGRS SASLKG.... .......... ...ILIHPGV IDSDYTGEIK
P07570-2    F..GLILGRS SITMKG.... .......... ...LQVYPGV IDNDYTGEIK
P10271-1    T..GLIIGRS SNYKKG.... .......... ...LEVLPGV IDSDFQGEIK
P21407-2    F..GLILAEP ALPSKG.... .......... ...IQVLPGI LDNDFEGEIH
P10265-1    V..GLILGRS SLNLKG.... .......... ...VQIHTSV VDSDYKGEIQ
P11204-4    F..GWVTGKS SMAKQG.... .......... ...LLINGGI IDEGYTGEIQ
P16088-4    W..GLIIGKS SIGSKG.... .......... ...LDVLGGV IDEGYRGEIG
JQ1162-4    W..AMIGTKS SFASKG.... .......... ...VFVQGGI VDSGYQGIIQ
P16901-4    W..AMVGTKS SFASKG.... .......... ...VFVQGGI IDSGYQGIIQ
P23427-4    W..AMIGTKS SFANKG.... .......... ...VFVQGGI IDSGYQGTIQ
P03370-4    W..AMIGTKS SFANKG.... .......... ...VFVQGGI IDSGYQGTIQ
P23426-4    W..AMIGTKS SFANKG.... .......... ...VFVQGGI IDSGYQGTIQ
P35956-4    W..AMIGTKS SFANKG.... .......... ...VFVQGGI IDSGYQGTIQ
P33459-4    W..AMIATKS SMAAKG.... .......... ...VFTQGGI IDSGYQGQIQ
P32208-1    Y..GRISPRS GLSLNYN... .......... ...IDIGGGV IDSDYRGEIG
P32518-1    Y..ARIAPRS GLAWKYS... .......... ...IDVGAGV IDADYRGPVG
P33317-1    Y..GRIAPRS GLAVKNG... .......... ...IQTGAGV VDRDYTGEVK
P43058-1    Y..GRVAPRS GLAVKHG... .......... ...ISTGAGV IDADYRGEVK
P33316-1    Y..GRVAPRS GLAAKHF... .......... ...IDVGAGV IDEDYRGNVG
P14597-1    Y..GRIAPRS GLAVKHF... .......... ...IDVGAGV IDEDYRGNVG
P21035-1    Y..GRIAPRS GLSLKG.... .......... ...IDIGGGV IDEDYRGNIG
S26429-1    Y..GRIAPRS GLAAKFF... .......... ...IDVGAGV IDPDYRGNVS
P28893-1    V..GIITPRS SQAKNF.... .......... .....VSTGI IDSDFRGHIH
Q00030-1    GYAIVLAQIS GLPHVGREPG NFSNITFTGN LANYYTAYGI VDSGYRGVVK

            101                                                150
P09254-1    CKFYVYNLTG DDIRIKTGDR LAQVLLIDHN TQ........ ..........
A37470-1    CRFVLRNVTQ EPLVAAAGQR VAQLLLLARR LE.WLPSGLN DREPFPTSPR
Q00030-2    CCFFILNINK YPVYITKGQR VAQLVLTEDI DEALIPTNVN YNTPFPTYSP
P28892-1    CCFFILNVNK YPVSITKGQR VAQLLLTEDI DDALIPPTVN YDNPFPTYSP
P10234-1    CAFVVYNLTG VPVTLEAGAK VAQLLVAGAD ALPWIPP... ..........
P11365-6    VLC...SSPK GVFSISKGDR IPQLLLL... .......... ..........
P06968-1    ISVW..NRGQ DSFTIQPGER IAQMIFVPVV Q......... ..........
P43792-1    VSMW..NRGN EPFKIEVGDR IAQLVFVPVV Q......... ..........
S44300-1    VSCW..NRGK EPYTINPGDR IAQLVVLPIL K......... ..........
P31625-2    ILA...SAPN KIIVINAGQR IAQLLLVPLV .......... ..........
P07570-2    IMA...KAVN NIVTVSQGNR IAQLILLPLI .......... ..........
P10271-1    VMV...KAAK NAVIIHKGER IAQLLLLPY. .......... ..........
P21407-2    IIL...STTK DLVTIPKGTR LAQIVILPLQ .......... ..........
P10265-1    LVI...SSSI PWSASPR.DR IAQLLLLPY. .......... ..........
P11204-4    VICT..NIGK SNIKLIEGQK FAQLIILQHH S......... ..........
P16088-4    VIMI..NVSR KSITLMERQK IAQLIILPCK H......... ..........
JQ1162-4    VVIY..NSND EEVIIPQGRK FAQLILMPLI H......... ..........
P16901-4    VVVY..NSND KEVIIPQGRK FAQLILMPLI H......... ..........
P23427-4    VVIY..NSNN KEVVIPQGRK FAQLILMPLI H......... ..........
P03370-4    VVIY..NSNN KEVVIPQGRK FAQLILMPLI H......... ..........
P23426-4    VVIY..NSNN KEVVIPQGRK FAQLILMPLI H......... ..........
P35956-4    VVIY..NSNN KEVVIPQGRK FAQLILMPLI H......... ..........
P33459-4    VIMY..NSNK IAVVIPQGRK FAQLILMDKK H......... ..........
P32208-1    IVFI..NNGC SDFNIKVGDR IAQIIFERVE Y......... ..........
P32518-1    VVLF..NHSE VDFEVKVGDR IAQLIVQKIV T......... ..........
P33317-1    VVLF..NHSQ RDFAIKKGDR VAQLILEKIV DD........ ..........
P43058-1    VVLF..NHSE KDFEIKEGDR IAQLVLEQIV NA........ ..........
P33316-1    VVLF..NFGK EKFEVKKGDR IAQLICERIF Y......... ..........
P14597-1    VVLF..NFGN SDFEVKKGDR IAQLICERIS C......... ..........
P21035-1    VILI..NNGK CTFNVNTGDR IAQLIYQRIY Y......... ..........
S26429-1    VVLF..NFSE SSFNIRRGDR VAQLILERIM V......... ..........
P28893-1    IMV....SAI ADFSVKKNQR IAQLVVTPCL T......... ..........
Q00030-1    AVQF...ANG VNTVVPPGCM SLGLVLVKLS T......... ..........

            151
P09254-1    .......... IHLKHNVLSN IAFPYAIRGK CGIPGVQ... ......
A37470-1    AAPPAPGAPR LRWRRVADLA AAVPPSARGP RGFGSTGL.. ......
Q00030-2    TGAVKHNPTP ILWKFTEAFD HDAPSSARSE GGFGST.... ......
P28892-1    SESTKAPQSP VLWKFTTDFD REAPSSLRAD GGFGSTGL.. ......
P10234-1    .......... ....DNFHGT KALRNYPRGV PDSTAEPR.. ......
P11365-6    .......... ......LPDN TREKSAGPEI KKMGS..... ......
P06968-1    .......... ....AEFNLV EDFDATDRGE GGFGHSGR.. ......
P43792-1    .......... ....AEFNIV EDFQQTERGE GGFGHSGK.. ......
S44300-1    .......... ....AQFAVV EEFELTERGA GGFGSSGQ.. ......
P31625-2    .......... ........IQ GKTINRDRQD KGFG...... ......
P07570-2    .......... ........ET DNKVQQPYRG QGSFGSSDI. ......
P10271-1    .......... ......LKLP NPVIKEERGS EGFG...... ......
P21407-2    .......... .......QIN SNFHKPYRGA SAPG...... ......
P10265-1    .......... ......IKGG NSEIKRIGGL VSTDP..... ......
P11204-4    .......... ....NSRQPW DENKISQRGD KGFGSTGVF. .WVENI
P16088-4    .......... ....EVLEQG KVVMDSERGD NGYGSTGVFS SWVDRI
JQ1162-4    .......... ....EELEPW GETRKTERGN QGFGSTGAY. .WIENI
P16901-4    .......... ....EDLEAW GETRRTERGN QGFGSTGAY. .WIENI
P23427-4    .......... ....EELKPW GETRKTERGE QGFGSTGMY. .WIENI
P03370-4    .......... ....EELEPW GETRKTERGE QGFGSTGMY. .WIENI
P23426-4    .......... ....EELEPW GETRKTERGE QGFGSTGMY. .WIENI
P35956-4    .......... ....EELEPW GETRKTERGE QGFGSTGMY. .WIENI
P33459-4    .......... ....GKLEPW GESRKTERGE KGFGSTGMY. .WIENI
P32208-1    .......... ....PIMEEV KCLEDTERGN SGFGSSGM.. ......
P32518-1    .......... ....PEVEQV DDLDSTVRGS GGFGSTGV.. ......
P33317-1    .......... ....AQIVVV DSLEESARGA GGFGSTGN.. ......
P43058-1    .......... ...DIKEISL EELDNTERGE GGFGSTGK.. ......
P33316-1    .......... ....PEIEEA QALDDTERGS GGFGSTGK.. ......
P14597-1    .......... ....PAVQEV NCLDNTDRGD SGFGSTGS.. ......
P21035-1    .......... ....PELEEV QSLDSTNRGD QGFGSTGL.. ......
S26429-1    .......... ....PELSEL TQLGETDRGA SGFGFTGM.. ......
P28893-1    .......... ...QSEVVPY ETLERTRRGT GGFGSSGQ.. ......
Q00030-1    .......... .......... ETINVTNINL TENGRSPRVN IFY...
blimps-3.9/examples/processor/process.csh000075500001460000012000000011771041506012200211600ustar00jorjastaff00000400000027#!/bin/csh
#	Block Processor script
#		process.csh 
#		m.a. must be in FASTA, CLUSTAL, MSF or STOCKHOLM format

setenv BLIMPS_DIR ../..
set bin = $BLIMPS_DIR/bin

#	1. mablock carves ungapped regions in all sequences out of m.a.
#	   Set min and max width of blocks
#	   Creates files $1.blks and $1.seqs
set minwidth=10
set maxwidth=60
$bin/mablock $1 $1 B $minwidth $maxwidth

#	2. Calibrate blocks for searching with blimps program
./calibrate.csh $1.blks $1.cblks > /dev/null

#	3. Add sequence weights to calibrated blocks
$bin/blweight $1.cblks $1.wblks P M > /dev/null

echo "Final blocks are in $1.wblks"

exit
blimps-3.9/examples/processor/stockholm.in000064400001460000012000000025621026224530500213420ustar00jorjastaff00000400000027# STOCKHOLM 1.0

BBP_PIEBR   -------NVYHDGACPE-----VKPVDNFDWSNYHGKWWEVAKYPNSVEK
ICYA_MANSE  ------GDIFYPGYCPD-----VKPVNDFDLSAFAGAWHEIAKLPLENEN
LACB_BOVIN  ---MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISL
MUP2_MOUSE  MKMLLLLCLGLTLVCVH-AEEASSTGRNFNVEKINGEWHTIILASDKREK
RETB_BOVIN  -----------ERDCRVSS---FRVKENFDKARFAGTWYAMAKKDPEGLF

BBP_PIEBR   YGKCG--WAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDS---KIGK
ICYA_MANSE  QGKCT--IAEYKYDGKKASVYNSFVSNGVKEYMEGDLEIAPDAKYTKQGK
LACB_BOVIN  LDAQSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAE---KT-K
MUP2_MOUSE  IEDNGN-FRLFLEQIHVLEKSLVLKFHTVRDEECSELSMVADK---TEKA
RETB_BOVIN  LQDNIVAEFSVDENGHMSATAKGRVRLLNNWDVCADMVGTFTD---TEDP

BBP_PIEBR   IYHKLTYGGVTKENVFN-----VLSTDNKNYIIGYYCKY-DEDKKGHQDF
ICYA_MANSE  YVMTFKFGQRVVNLVPW-----VLATDYKNYAINYNCDY-HPDKKAHSIH
LACB_BOVIN  IPAVFKIDALNENKVL------VLDTDYKKYLL--FCME-NSAEPEQSLA
MUP2_MOUSE  GEYSVTYDGFNTFTIP--------KTDYDNFLMAHLINE-KDGETFQ--L
RETB_BOVIN  AKFKMKYWGVASFLQKGNDDHWIIDTDYETFAVQYSCRLLNLDGTCADSY

BBP_PIEBR   VWVLSRSKV-LTGEAKTAVENYLIG-SPVVDSQKLVYSDFSEAACKVN--
ICYA_MANSE  AWILSKSKV-LEGNTKEVVDNVLKTFSHLIDASKFISNDFSEAACQYSTT
LACB_BOVIN  CQCLVRTPE-VDDEALEKFDKALKA-LPMHIRLSFNPTQL-EEQCHI---
MUP2_MOUSE  MGLYGREPD-LSSDIKERFAKLCEE--HGILRENIIDLSN-ANRCLQARE
RETB_BOVIN  SFVFARDPSGFSPEVQKIVRQRQEE-LCLARQYRLIPHNG---YCDGKSE

BBP_PIEBR   ---------
ICYA_MANSE  YSLTGPDRH
LACB_BOVIN  ---------
MUP2_MOUSE  ---------
RETB_BOVIN  RNIL-----
//
blimps-3.9/examples/processor/README000064400001460000012000000002671041506407500176720ustar00jorjastaff00000400000027
Block Processor Example

To test the installation:	test.csh

To run your own example:
process.csh 
	m.a. must be in FASTA, CLUSTAL, MSF or STOCKHOLM format

blimps-3.9/examples/processor/distribution/000075500001460000012000000000001062461223400215225ustar00jorjastaff00000400000027blimps-3.9/examples/processor/distribution/fasta.in.blks000064400001460000012000000051121062461143200241000ustar00jorjastaff00000400000027ID   fastaxin; BLOCK
AC   fastaxinA; distance from previous block=(22,22)
DE   fasta.in
BL   UNK motif;  width=33; seqs=5; 99.5%=0; strength=0 
BBP_PIEBR            (  22) VKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCG 5.950000
ICYA_MANSE           (  22) VKPVNDFDLSAFAGAWHEIAKLPLENENQGKCT 5.658333
LACB_BOVIN           (  22) TQTMKGLDIQKVAGTWYSLAMAASDISLLDAQS 7.561111
MUP2_MOUSE           (  22) SSTGRNFNVEKINGEWHTIILASDKREKIEDNG 7.255556
RETB_BOVIN           (  22) FRVKENFDKARFAGTWYAMAKKDPEGLFLQDNI 6.575000
//
ID   fastaxin; BLOCK
AC   fastaxinB; distance from previous block=(2,2)
DE   fasta.in
BL   UNK motif;  width=36; seqs=5; 99.5%=0; strength=0 
BBP_PIEBR            (  57) WAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDS 6.361111
ICYA_MANSE           (  57) IAEYKYDGKKASVYNSFVSNGVKEYMEGDLEIAPDA 6.527778
LACB_BOVIN           (  57) LRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAE 7.555556
MUP2_MOUSE           (  57) FRLFLEQIHVLEKSLVLKFHTVRDEECSELSMVADK 7.597222
RETB_BOVIN           (  57) EFSVDENGHMSATAKGRVRLLNNWDVCADMVGTFTD 7.958333
//
ID   fastaxin; BLOCK
AC   fastaxinC; distance from previous block=(6,6)
DE   fasta.in
BL   UNK motif;  width=17; seqs=5; 99.5%=0; strength=0 
BBP_PIEBR            (  99) KIYHKLTYGGVTKENVF 3.169444
ICYA_MANSE           (  99) KYVMTFKFGQRVVNLVP 3.363889
LACB_BOVIN           (  99) KIPAVFKIDALNENKVL 3.363889
MUP2_MOUSE           (  99) AGEYSVTYDGFNTFTIP 3.572222
RETB_BOVIN           (  99) PAKFKMKYWGVASFLQK 3.530556
//
ID   fastaxin; BLOCK
AC   fastaxinD; distance from previous block=(33,33)
DE   fasta.in
BL   UNK motif;  width=10; seqs=5; 99.5%=0; strength=0 
BBP_PIEBR            ( 149) FVWVLSRSKV 1.511111
ICYA_MANSE           ( 149) HAWILSKSKV 2.011111
LACB_BOVIN           ( 149) ACQCLVRTPE 2.052778
MUP2_MOUSE           ( 149) LMGLYGREPD 2.275000
RETB_BOVIN           ( 149) YSFVFARDPS 2.150000
//
ID   fastaxin; BLOCK
AC   fastaxinE; distance from previous block=(1,1)
DE   fasta.in
BL   UNK motif;  width=15; seqs=5; 99.5%=0; strength=0 
BBP_PIEBR            ( 160) LTGEAKTAVENYLIG 2.844444
ICYA_MANSE           ( 160) LEGNTKEVVDNVLKT 2.677778
LACB_BOVIN           ( 160) VDDEALEKFDKALKA 2.983333
MUP2_MOUSE           ( 160) LSSDIKERFAKLCEE 2.983333
RETB_BOVIN           ( 160) FSPEVQKIVRQRQEE 3.511111
//
ID   fastaxin; BLOCK
AC   fastaxinF; distance from previous block=(2,2)
DE   fasta.in
BL   UNK motif;  width=13; seqs=5; 99.5%=0; strength=0 
BBP_PIEBR            ( 177) PVVDSQKLVYSDF 2.566667
ICYA_MANSE           ( 177) HLIDASKFISNDF 2.094444
LACB_BOVIN           ( 177) PMHIRLSFNPTQL 2.816667
MUP2_MOUSE           ( 177) HGILRENIIDLSN 2.761111
RETB_BOVIN           ( 177) CLARQYRLIPHNG 2.761111
//
blimps-3.9/examples/processor/distribution/stockholm.in.blks000064400001460000012000000051561062461143300250160ustar00jorjastaff00000400000027ID   stockholm; BLOCK
AC   stockholmA; distance from previous block=(22,22)
DE   stockholm.in
BL   UNK motif;  width=33; seqs=5; 99.5%=0; strength=0 
BBP_PIEBR            (  22) VKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCG 5.950000
ICYA_MANSE           (  22) VKPVNDFDLSAFAGAWHEIAKLPLENENQGKCT 5.658333
LACB_BOVIN           (  22) TQTMKGLDIQKVAGTWYSLAMAASDISLLDAQS 7.561111
MUP2_MOUSE           (  22) SSTGRNFNVEKINGEWHTIILASDKREKIEDNG 7.255556
RETB_BOVIN           (  22) FRVKENFDKARFAGTWYAMAKKDPEGLFLQDNI 6.575000
//
ID   stockholm; BLOCK
AC   stockholmB; distance from previous block=(2,2)
DE   stockholm.in
BL   UNK motif;  width=36; seqs=5; 99.5%=0; strength=0 
BBP_PIEBR            (  57) WAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDS 6.361111
ICYA_MANSE           (  57) IAEYKYDGKKASVYNSFVSNGVKEYMEGDLEIAPDA 6.527778
LACB_BOVIN           (  57) LRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAE 7.555556
MUP2_MOUSE           (  57) FRLFLEQIHVLEKSLVLKFHTVRDEECSELSMVADK 7.597222
RETB_BOVIN           (  57) EFSVDENGHMSATAKGRVRLLNNWDVCADMVGTFTD 7.958333
//
ID   stockholm; BLOCK
AC   stockholmC; distance from previous block=(6,6)
DE   stockholm.in
BL   UNK motif;  width=17; seqs=5; 99.5%=0; strength=0 
BBP_PIEBR            (  99) KIYHKLTYGGVTKENVF 3.169444
ICYA_MANSE           (  99) KYVMTFKFGQRVVNLVP 3.363889
LACB_BOVIN           (  99) KIPAVFKIDALNENKVL 3.363889
MUP2_MOUSE           (  99) AGEYSVTYDGFNTFTIP 3.572222
RETB_BOVIN           (  99) PAKFKMKYWGVASFLQK 3.530556
//
ID   stockholm; BLOCK
AC   stockholmD; distance from previous block=(33,33)
DE   stockholm.in
BL   UNK motif;  width=10; seqs=5; 99.5%=0; strength=0 
BBP_PIEBR            ( 149) FVWVLSRSKV 1.511111
ICYA_MANSE           ( 149) HAWILSKSKV 2.011111
LACB_BOVIN           ( 149) ACQCLVRTPE 2.052778
MUP2_MOUSE           ( 149) LMGLYGREPD 2.275000
RETB_BOVIN           ( 149) YSFVFARDPS 2.150000
//
ID   stockholm; BLOCK
AC   stockholmE; distance from previous block=(1,1)
DE   stockholm.in
BL   UNK motif;  width=15; seqs=5; 99.5%=0; strength=0 
BBP_PIEBR            ( 160) LTGEAKTAVENYLIG 2.844444
ICYA_MANSE           ( 160) LEGNTKEVVDNVLKT 2.677778
LACB_BOVIN           ( 160) VDDEALEKFDKALKA 2.983333
MUP2_MOUSE           ( 160) LSSDIKERFAKLCEE 2.983333
RETB_BOVIN           ( 160) FSPEVQKIVRQRQEE 3.511111
//
ID   stockholm; BLOCK
AC   stockholmF; distance from previous block=(2,2)
DE   stockholm.in
BL   UNK motif;  width=13; seqs=5; 99.5%=0; strength=0 
BBP_PIEBR            ( 177) PVVDSQKLVYSDF 2.566667
ICYA_MANSE           ( 177) HLIDASKFISNDF 2.094444
LACB_BOVIN           ( 177) PMHIRLSFNPTQL 2.816667
MUP2_MOUSE           ( 177) HGILRENIIDLSN 2.761111
RETB_BOVIN           ( 177) CLARQYRLIPHNG 2.761111
//
blimps-3.9/examples/processor/distribution/fasta.in.cblks000064400001460000012000000046601062461143200242520ustar00jorjastaff00000400000027ID   fastaxin; BLOCK
AC   fastaxinA; distance from previous block=(22,22)
DE   fasta.in
BL   UNK;  width=33; seqs=5; 99.5%=1384; strength=1370 
BBP_PIEBR            (  22) VKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCG   6
ICYA_MANSE           (  22) VKPVNDFDLSAFAGAWHEIAKLPLENENQGKCT   6
LACB_BOVIN           (  22) TQTMKGLDIQKVAGTWYSLAMAASDISLLDAQS   8
MUP2_MOUSE           (  22) SSTGRNFNVEKINGEWHTIILASDKREKIEDNG   7
RETB_BOVIN           (  22) FRVKENFDKARFAGTWYAMAKKDPEGLFLQDNI   7
//
ID   fastaxin; BLOCK
AC   fastaxinB; distance from previous block=(2,2)
DE   fasta.in
BL   UNK;  width=36; seqs=5; 99.5%=1455; strength=1441 
BBP_PIEBR            (  57) WAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDS   6
ICYA_MANSE           (  57) IAEYKYDGKKASVYNSFVSNGVKEYMEGDLEIAPDA   7
LACB_BOVIN           (  57) LRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAE   8
MUP2_MOUSE           (  57) FRLFLEQIHVLEKSLVLKFHTVRDEECSELSMVADK   8
RETB_BOVIN           (  57) EFSVDENGHMSATAKGRVRLLNNWDVCADMVGTFTD   8
//
ID   fastaxin; BLOCK
AC   fastaxinC; distance from previous block=(6,6)
DE   fasta.in
BL   UNK;  width=17; seqs=5; 99.5%=896; strength=1303 
BBP_PIEBR            (  99) KIYHKLTYGGVTKENVF   3
ICYA_MANSE           (  99) KYVMTFKFGQRVVNLVP   3
LACB_BOVIN           (  99) KIPAVFKIDALNENKVL   3
MUP2_MOUSE           (  99) AGEYSVTYDGFNTFTIP   4
RETB_BOVIN           (  99) PAKFKMKYWGVASFLQK   4
//
ID   fastaxin; BLOCK
AC   fastaxinD; distance from previous block=(33,33)
DE   fasta.in
BL   UNK;  width=10; seqs=5; 99.5%=558; strength=1146 
BBP_PIEBR            ( 149) FVWVLSRSKV   2
ICYA_MANSE           ( 149) HAWILSKSKV   2
LACB_BOVIN           ( 149) ACQCLVRTPE   2
MUP2_MOUSE           ( 149) LMGLYGREPD   2
RETB_BOVIN           ( 149) YSFVFARDPS   2
//
ID   fastaxin; BLOCK
AC   fastaxinE; distance from previous block=(1,1)
DE   fasta.in
BL   UNK;  width=15; seqs=5; 99.5%=909; strength=1232 
BBP_PIEBR            ( 160) LTGEAKTAVENYLIG   3
ICYA_MANSE           ( 160) LEGNTKEVVDNVLKT   3
LACB_BOVIN           ( 160) VDDEALEKFDKALKA   3
MUP2_MOUSE           ( 160) LSSDIKERFAKLCEE   3
RETB_BOVIN           ( 160) FSPEVQKIVRQRQEE   4
//
ID   fastaxin; BLOCK
AC   fastaxinF; distance from previous block=(2,2)
DE   fasta.in
BL   UNK;  width=13; seqs=5; 99.5%=769; strength=1192 
BBP_PIEBR            ( 177) PVVDSQKLVYSDF   3
ICYA_MANSE           ( 177) HLIDASKFISNDF   2
LACB_BOVIN           ( 177) PMHIRLSFNPTQL   3
MUP2_MOUSE           ( 177) HGILRENIIDLSN   3
RETB_BOVIN           ( 177) CLARQYRLIPHNG   3
//
NNWDVCADMVGTFTD   8
//
ID   fastaxin; BLOCK
AC   fastaxinC; distance from previoblimps-3.9/examples/processor/distribution/fasta.in.wblks000064400001460000012000000046661062461143200243040ustar00jorjastaff00000400000027ID   fastaxin; BLOCK
AC   fastaxinA; distance from previous block=(22,22)
DE   fasta.in
BL   UNK;   width=33; seqs=5; 99.5%=1384; strength=1370 
BBP_PIEBR            (  22) VKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCG  79
ICYA_MANSE           (  22) VKPVNDFDLSAFAGAWHEIAKLPLENENQGKCT  75
LACB_BOVIN           (  22) TQTMKGLDIQKVAGTWYSLAMAASDISLLDAQS 100
MUP2_MOUSE           (  22) SSTGRNFNVEKINGEWHTIILASDKREKIEDNG  96
RETB_BOVIN           (  22) FRVKENFDKARFAGTWYAMAKKDPEGLFLQDNI  87
//
ID   fastaxin; BLOCK
AC   fastaxinB; distance from previous block=(2,2)
DE   fasta.in
BL   UNK;   width=36; seqs=5; 99.5%=1455; strength=1441 
BBP_PIEBR            (  57) WAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDS  80
ICYA_MANSE           (  57) IAEYKYDGKKASVYNSFVSNGVKEYMEGDLEIAPDA  82
LACB_BOVIN           (  57) LRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAE  95
MUP2_MOUSE           (  57) FRLFLEQIHVLEKSLVLKFHTVRDEECSELSMVADK  95
RETB_BOVIN           (  57) EFSVDENGHMSATAKGRVRLLNNWDVCADMVGTFTD 100
//
ID   fastaxin; BLOCK
AC   fastaxinC; distance from previous block=(6,6)
DE   fasta.in
BL   UNK;   width=17; seqs=5; 99.5%=896; strength=1303 
BBP_PIEBR            (  99) KIYHKLTYGGVTKENVF  89
ICYA_MANSE           (  99) KYVMTFKFGQRVVNLVP  94
LACB_BOVIN           (  99) KIPAVFKIDALNENKVL  94
MUP2_MOUSE           (  99) AGEYSVTYDGFNTFTIP 100
RETB_BOVIN           (  99) PAKFKMKYWGVASFLQK  99
//
ID   fastaxin; BLOCK
AC   fastaxinD; distance from previous block=(33,33)
DE   fasta.in
BL   UNK;   width=10; seqs=5; 99.5%=558; strength=1146 
BBP_PIEBR            ( 149) FVWVLSRSKV  66
ICYA_MANSE           ( 149) HAWILSKSKV  88
LACB_BOVIN           ( 149) ACQCLVRTPE  90
MUP2_MOUSE           ( 149) LMGLYGREPD 100
RETB_BOVIN           ( 149) YSFVFARDPS  95
//
ID   fastaxin; BLOCK
AC   fastaxinE; distance from previous block=(1,1)
DE   fasta.in
BL   UNK;   width=15; seqs=5; 99.5%=909; strength=1232 
BBP_PIEBR            ( 160) LTGEAKTAVENYLIG  81
ICYA_MANSE           ( 160) LEGNTKEVVDNVLKT  76
LACB_BOVIN           ( 160) VDDEALEKFDKALKA  85
MUP2_MOUSE           ( 160) LSSDIKERFAKLCEE  85
RETB_BOVIN           ( 160) FSPEVQKIVRQRQEE 100
//
ID   fastaxin; BLOCK
AC   fastaxinF; distance from previous block=(2,2)
DE   fasta.in
BL   UNK;   width=13; seqs=5; 99.5%=769; strength=1192 
BBP_PIEBR            ( 177) PVVDSQKLVYSDF  91
ICYA_MANSE           ( 177) HLIDASKFISNDF  74
LACB_BOVIN           ( 177) PMHIRLSFNPTQL 100
MUP2_MOUSE           ( 177) HGILRENIIDLSN  98
RETB_BOVIN           ( 177) CLARQYRLIPHNG  98
//
blimps-3.9/examples/processor/distribution/stockholm.in.cblks000064400001460000012000000047241062461143400251620ustar00jorjastaff00000400000027ID   stockholm; BLOCK
AC   stockholmA; distance from previous block=(22,22)
DE   stockholm.in
BL   UNK;  width=33; seqs=5; 99.5%=1384; strength=1370 
BBP_PIEBR            (  22) VKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCG   6
ICYA_MANSE           (  22) VKPVNDFDLSAFAGAWHEIAKLPLENENQGKCT   6
LACB_BOVIN           (  22) TQTMKGLDIQKVAGTWYSLAMAASDISLLDAQS   8
MUP2_MOUSE           (  22) SSTGRNFNVEKINGEWHTIILASDKREKIEDNG   7
RETB_BOVIN           (  22) FRVKENFDKARFAGTWYAMAKKDPEGLFLQDNI   7
//
ID   stockholm; BLOCK
AC   stockholmB; distance from previous block=(2,2)
DE   stockholm.in
BL   UNK;  width=36; seqs=5; 99.5%=1455; strength=1441 
BBP_PIEBR            (  57) WAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDS   6
ICYA_MANSE           (  57) IAEYKYDGKKASVYNSFVSNGVKEYMEGDLEIAPDA   7
LACB_BOVIN           (  57) LRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAE   8
MUP2_MOUSE           (  57) FRLFLEQIHVLEKSLVLKFHTVRDEECSELSMVADK   8
RETB_BOVIN           (  57) EFSVDENGHMSATAKGRVRLLNNWDVCADMVGTFTD   8
//
ID   stockholm; BLOCK
AC   stockholmC; distance from previous block=(6,6)
DE   stockholm.in
BL   UNK;  width=17; seqs=5; 99.5%=896; strength=1303 
BBP_PIEBR            (  99) KIYHKLTYGGVTKENVF   3
ICYA_MANSE           (  99) KYVMTFKFGQRVVNLVP   3
LACB_BOVIN           (  99) KIPAVFKIDALNENKVL   3
MUP2_MOUSE           (  99) AGEYSVTYDGFNTFTIP   4
RETB_BOVIN           (  99) PAKFKMKYWGVASFLQK   4
//
ID   stockholm; BLOCK
AC   stockholmD; distance from previous block=(33,33)
DE   stockholm.in
BL   UNK;  width=10; seqs=5; 99.5%=558; strength=1146 
BBP_PIEBR            ( 149) FVWVLSRSKV   2
ICYA_MANSE           ( 149) HAWILSKSKV   2
LACB_BOVIN           ( 149) ACQCLVRTPE   2
MUP2_MOUSE           ( 149) LMGLYGREPD   2
RETB_BOVIN           ( 149) YSFVFARDPS   2
//
ID   stockholm; BLOCK
AC   stockholmE; distance from previous block=(1,1)
DE   stockholm.in
BL   UNK;  width=15; seqs=5; 99.5%=909; strength=1232 
BBP_PIEBR            ( 160) LTGEAKTAVENYLIG   3
ICYA_MANSE           ( 160) LEGNTKEVVDNVLKT   3
LACB_BOVIN           ( 160) VDDEALEKFDKALKA   3
MUP2_MOUSE           ( 160) LSSDIKERFAKLCEE   3
RETB_BOVIN           ( 160) FSPEVQKIVRQRQEE   4
//
ID   stockholm; BLOCK
AC   stockholmF; distance from previous block=(2,2)
DE   stockholm.in
BL   UNK;  width=13; seqs=5; 99.5%=769; strength=1192 
BBP_PIEBR            ( 177) PVVDSQKLVYSDF   3
ICYA_MANSE           ( 177) HLIDASKFISNDF   2
LACB_BOVIN           ( 177) PMHIRLSFNPTQL   3
MUP2_MOUSE           ( 177) HGILRENIIDLSN   3
RETB_BOVIN           ( 177) CLARQYRLIPHNG   3
//
blimps-3.9/examples/processor/distribution/stockholm.in.wblks000064400001460000012000000047321062461143400252050ustar00jorjastaff00000400000027ID   stockholm; BLOCK
AC   stockholmA; distance from previous block=(22,22)
DE   stockholm.in
BL   UNK;   width=33; seqs=5; 99.5%=1384; strength=1370 
BBP_PIEBR            (  22) VKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCG  79
ICYA_MANSE           (  22) VKPVNDFDLSAFAGAWHEIAKLPLENENQGKCT  75
LACB_BOVIN           (  22) TQTMKGLDIQKVAGTWYSLAMAASDISLLDAQS 100
MUP2_MOUSE           (  22) SSTGRNFNVEKINGEWHTIILASDKREKIEDNG  96
RETB_BOVIN           (  22) FRVKENFDKARFAGTWYAMAKKDPEGLFLQDNI  87
//
ID   stockholm; BLOCK
AC   stockholmB; distance from previous block=(2,2)
DE   stockholm.in
BL   UNK;   width=36; seqs=5; 99.5%=1455; strength=1441 
BBP_PIEBR            (  57) WAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDS  80
ICYA_MANSE           (  57) IAEYKYDGKKASVYNSFVSNGVKEYMEGDLEIAPDA  82
LACB_BOVIN           (  57) LRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAE  95
MUP2_MOUSE           (  57) FRLFLEQIHVLEKSLVLKFHTVRDEECSELSMVADK  95
RETB_BOVIN           (  57) EFSVDENGHMSATAKGRVRLLNNWDVCADMVGTFTD 100
//
ID   stockholm; BLOCK
AC   stockholmC; distance from previous block=(6,6)
DE   stockholm.in
BL   UNK;   width=17; seqs=5; 99.5%=896; strength=1303 
BBP_PIEBR            (  99) KIYHKLTYGGVTKENVF  89
ICYA_MANSE           (  99) KYVMTFKFGQRVVNLVP  94
LACB_BOVIN           (  99) KIPAVFKIDALNENKVL  94
MUP2_MOUSE           (  99) AGEYSVTYDGFNTFTIP 100
RETB_BOVIN           (  99) PAKFKMKYWGVASFLQK  99
//
ID   stockholm; BLOCK
AC   stockholmD; distance from previous block=(33,33)
DE   stockholm.in
BL   UNK;   width=10; seqs=5; 99.5%=558; strength=1146 
BBP_PIEBR            ( 149) FVWVLSRSKV  66
ICYA_MANSE           ( 149) HAWILSKSKV  88
LACB_BOVIN           ( 149) ACQCLVRTPE  90
MUP2_MOUSE           ( 149) LMGLYGREPD 100
RETB_BOVIN           ( 149) YSFVFARDPS  95
//
ID   stockholm; BLOCK
AC   stockholmE; distance from previous block=(1,1)
DE   stockholm.in
BL   UNK;   width=15; seqs=5; 99.5%=909; strength=1232 
BBP_PIEBR            ( 160) LTGEAKTAVENYLIG  81
ICYA_MANSE           ( 160) LEGNTKEVVDNVLKT  76
LACB_BOVIN           ( 160) VDDEALEKFDKALKA  85
MUP2_MOUSE           ( 160) LSSDIKERFAKLCEE  85
RETB_BOVIN           ( 160) FSPEVQKIVRQRQEE 100
//
ID   stockholm; BLOCK
AC   stockholmF; distance from previous block=(2,2)
DE   stockholm.in
BL   UNK;   width=13; seqs=5; 99.5%=769; strength=1192 
BBP_PIEBR            ( 177) PVVDSQKLVYSDF  91
ICYA_MANSE           ( 177) HLIDASKFISNDF  74
LACB_BOVIN           ( 177) PMHIRLSFNPTQL 100
MUP2_MOUSE           ( 177) HGILRENIIDLSN  98
RETB_BOVIN           ( 177) CLARQYRLIPHNG  98
//
blimps-3.9/examples/processor/distribution/fasta.in.seqs000064400001460000012000000021651062461143200241250ustar00jorjastaff00000400000027>BBP_PIEBR   
-------NVYHDGACPE-----VKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCG--WAE
YTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDS---KIGKIYHKLTYGGVTKENVFN---
--VLSTDNKNYIIGYYCKY-DEDKKGHQDFVWVLSRSKV-LTGEAKTAVENYLIG-SPVV
DSQKLVYSDFSEAACKVN-----------
>ICYA_MANSE   
------GDIFYPGYCPD-----VKPVNDFDLSAFAGAWHEIAKLPLENENQGKCT--IAE
YKYDGKKASVYNSFVSNGVKEYMEGDLEIAPDAKYTKQGKYVMTFKFGQRVVNLVPW---
--VLATDYKNYAINYNCDY-HPDKKAHSIHAWILSKSKV-LEGNTKEVVDNVLKTFSHLI
DASKFISNDFSEAACQYSTTYSLTGPDRH
>LACB_BOVIN   
---MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRV
YVEELKPTPEGDLEILLQKWENGECAQKKIIAE---KT-KIPAVFKIDALNENKVL----
--VLDTDYKKYLL--FCME-NSAEPEQSLACQCLVRTPE-VDDEALEKFDKALKA-LPMH
IRLSFNPTQL-EEQCHI------------
>MUP2_MOUSE   
MKMLLLLCLGLTLVCVH-AEEASSTGRNFNVEKINGEWHTIILASDKREKIEDNGN-FRL
FLEQIHVLEKSLVLKFHTVRDEECSELSMVADK---TEKAGEYSVTYDGFNTFTIP----
----KTDYDNFLMAHLINE-KDGETFQ--LMGLYGREPD-LSSDIKERFAKLCEE--HGI
LRENIIDLSN-ANRCLQARE---------
>RETB_BOVIN   
-----------ERDCRVSS---FRVKENFDKARFAGTWYAMAKKDPEGLFLQDNIVAEFS
VDENGHMSATAKGRVRLLNNWDVCADMVGTFTD---TEDPAKFKMKYWGVASFLQKGNDD
HWIIDTDYETFAVQYSCRLLNLDGTCADSYSFVFARDPSGFSPEVQKIVRQRQEE-LCLA
RQYRLIPHNG---YCDGKSERNIL-----


blimps-3.9/examples/processor/distribution/stockholm.in.seqs000064400001460000012000000021651062461143300250330ustar00jorjastaff00000400000027>BBP_PIEBR   
-------NVYHDGACPE-----VKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCG--WAE
YTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDS---KIGKIYHKLTYGGVTKENVFN---
--VLSTDNKNYIIGYYCKY-DEDKKGHQDFVWVLSRSKV-LTGEAKTAVENYLIG-SPVV
DSQKLVYSDFSEAACKVN-----------
>ICYA_MANSE   
------GDIFYPGYCPD-----VKPVNDFDLSAFAGAWHEIAKLPLENENQGKCT--IAE
YKYDGKKASVYNSFVSNGVKEYMEGDLEIAPDAKYTKQGKYVMTFKFGQRVVNLVPW---
--VLATDYKNYAINYNCDY-HPDKKAHSIHAWILSKSKV-LEGNTKEVVDNVLKTFSHLI
DASKFISNDFSEAACQYSTTYSLTGPDRH
>LACB_BOVIN   
---MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRV
YVEELKPTPEGDLEILLQKWENGECAQKKIIAE---KT-KIPAVFKIDALNENKVL----
--VLDTDYKKYLL--FCME-NSAEPEQSLACQCLVRTPE-VDDEALEKFDKALKA-LPMH
IRLSFNPTQL-EEQCHI------------
>MUP2_MOUSE   
MKMLLLLCLGLTLVCVH-AEEASSTGRNFNVEKINGEWHTIILASDKREKIEDNGN-FRL
FLEQIHVLEKSLVLKFHTVRDEECSELSMVADK---TEKAGEYSVTYDGFNTFTIP----
----KTDYDNFLMAHLINE-KDGETFQ--LMGLYGREPD-LSSDIKERFAKLCEE--HGI
LRENIIDLSN-ANRCLQARE---------
>RETB_BOVIN   
-----------ERDCRVSS---FRVKENFDKARFAGTWYAMAKKDPEGLFLQDNIVAEFS
VDENGHMSATAKGRVRLLNNWDVCADMVGTFTD---TEDPAKFKMKYWGVASFLQKGNDD
HWIIDTDYETFAVQYSCRLLNLDGTCADSYSFVFARDPSGFSPEVQKIVRQRQEE-LCLA
RQYRLIPHNG---YCDGKSERNIL-----


blimps-3.9/examples/processor/distribution/clustal.in.blks000064400001460000012000000056341062461143000244600ustar00jorjastaff00000400000027ID   clustalxi; BLOCK
AC   clustalxiA; distance from previous block=(20,20)
DE   clustal.in
BL   UNK motif;  width=27; seqs=10; 99.5%=0; strength=0 
MTCH_ARATH           (  20) LPLPGTVYTVCGGPPCQGISGYNRYRN 3.738095
MTCH_ARAAR           (  20) LPLPGTVYSVCGGPPCQGISGYNRFRN 3.293651
MTDM_ARATH           (  20) LPLPGQVDFINGGPPCQGFSGMNRFNQ 2.694841
MET2_ARATH           (  20) LPLPGQVDFINGGPPCQGFSGMNRFSH 2.980556
MTDM_PISAT           (  20) LPLPGQVDFINGGPPCQGFSGMNRFNT 2.694841
MTDM_MOUSE           (  20) LPQKGDVEMLCGGPPCQGFSGMNRFNS 2.289603
MTDM_HUMAN           (  20) LPQKGDVEMLCGGPPCQGFSGMNRFNS 2.289603
MTDM_XENLA           (  20) LPQKGDVEMLCGGPPCQGFSGMNRFNS 2.289603
MTDM_PARLI           (  20) LPQKGDVELLCGGPPCQGFSGMNRFNS 2.439603
MTDM_CHICK           (  20) LPQKGDVEMLCGGPPCQGFSGMNRFNS 2.289603
//
ID   clustalxi; BLOCK
AC   clustalxiB; distance from previous block=(2,2)
DE   clustal.in
BL   UNK motif;  width=60; seqs=10; 99.5%=0; strength=0 
MTCH_ARATH           (  49) APLEDQKNQQLLVFLDIIDFLKPNYVLMENVVDLLRFSKGFLARHAVASFVAMNYQTRLG 9.248214
MTCH_ARAAR           (  49) APLEDKKNQQLLVFLDIIDFLKPSYVLMENVVDLLRFSKGYLARHAVASFVAMNYQTRLG 9.248214
MTDM_ARATH           (  49) SSWSKVQCEMILAFLSFADYFRPRYFLLENVRTFVSFNKGQTFQLTLASLLEMGYQVRFG 5.573810
MET2_ARATH           (  49) GSWSKVQCEMILAFLSFADYFRPKYFLLENVKKFVTYNKGRTFQLTMASLLEMGYQVRFG 6.834524
MTDM_PISAT           (  49) STWSKVQCEMILAFLSFADYFRPRYFLLENVRNFVSFNKGQTFRLTLASLLEMGYQVRFG 5.234921
MTDM_MOUSE           (  49) RTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSYRRSMVLKLTLRCLVRMGYQCTFG 4.719365
MTDM_HUMAN           (  49) RTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFG 4.436627
MTDM_XENLA           (  49) RTYSKFKNSLVVSYLSYCDYYRPKYFLLENVRNFVSFKKSMVLKLTLRCLVRMGYQCTFG 4.570556
MTDM_PARLI           (  49) REYSKFKNSLISSYLSYCDYYRPRFFLLENVRNFVSYKKNMVLKLALRCLIRMGYQCTFG 5.697143
MTDM_CHICK           (  49) RTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFG 4.436627
//
ID   clustalxi; BLOCK
AC   clustalxiC; distance from previous block=(0,0)
DE   clustal.in
BL   UNK motif;  width=51; seqs=10; 99.5%=0; strength=0 
MTCH_ARATH           ( 109) MMAAGSYGLPQLRNRVFLWAAQPSEKLPPYPLPTHEVAKKFNTPKEFKDLQ 6.821151
MTCH_ARAAR           ( 109) MMTAGSYGLPQVRNRVFLWAAQPTEKLPPYPLPTHEVEKKYNTPKEFEDLQ 6.897817
MTDM_ARATH           ( 109) ILEAGAYGVSQSRKRAFIWAAAPEEVLPEWPEPMHVFGVPKLKISLSQGLH 5.263492
MET2_ARATH           ( 109) ILEAGTYGVSQPRKRVIIWAASPEEVLPEWPEPMHVFDNPGSKISLPRGLR 5.778175
MTDM_PISAT           ( 109) ILEAGAFGVSQSRKRAFIWAASPEDVLPEWPEPMHVFSAPELKITLAENVQ 6.608929
MTDM_MOUSE           ( 109) VLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDK 3.702421
MTDM_HUMAN           ( 109) VLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDK 3.702421
MTDM_XENLA           ( 109) VLQAGQYGVAQTRRRAIVLAAAPGEKLPMFPEPLHVFAPRACTLSVVVDEK 3.855198
MTDM_PARLI           ( 109) ILQAGQYGVPQTRRRAIILAAAPGEKLPFYPEPLHVFSSRACSLSVMIGEK 4.556865
MTDM_CHICK           ( 109) VLQAGQYGVAQTRRRAIVLAAAPGEKLPMFPEPLHVFAPRACQLSVVVDDK 3.813532
//
blimps-3.9/examples/processor/distribution/clustal.in.blks.cum000064400001460000012000002102041062461143200252340ustar00jorjastaff00000400000027>clustalxiA
2100 8.7e-37
2099 8.7e-37
2098 4.4e-36
2097 7.2e-36
2096 1.1e-35
2095 2.3e-35
2094 3.4e-35
2093  5e-35
2092 6.4e-35
2091  1e-34
2090 1.3e-34
2089 1.6e-34
2088 2.2e-34
2087 2.7e-34
2086 3.4e-34
2085  4e-34
2084 5.3e-34
2083  6e-34
2082 7.3e-34
2081 8.6e-34
2080  1e-33
2079 1.2e-33
2078 1.3e-33
2077 1.6e-33
2076 1.8e-33
2075 2.1e-33
2074 2.3e-33
2073 2.8e-33
2072 3.1e-33
2071 3.7e-33
2070 4.3e-33
2069 4.9e-33
2068 5.6e-33
2067 6.4e-33
2066 7.5e-33
2065 8.5e-33
2064  1e-32
2063 1.1e-32
2062 1.3e-32
2061 1.5e-32
2060 1.7e-32
2059  2e-32
2058 2.2e-32
2057 2.6e-32
2056 2.9e-32
2055 3.3e-32
2054 3.7e-32
2053 4.3e-32
2052 4.8e-32
2051 5.5e-32
2050 6.2e-32
2049  7e-32
2048 7.9e-32
2047 8.9e-32
2046  1e-31
2045 1.1e-31
2044 1.3e-31
2043 1.5e-31
2042 1.6e-31
2041 1.8e-31
2040 2.1e-31
2039 2.3e-31
2038 2.6e-31
2037  3e-31
2036 3.3e-31
2035 3.7e-31
2034 4.2e-31
2033 4.7e-31
2032 5.2e-31
2031 5.9e-31
2030 6.6e-31
2029 7.3e-31
2028 8.2e-31
2027 9.2e-31
2026  1e-30
2025 1.1e-30
2024 1.3e-30
2023 1.4e-30
2022 1.6e-30
2021 1.8e-30
2020  2e-30
2019 2.2e-30
2018 2.5e-30
2017 2.8e-30
2016 3.1e-30
2015 3.5e-30
2014 3.8e-30
2013 4.3e-30
2012 4.7e-30
2011 5.3e-30
2010 5.9e-30
2009 6.5e-30
2008 7.2e-30
2007  8e-30
2006 8.9e-30
2005 9.9e-30
2004 1.1e-29
2003 1.2e-29
2002 1.4e-29
2001 1.5e-29
2000 1.7e-29
1999 1.8e-29
1998  2e-29
1997 2.3e-29
1996 2.5e-29
1995 2.8e-29
1994 3.1e-29
1993 3.4e-29
1992 3.8e-29
1991 4.2e-29
1990 4.6e-29
1989 5.1e-29
1988 5.6e-29
1987 6.2e-29
1986 6.8e-29
1985 7.5e-29
1984 8.3e-29
1983 9.2e-29
1982  1e-28
1981 1.1e-28
1980 1.2e-28
1979 1.4e-28
1978 1.5e-28
1977 1.6e-28
1976 1.8e-28
1975  2e-28
1974 2.2e-28
1973 2.4e-28
1972 2.7e-28
1971 2.9e-28
1970 3.2e-28
1969 3.6e-28
1968 3.9e-28
1967 4.3e-28
1966 4.7e-28
1965 5.2e-28
1964 5.7e-28
1963 6.3e-28
1962 6.9e-28
1961 7.6e-28
1960 8.3e-28
1959 9.1e-28
1958  1e-27
1957 1.1e-27
1956 1.2e-27
1955 1.3e-27
1954 1.4e-27
1953 1.6e-27
1952 1.7e-27
1951 1.9e-27
1950 2.1e-27
1949 2.3e-27
1948 2.5e-27
1947 2.7e-27
1946  3e-27
1945 3.3e-27
1944 3.6e-27
1943 3.9e-27
1942 4.3e-27
1941 4.7e-27
1940 5.2e-27
1939 5.7e-27
1938 6.2e-27
1937 6.8e-27
1936 7.4e-27
1935 8.1e-27
1934 8.8e-27
1933 9.7e-27
1932 1.1e-26
1931 1.2e-26
1930 1.3e-26
1929 1.4e-26
1928 1.5e-26
1927 1.6e-26
1926 1.8e-26
1925  2e-26
1924 2.1e-26
1923 2.3e-26
1922 2.5e-26
1921 2.8e-26
1920  3e-26
1919 3.3e-26
1918 3.6e-26
1917 3.9e-26
1916 4.3e-26
1915 4.6e-26
1914 5.1e-26
1913 5.5e-26
1912  6e-26
1911 6.5e-26
1910 7.1e-26
1909 7.8e-26
1908 8.5e-26
1907 9.2e-26
1906  1e-25
1905 1.1e-25
1904 1.2e-25
1903 1.3e-25
1902 1.4e-25
1901 1.5e-25
1900 1.7e-25
1899 1.8e-25
1898  2e-25
1897 2.1e-25
1896 2.3e-25
1895 2.5e-25
1894 2.7e-25
1893  3e-25
1892 3.2e-25
1891 3.5e-25
1890 3.8e-25
1889 4.1e-25
1888 4.5e-25
1887 4.9e-25
1886 5.3e-25
1885 5.8e-25
1884 6.3e-25
1883 6.8e-25
1882 7.4e-25
1881  8e-25
1880 8.7e-25
1879 9.4e-25
1878  1e-24
1877 1.1e-24
1876 1.2e-24
1875 1.3e-24
1874 1.4e-24
1873 1.5e-24
1872 1.7e-24
1871 1.8e-24
1870 1.9e-24
1869 2.1e-24
1868 2.3e-24
1867 2.5e-24
1866 2.7e-24
1865 2.9e-24
1864 3.1e-24
1863 3.4e-24
1862 3.7e-24
1861  4e-24
1860 4.3e-24
1859 4.7e-24
1858 5.1e-24
1857 5.5e-24
1856 5.9e-24
1855 6.4e-24
1854 6.9e-24
1853 7.5e-24
1852 8.1e-24
1851 8.8e-24
1850 9.5e-24
1849  1e-23
1848 1.1e-23
1847 1.2e-23
1846 1.3e-23
1845 1.4e-23
1844 1.5e-23
1843 1.6e-23
1842 1.8e-23
1841 1.9e-23
1840 2.1e-23
1839 2.2e-23
1838 2.4e-23
1837 2.6e-23
1836 2.8e-23
1835  3e-23
1834 3.3e-23
1833 3.5e-23
1832 3.8e-23
1831 4.1e-23
1830 4.5e-23
1829 4.8e-23
1828 5.2e-23
1827 5.6e-23
1826  6e-23
1825 6.5e-23
1824  7e-23
1823 7.6e-23
1822 8.2e-23
1821 8.8e-23
1820 9.5e-23
1819  1e-22
1818 1.1e-22
1817 1.2e-22
1816 1.3e-22
1815 1.4e-22
1814 1.5e-22
1813 1.6e-22
1812 1.7e-22
1811 1.9e-22
1810  2e-22
1809 2.2e-22
1808 2.3e-22
1807 2.5e-22
1806 2.7e-22
1805 2.9e-22
1804 3.1e-22
1803 3.4e-22
1802 3.6e-22
1801 3.9e-22
1800 4.2e-22
1799 4.5e-22
1798 4.9e-22
1797 5.2e-22
1796 5.6e-22
1795 6.1e-22
1794 6.5e-22
1793  7e-22
1792 7.5e-22
1791 8.1e-22
1790 8.7e-22
1789 9.4e-22
1788  1e-21
1787 1.1e-21
1786 1.2e-21
1785 1.3e-21
1784 1.3e-21
1783 1.4e-21
1782 1.6e-21
1781 1.7e-21
1780 1.8e-21
1779 1.9e-21
1778 2.1e-21
1777 2.2e-21
1776 2.4e-21
1775 2.6e-21
1774 2.8e-21
1773  3e-21
1772 3.2e-21
1771 3.4e-21
1770 3.7e-21
1769 3.9e-21
1768 4.2e-21
1767 4.5e-21
1766 4.9e-21
1765 5.2e-21
1764 5.6e-21
1763  6e-21
1762 6.5e-21
1761 6.9e-21
1760 7.4e-21
1759  8e-21
1758 8.6e-21
1757 9.2e-21
1756 9.9e-21
1755 1.1e-20
1754 1.1e-20
1753 1.2e-20
1752 1.3e-20
1751 1.4e-20
1750 1.5e-20
1749 1.6e-20
1748 1.7e-20
1747 1.8e-20
1746  2e-20
1745 2.1e-20
1744 2.3e-20
1743 2.4e-20
1742 2.6e-20
1741 2.8e-20
1740  3e-20
1739 3.2e-20
1738 3.4e-20
1737 3.7e-20
1736 3.9e-20
1735 4.2e-20
1734 4.5e-20
1733 4.8e-20
1732 5.2e-20
1731 5.5e-20
1730 5.9e-20
1729 6.3e-20
1728 6.8e-20
1727 7.3e-20
1726 7.8e-20
1725 8.3e-20
1724 8.9e-20
1723 9.5e-20
1722  1e-19
1721 1.1e-19
1720 1.2e-19
1719 1.2e-19
1718 1.3e-19
1717 1.4e-19
1716 1.5e-19
1715 1.6e-19
1714 1.7e-19
1713 1.9e-19
1712  2e-19
1711 2.1e-19
1710 2.3e-19
1709 2.4e-19
1708 2.6e-19
1707 2.8e-19
1706  3e-19
1705 3.2e-19
1704 3.4e-19
1703 3.6e-19
1702 3.9e-19
1701 4.1e-19
1700 4.4e-19
1699 4.7e-19
1698 5.1e-19
1697 5.4e-19
1696 5.8e-19
1695 6.2e-19
1694 6.6e-19
1693  7e-19
1692 7.5e-19
1691  8e-19
1690 8.6e-19
1689 9.1e-19
1688 9.7e-19
1687  1e-18
1686 1.1e-18
1685 1.2e-18
1684 1.3e-18
1683 1.3e-18
1682 1.4e-18
1681 1.5e-18
1680 1.6e-18
1679 1.7e-18
1678 1.9e-18
1677  2e-18
1676 2.1e-18
1675 2.3e-18
1674 2.4e-18
1673 2.6e-18
1672 2.7e-18
1671 2.9e-18
1670 3.1e-18
1669 3.3e-18
1668 3.5e-18
1667 3.8e-18
1666  4e-18
1665 4.3e-18
1664 4.6e-18
1663 4.9e-18
1662 5.2e-18
1661 5.5e-18
1660 5.9e-18
1659 6.3e-18
1658 6.7e-18
1657 7.2e-18
1656 7.6e-18
1655 8.1e-18
1654 8.6e-18
1653 9.2e-18
1652 9.8e-18
1651  1e-17
1650 1.1e-17
1649 1.2e-17
1648 1.3e-17
1647 1.3e-17
1646 1.4e-17
1645 1.5e-17
1644 1.6e-17
1643 1.7e-17
1642 1.8e-17
1641  2e-17
1640 2.1e-17
1639 2.2e-17
1638 2.4e-17
1637 2.5e-17
1636 2.7e-17
1635 2.8e-17
1634  3e-17
1633 3.2e-17
1632 3.4e-17
1631 3.6e-17
1630 3.9e-17
1629 4.1e-17
1628 4.4e-17
1627 4.7e-17
1626  5e-17
1625 5.3e-17
1624 5.6e-17
1623  6e-17
1622 6.3e-17
1621 6.7e-17
1620 7.2e-17
1619 7.6e-17
1618 8.1e-17
1617 8.6e-17
1616 9.1e-17
1615 9.7e-17
1614  1e-16
1613 1.1e-16
1612 1.2e-16
1611 1.2e-16
1610 1.3e-16
1609 1.4e-16
1608 1.5e-16
1607 1.6e-16
1606 1.7e-16
1605 1.8e-16
1604 1.9e-16
1603  2e-16
1602 2.1e-16
1601 2.3e-16
1600 2.4e-16
1599 2.6e-16
1598 2.7e-16
1597 2.9e-16
1596 3.1e-16
1595 3.2e-16
1594 3.4e-16
1593 3.7e-16
1592 3.9e-16
1591 4.1e-16
1590 4.4e-16
1589 4.6e-16
1588 4.9e-16
1587 5.2e-16
1586 5.5e-16
1585 5.9e-16
1584 6.2e-16
1583 6.6e-16
1582  7e-16
1581 7.5e-16
1580 7.9e-16
1579 8.4e-16
1578 8.9e-16
1577 9.4e-16
1576  1e-15
1575 1.1e-15
1574 1.1e-15
1573 1.2e-15
1572 1.3e-15
1571 1.3e-15
1570 1.4e-15
1569 1.5e-15
1568 1.6e-15
1567 1.7e-15
1566 1.8e-15
1565 1.9e-15
1564  2e-15
1563 2.1e-15
1562 2.3e-15
1561 2.4e-15
1560 2.5e-15
1559 2.7e-15
1558 2.9e-15
1557  3e-15
1556 3.2e-15
1555 3.4e-15
1554 3.6e-15
1553 3.8e-15
1552  4e-15
1551 4.3e-15
1550 4.5e-15
1549 4.8e-15
1548 5.1e-15
1547 5.4e-15
1546 5.7e-15
1545  6e-15
1544 6.4e-15
1543 6.8e-15
1542 7.1e-15
1541 7.6e-15
1540  8e-15
1539 8.5e-15
1538  9e-15
1537 9.5e-15
1536  1e-14
1535 1.1e-14
1534 1.1e-14
1533 1.2e-14
1532 1.3e-14
1531 1.3e-14
1530 1.4e-14
1529 1.5e-14
1528 1.6e-14
1527 1.7e-14
1526 1.8e-14
1525 1.9e-14
1524  2e-14
1523 2.1e-14
1522 2.2e-14
1521 2.3e-14
1520 2.5e-14
1519 2.6e-14
1518 2.8e-14
1517 2.9e-14
1516 3.1e-14
1515 3.3e-14
1514 3.5e-14
1513 3.7e-14
1512 3.9e-14
1511 4.1e-14
1510 4.3e-14
1509 4.6e-14
1508 4.8e-14
1507 5.1e-14
1506 5.4e-14
1505 5.7e-14
1504  6e-14
1503 6.3e-14
1502 6.7e-14
1501 7.1e-14
1500 7.5e-14
1499 7.9e-14
1498 8.3e-14
1497 8.8e-14
1496 9.3e-14
1495 9.8e-14
1494  1e-13
1493 1.1e-13
1492 1.2e-13
1491 1.2e-13
1490 1.3e-13
1489 1.4e-13
1488 1.4e-13
1487 1.5e-13
1486 1.6e-13
1485 1.7e-13
1484 1.8e-13
1483 1.9e-13
1482  2e-13
1481 2.1e-13
1480 2.2e-13
1479 2.3e-13
1478 2.5e-13
1477 2.6e-13
1476 2.8e-13
1475 2.9e-13
1474 3.1e-13
1473 3.2e-13
1472 3.4e-13
1471 3.6e-13
1470 3.8e-13
1469  4e-13
1468 4.2e-13
1467 4.5e-13
1466 4.7e-13
1465  5e-13
1464 5.2e-13
1463 5.5e-13
1462 5.8e-13
1461 6.1e-13
1460 6.5e-13
1459 6.8e-13
1458 7.2e-13
1457 7.6e-13
1456  8e-13
1455 8.4e-13
1454 8.9e-13
1453 9.3e-13
1452 9.8e-13
1451  1e-12
1450 1.1e-12
1449 1.2e-12
1448 1.2e-12
1447 1.3e-12
1446 1.3e-12
1445 1.4e-12
1444 1.5e-12
1443 1.6e-12
1442 1.7e-12
1441 1.8e-12
1440 1.8e-12
1439 1.9e-12
1438  2e-12
1437 2.2e-12
1436 2.3e-12
1435 2.4e-12
1434 2.5e-12
1433 2.6e-12
1432 2.8e-12
1431 2.9e-12
1430 3.1e-12
1429 3.3e-12
1428 3.4e-12
1427 3.6e-12
1426 3.8e-12
1425  4e-12
1424 4.2e-12
1423 4.4e-12
1422 4.7e-12
1421 4.9e-12
1420 5.2e-12
1419 5.4e-12
1418 5.7e-12
1417  6e-12
1416 6.3e-12
1415 6.7e-12
1414  7e-12
1413 7.4e-12
1412 7.8e-12
1411 8.2e-12
1410 8.6e-12
1409  9e-12
1408 9.5e-12
1407  1e-11
1406 1.1e-11
1405 1.1e-11
1404 1.2e-11
1403 1.2e-11
1402 1.3e-11
1401 1.4e-11
1400 1.4e-11
1399 1.5e-11
1398 1.6e-11
1397 1.7e-11
1396 1.7e-11
1395 1.8e-11
1394 1.9e-11
1393  2e-11
1392 2.1e-11
1391 2.2e-11
1390 2.3e-11
1389 2.5e-11
1388 2.6e-11
1387 2.7e-11
1386 2.9e-11
1385  3e-11
1384 3.2e-11
1383 3.3e-11
1382 3.5e-11
1381 3.7e-11
1380 3.8e-11
1379  4e-11
1378 4.2e-11
1377 4.4e-11
1376 4.7e-11
1375 4.9e-11
1374 5.2e-11
1373 5.4e-11
1372 5.7e-11
1371  6e-11
1370 6.3e-11
1369 6.6e-11
1368 6.9e-11
1367 7.2e-11
1366 7.6e-11
1365  8e-11
1364 8.4e-11
1363 8.8e-11
1362 9.2e-11
1361 9.7e-11
1360  1e-10
1359 1.1e-10
1358 1.1e-10
1357 1.2e-10
1356 1.2e-10
1355 1.3e-10
1354 1.4e-10
1353 1.4e-10
1352 1.5e-10
1351 1.6e-10
1350 1.6e-10
1349 1.7e-10
1348 1.8e-10
1347 1.9e-10
1346  2e-10
1345 2.1e-10
1344 2.2e-10
1343 2.3e-10
1342 2.4e-10
1341 2.5e-10
1340 2.7e-10
1339 2.8e-10
1338 2.9e-10
1337 3.1e-10
1336 3.2e-10
1335 3.4e-10
1334 3.5e-10
1333 3.7e-10
1332 3.9e-10
1331 4.1e-10
1330 4.2e-10
1329 4.5e-10
1328 4.7e-10
1327 4.9e-10
1326 5.1e-10
1325 5.4e-10
1324 5.6e-10
1323 5.9e-10
1322 6.2e-10
1321 6.5e-10
1320 6.8e-10
1319 7.1e-10
1318 7.4e-10
1317 7.8e-10
1316 8.2e-10
1315 8.6e-10
1314  9e-10
1313 9.4e-10
1312 9.8e-10
1311  1e-09
1310 1.1e-09
1309 1.1e-09
1308 1.2e-09
1307 1.2e-09
1306 1.3e-09
1305 1.4e-09
1304 1.4e-09
1303 1.5e-09
1302 1.6e-09
1301 1.6e-09
1300 1.7e-09
1299 1.8e-09
1298 1.9e-09
1297  2e-09
1296  2e-09
1295 2.1e-09
1294 2.2e-09
1293 2.3e-09
1292 2.5e-09
1291 2.6e-09
1290 2.7e-09
1289 2.8e-09
1288 2.9e-09
1287 3.1e-09
1286 3.2e-09
1285 3.4e-09
1284 3.5e-09
1283 3.7e-09
1282 3.8e-09
1281  4e-09
1280 4.2e-09
1279 4.4e-09
1278 4.6e-09
1277 4.8e-09
1276  5e-09
1275 5.3e-09
1274 5.5e-09
1273 5.7e-09
1272  6e-09
1271 6.3e-09
1270 6.6e-09
1269 6.9e-09
1268 7.2e-09
1267 7.5e-09
1266 7.8e-09
1265 8.2e-09
1264 8.6e-09
1263 8.9e-09
1262 9.3e-09
1261 9.8e-09
1260  1e-08
1259 1.1e-08
1258 1.1e-08
1257 1.2e-08
1256 1.2e-08
1255 1.3e-08
1254 1.3e-08
1253 1.4e-08
1252 1.4e-08
1251 1.5e-08
1250 1.6e-08
1249 1.6e-08
1248 1.7e-08
1247 1.8e-08
1246 1.9e-08
1245  2e-08
1244  2e-08
1243 2.1e-08
1242 2.2e-08
1241 2.3e-08
1240 2.4e-08
1239 2.5e-08
1238 2.7e-08
1237 2.8e-08
1236 2.9e-08
1235  3e-08
1234 3.1e-08
1233 3.3e-08
1232 3.4e-08
1231 3.6e-08
1230 3.7e-08
1229 3.9e-08
1228 4.1e-08
1227 4.2e-08
1226 4.4e-08
1225 4.6e-08
1224 4.8e-08
1223  5e-08
1222 5.2e-08
1221 5.5e-08
1220 5.7e-08
1219 5.9e-08
1218 6.2e-08
1217 6.5e-08
1216 6.7e-08
1215  7e-08
1214 7.3e-08
1213 7.6e-08
1212  8e-08
1211 8.3e-08
1210 8.7e-08
1209  9e-08
1208 9.4e-08
1207 9.8e-08
1206  1e-07
1205 1.1e-07
1204 1.1e-07
1203 1.2e-07
1202 1.2e-07
1201 1.3e-07
1200 1.3e-07
1199 1.4e-07
1198 1.4e-07
1197 1.5e-07
1196 1.5e-07
1195 1.6e-07
1194 1.7e-07
1193 1.7e-07
1192 1.8e-07
1191 1.9e-07
1190  2e-07
1189 2.1e-07
1188 2.1e-07
1187 2.2e-07
1186 2.3e-07
1185 2.4e-07
1184 2.5e-07
1183 2.6e-07
1182 2.7e-07
1181 2.8e-07
1180  3e-07
1179 3.1e-07
1178 3.2e-07
1177 3.3e-07
1176 3.5e-07
1175 3.6e-07
1174 3.8e-07
1173 3.9e-07
1172 4.1e-07
1171 4.3e-07
1170 4.4e-07
1169 4.6e-07
1168 4.8e-07
1167  5e-07
1166 5.2e-07
1165 5.4e-07
1164 5.6e-07
1163 5.8e-07
1162 6.1e-07
1161 6.3e-07
1160 6.6e-07
1159 6.8e-07
1158 7.1e-07
1157 7.4e-07
1156 7.7e-07
1155  8e-07
1154 8.3e-07
1153 8.7e-07
1152  9e-07
1151 9.4e-07
1150 9.7e-07
1149  1e-06
1148 1.1e-06
1147 1.1e-06
1146 1.1e-06
1145 1.2e-06
1144 1.2e-06
1143 1.3e-06
1142 1.3e-06
1141 1.4e-06
1140 1.4e-06
1139 1.5e-06
1138 1.5e-06
1137 1.6e-06
1136 1.7e-06
1135 1.7e-06
1134 1.8e-06
1133 1.9e-06
1132 1.9e-06
1131  2e-06
1130 2.1e-06
1129 2.2e-06
1128 2.3e-06
1127 2.4e-06
1126 2.4e-06
1125 2.5e-06
1124 2.6e-06
1123 2.7e-06
1122 2.8e-06
1121  3e-06
1120 3.1e-06
1119 3.2e-06
1118 3.3e-06
1117 3.4e-06
1116 3.6e-06
1115 3.7e-06
1114 3.8e-06
1113  4e-06
1112 4.1e-06
1111 4.3e-06
1110 4.5e-06
1109 4.6e-06
1108 4.8e-06
1107  5e-06
1106 5.2e-06
1105 5.4e-06
1104 5.6e-06
1103 5.8e-06
1102  6e-06
1101 6.2e-06
1100 6.5e-06
1099 6.7e-06
1098 6.9e-06
1097 7.2e-06
1096 7.5e-06
1095 7.8e-06
1094  8e-06
1093 8.3e-06
1092 8.6e-06
1091  9e-06
1090 9.3e-06
1089 9.6e-06
1088  1e-05
1087  1e-05
1086 1.1e-05
1085 1.1e-05
1084 1.2e-05
1083 1.2e-05
1082 1.2e-05
1081 1.3e-05
1080 1.3e-05
1079 1.4e-05
1078 1.4e-05
1077 1.5e-05
1076 1.5e-05
1075 1.6e-05
1074 1.7e-05
1073 1.7e-05
1072 1.8e-05
1071 1.8e-05
1070 1.9e-05
1069  2e-05
1068  2e-05
1067 2.1e-05
1066 2.2e-05
1065 2.3e-05
1064 2.3e-05
1063 2.4e-05
1062 2.5e-05
1061 2.6e-05
1060 2.7e-05
1059 2.8e-05
1058 2.9e-05
1057  3e-05
1056 3.1e-05
1055 3.2e-05
1054 3.3e-05
1053 3.4e-05
1052 3.6e-05
1051 3.7e-05
1050 3.8e-05
1049  4e-05
1048 4.1e-05
1047 4.2e-05
1046 4.4e-05
1045 4.5e-05
1044 4.7e-05
1043 4.9e-05
1042  5e-05
1041 5.2e-05
1040 5.4e-05
1039 5.6e-05
1038 5.8e-05
1037 5.9e-05
1036 6.2e-05
1035 6.4e-05
1034 6.6e-05
1033 6.8e-05
1032  7e-05
1031 7.3e-05
1030 7.5e-05
1029 7.8e-05
1028  8e-05
1027 8.3e-05
1026 8.6e-05
1025 8.9e-05
1024 9.2e-05
1023 9.5e-05
1022 9.8e-05
1021 0.0001
1020 0.0001
1019 0.00011
1018 0.00011
1017 0.00012
1016 0.00012
1015 0.00012
1014 0.00013
1013 0.00013
1012 0.00014
1011 0.00014
1010 0.00015
1009 0.00015
1008 0.00016
1007 0.00016
1006 0.00017
1005 0.00017
1004 0.00018
1003 0.00018
1002 0.00019
1001 0.00019
1000 0.0002
999 0.00021
998 0.00021
997 0.00022
996 0.00023
995 0.00024
994 0.00024
993 0.00025
992 0.00026
991 0.00027
990 0.00028
989 0.00028
988 0.00029
987 0.0003
986 0.00031
985 0.00032
984 0.00033
983 0.00034
982 0.00035
981 0.00037
980 0.00038
979 0.00039
978 0.0004
977 0.00041
976 0.00043
975 0.00044
974 0.00045
973 0.00047
972 0.00048
971 0.0005
>clustalxiB
4685 9.3e-82
4684 5.3e-81
4683 1.6e-80
4682  4e-80
4681 8.3e-80
4680 1.6e-79
4679  3e-79
4678 5.4e-79
4677 9.8e-79
4676 1.7e-78
4675 2.9e-78
4674  5e-78
4673 8.1e-78
4672 1.3e-77
4671 2.1e-77
4670 3.3e-77
4669 5.1e-77
4668 7.9e-77
4667 1.2e-76
4666 1.8e-76
4665 2.7e-76
4664  4e-76
4663 5.9e-76
4662 8.6e-76
4661 1.2e-75
4660 1.8e-75
4659 2.6e-75
4658 3.7e-75
4657 5.2e-75
4656 7.3e-75
4655  1e-74
4654 1.4e-74
4653  2e-74
4652 2.7e-74
4651 3.7e-74
4650 5.1e-74
4649  7e-74
4648 9.4e-74
4647 1.3e-73
4646 1.7e-73
4645 2.3e-73
4644 3.1e-73
4643 4.1e-73
4642 5.4e-73
4641 7.2e-73
4640 9.5e-73
4639 1.2e-72
4638 1.6e-72
4637 2.1e-72
4636 2.8e-72
4635 3.6e-72
4634 4.7e-72
4633 6.1e-72
4632 7.8e-72
4631  1e-71
4630 1.3e-71
4629 1.7e-71
4628 2.1e-71
4627 2.7e-71
4626 3.5e-71
4625 4.4e-71
4624 5.6e-71
4623  7e-71
4622 8.9e-71
4621 1.1e-70
4620 1.4e-70
4619 1.8e-70
4618 2.2e-70
4617 2.8e-70
4616 3.5e-70
4615 4.3e-70
4614 5.4e-70
4613 6.7e-70
4612 8.3e-70
4611  1e-69
4610 1.3e-69
4609 1.6e-69
4608 1.9e-69
4607 2.4e-69
4606 2.9e-69
4605 3.6e-69
4604 4.4e-69
4603 5.4e-69
4602 6.7e-69
4601 8.1e-69
4600 9.9e-69
4599 1.2e-68
4598 1.5e-68
4597 1.8e-68
4596 2.2e-68
4595 2.7e-68
4594 3.2e-68
4593 3.9e-68
4592 4.7e-68
4591 5.7e-68
4590 6.9e-68
4589 8.3e-68
4588  1e-67
4587 1.2e-67
4586 1.5e-67
4585 1.7e-67
4584 2.1e-67
4583 2.5e-67
4582  3e-67
4581 3.6e-67
4580 4.3e-67
4579 5.2e-67
4578 6.2e-67
4577 7.3e-67
4576 8.8e-67
4575  1e-66
4574 1.2e-66
4573 1.5e-66
4572 1.8e-66
4571 2.1e-66
4570 2.5e-66
4569 2.9e-66
4568 3.5e-66
4567 4.1e-66
4566 4.9e-66
4565 5.8e-66
4564 6.8e-66
4563 8.1e-66
4562 9.5e-66
4561 1.1e-65
4560 1.3e-65
4559 1.6e-65
4558 1.8e-65
4557 2.2e-65
4556 2.5e-65
4555  3e-65
4554 3.5e-65
4553 4.1e-65
4552 4.8e-65
4551 5.7e-65
4550 6.6e-65
4549 7.8e-65
4548 9.1e-65
4547 1.1e-64
4546 1.2e-64
4545 1.5e-64
4544 1.7e-64
4543  2e-64
4542 2.3e-64
4541 2.7e-64
4540 3.2e-64
4539 3.7e-64
4538 4.3e-64
4537  5e-64
4536 5.8e-64
4535 6.7e-64
4534 7.8e-64
4533 9.1e-64
4532 1.1e-63
4531 1.2e-63
4530 1.4e-63
4529 1.7e-63
4528 1.9e-63
4527 2.2e-63
4526 2.6e-63
4525  3e-63
4524 3.4e-63
4523  4e-63
4522 4.6e-63
4521 5.3e-63
4520 6.2e-63
4519 7.1e-63
4518 8.2e-63
4517 9.5e-63
4516 1.1e-62
4515 1.3e-62
4514 1.5e-62
4513 1.7e-62
4512 1.9e-62
4511 2.2e-62
4510 2.6e-62
4509 2.9e-62
4508 3.4e-62
4507 3.9e-62
4506 4.5e-62
4505 5.2e-62
4504 5.9e-62
4503 6.8e-62
4502 7.8e-62
4501  9e-62
4500  1e-61
4499 1.2e-61
4498 1.4e-61
4497 1.5e-61
4496 1.8e-61
4495  2e-61
4494 2.3e-61
4493 2.7e-61
4492  3e-61
4491 3.5e-61
4490  4e-61
4489 4.6e-61
4488 5.2e-61
4487  6e-61
4486 6.8e-61
4485 7.8e-61
4484 8.9e-61
4483  1e-60
4482 1.2e-60
4481 1.3e-60
4480 1.5e-60
4479 1.7e-60
4478  2e-60
4477 2.2e-60
4476 2.5e-60
4475 2.9e-60
4474 3.3e-60
4473 3.7e-60
4472 4.3e-60
4471 4.8e-60
4470 5.5e-60
4469 6.3e-60
4468 7.1e-60
4467 8.1e-60
4466 9.2e-60
4465  1e-59
4464 1.2e-59
4463 1.3e-59
4462 1.5e-59
4461 1.7e-59
4460  2e-59
4459 2.2e-59
4458 2.5e-59
4457 2.9e-59
4456 3.2e-59
4455 3.7e-59
4454 4.2e-59
4453 4.7e-59
4452 5.3e-59
4451  6e-59
4450 6.8e-59
4449 7.7e-59
4448 8.8e-59
4447 9.9e-59
4446 1.1e-58
4445 1.3e-58
4444 1.4e-58
4443 1.6e-58
4442 1.8e-58
4441 2.1e-58
4440 2.3e-58
4439 2.6e-58
4438  3e-58
4437 3.4e-58
4436 3.8e-58
4435 4.3e-58
4434 4.8e-58
4433 5.4e-58
4432 6.1e-58
4431 6.9e-58
4430 7.8e-58
4429 8.8e-58
4428 9.9e-58
4427 1.1e-57
4426 1.3e-57
4425 1.4e-57
4424 1.6e-57
4423 1.8e-57
4422  2e-57
4421 2.3e-57
4420 2.5e-57
4419 2.9e-57
4418 3.2e-57
4417 3.6e-57
4416 4.1e-57
4415 4.6e-57
4414 5.1e-57
4413 5.8e-57
4412 6.5e-57
4411 7.3e-57
4410 8.2e-57
4409 9.2e-57
4408  1e-56
4407 1.2e-56
4406 1.3e-56
4405 1.5e-56
4404 1.6e-56
4403 1.8e-56
4402  2e-56
4401 2.3e-56
4400 2.6e-56
4399 2.9e-56
4398 3.2e-56
4397 3.6e-56
4396 4.1e-56
4395 4.5e-56
4394 5.1e-56
4393 5.7e-56
4392 6.4e-56
4391 7.1e-56
4390  8e-56
4389 8.9e-56
4388  1e-55
4387 1.1e-55
4386 1.2e-55
4385 1.4e-55
4384 1.6e-55
4383 1.7e-55
4382  2e-55
4381 2.2e-55
4380 2.4e-55
4379 2.7e-55
4378  3e-55
4377 3.4e-55
4376 3.8e-55
4375 4.2e-55
4374 4.7e-55
4373 5.3e-55
4372 5.9e-55
4371 6.6e-55
4370 7.3e-55
4369 8.2e-55
4368 9.1e-55
4367  1e-54
4366 1.1e-54
4365 1.3e-54
4364 1.4e-54
4363 1.6e-54
4362 1.7e-54
4361 1.9e-54
4360 2.2e-54
4359 2.4e-54
4358 2.7e-54
4357  3e-54
4356 3.3e-54
4355 3.7e-54
4354 4.1e-54
4353 4.6e-54
4352 5.1e-54
4351 5.7e-54
4350 6.3e-54
4349  7e-54
4348 7.8e-54
4347 8.7e-54
4346 9.7e-54
4345 1.1e-53
4344 1.2e-53
4343 1.3e-53
4342 1.5e-53
4341 1.6e-53
4340 1.8e-53
4339  2e-53
4338 2.3e-53
4337 2.5e-53
4336 2.8e-53
4335 3.1e-53
4334 3.4e-53
4333 3.8e-53
4332 4.2e-53
4331 4.7e-53
4330 5.2e-53
4329 5.8e-53
4328 6.4e-53
4327 7.1e-53
4326 7.9e-53
4325 8.7e-53
4324 9.7e-53
4323 1.1e-52
4322 1.2e-52
4321 1.3e-52
4320 1.5e-52
4319 1.6e-52
4318 1.8e-52
4317  2e-52
4316 2.2e-52
4315 2.4e-52
4314 2.7e-52
4313  3e-52
4312 3.3e-52
4311 3.7e-52
4310 4.1e-52
4309 4.5e-52
4308  5e-52
4307 5.5e-52
4306 6.1e-52
4305 6.7e-52
4304 7.4e-52
4303 8.2e-52
4302 9.1e-52
4301  1e-51
4300 1.1e-51
4299 1.2e-51
4298 1.4e-51
4297 1.5e-51
4296 1.7e-51
4295 1.8e-51
4294  2e-51
4293 2.2e-51
4292 2.5e-51
4291 2.7e-51
4290  3e-51
4289 3.3e-51
4288 3.7e-51
4287 4.1e-51
4286 4.5e-51
4285  5e-51
4284 5.5e-51
4283  6e-51
4282 6.7e-51
4281 7.4e-51
4280 8.1e-51
4279  9e-51
4278 9.9e-51
4277 1.1e-50
4276 1.2e-50
4275 1.3e-50
4274 1.5e-50
4273 1.6e-50
4272 1.8e-50
4271  2e-50
4270 2.2e-50
4269 2.4e-50
4268 2.6e-50
4267 2.9e-50
4266 3.2e-50
4265 3.5e-50
4264 3.9e-50
4263 4.3e-50
4262 4.7e-50
4261 5.2e-50
4260 5.7e-50
4259 6.3e-50
4258 6.9e-50
4257 7.6e-50
4256 8.4e-50
4255 9.2e-50
4254  1e-49
4253 1.1e-49
4252 1.2e-49
4251 1.3e-49
4250 1.5e-49
4249 1.6e-49
4248 1.8e-49
4247  2e-49
4246 2.2e-49
4245 2.4e-49
4244 2.6e-49
4243 2.9e-49
4242 3.2e-49
4241 3.5e-49
4240 3.8e-49
4239 4.2e-49
4238 4.6e-49
4237 5.1e-49
4236 5.6e-49
4235 6.1e-49
4234 6.8e-49
4233 7.4e-49
4232 8.1e-49
4231 8.9e-49
4230 9.8e-49
4229 1.1e-48
4228 1.2e-48
4227 1.3e-48
4226 1.4e-48
4225 1.6e-48
4224 1.7e-48
4223 1.9e-48
4222 2.1e-48
4221 2.3e-48
4220 2.5e-48
4219 2.7e-48
4218  3e-48
4217 3.3e-48
4216 3.6e-48
4215  4e-48
4214 4.3e-48
4213 4.8e-48
4212 5.2e-48
4211 5.7e-48
4210 6.3e-48
4209 6.9e-48
4208 7.5e-48
4207 8.3e-48
4206 9.1e-48
4205 9.9e-48
4204 1.1e-47
4203 1.2e-47
4202 1.3e-47
4201 1.4e-47
4200 1.6e-47
4199 1.7e-47
4198 1.9e-47
4197 2.1e-47
4196 2.3e-47
4195 2.5e-47
4194 2.7e-47
4193  3e-47
4192 3.2e-47
4191 3.5e-47
4190 3.9e-47
4189 4.2e-47
4188 4.6e-47
4187 5.1e-47
4186 5.6e-47
4185 6.1e-47
4184 6.6e-47
4183 7.3e-47
4182  8e-47
4181 8.7e-47
4180 9.5e-47
4179  1e-46
4178 1.1e-46
4177 1.2e-46
4176 1.4e-46
4175 1.5e-46
4174 1.6e-46
4173 1.8e-46
4172 1.9e-46
4171 2.1e-46
4170 2.3e-46
4169 2.5e-46
4168 2.8e-46
4167  3e-46
4166 3.3e-46
4165 3.6e-46
4164 3.9e-46
4163 4.3e-46
4162 4.7e-46
4161 5.1e-46
4160 5.6e-46
4159 6.1e-46
4158 6.7e-46
4157 7.3e-46
4156  8e-46
4155 8.7e-46
4154 9.5e-46
4153  1e-45
4152 1.1e-45
4151 1.2e-45
4150 1.3e-45
4149 1.5e-45
4148 1.6e-45
4147 1.7e-45
4146 1.9e-45
4145 2.1e-45
4144 2.3e-45
4143 2.5e-45
4142 2.7e-45
4141 2.9e-45
4140 3.2e-45
4139 3.5e-45
4138 3.8e-45
4137 4.2e-45
4136 4.5e-45
4135 4.9e-45
4134 5.4e-45
4133 5.9e-45
4132 6.4e-45
4131  7e-45
4130 7.6e-45
4129 8.3e-45
4128  9e-45
4127 9.8e-45
4126 1.1e-44
4125 1.2e-44
4124 1.3e-44
4123 1.4e-44
4122 1.5e-44
4121 1.6e-44
4120 1.8e-44
4119 1.9e-44
4118 2.1e-44
4117 2.3e-44
4116 2.5e-44
4115 2.7e-44
4114  3e-44
4113 3.2e-44
4112 3.5e-44
4111 3.8e-44
4110 4.2e-44
4109 4.5e-44
4108 4.9e-44
4107 5.4e-44
4106 5.8e-44
4105 6.4e-44
4104 6.9e-44
4103 7.5e-44
4102 8.2e-44
4101 8.9e-44
4100 9.7e-44
4099 1.1e-43
4098 1.1e-43
4097 1.2e-43
4096 1.4e-43
4095 1.5e-43
4094 1.6e-43
4093 1.7e-43
4092 1.9e-43
4091 2.1e-43
4090 2.2e-43
4089 2.4e-43
4088 2.6e-43
4087 2.9e-43
4086 3.1e-43
4085 3.4e-43
4084 3.7e-43
4083  4e-43
4082 4.3e-43
4081 4.7e-43
4080 5.1e-43
4079 5.5e-43
4078  6e-43
4077 6.5e-43
4076 7.1e-43
4075 7.7e-43
4074 8.4e-43
4073 9.1e-43
4072 9.9e-43
4071 1.1e-42
4070 1.2e-42
4069 1.3e-42
4068 1.4e-42
4067 1.5e-42
4066 1.6e-42
4065 1.7e-42
4064 1.9e-42
4063 2.1e-42
4062 2.2e-42
4061 2.4e-42
4060 2.6e-42
4059 2.9e-42
4058 3.1e-42
4057 3.4e-42
4056 3.6e-42
4055 3.9e-42
4054 4.3e-42
4053 4.6e-42
4052  5e-42
4051 5.5e-42
4050 5.9e-42
4049 6.4e-42
4048  7e-42
4047 7.5e-42
4046 8.2e-42
4045 8.9e-42
4044 9.6e-42
4043  1e-41
4042 1.1e-41
4041 1.2e-41
4040 1.3e-41
4039 1.4e-41
4038 1.6e-41
4037 1.7e-41
4036 1.8e-41
4035  2e-41
4034 2.1e-41
4033 2.3e-41
4032 2.5e-41
4031 2.7e-41
4030 2.9e-41
4029 3.2e-41
4028 3.4e-41
4027 3.7e-41
4026  4e-41
4025 4.4e-41
4024 4.7e-41
4023 5.1e-41
4022 5.5e-41
4021  6e-41
4020 6.5e-41
4019  7e-41
4018 7.6e-41
4017 8.2e-41
4016 8.9e-41
4015 9.6e-41
4014  1e-40
4013 1.1e-40
4012 1.2e-40
4011 1.3e-40
4010 1.4e-40
4009 1.5e-40
4008 1.7e-40
4007 1.8e-40
4006  2e-40
4005 2.1e-40
4004 2.3e-40
4003 2.5e-40
4002 2.7e-40
4001 2.9e-40
4000 3.1e-40
3999 3.4e-40
3998 3.7e-40
3997 3.9e-40
3996 4.3e-40
3995 4.6e-40
3994  5e-40
3993 5.4e-40
3992 5.8e-40
3991 6.3e-40
3990 6.8e-40
3989 7.3e-40
3988 7.9e-40
3987 8.6e-40
3986 9.3e-40
3985  1e-39
3984 1.1e-39
3983 1.2e-39
3982 1.3e-39
3981 1.4e-39
3980 1.5e-39
3979 1.6e-39
3978 1.7e-39
3977 1.9e-39
3976  2e-39
3975 2.2e-39
3974 2.3e-39
3973 2.5e-39
3972 2.7e-39
3971 2.9e-39
3970 3.2e-39
3969 3.4e-39
3968 3.7e-39
3967  4e-39
3966 4.3e-39
3965 4.6e-39
3964  5e-39
3963 5.4e-39
3962 5.8e-39
3961 6.3e-39
3960 6.8e-39
3959 7.3e-39
3958 7.9e-39
3957 8.5e-39
3956 9.2e-39
3955 9.9e-39
3954 1.1e-38
3953 1.2e-38
3952 1.2e-38
3951 1.3e-38
3950 1.4e-38
3949 1.6e-38
3948 1.7e-38
3947 1.8e-38
3946 1.9e-38
3945 2.1e-38
3944 2.3e-38
3943 2.4e-38
3942 2.6e-38
3941 2.8e-38
3940 3.1e-38
3939 3.3e-38
3938 3.6e-38
3937 3.8e-38
3936 4.1e-38
3935 4.4e-38
3934 4.8e-38
3933 5.2e-38
3932 5.6e-38
3931  6e-38
3930 6.5e-38
3929  7e-38
3928 7.5e-38
3927 8.1e-38
3926 8.7e-38
3925 9.4e-38
3924  1e-37
3923 1.1e-37
3922 1.2e-37
3921 1.3e-37
3920 1.4e-37
3919 1.5e-37
3918 1.6e-37
3917 1.7e-37
3916 1.8e-37
3915  2e-37
3914 2.1e-37
3913 2.3e-37
3912 2.4e-37
3911 2.6e-37
3910 2.8e-37
3909  3e-37
3908 3.3e-37
3907 3.5e-37
3906 3.8e-37
3905 4.1e-37
3904 4.4e-37
3903 4.7e-37
3902 5.1e-37
3901 5.5e-37
3900 5.9e-37
3899 6.3e-37
3898 6.8e-37
3897 7.3e-37
3896 7.9e-37
3895 8.5e-37
3894 9.1e-37
3893 9.8e-37
3892 1.1e-36
3891 1.1e-36
3890 1.2e-36
3889 1.3e-36
3888 1.4e-36
3887 1.5e-36
3886 1.6e-36
3885 1.8e-36
3884 1.9e-36
3883  2e-36
3882 2.2e-36
3881 2.3e-36
3880 2.5e-36
3879 2.7e-36
3878 2.9e-36
3877 3.1e-36
3876 3.3e-36
3875 3.6e-36
3874 3.9e-36
3873 4.2e-36
3872 4.5e-36
3871 4.8e-36
3870 5.2e-36
3869 5.5e-36
3868 5.9e-36
3867 6.4e-36
3866 6.9e-36
3865 7.4e-36
3864 7.9e-36
3863 8.5e-36
3862 9.1e-36
3861 9.8e-36
3860 1.1e-35
3859 1.1e-35
3858 1.2e-35
3857 1.3e-35
3856 1.4e-35
3855 1.5e-35
3854 1.6e-35
3853 1.7e-35
3852 1.9e-35
3851  2e-35
3850 2.1e-35
3849 2.3e-35
3848 2.5e-35
3847 2.6e-35
3846 2.8e-35
3845  3e-35
3844 3.3e-35
3843 3.5e-35
3842 3.8e-35
3841  4e-35
3840 4.3e-35
3839 4.6e-35
3838  5e-35
3837 5.3e-35
3836 5.7e-35
3835 6.2e-35
3834 6.6e-35
3833 7.1e-35
3832 7.6e-35
3831 8.1e-35
3830 8.7e-35
3829 9.4e-35
3828  1e-34
3827 1.1e-34
3826 1.2e-34
3825 1.2e-34
3824 1.3e-34
3823 1.4e-34
3822 1.5e-34
3821 1.6e-34
3820 1.8e-34
3819 1.9e-34
3818  2e-34
3817 2.2e-34
3816 2.3e-34
3815 2.5e-34
3814 2.7e-34
3813 2.8e-34
3812 3.1e-34
3811 3.3e-34
3810 3.5e-34
3809 3.8e-34
3808  4e-34
3807 4.3e-34
3806 4.6e-34
3805 4.9e-34
3804 5.3e-34
3803 5.7e-34
3802 6.1e-34
3801 6.5e-34
3800  7e-34
3799 7.5e-34
3798  8e-34
3797 8.6e-34
3796 9.2e-34
3795 9.8e-34
3794 1.1e-33
3793 1.1e-33
3792 1.2e-33
3791 1.3e-33
3790 1.4e-33
3789 1.5e-33
3788 1.6e-33
3787 1.7e-33
3786 1.8e-33
3785 1.9e-33
3784 2.1e-33
3783 2.2e-33
3782 2.4e-33
3781 2.6e-33
3780 2.7e-33
3779 2.9e-33
3778 3.1e-33
3777 3.3e-33
3776 3.6e-33
3775 3.8e-33
3774 4.1e-33
3773 4.4e-33
3772 4.7e-33
3771  5e-33
3770 5.4e-33
3769 5.8e-33
3768 6.2e-33
3767 6.6e-33
3766  7e-33
3765 7.5e-33
3764 8.1e-33
3763 8.6e-33
3762 9.2e-33
3761 9.9e-33
3760 1.1e-32
3759 1.1e-32
3758 1.2e-32
3757 1.3e-32
3756 1.4e-32
3755 1.5e-32
3754 1.6e-32
3753 1.7e-32
3752 1.8e-32
3751 1.9e-32
3750 2.1e-32
3749 2.2e-32
3748 2.3e-32
3747 2.5e-32
3746 2.7e-32
3745 2.9e-32
3744 3.1e-32
3743 3.3e-32
3742 3.5e-32
3741 3.7e-32
3740  4e-32
3739 4.3e-32
3738 4.6e-32
3737 4.9e-32
3736 5.2e-32
3735 5.6e-32
3734 5.9e-32
3733 6.4e-32
3732 6.8e-32
3731 7.2e-32
3730 7.7e-32
3729 8.3e-32
3728 8.8e-32
3727 9.4e-32
3726  1e-31
3725 1.1e-31
3724 1.1e-31
3723 1.2e-31
3722 1.3e-31
3721 1.4e-31
3720 1.5e-31
3719 1.6e-31
3718 1.7e-31
3717 1.8e-31
3716 1.9e-31
3715 2.1e-31
3714 2.2e-31
3713 2.4e-31
3712 2.5e-31
3711 2.7e-31
3710 2.9e-31
3709 3.1e-31
3708 3.3e-31
3707 3.5e-31
3706 3.7e-31
3705  4e-31
3704 4.2e-31
3703 4.5e-31
3702 4.8e-31
3701 5.2e-31
3700 5.5e-31
3699 5.9e-31
3698 6.3e-31
3697 6.7e-31
3696 7.1e-31
3695 7.6e-31
3694 8.1e-31
3693 8.6e-31
3692 9.2e-31
3691 9.8e-31
3690  1e-30
3689 1.1e-30
3688 1.2e-30
3687 1.3e-30
3686 1.4e-30
3685 1.4e-30
3684 1.5e-30
3683 1.6e-30
3682 1.8e-30
3681 1.9e-30
3680  2e-30
3679 2.1e-30
3678 2.3e-30
3677 2.4e-30
3676 2.6e-30
3675 2.7e-30
3674 2.9e-30
3673 3.1e-30
3672 3.3e-30
3671 3.5e-30
3670 3.8e-30
3669  4e-30
3668 4.3e-30
3667 4.6e-30
3666 4.9e-30
3665 5.2e-30
3664 5.5e-30
3663 5.9e-30
3662 6.3e-30
3661 6.7e-30
3660 7.1e-30
3659 7.6e-30
3658 8.1e-30
3657 8.6e-30
3656 9.2e-30
3655 9.8e-30
3654  1e-29
3653 1.1e-29
3652 1.2e-29
3651 1.3e-29
3650 1.3e-29
3649 1.4e-29
3648 1.5e-29
3647 1.6e-29
3646 1.7e-29
3645 1.8e-29
3644  2e-29
3643 2.1e-29
3642 2.2e-29
3641 2.4e-29
3640 2.5e-29
3639 2.7e-29
3638 2.8e-29
3637  3e-29
3636 3.2e-29
3635 3.4e-29
3634 3.7e-29
3633 3.9e-29
3632 4.1e-29
3631 4.4e-29
3630 4.7e-29
3629  5e-29
3628 5.3e-29
3627 5.7e-29
3626  6e-29
3625 6.4e-29
3624 6.8e-29
3623 7.2e-29
3622 7.7e-29
3621 8.2e-29
3620 8.7e-29
3619 9.3e-29
3618 9.9e-29
3617 1.1e-28
3616 1.1e-28
3615 1.2e-28
3614 1.3e-28
3613 1.3e-28
3612 1.4e-28
3611 1.5e-28
3610 1.6e-28
3609 1.7e-28
3608 1.8e-28
3607 1.9e-28
3606 2.1e-28
3605 2.2e-28
3604 2.3e-28
3603 2.5e-28
3602 2.6e-28
3601 2.8e-28
3600  3e-28
3599 3.2e-28
3598 3.4e-28
3597 3.6e-28
3596 3.8e-28
3595 4.1e-28
3594 4.3e-28
3593 4.6e-28
3592 4.9e-28
3591 5.2e-28
3590 5.5e-28
3589 5.9e-28
3588 6.2e-28
3587 6.6e-28
3586  7e-28
3585 7.5e-28
3584 7.9e-28
3583 8.4e-28
3582  9e-28
3581 9.5e-28
3580  1e-27
3579 1.1e-27
3578 1.1e-27
3577 1.2e-27
3576 1.3e-27
3575 1.4e-27
3574 1.5e-27
3573 1.5e-27
3572 1.6e-27
3571 1.7e-27
3570 1.9e-27
3569  2e-27
3568 2.1e-27
3567 2.2e-27
3566 2.4e-27
3565 2.5e-27
3564 2.7e-27
3563 2.8e-27
3562  3e-27
3561 3.2e-27
3560 3.4e-27
3559 3.6e-27
3558 3.8e-27
3557  4e-27
3556 4.3e-27
3555 4.6e-27
3554 4.8e-27
3553 5.1e-27
3552 5.4e-27
3551 5.8e-27
3550 6.1e-27
3549 6.5e-27
3548 6.9e-27
3547 7.3e-27
3546 7.8e-27
3545 8.3e-27
3544 8.8e-27
3543 9.3e-27
3542 9.9e-27
3541  1e-26
3540 1.1e-26
3539 1.2e-26
3538 1.3e-26
3537 1.3e-26
3536 1.4e-26
3535 1.5e-26
3534 1.6e-26
3533 1.7e-26
3532 1.8e-26
3531 1.9e-26
3530  2e-26
3529 2.1e-26
3528 2.3e-26
3527 2.4e-26
3526 2.5e-26
3525 2.7e-26
3524 2.9e-26
3523  3e-26
3522 3.2e-26
3521 3.4e-26
3520 3.6e-26
3519 3.8e-26
3518 4.1e-26
3517 4.3e-26
3516 4.6e-26
3515 4.8e-26
3514 5.1e-26
3513 5.4e-26
3512 5.8e-26
3511 6.1e-26
3510 6.5e-26
3509 6.9e-26
3508 7.3e-26
3507 7.7e-26
3506 8.2e-26
3505 8.7e-26
3504 9.2e-26
3503 9.7e-26
3502  1e-25
3501 1.1e-25
3500 1.2e-25
3499 1.2e-25
3498 1.3e-25
3497 1.4e-25
3496 1.5e-25
3495 1.5e-25
3494 1.6e-25
3493 1.7e-25
3492 1.8e-25
3491  2e-25
3490 2.1e-25
3489 2.2e-25
3488 2.3e-25
3487 2.5e-25
3486 2.6e-25
3485 2.8e-25
3484 2.9e-25
3483 3.1e-25
3482 3.3e-25
3481 3.5e-25
3480 3.7e-25
3479 3.9e-25
3478 4.1e-25
3477 4.4e-25
3476 4.6e-25
3475 4.9e-25
3474 5.2e-25
3473 5.5e-25
3472 5.8e-25
3471 6.1e-25
3470 6.5e-25
3469 6.9e-25
3468 7.3e-25
3467 7.7e-25
3466 8.2e-25
3465 8.7e-25
3464 9.2e-25
3463 9.7e-25
3462  1e-24
3461 1.1e-24
3460 1.1e-24
3459 1.2e-24
3458 1.3e-24
3457 1.4e-24
3456 1.4e-24
3455 1.5e-24
3454 1.6e-24
3453 1.7e-24
3452 1.8e-24
3451 1.9e-24
3450  2e-24
3449 2.1e-24
3448 2.3e-24
3447 2.4e-24
3446 2.5e-24
3445 2.7e-24
3444 2.8e-24
3443  3e-24
3442 3.2e-24
3441 3.4e-24
3440 3.6e-24
3439 3.8e-24
3438  4e-24
3437 4.2e-24
3436 4.4e-24
3435 4.7e-24
3434  5e-24
3433 5.3e-24
3432 5.6e-24
3431 5.9e-24
3430 6.2e-24
3429 6.6e-24
3428  7e-24
3427 7.4e-24
3426 7.8e-24
3425 8.2e-24
3424 8.7e-24
3423 9.2e-24
3422 9.7e-24
3421  1e-23
3420 1.1e-23
3419 1.1e-23
3418 1.2e-23
3417 1.3e-23
3416 1.4e-23
3415 1.4e-23
3414 1.5e-23
3413 1.6e-23
3412 1.7e-23
3411 1.8e-23
3410 1.9e-23
3409  2e-23
3408 2.1e-23
3407 2.2e-23
3406 2.4e-23
3405 2.5e-23
3404 2.6e-23
3403 2.8e-23
3402 2.9e-23
3401 3.1e-23
3400 3.3e-23
3399 3.5e-23
3398 3.7e-23
3397 3.9e-23
3396 4.1e-23
3395 4.3e-23
3394 4.5e-23
3393 4.8e-23
3392 5.1e-23
3391 5.4e-23
3390 5.7e-23
3389  6e-23
3388 6.3e-23
3387 6.7e-23
3386  7e-23
3385 7.4e-23
3384 7.8e-23
3383 8.3e-23
3382 8.7e-23
3381 9.2e-23
3380 9.8e-23
3379  1e-22
3378 1.1e-22
3377 1.1e-22
3376 1.2e-22
3375 1.3e-22
3374 1.4e-22
3373 1.4e-22
3372 1.5e-22
3371 1.6e-22
3370 1.7e-22
3369 1.8e-22
3368 1.9e-22
3367  2e-22
3366 2.1e-22
3365 2.2e-22
3364 2.3e-22
3363 2.4e-22
3362 2.6e-22
3361 2.7e-22
3360 2.9e-22
3359  3e-22
3358 3.2e-22
3357 3.4e-22
3356 3.6e-22
3355 3.8e-22
3354  4e-22
3353 4.2e-22
3352 4.4e-22
3351 4.7e-22
3350 4.9e-22
3349 5.2e-22
3348 5.5e-22
3347 5.8e-22
3346 6.1e-22
3345 6.4e-22
3344 6.8e-22
3343 7.1e-22
3342 7.5e-22
3341 7.9e-22
3340 8.4e-22
3339 8.8e-22
3338 9.3e-22
3337 9.8e-22
3336  1e-21
3335 1.1e-21
3334 1.1e-21
3333 1.2e-21
3332 1.3e-21
3331 1.3e-21
3330 1.4e-21
3329 1.5e-21
3328 1.6e-21
3327 1.7e-21
3326 1.8e-21
3325 1.8e-21
3324 1.9e-21
3323 2.1e-21
3322 2.2e-21
3321 2.3e-21
3320 2.4e-21
3319 2.5e-21
3318 2.7e-21
3317 2.8e-21
3316  3e-21
3315 3.1e-21
3314 3.3e-21
3313 3.5e-21
3312 3.7e-21
3311 3.9e-21
3310 4.1e-21
3309 4.3e-21
3308 4.5e-21
3307 4.8e-21
3306  5e-21
3305 5.3e-21
3304 5.6e-21
3303 5.9e-21
3302 6.2e-21
3301 6.5e-21
3300 6.8e-21
3299 7.2e-21
3298 7.6e-21
3297  8e-21
3296 8.4e-21
3295 8.9e-21
3294 9.3e-21
3293 9.8e-21
3292  1e-20
3291 1.1e-20
3290 1.1e-20
3289 1.2e-20
3288 1.3e-20
3287 1.3e-20
3286 1.4e-20
3285 1.5e-20
3284 1.6e-20
3283 1.6e-20
3282 1.7e-20
3281 1.8e-20
3280 1.9e-20
3279  2e-20
3278 2.1e-20
3277 2.2e-20
3276 2.4e-20
3275 2.5e-20
3274 2.6e-20
3273 2.8e-20
3272 2.9e-20
3271 3.1e-20
3270 3.2e-20
3269 3.4e-20
3268 3.6e-20
3267 3.7e-20
3266 3.9e-20
3265 4.1e-20
3264 4.4e-20
3263 4.6e-20
3262 4.8e-20
3261 5.1e-20
3260 5.3e-20
3259 5.6e-20
3258 5.9e-20
3257 6.2e-20
3256 6.6e-20
3255 6.9e-20
3254 7.3e-20
3253 7.6e-20
3252  8e-20
3251 8.4e-20
3250 8.9e-20
3249 9.3e-20
3248 9.8e-20
3247  1e-19
3246 1.1e-19
3245 1.1e-19
3244 1.2e-19
3243 1.3e-19
3242 1.3e-19
3241 1.4e-19
3240 1.5e-19
3239 1.5e-19
3238 1.6e-19
3237 1.7e-19
3236 1.8e-19
3235 1.9e-19
3234  2e-19
3233 2.1e-19
3232 2.2e-19
3231 2.3e-19
3230 2.4e-19
3229 2.6e-19
3228 2.7e-19
3227 2.8e-19
3226  3e-19
3225 3.1e-19
3224 3.3e-19
3223 3.4e-19
3222 3.6e-19
3221 3.8e-19
3220  4e-19
3219 4.2e-19
3218 4.4e-19
3217 4.6e-19
3216 4.9e-19
3215 5.1e-19
3214 5.4e-19
3213 5.7e-19
3212 5.9e-19
3211 6.2e-19
3210 6.6e-19
3209 6.9e-19
3208 7.2e-19
3207 7.6e-19
3206  8e-19
3205 8.4e-19
3204 8.8e-19
3203 9.3e-19
3202 9.7e-19
3201  1e-18
3200 1.1e-18
3199 1.1e-18
3198 1.2e-18
3197 1.2e-18
3196 1.3e-18
3195 1.4e-18
3194 1.4e-18
3193 1.5e-18
3192 1.6e-18
3191 1.7e-18
3190 1.8e-18
3189 1.8e-18
3188 1.9e-18
3187  2e-18
3186 2.1e-18
3185 2.2e-18
3184 2.3e-18
3183 2.5e-18
3182 2.6e-18
3181 2.7e-18
3180 2.9e-18
3179  3e-18
3178 3.1e-18
3177 3.3e-18
3176 3.5e-18
3175 3.6e-18
3174 3.8e-18
3173  4e-18
3172 4.2e-18
3171 4.4e-18
3170 4.6e-18
3169 4.9e-18
3168 5.1e-18
3167 5.4e-18
3166 5.6e-18
3165 5.9e-18
3164 6.2e-18
3163 6.5e-18
3162 6.8e-18
3161 7.2e-18
3160 7.5e-18
3159 7.9e-18
3158 8.3e-18
3157 8.7e-18
3156 9.1e-18
3155 9.5e-18
3154  1e-17
3153  1e-17
3152 1.1e-17
3151 1.2e-17
3150 1.2e-17
3149 1.3e-17
3148 1.3e-17
3147 1.4e-17
3146 1.5e-17
3145 1.5e-17
3144 1.6e-17
3143 1.7e-17
3142 1.8e-17
3141 1.9e-17
3140  2e-17
3139  2e-17
3138 2.1e-17
3137 2.2e-17
3136 2.4e-17
3135 2.5e-17
3134 2.6e-17
3133 2.7e-17
3132 2.9e-17
3131  3e-17
3130 3.1e-17
3129 3.3e-17
3128 3.4e-17
3127 3.6e-17
3126 3.8e-17
3125  4e-17
3124 4.2e-17
3123 4.4e-17
3122 4.6e-17
3121 4.8e-17
3120  5e-17
3119 5.3e-17
3118 5.5e-17
3117 5.8e-17
3116 6.1e-17
3115 6.3e-17
3114 6.6e-17
3113  7e-17
3112 7.3e-17
3111 7.6e-17
3110  8e-17
3109 8.4e-17
3108 8.8e-17
3107 9.2e-17
3106 9.7e-17
3105  1e-16
3104 1.1e-16
3103 1.1e-16
3102 1.2e-16
3101 1.2e-16
3100 1.3e-16
3099 1.3e-16
3098 1.4e-16
3097 1.5e-16
3096 1.5e-16
3095 1.6e-16
3094 1.7e-16
3093 1.8e-16
3092 1.8e-16
3091 1.9e-16
3090  2e-16
3089 2.1e-16
3088 2.2e-16
3087 2.3e-16
3086 2.4e-16
3085 2.6e-16
3084 2.7e-16
3083 2.8e-16
3082 2.9e-16
3081 3.1e-16
3080 3.2e-16
3079 3.4e-16
3078 3.5e-16
3077 3.7e-16
3076 3.9e-16
3075  4e-16
3074 4.2e-16
3073 4.4e-16
3072 4.6e-16
3071 4.8e-16
3070 5.1e-16
3069 5.3e-16
3068 5.6e-16
3067 5.8e-16
3066 6.1e-16
3065 6.4e-16
3064 6.7e-16
3063  7e-16
3062 7.3e-16
3061 7.6e-16
3060  8e-16
3059 8.4e-16
3058 8.8e-16
3057 9.2e-16
3056 9.6e-16
3055  1e-15
3054  1e-15
3053 1.1e-15
3052 1.1e-15
3051 1.2e-15
3050 1.3e-15
3049 1.3e-15
3048 1.4e-15
3047 1.4e-15
3046 1.5e-15
3045 1.6e-15
3044 1.6e-15
3043 1.7e-15
3042 1.8e-15
3041 1.9e-15
3040  2e-15
3039 2.1e-15
3038 2.2e-15
3037 2.3e-15
3036 2.4e-15
3035 2.5e-15
3034 2.6e-15
3033 2.7e-15
3032 2.8e-15
3031 2.9e-15
3030 3.1e-15
3029 3.2e-15
3028 3.4e-15
3027 3.5e-15
3026 3.7e-15
3025 3.8e-15
3024  4e-15
3023 4.2e-15
3022 4.4e-15
3021 4.6e-15
3020 4.8e-15
3019  5e-15
3018 5.2e-15
3017 5.5e-15
3016 5.7e-15
3015  6e-15
3014 6.2e-15
3013 6.5e-15
3012 6.8e-15
3011 7.1e-15
3010 7.5e-15
3009 7.8e-15
3008 8.1e-15
3007 8.5e-15
3006 8.9e-15
3005 9.3e-15
3004 9.7e-15
3003  1e-14
3002 1.1e-14
3001 1.1e-14
3000 1.2e-14
2999 1.2e-14
2998 1.3e-14
2997 1.3e-14
2996 1.4e-14
2995 1.4e-14
2994 1.5e-14
2993 1.6e-14
2992 1.6e-14
2991 1.7e-14
2990 1.8e-14
2989 1.9e-14
2988 1.9e-14
2987  2e-14
2986 2.1e-14
2985 2.2e-14
2984 2.3e-14
2983 2.4e-14
2982 2.5e-14
2981 2.6e-14
2980 2.8e-14
2979 2.9e-14
2978  3e-14
2977 3.1e-14
2976 3.3e-14
2975 3.4e-14
2974 3.6e-14
2973 3.7e-14
2972 3.9e-14
2971 4.1e-14
2970 4.2e-14
2969 4.4e-14
2968 4.6e-14
2967 4.8e-14
2966  5e-14
2965 5.2e-14
2964 5.5e-14
2963 5.7e-14
2962  6e-14
2961 6.2e-14
2960 6.5e-14
2959 6.8e-14
2958 7.1e-14
2957 7.4e-14
2956 7.7e-14
2955  8e-14
2954 8.4e-14
2953 8.8e-14
2952 9.1e-14
2951 9.5e-14
2950 9.9e-14
2949  1e-13
2948 1.1e-13
2947 1.1e-13
2946 1.2e-13
2945 1.2e-13
2944 1.3e-13
2943 1.3e-13
2942 1.4e-13
2941 1.5e-13
2940 1.5e-13
2939 1.6e-13
2938 1.6e-13
2937 1.7e-13
2936 1.8e-13
2935 1.9e-13
2934  2e-13
2933  2e-13
2932 2.1e-13
2931 2.2e-13
2930 2.3e-13
2929 2.4e-13
2928 2.5e-13
2927 2.6e-13
2926 2.7e-13
2925 2.8e-13
2924  3e-13
2923 3.1e-13
2922 3.2e-13
2921 3.4e-13
2920 3.5e-13
2919 3.6e-13
2918 3.8e-13
2917  4e-13
2916 4.1e-13
2915 4.3e-13
2914 4.5e-13
2913 4.7e-13
2912 4.9e-13
2911 5.1e-13
2910 5.3e-13
2909 5.5e-13
2908 5.8e-13
2907  6e-13
2906 6.2e-13
2905 6.5e-13
2904 6.8e-13
2903 7.1e-13
2902 7.4e-13
2901 7.7e-13
2900  8e-13
2899 8.3e-13
2898 8.7e-13
2897  9e-13
2896 9.4e-13
2895 9.8e-13
2894  1e-12
2893 1.1e-12
2892 1.1e-12
2891 1.2e-12
2890 1.2e-12
2889 1.3e-12
2888 1.3e-12
2887 1.4e-12
2886 1.4e-12
2885 1.5e-12
2884 1.5e-12
2883 1.6e-12
2882 1.7e-12
2881 1.7e-12
2880 1.8e-12
2879 1.9e-12
2878  2e-12
2877  2e-12
2876 2.1e-12
2875 2.2e-12
2874 2.3e-12
2873 2.4e-12
2872 2.5e-12
2871 2.6e-12
2870 2.7e-12
2869 2.8e-12
2868 2.9e-12
2867 3.1e-12
2866 3.2e-12
2865 3.3e-12
2864 3.4e-12
2863 3.6e-12
2862 3.7e-12
2861 3.9e-12
2860  4e-12
2859 4.2e-12
2858 4.4e-12
2857 4.6e-12
2856 4.7e-12
2855 4.9e-12
2854 5.1e-12
2853 5.3e-12
2852 5.6e-12
2851 5.8e-12
2850  6e-12
2849 6.3e-12
2848 6.5e-12
2847 6.8e-12
2846  7e-12
2845 7.3e-12
2844 7.6e-12
2843 7.9e-12
2842 8.3e-12
2841 8.6e-12
2840 8.9e-12
2839 9.3e-12
2838 9.7e-12
2837  1e-11
2836  1e-11
2835 1.1e-11
2834 1.1e-11
2833 1.2e-11
2832 1.2e-11
2831 1.3e-11
2830 1.3e-11
2829 1.4e-11
2828 1.4e-11
2827 1.5e-11
2826 1.5e-11
2825 1.6e-11
2824 1.7e-11
2823 1.7e-11
2822 1.8e-11
2821 1.9e-11
2820  2e-11
2819  2e-11
2818 2.1e-11
2817 2.2e-11
2816 2.3e-11
2815 2.4e-11
2814 2.5e-11
2813 2.6e-11
2812 2.7e-11
2811 2.8e-11
2810 2.9e-11
2809  3e-11
2808 3.1e-11
2807 3.2e-11
2806 3.4e-11
2805 3.5e-11
2804 3.6e-11
2803 3.8e-11
2802 3.9e-11
2801 4.1e-11
2800 4.2e-11
2799 4.4e-11
2798 4.6e-11
2797 4.7e-11
2796 4.9e-11
2795 5.1e-11
2794 5.3e-11
2793 5.5e-11
2792 5.7e-11
2791  6e-11
2790 6.2e-11
2789 6.4e-11
2788 6.7e-11
2787 6.9e-11
2786 7.2e-11
2785 7.5e-11
2784 7.8e-11
2783 8.1e-11
2782 8.4e-11
2781 8.7e-11
2780 9.1e-11
2779 9.4e-11
2778 9.8e-11
2777  1e-10
2776 1.1e-10
2775 1.1e-10
2774 1.1e-10
2773 1.2e-10
2772 1.2e-10
2771 1.3e-10
2770 1.3e-10
2769 1.4e-10
2768 1.4e-10
2767 1.5e-10
2766 1.5e-10
2765 1.6e-10
2764 1.7e-10
2763 1.7e-10
2762 1.8e-10
2761 1.8e-10
2760 1.9e-10
2759  2e-10
2758 2.1e-10
2757 2.1e-10
2756 2.2e-10
2755 2.3e-10
2754 2.4e-10
2753 2.5e-10
2752 2.6e-10
2751 2.7e-10
2750 2.8e-10
2749 2.9e-10
2748  3e-10
2747 3.1e-10
2746 3.2e-10
2745 3.3e-10
2744 3.5e-10
2743 3.6e-10
2742 3.7e-10
2741 3.9e-10
2740  4e-10
2739 4.2e-10
2738 4.3e-10
2737 4.5e-10
2736 4.7e-10
2735 4.8e-10
2734  5e-10
2733 5.2e-10
2732 5.4e-10
2731 5.6e-10
2730 5.8e-10
2729  6e-10
2728 6.2e-10
2727 6.5e-10
2726 6.7e-10
2725  7e-10
2724 7.2e-10
2723 7.5e-10
2722 7.8e-10
2721  8e-10
2720 8.3e-10
2719 8.6e-10
2718  9e-10
2717 9.3e-10
2716 9.6e-10
2715  1e-09
2714  1e-09
2713 1.1e-09
2712 1.1e-09
2711 1.2e-09
2710 1.2e-09
2709 1.2e-09
2708 1.3e-09
2707 1.3e-09
2706 1.4e-09
2705 1.4e-09
2704 1.5e-09
2703 1.5e-09
2702 1.6e-09
2701 1.6e-09
2700 1.7e-09
2699 1.8e-09
2698 1.8e-09
2697 1.9e-09
2696  2e-09
2695  2e-09
2694 2.1e-09
2693 2.2e-09
2692 2.3e-09
2691 2.4e-09
2690 2.4e-09
2689 2.5e-09
2688 2.6e-09
2687 2.7e-09
2686 2.8e-09
2685 2.9e-09
2684  3e-09
2683 3.1e-09
2682 3.2e-09
2681 3.3e-09
2680 3.5e-09
2679 3.6e-09
2678 3.7e-09
2677 3.8e-09
2676  4e-09
2675 4.1e-09
2674 4.3e-09
2673 4.4e-09
2672 4.6e-09
2671 4.7e-09
2670 4.9e-09
2669 5.1e-09
2668 5.3e-09
2667 5.5e-09
2666 5.6e-09
2665 5.8e-09
2664 6.1e-09
2663 6.3e-09
2662 6.5e-09
2661 6.7e-09
2660  7e-09
2659 7.2e-09
2658 7.4e-09
2657 7.7e-09
2656  8e-09
2655 8.3e-09
2654 8.5e-09
2653 8.8e-09
2652 9.2e-09
2651 9.5e-09
2650 9.8e-09
2649  1e-08
2648  1e-08
2647 1.1e-08
2646 1.1e-08
2645 1.2e-08
2644 1.2e-08
2643 1.2e-08
2642 1.3e-08
2641 1.3e-08
2640 1.4e-08
2639 1.4e-08
2638 1.5e-08
2637 1.5e-08
2636 1.6e-08
2635 1.6e-08
2634 1.7e-08
2633 1.7e-08
2632 1.8e-08
2631 1.9e-08
2630 1.9e-08
2629  2e-08
2628 2.1e-08
2627 2.1e-08
2626 2.2e-08
2625 2.3e-08
2624 2.4e-08
2623 2.4e-08
2622 2.5e-08
2621 2.6e-08
2620 2.7e-08
2619 2.8e-08
2618 2.9e-08
2617  3e-08
2616 3.1e-08
2615 3.2e-08
2614 3.3e-08
2613 3.4e-08
2612 3.5e-08
2611 3.6e-08
2610 3.8e-08
2609 3.9e-08
2608  4e-08
2607 4.2e-08
2606 4.3e-08
2605 4.5e-08
2604 4.6e-08
2603 4.8e-08
2602 4.9e-08
2601 5.1e-08
2600 5.2e-08
2599 5.4e-08
2598 5.6e-08
2597 5.8e-08
2596  6e-08
2595 6.2e-08
2594 6.4e-08
2593 6.6e-08
2592 6.8e-08
2591  7e-08
2590 7.3e-08
2589 7.5e-08
2588 7.8e-08
2587  8e-08
2586 8.3e-08
2585 8.6e-08
2584 8.8e-08
2583 9.1e-08
2582 9.4e-08
2581 9.7e-08
2580  1e-07
2579  1e-07
2578 1.1e-07
2577 1.1e-07
2576 1.1e-07
2575 1.2e-07
2574 1.2e-07
2573 1.3e-07
2572 1.3e-07
2571 1.3e-07
2570 1.4e-07
2569 1.4e-07
2568 1.5e-07
2567 1.5e-07
2566 1.6e-07
2565 1.6e-07
2564 1.7e-07
2563 1.7e-07
2562 1.8e-07
2561 1.8e-07
2560 1.9e-07
2559  2e-07
2558  2e-07
2557 2.1e-07
2556 2.2e-07
2555 2.2e-07
2554 2.3e-07
2553 2.4e-07
2552 2.5e-07
2551 2.5e-07
2550 2.6e-07
2549 2.7e-07
2548 2.8e-07
2547 2.9e-07
2546  3e-07
2545 3.1e-07
2544 3.2e-07
2543 3.3e-07
2542 3.4e-07
2541 3.5e-07
2540 3.6e-07
2539 3.7e-07
2538 3.8e-07
2537 3.9e-07
2536 4.1e-07
2535 4.2e-07
2534 4.3e-07
2533 4.4e-07
2532 4.6e-07
2531 4.7e-07
2530 4.9e-07
2529  5e-07
2528 5.2e-07
2527 5.4e-07
2526 5.5e-07
2525 5.7e-07
2524 5.9e-07
2523 6.1e-07
2522 6.2e-07
2521 6.4e-07
2520 6.6e-07
2519 6.8e-07
2518 7.1e-07
2517 7.3e-07
2516 7.5e-07
2515 7.7e-07
2514  8e-07
2513 8.2e-07
2512 8.5e-07
2511 8.7e-07
2510  9e-07
2509 9.3e-07
2508 9.6e-07
2507 9.8e-07
2506  1e-06
2505  1e-06
2504 1.1e-06
2503 1.1e-06
2502 1.1e-06
2501 1.2e-06
2500 1.2e-06
2499 1.3e-06
2498 1.3e-06
2497 1.3e-06
2496 1.4e-06
2495 1.4e-06
2494 1.5e-06
2493 1.5e-06
2492 1.5e-06
2491 1.6e-06
2490 1.6e-06
2489 1.7e-06
2488 1.7e-06
2487 1.8e-06
2486 1.8e-06
2485 1.9e-06
2484  2e-06
2483  2e-06
2482 2.1e-06
2481 2.1e-06
2480 2.2e-06
2479 2.3e-06
2478 2.3e-06
2477 2.4e-06
2476 2.5e-06
2475 2.6e-06
2474 2.6e-06
2473 2.7e-06
2472 2.8e-06
2471 2.9e-06
2470  3e-06
2469  3e-06
2468 3.1e-06
2467 3.2e-06
2466 3.3e-06
2465 3.4e-06
2464 3.5e-06
2463 3.6e-06
2462 3.7e-06
2461 3.8e-06
2460 3.9e-06
2459 4.1e-06
2458 4.2e-06
2457 4.3e-06
2456 4.4e-06
2455 4.6e-06
2454 4.7e-06
2453 4.8e-06
2452  5e-06
2451 5.1e-06
2450 5.3e-06
2449 5.4e-06
2448 5.6e-06
2447 5.7e-06
2446 5.9e-06
2445 6.1e-06
2444 6.2e-06
2443 6.4e-06
2442 6.6e-06
2441 6.8e-06
2440  7e-06
2439 7.2e-06
2438 7.4e-06
2437 7.6e-06
2436 7.8e-06
2435  8e-06
2434 8.3e-06
2433 8.5e-06
2432 8.7e-06
2431  9e-06
2430 9.2e-06
2429 9.5e-06
2428 9.8e-06
2427  1e-05
2426  1e-05
2425 1.1e-05
2424 1.1e-05
2423 1.1e-05
2422 1.2e-05
2421 1.2e-05
2420 1.2e-05
2419 1.3e-05
2418 1.3e-05
2417 1.3e-05
2416 1.4e-05
2415 1.4e-05
2414 1.4e-05
2413 1.5e-05
2412 1.5e-05
2411 1.6e-05
2410 1.6e-05
2409 1.6e-05
2408 1.7e-05
2407 1.7e-05
2406 1.8e-05
2405 1.8e-05
2404 1.9e-05
2403 1.9e-05
2402  2e-05
2401  2e-05
2400 2.1e-05
2399 2.2e-05
2398 2.2e-05
2397 2.3e-05
2396 2.3e-05
2395 2.4e-05
2394 2.5e-05
2393 2.5e-05
2392 2.6e-05
2391 2.7e-05
2390 2.8e-05
2389 2.8e-05
2388 2.9e-05
2387  3e-05
2386 3.1e-05
2385 3.1e-05
2384 3.2e-05
2383 3.3e-05
2382 3.4e-05
2381 3.5e-05
2380 3.6e-05
2379 3.7e-05
2378 3.8e-05
2377 3.9e-05
2376  4e-05
2375 4.1e-05
2374 4.2e-05
2373 4.3e-05
2372 4.4e-05
2371 4.6e-05
2370 4.7e-05
2369 4.8e-05
2368 4.9e-05
2367 5.1e-05
2366 5.2e-05
2365 5.3e-05
2364 5.5e-05
2363 5.6e-05
2362 5.8e-05
2361 5.9e-05
2360 6.1e-05
2359 6.2e-05
2358 6.4e-05
2357 6.5e-05
2356 6.7e-05
2355 6.9e-05
2354 7.1e-05
2353 7.3e-05
2352 7.4e-05
2351 7.6e-05
2350 7.8e-05
2349  8e-05
2348 8.2e-05
2347 8.4e-05
2346 8.7e-05
2345 8.9e-05
2344 9.1e-05
2343 9.4e-05
2342 9.6e-05
2341 9.8e-05
2340 0.0001
2339 0.0001
2338 0.00011
2337 0.00011
2336 0.00011
2335 0.00011
2334 0.00012
2333 0.00012
2332 0.00012
2331 0.00013
2330 0.00013
2329 0.00013
2328 0.00014
2327 0.00014
2326 0.00014
2325 0.00015
2324 0.00015
2323 0.00015
2322 0.00016
2321 0.00016
2320 0.00017
2319 0.00017
2318 0.00017
2317 0.00018
2316 0.00018
2315 0.00019
2314 0.00019
2313 0.0002
2312 0.0002
2311 0.00021
2310 0.00021
2309 0.00022
2308 0.00022
2307 0.00023
2306 0.00023
2305 0.00024
2304 0.00024
2303 0.00025
2302 0.00026
2301 0.00026
2300 0.00027
2299 0.00028
2298 0.00028
2297 0.00029
2296 0.0003
2295 0.0003
2294 0.00031
2293 0.00032
2292 0.00033
2291 0.00033
2290 0.00034
2289 0.00035
2288 0.00036
2287 0.00037
2286 0.00038
2285 0.00038
2284 0.00039
2283 0.0004
2282 0.00041
2281 0.00042
2280 0.00043
2279 0.00044
2278 0.00045
2277 0.00046
2276 0.00047
2275 0.00048
2274 0.0005
>clustalxiC
3808 1.1e-66
3807 4.3e-66
3806 8.8e-66
3805 2.5e-65
3804 6.9e-65
3803 1.4e-64
3802 2.7e-64
3801 5.5e-64
3800  1e-63
3799 1.8e-63
3798 3.1e-63
3797 5.3e-63
3796 8.6e-63
3795 1.4e-62
3794 2.2e-62
3793 3.4e-62
3792 5.1e-62
3791 7.7e-62
3790 1.1e-61
3789 1.7e-61
3788 2.5e-61
3787 3.6e-61
3786 5.1e-61
3785 7.2e-61
3784  1e-60
3783 1.4e-60
3782  2e-60
3781 2.8e-60
3780 3.8e-60
3779 5.2e-60
3778 7.1e-60
3777 9.6e-60
3776 1.3e-59
3775 1.7e-59
3774 2.3e-59
3773 3.1e-59
3772 4.1e-59
3771 5.5e-59
3770 7.2e-59
3769 9.4e-59
3768 1.2e-58
3767 1.6e-58
3766 2.1e-58
3765 2.7e-58
3764 3.5e-58
3763 4.5e-58
3762 5.8e-58
3761 7.5e-58
3760 9.6e-58
3759 1.2e-57
3758 1.6e-57
3757  2e-57
3756 2.5e-57
3755 3.2e-57
3754  4e-57
3753  5e-57
3752 6.3e-57
3751 7.9e-57
3750 9.9e-57
3749 1.2e-56
3748 1.5e-56
3747 1.9e-56
3746 2.4e-56
3745  3e-56
3744 3.7e-56
3743 4.5e-56
3742 5.6e-56
3741 6.9e-56
3740 8.5e-56
3739  1e-55
3738 1.3e-55
3737 1.6e-55
3736 1.9e-55
3735 2.3e-55
3734 2.9e-55
3733 3.5e-55
3732 4.2e-55
3731 5.1e-55
3730 6.3e-55
3729 7.6e-55
3728 9.2e-55
3727 1.1e-54
3726 1.3e-54
3725 1.6e-54
3724  2e-54
3723 2.4e-54
3722 2.8e-54
3721 3.4e-54
3720 4.1e-54
3719 4.9e-54
3718 5.9e-54
3717  7e-54
3716 8.4e-54
3715  1e-53
3714 1.2e-53
3713 1.4e-53
3712 1.7e-53
3711  2e-53
3710 2.4e-53
3709 2.9e-53
3708 3.4e-53
3707  4e-53
3706 4.8e-53
3705 5.7e-53
3704 6.7e-53
3703 7.9e-53
3702 9.4e-53
3701 1.1e-52
3700 1.3e-52
3699 1.5e-52
3698 1.8e-52
3697 2.1e-52
3696 2.5e-52
3695  3e-52
3694 3.5e-52
3693 4.1e-52
3692 4.8e-52
3691 5.6e-52
3690 6.6e-52
3689 7.7e-52
3688  9e-52
3687 1.1e-51
3686 1.2e-51
3685 1.4e-51
3684 1.7e-51
3683  2e-51
3682 2.3e-51
3681 2.7e-51
3680 3.1e-51
3679 3.6e-51
3678 4.2e-51
3677 4.9e-51
3676 5.7e-51
3675 6.6e-51
3674 7.7e-51
3673 8.9e-51
3672  1e-50
3671 1.2e-50
3670 1.4e-50
3669 1.6e-50
3668 1.9e-50
3667 2.2e-50
3666 2.5e-50
3665 2.9e-50
3664 3.3e-50
3663 3.9e-50
3662 4.4e-50
3661 5.1e-50
3660 5.9e-50
3659 6.8e-50
3658 7.9e-50
3657 9.1e-50
3656  1e-49
3655 1.2e-49
3654 1.4e-49
3653 1.6e-49
3652 1.8e-49
3651 2.1e-49
3650 2.4e-49
3649 2.8e-49
3648 3.2e-49
3647 3.6e-49
3646 4.2e-49
3645 4.8e-49
3644 5.5e-49
3643 6.3e-49
3642 7.2e-49
3641 8.2e-49
3640 9.4e-49
3639 1.1e-48
3638 1.2e-48
3637 1.4e-48
3636 1.6e-48
3635 1.8e-48
3634 2.1e-48
3633 2.4e-48
3632 2.7e-48
3631 3.1e-48
3630 3.5e-48
3629  4e-48
3628 4.6e-48
3627 5.2e-48
3626 5.9e-48
3625 6.8e-48
3624 7.7e-48
3623 8.8e-48
3622  1e-47
3621 1.1e-47
3620 1.3e-47
3619 1.5e-47
3618 1.7e-47
3617 1.9e-47
3616 2.1e-47
3615 2.4e-47
3614 2.8e-47
3613 3.1e-47
3612 3.5e-47
3611  4e-47
3610 4.5e-47
3609 5.1e-47
3608 5.8e-47
3607 6.6e-47
3606 7.5e-47
3605 8.4e-47
3604 9.5e-47
3603 1.1e-46
3602 1.2e-46
3601 1.4e-46
3600 1.6e-46
3599 1.8e-46
3598  2e-46
3597 2.2e-46
3596 2.5e-46
3595 2.9e-46
3594 3.2e-46
3593 3.6e-46
3592 4.1e-46
3591 4.6e-46
3590 5.2e-46
3589 5.9e-46
3588 6.6e-46
3587 7.4e-46
3586 8.4e-46
3585 9.4e-46
3584 1.1e-45
3583 1.2e-45
3582 1.3e-45
3581 1.5e-45
3580 1.7e-45
3579 1.9e-45
3578 2.1e-45
3577 2.4e-45
3576 2.7e-45
3575  3e-45
3574 3.4e-45
3573 3.8e-45
3572 4.3e-45
3571 4.8e-45
3570 5.4e-45
3569  6e-45
3568 6.8e-45
3567 7.6e-45
3566 8.5e-45
3565 9.5e-45
3564 1.1e-44
3563 1.2e-44
3562 1.3e-44
3561 1.5e-44
3560 1.7e-44
3559 1.9e-44
3558 2.1e-44
3557 2.4e-44
3556 2.6e-44
3555 2.9e-44
3554 3.3e-44
3553 3.7e-44
3552 4.1e-44
3551 4.6e-44
3550 5.1e-44
3549 5.7e-44
3548 6.4e-44
3547 7.1e-44
3546  8e-44
3545 8.9e-44
3544 9.9e-44
3543 1.1e-43
3542 1.2e-43
3541 1.4e-43
3540 1.5e-43
3539 1.7e-43
3538 1.9e-43
3537 2.1e-43
3536 2.4e-43
3535 2.6e-43
3534 2.9e-43
3533 3.3e-43
3532 3.6e-43
3531 4.1e-43
3530 4.5e-43
3529  5e-43
3528 5.6e-43
3527 6.2e-43
3526 6.9e-43
3525 7.7e-43
3524 8.5e-43
3523 9.5e-43
3522 1.1e-42
3521 1.2e-42
3520 1.3e-42
3519 1.4e-42
3518 1.6e-42
3517 1.8e-42
3516  2e-42
3515 2.2e-42
3514 2.4e-42
3513 2.7e-42
3512  3e-42
3511 3.3e-42
3510 3.7e-42
3509 4.1e-42
3508 4.6e-42
3507 5.1e-42
3506 5.6e-42
3505 6.2e-42
3504 6.9e-42
3503 7.6e-42
3502 8.4e-42
3501 9.4e-42
3500  1e-41
3499 1.1e-41
3498 1.3e-41
3497 1.4e-41
3496 1.6e-41
3495 1.7e-41
3494 1.9e-41
3493 2.1e-41
3492 2.3e-41
3491 2.6e-41
3490 2.9e-41
3489 3.2e-41
3488 3.5e-41
3487 3.9e-41
3486 4.3e-41
3485 4.7e-41
3484 5.2e-41
3483 5.8e-41
3482 6.4e-41
3481  7e-41
3480 7.8e-41
3479 8.6e-41
3478 9.5e-41
3477  1e-40
3476 1.2e-40
3475 1.3e-40
3474 1.4e-40
3473 1.6e-40
3472 1.7e-40
3471 1.9e-40
3470 2.1e-40
3469 2.3e-40
3468 2.5e-40
3467 2.8e-40
3466 3.1e-40
3465 3.4e-40
3464 3.7e-40
3463 4.1e-40
3462 4.5e-40
3461  5e-40
3460 5.5e-40
3459 6.1e-40
3458 6.7e-40
3457 7.4e-40
3456 8.1e-40
3455 8.9e-40
3454 9.8e-40
3453 1.1e-39
3452 1.2e-39
3451 1.3e-39
3450 1.4e-39
3449 1.6e-39
3448 1.7e-39
3447 1.9e-39
3446 2.1e-39
3445 2.3e-39
3444 2.5e-39
3443 2.8e-39
3442 3.1e-39
3441 3.4e-39
3440 3.7e-39
3439 4.1e-39
3438 4.5e-39
3437 4.9e-39
3436 5.4e-39
3435 5.9e-39
3434 6.5e-39
3433 7.2e-39
3432 7.9e-39
3431 8.6e-39
3430 9.5e-39
3429  1e-38
3428 1.1e-38
3427 1.3e-38
3426 1.4e-38
3425 1.5e-38
3424 1.7e-38
3423 1.8e-38
3422  2e-38
3421 2.2e-38
3420 2.4e-38
3419 2.6e-38
3418 2.9e-38
3417 3.2e-38
3416 3.5e-38
3415 3.8e-38
3414 4.2e-38
3413 4.5e-38
3412  5e-38
3411 5.5e-38
3410  6e-38
3409 6.5e-38
3408 7.2e-38
3407 7.8e-38
3406 8.6e-38
3405 9.4e-38
3404  1e-37
3403 1.1e-37
3402 1.2e-37
3401 1.3e-37
3400 1.5e-37
3399 1.6e-37
3398 1.8e-37
3397 1.9e-37
3396 2.1e-37
3395 2.3e-37
3394 2.5e-37
3393 2.8e-37
3392  3e-37
3391 3.3e-37
3390 3.6e-37
3389 3.9e-37
3388 4.3e-37
3387 4.7e-37
3386 5.1e-37
3385 5.6e-37
3384 6.1e-37
3383 6.7e-37
3382 7.3e-37
3381  8e-37
3380 8.7e-37
3379 9.5e-37
3378  1e-36
3377 1.1e-36
3376 1.2e-36
3375 1.4e-36
3374 1.5e-36
3373 1.6e-36
3372 1.8e-36
3371 1.9e-36
3370 2.1e-36
3369 2.3e-36
3368 2.5e-36
3367 2.7e-36
3366  3e-36
3365 3.2e-36
3364 3.5e-36
3363 3.8e-36
3362 4.2e-36
3361 4.6e-36
3360  5e-36
3359 5.4e-36
3358 5.9e-36
3357 6.5e-36
3356  7e-36
3355 7.7e-36
3354 8.3e-36
3353 9.1e-36
3352 9.9e-36
3351 1.1e-35
3350 1.2e-35
3349 1.3e-35
3348 1.4e-35
3347 1.5e-35
3346 1.7e-35
3345 1.8e-35
3344  2e-35
3343 2.1e-35
3342 2.3e-35
3341 2.5e-35
3340 2.7e-35
3339  3e-35
3338 3.2e-35
3337 3.5e-35
3336 3.8e-35
3335 4.2e-35
3334 4.5e-35
3333 4.9e-35
3332 5.4e-35
3331 5.8e-35
3330 6.3e-35
3329 6.9e-35
3328 7.5e-35
3327 8.2e-35
3326 8.9e-35
3325 9.6e-35
3324  1e-34
3323 1.1e-34
3322 1.2e-34
3321 1.3e-34
3320 1.5e-34
3319 1.6e-34
3318 1.7e-34
3317 1.9e-34
3316  2e-34
3315 2.2e-34
3314 2.4e-34
3313 2.6e-34
3312 2.8e-34
3311 3.1e-34
3310 3.3e-34
3309 3.6e-34
3308 3.9e-34
3307 4.2e-34
3306 4.6e-34
3305  5e-34
3304 5.4e-34
3303 5.9e-34
3302 6.4e-34
3301 6.9e-34
3300 7.5e-34
3299 8.1e-34
3298 8.8e-34
3297 9.6e-34
3296  1e-33
3295 1.1e-33
3294 1.2e-33
3293 1.3e-33
3292 1.4e-33
3291 1.6e-33
3290 1.7e-33
3289 1.8e-33
3288  2e-33
3287 2.1e-33
3286 2.3e-33
3285 2.5e-33
3284 2.7e-33
3283  3e-33
3282 3.2e-33
3281 3.5e-33
3280 3.8e-33
3279 4.1e-33
3278 4.4e-33
3277 4.8e-33
3276 5.2e-33
3275 5.6e-33
3274  6e-33
3273 6.5e-33
3272 7.1e-33
3271 7.7e-33
3270 8.3e-33
3269  9e-33
3268 9.7e-33
3267 1.1e-32
3266 1.1e-32
3265 1.2e-32
3264 1.3e-32
3263 1.4e-32
3262 1.6e-32
3261 1.7e-32
3260 1.8e-32
3259  2e-32
3258 2.1e-32
3257 2.3e-32
3256 2.5e-32
3255 2.7e-32
3254 2.9e-32
3253 3.1e-32
3252 3.4e-32
3251 3.7e-32
3250  4e-32
3249 4.3e-32
3248 4.6e-32
3247  5e-32
3246 5.4e-32
3245 5.8e-32
3244 6.3e-32
3243 6.8e-32
3242 7.4e-32
3241  8e-32
3240 8.6e-32
3239 9.3e-32
3238  1e-31
3237 1.1e-31
3236 1.2e-31
3235 1.3e-31
3234 1.4e-31
3233 1.5e-31
3232 1.6e-31
3231 1.7e-31
3230 1.8e-31
3229  2e-31
3228 2.2e-31
3227 2.3e-31
3226 2.5e-31
3225 2.7e-31
3224 2.9e-31
3223 3.1e-31
3222 3.4e-31
3221 3.7e-31
3220 3.9e-31
3219 4.3e-31
3218 4.6e-31
3217 4.9e-31
3216 5.3e-31
3215 5.8e-31
3214 6.2e-31
3213 6.7e-31
3212 7.2e-31
3211 7.8e-31
3210 8.4e-31
3209  9e-31
3208 9.7e-31
3207  1e-30
3206 1.1e-30
3205 1.2e-30
3204 1.3e-30
3203 1.4e-30
3202 1.5e-30
3201 1.6e-30
3200 1.8e-30
3199 1.9e-30
3198 2.1e-30
3197 2.2e-30
3196 2.4e-30
3195 2.6e-30
3194 2.8e-30
3193  3e-30
3192 3.2e-30
3191 3.4e-30
3190 3.7e-30
3189  4e-30
3188 4.3e-30
3187 4.6e-30
3186  5e-30
3185 5.4e-30
3184 5.8e-30
3183 6.2e-30
3182 6.7e-30
3181 7.2e-30
3180 7.7e-30
3179 8.3e-30
3178 8.9e-30
3177 9.6e-30
3176  1e-29
3175 1.1e-29
3174 1.2e-29
3173 1.3e-29
3172 1.4e-29
3171 1.5e-29
3170 1.6e-29
3169 1.7e-29
3168 1.9e-29
3167  2e-29
3166 2.1e-29
3165 2.3e-29
3164 2.5e-29
3163 2.7e-29
3162 2.9e-29
3161 3.1e-29
3160 3.3e-29
3159 3.5e-29
3158 3.8e-29
3157 4.1e-29
3156 4.4e-29
3155 4.7e-29
3154 5.1e-29
3153 5.5e-29
3152 5.9e-29
3151 6.3e-29
3150 6.8e-29
3149 7.3e-29
3148 7.8e-29
3147 8.4e-29
3146  9e-29
3145 9.7e-29
3144  1e-28
3143 1.1e-28
3142 1.2e-28
3141 1.3e-28
3140 1.4e-28
3139 1.5e-28
3138 1.6e-28
3137 1.7e-28
3136 1.8e-28
3135  2e-28
3134 2.1e-28
3133 2.3e-28
3132 2.4e-28
3131 2.6e-28
3130 2.8e-28
3129  3e-28
3128 3.2e-28
3127 3.4e-28
3126 3.7e-28
3125  4e-28
3124 4.2e-28
3123 4.6e-28
3122 4.9e-28
3121 5.2e-28
3120 5.6e-28
3119  6e-28
3118 6.5e-28
3117 6.9e-28
3116 7.4e-28
3115  8e-28
3114 8.5e-28
3113 9.1e-28
3112 9.8e-28
3111 1.1e-27
3110 1.1e-27
3109 1.2e-27
3108 1.3e-27
3107 1.4e-27
3106 1.5e-27
3105 1.6e-27
3104 1.7e-27
3103 1.8e-27
3102  2e-27
3101 2.1e-27
3100 2.2e-27
3099 2.4e-27
3098 2.6e-27
3097 2.8e-27
3096  3e-27
3095 3.2e-27
3094 3.4e-27
3093 3.6e-27
3092 3.9e-27
3091 4.2e-27
3090 4.5e-27
3089 4.8e-27
3088 5.1e-27
3087 5.5e-27
3086 5.8e-27
3085 6.3e-27
3084 6.7e-27
3083 7.2e-27
3082 7.7e-27
3081 8.2e-27
3080 8.8e-27
3079 9.4e-27
3078  1e-26
3077 1.1e-26
3076 1.2e-26
3075 1.2e-26
3074 1.3e-26
3073 1.4e-26
3072 1.5e-26
3071 1.6e-26
3070 1.7e-26
3069 1.8e-26
3068  2e-26
3067 2.1e-26
3066 2.3e-26
3065 2.4e-26
3064 2.6e-26
3063 2.8e-26
3062 2.9e-26
3061 3.2e-26
3060 3.4e-26
3059 3.6e-26
3058 3.9e-26
3057 4.1e-26
3056 4.4e-26
3055 4.7e-26
3054  5e-26
3053 5.4e-26
3052 5.7e-26
3051 6.1e-26
3050 6.6e-26
3049  7e-26
3048 7.5e-26
3047  8e-26
3046 8.5e-26
3045 9.1e-26
3044 9.7e-26
3043  1e-25
3042 1.1e-25
3041 1.2e-25
3040 1.3e-25
3039 1.4e-25
3038 1.4e-25
3037 1.5e-25
3036 1.6e-25
3035 1.8e-25
3034 1.9e-25
3033  2e-25
3032 2.1e-25
3031 2.3e-25
3030 2.4e-25
3029 2.6e-25
3028 2.8e-25
3027  3e-25
3026 3.2e-25
3025 3.4e-25
3024 3.6e-25
3023 3.9e-25
3022 4.1e-25
3021 4.4e-25
3020 4.7e-25
3019  5e-25
3018 5.3e-25
3017 5.7e-25
3016 6.1e-25
3015 6.5e-25
3014 6.9e-25
3013 7.4e-25
3012 7.8e-25
3011 8.4e-25
3010 8.9e-25
3009 9.5e-25
3008  1e-24
3007 1.1e-24
3006 1.2e-24
3005 1.2e-24
3004 1.3e-24
3003 1.4e-24
3002 1.5e-24
3001 1.6e-24
3000 1.7e-24
2999 1.8e-24
2998 1.9e-24
2997 2.1e-24
2996 2.2e-24
2995 2.3e-24
2994 2.5e-24
2993 2.6e-24
2992 2.8e-24
2991  3e-24
2990 3.2e-24
2989 3.4e-24
2988 3.6e-24
2987 3.9e-24
2986 4.1e-24
2985 4.4e-24
2984 4.7e-24
2983  5e-24
2982 5.3e-24
2981 5.7e-24
2980  6e-24
2979 6.4e-24
2978 6.8e-24
2977 7.3e-24
2976 7.8e-24
2975 8.3e-24
2974 8.8e-24
2973 9.4e-24
2972  1e-23
2971 1.1e-23
2970 1.1e-23
2969 1.2e-23
2968 1.3e-23
2967 1.4e-23
2966 1.5e-23
2965 1.5e-23
2964 1.6e-23
2963 1.7e-23
2962 1.9e-23
2961  2e-23
2960 2.1e-23
2959 2.2e-23
2958 2.4e-23
2957 2.5e-23
2956 2.7e-23
2955 2.9e-23
2954 3.1e-23
2953 3.3e-23
2952 3.5e-23
2951 3.7e-23
2950 3.9e-23
2949 4.2e-23
2948 4.4e-23
2947 4.7e-23
2946  5e-23
2945 5.3e-23
2944 5.7e-23
2943  6e-23
2942 6.4e-23
2941 6.8e-23
2940 7.2e-23
2939 7.7e-23
2938 8.2e-23
2937 8.7e-23
2936 9.3e-23
2935 9.8e-23
2934  1e-22
2933 1.1e-22
2932 1.2e-22
2931 1.3e-22
2930 1.3e-22
2929 1.4e-22
2928 1.5e-22
2927 1.6e-22
2926 1.7e-22
2925 1.8e-22
2924 1.9e-22
2923  2e-22
2922 2.2e-22
2921 2.3e-22
2920 2.4e-22
2919 2.6e-22
2918 2.8e-22
2917 2.9e-22
2916 3.1e-22
2915 3.3e-22
2914 3.5e-22
2913 3.7e-22
2912  4e-22
2911 4.2e-22
2910 4.5e-22
2909 4.7e-22
2908  5e-22
2907 5.3e-22
2906 5.7e-22
2905  6e-22
2904 6.4e-22
2903 6.8e-22
2902 7.2e-22
2901 7.7e-22
2900 8.1e-22
2899 8.6e-22
2898 9.2e-22
2897 9.7e-22
2896  1e-21
2895 1.1e-21
2894 1.2e-21
2893 1.2e-21
2892 1.3e-21
2891 1.4e-21
2890 1.5e-21
2889 1.6e-21
2888 1.7e-21
2887 1.8e-21
2886 1.9e-21
2885  2e-21
2884 2.1e-21
2883 2.2e-21
2882 2.4e-21
2881 2.5e-21
2880 2.7e-21
2879 2.8e-21
2878  3e-21
2877 3.2e-21
2876 3.4e-21
2875 3.6e-21
2874 3.8e-21
2873  4e-21
2872 4.2e-21
2871 4.5e-21
2870 4.8e-21
2869 5.1e-21
2868 5.4e-21
2867 5.7e-21
2866  6e-21
2865 6.4e-21
2864 6.8e-21
2863 7.2e-21
2862 7.6e-21
2861 8.1e-21
2860 8.5e-21
2859 9.1e-21
2858 9.6e-21
2857  1e-20
2856 1.1e-20
2855 1.1e-20
2854 1.2e-20
2853 1.3e-20
2852 1.4e-20
2851 1.4e-20
2850 1.5e-20
2849 1.6e-20
2848 1.7e-20
2847 1.8e-20
2846 1.9e-20
2845  2e-20
2844 2.2e-20
2843 2.3e-20
2842 2.4e-20
2841 2.6e-20
2840 2.7e-20
2839 2.9e-20
2838  3e-20
2837 3.2e-20
2836 3.4e-20
2835 3.6e-20
2834 3.8e-20
2833  4e-20
2832 4.3e-20
2831 4.5e-20
2830 4.8e-20
2829 5.1e-20
2828 5.4e-20
2827 5.7e-20
2826  6e-20
2825 6.4e-20
2824 6.7e-20
2823 7.1e-20
2822 7.5e-20
2821  8e-20
2820 8.4e-20
2819 8.9e-20
2818 9.4e-20
2817  1e-19
2816 1.1e-19
2815 1.1e-19
2814 1.2e-19
2813 1.3e-19
2812 1.3e-19
2811 1.4e-19
2810 1.5e-19
2809 1.6e-19
2808 1.7e-19
2807 1.8e-19
2806 1.9e-19
2805  2e-19
2804 2.1e-19
2803 2.2e-19
2802 2.3e-19
2801 2.4e-19
2800 2.6e-19
2799 2.7e-19
2798 2.9e-19
2797 3.1e-19
2796 3.2e-19
2795 3.4e-19
2794 3.6e-19
2793 3.8e-19
2792  4e-19
2791 4.3e-19
2790 4.5e-19
2789 4.8e-19
2788  5e-19
2787 5.3e-19
2786 5.6e-19
2785 5.9e-19
2784 6.3e-19
2783 6.6e-19
2782  7e-19
2781 7.4e-19
2780 7.8e-19
2779 8.3e-19
2778 8.7e-19
2777 9.2e-19
2776 9.8e-19
2775  1e-18
2774 1.1e-18
2773 1.1e-18
2772 1.2e-18
2771 1.3e-18
2770 1.4e-18
2769 1.4e-18
2768 1.5e-18
2767 1.6e-18
2766 1.7e-18
2765 1.8e-18
2764 1.9e-18
2763  2e-18
2762 2.1e-18
2761 2.2e-18
2760 2.3e-18
2759 2.5e-18
2758 2.6e-18
2757 2.7e-18
2756 2.9e-18
2755 3.1e-18
2754 3.2e-18
2753 3.4e-18
2752 3.6e-18
2751 3.8e-18
2750  4e-18
2749 4.2e-18
2748 4.5e-18
2747 4.7e-18
2746  5e-18
2745 5.2e-18
2744 5.5e-18
2743 5.8e-18
2742 6.2e-18
2741 6.5e-18
2740 6.9e-18
2739 7.2e-18
2738 7.6e-18
2737  8e-18
2736 8.5e-18
2735  9e-18
2734 9.4e-18
2733  1e-17
2732 1.1e-17
2731 1.1e-17
2730 1.2e-17
2729 1.2e-17
2728 1.3e-17
2727 1.4e-17
2726 1.4e-17
2725 1.5e-17
2724 1.6e-17
2723 1.7e-17
2722 1.8e-17
2721 1.9e-17
2720  2e-17
2719 2.1e-17
2718 2.2e-17
2717 2.3e-17
2716 2.4e-17
2715 2.6e-17
2714 2.7e-17
2713 2.9e-17
2712  3e-17
2711 3.2e-17
2710 3.4e-17
2709 3.5e-17
2708 3.7e-17
2707 3.9e-17
2706 4.1e-17
2705 4.4e-17
2704 4.6e-17
2703 4.8e-17
2702 5.1e-17
2701 5.4e-17
2700 5.7e-17
2699  6e-17
2698 6.3e-17
2697 6.6e-17
2696  7e-17
2695 7.3e-17
2694 7.7e-17
2693 8.1e-17
2692 8.6e-17
2691  9e-17
2690 9.5e-17
2689  1e-16
2688 1.1e-16
2687 1.1e-16
2686 1.2e-16
2685 1.2e-16
2684 1.3e-16
2683 1.4e-16
2682 1.4e-16
2681 1.5e-16
2680 1.6e-16
2679 1.7e-16
2678 1.8e-16
2677 1.9e-16
2676  2e-16
2675 2.1e-16
2674 2.2e-16
2673 2.3e-16
2672 2.4e-16
2671 2.5e-16
2670 2.7e-16
2669 2.8e-16
2668 2.9e-16
2667 3.1e-16
2666 3.3e-16
2665 3.4e-16
2664 3.6e-16
2663 3.8e-16
2662  4e-16
2661 4.2e-16
2660 4.4e-16
2659 4.6e-16
2658 4.9e-16
2657 5.1e-16
2656 5.4e-16
2655 5.7e-16
2654  6e-16
2653 6.3e-16
2652 6.6e-16
2651  7e-16
2650 7.3e-16
2649 7.7e-16
2648 8.1e-16
2647 8.5e-16
2646 8.9e-16
2645 9.4e-16
2644 9.9e-16
2643  1e-15
2642 1.1e-15
2641 1.1e-15
2640 1.2e-15
2639 1.3e-15
2638 1.3e-15
2637 1.4e-15
2636 1.5e-15
2635 1.6e-15
2634 1.6e-15
2633 1.7e-15
2632 1.8e-15
2631 1.9e-15
2630  2e-15
2629 2.1e-15
2628 2.2e-15
2627 2.3e-15
2626 2.4e-15
2625 2.5e-15
2624 2.7e-15
2623 2.8e-15
2622  3e-15
2621 3.1e-15
2620 3.3e-15
2619 3.4e-15
2618 3.6e-15
2617 3.8e-15
2616  4e-15
2615 4.2e-15
2614 4.4e-15
2613 4.6e-15
2612 4.8e-15
2611 5.1e-15
2610 5.3e-15
2609 5.6e-15
2608 5.9e-15
2607 6.2e-15
2606 6.5e-15
2605 6.8e-15
2604 7.1e-15
2603 7.5e-15
2602 7.9e-15
2601 8.3e-15
2600 8.7e-15
2599 9.1e-15
2598 9.6e-15
2597  1e-14
2596 1.1e-14
2595 1.1e-14
2594 1.2e-14
2593 1.2e-14
2592 1.3e-14
2591 1.3e-14
2590 1.4e-14
2589 1.5e-14
2588 1.6e-14
2587 1.6e-14
2586 1.7e-14
2585 1.8e-14
2584 1.9e-14
2583  2e-14
2582 2.1e-14
2581 2.2e-14
2580 2.3e-14
2579 2.4e-14
2578 2.5e-14
2577 2.6e-14
2576 2.8e-14
2575 2.9e-14
2574  3e-14
2573 3.2e-14
2572 3.3e-14
2571 3.5e-14
2570 3.7e-14
2569 3.9e-14
2568  4e-14
2567 4.2e-14
2566 4.4e-14
2565 4.7e-14
2564 4.9e-14
2563 5.1e-14
2562 5.4e-14
2561 5.6e-14
2560 5.9e-14
2559 6.2e-14
2558 6.5e-14
2557 6.8e-14
2556 7.1e-14
2555 7.5e-14
2554 7.8e-14
2553 8.2e-14
2552 8.6e-14
2551  9e-14
2550 9.5e-14
2549 9.9e-14
2548  1e-13
2547 1.1e-13
2546 1.1e-13
2545 1.2e-13
2544 1.3e-13
2543 1.3e-13
2542 1.4e-13
2541 1.4e-13
2540 1.5e-13
2539 1.6e-13
2538 1.7e-13
2537 1.7e-13
2536 1.8e-13
2535 1.9e-13
2534  2e-13
2533 2.1e-13
2532 2.2e-13
2531 2.3e-13
2530 2.4e-13
2529 2.5e-13
2528 2.6e-13
2527 2.8e-13
2526 2.9e-13
2525  3e-13
2524 3.2e-13
2523 3.3e-13
2522 3.5e-13
2521 3.6e-13
2520 3.8e-13
2519  4e-13
2518 4.2e-13
2517 4.4e-13
2516 4.6e-13
2515 4.8e-13
2514  5e-13
2513 5.2e-13
2512 5.5e-13
2511 5.7e-13
2510  6e-13
2509 6.3e-13
2508 6.6e-13
2507 6.9e-13
2506 7.2e-13
2505 7.5e-13
2504 7.9e-13
2503 8.3e-13
2502 8.6e-13
2501  9e-13
2500 9.5e-13
2499 9.9e-13
2498  1e-12
2497 1.1e-12
2496 1.1e-12
2495 1.2e-12
2494 1.2e-12
2493 1.3e-12
2492 1.4e-12
2491 1.4e-12
2490 1.5e-12
2489 1.6e-12
2488 1.6e-12
2487 1.7e-12
2486 1.8e-12
2485 1.9e-12
2484 1.9e-12
2483  2e-12
2482 2.1e-12
2481 2.2e-12
2480 2.3e-12
2479 2.4e-12
2478 2.5e-12
2477 2.7e-12
2476 2.8e-12
2475 2.9e-12
2474  3e-12
2473 3.2e-12
2472 3.3e-12
2471 3.5e-12
2470 3.6e-12
2469 3.8e-12
2468  4e-12
2467 4.1e-12
2466 4.3e-12
2465 4.5e-12
2464 4.7e-12
2463 4.9e-12
2462 5.2e-12
2461 5.4e-12
2460 5.6e-12
2459 5.9e-12
2458 6.1e-12
2457 6.4e-12
2456 6.7e-12
2455  7e-12
2454 7.3e-12
2453 7.7e-12
2452  8e-12
2451 8.4e-12
2450 8.7e-12
2449 9.1e-12
2448 9.5e-12
2447 9.9e-12
2446  1e-11
2445 1.1e-11
2444 1.1e-11
2443 1.2e-11
2442 1.2e-11
2441 1.3e-11
2440 1.3e-11
2439 1.4e-11
2438 1.5e-11
2437 1.5e-11
2436 1.6e-11
2435 1.7e-11
2434 1.7e-11
2433 1.8e-11
2432 1.9e-11
2431  2e-11
2430 2.1e-11
2429 2.2e-11
2428 2.3e-11
2427 2.4e-11
2426 2.5e-11
2425 2.6e-11
2424 2.7e-11
2423 2.8e-11
2422 2.9e-11
2421  3e-11
2420 3.2e-11
2419 3.3e-11
2418 3.5e-11
2417 3.6e-11
2416 3.8e-11
2415 3.9e-11
2414 4.1e-11
2413 4.3e-11
2412 4.5e-11
2411 4.7e-11
2410 4.9e-11
2409 5.1e-11
2408 5.3e-11
2407 5.5e-11
2406 5.8e-11
2405  6e-11
2404 6.3e-11
2403 6.5e-11
2402 6.8e-11
2401 7.1e-11
2400 7.4e-11
2399 7.7e-11
2398 8.1e-11
2397 8.4e-11
2396 8.8e-11
2395 9.1e-11
2394 9.5e-11
2393 9.9e-11
2392  1e-10
2391 1.1e-10
2390 1.1e-10
2389 1.2e-10
2388 1.2e-10
2387 1.3e-10
2386 1.3e-10
2385 1.4e-10
2384 1.4e-10
2383 1.5e-10
2382 1.6e-10
2381 1.6e-10
2380 1.7e-10
2379 1.8e-10
2378 1.8e-10
2377 1.9e-10
2376  2e-10
2375 2.1e-10
2374 2.2e-10
2373 2.3e-10
2372 2.4e-10
2371 2.5e-10
2370 2.6e-10
2369 2.7e-10
2368 2.8e-10
2367 2.9e-10
2366  3e-10
2365 3.1e-10
2364 3.3e-10
2363 3.4e-10
2362 3.6e-10
2361 3.7e-10
2360 3.9e-10
2359  4e-10
2358 4.2e-10
2357 4.4e-10
2356 4.5e-10
2355 4.7e-10
2354 4.9e-10
2353 5.1e-10
2352 5.3e-10
2351 5.6e-10
2350 5.8e-10
2349  6e-10
2348 6.3e-10
2347 6.5e-10
2346 6.8e-10
2345 7.1e-10
2344 7.4e-10
2343 7.7e-10
2342  8e-10
2341 8.3e-10
2340 8.6e-10
2339  9e-10
2338 9.4e-10
2337 9.7e-10
2336  1e-09
2335 1.1e-09
2334 1.1e-09
2333 1.1e-09
2332 1.2e-09
2331 1.2e-09
2330 1.3e-09
2329 1.3e-09
2328 1.4e-09
2327 1.4e-09
2326 1.5e-09
2325 1.6e-09
2324 1.6e-09
2323 1.7e-09
2322 1.8e-09
2321 1.8e-09
2320 1.9e-09
2319  2e-09
2318 2.1e-09
2317 2.1e-09
2316 2.2e-09
2315 2.3e-09
2314 2.4e-09
2313 2.5e-09
2312 2.6e-09
2311 2.7e-09
2310 2.8e-09
2309 2.9e-09
2308 3.1e-09
2307 3.2e-09
2306 3.3e-09
2305 3.4e-09
2304 3.6e-09
2303 3.7e-09
2302 3.9e-09
2301  4e-09
2300 4.2e-09
2299 4.3e-09
2298 4.5e-09
2297 4.7e-09
2296 4.9e-09
2295  5e-09
2294 5.2e-09
2293 5.5e-09
2292 5.7e-09
2291 5.9e-09
2290 6.1e-09
2289 6.4e-09
2288 6.6e-09
2287 6.9e-09
2286 7.1e-09
2285 7.4e-09
2284 7.7e-09
2283  8e-09
2282 8.3e-09
2281 8.6e-09
2280  9e-09
2279 9.3e-09
2278 9.7e-09
2277  1e-08
2276  1e-08
2275 1.1e-08
2274 1.1e-08
2273 1.2e-08
2272 1.2e-08
2271 1.3e-08
2270 1.3e-08
2269 1.4e-08
2268 1.4e-08
2267 1.5e-08
2266 1.5e-08
2265 1.6e-08
2264 1.6e-08
2263 1.7e-08
2262 1.8e-08
2261 1.8e-08
2260 1.9e-08
2259  2e-08
2258  2e-08
2257 2.1e-08
2256 2.2e-08
2255 2.3e-08
2254 2.4e-08
2253 2.5e-08
2252 2.6e-08
2251 2.7e-08
2250 2.8e-08
2249 2.9e-08
2248  3e-08
2247 3.1e-08
2246 3.2e-08
2245 3.3e-08
2244 3.4e-08
2243 3.6e-08
2242 3.7e-08
2241 3.8e-08
2240  4e-08
2239 4.1e-08
2238 4.3e-08
2237 4.4e-08
2236 4.6e-08
2235 4.8e-08
2234  5e-08
2233 5.1e-08
2232 5.3e-08
2231 5.5e-08
2230 5.7e-08
2229 5.9e-08
2228 6.2e-08
2227 6.4e-08
2226 6.6e-08
2225 6.9e-08
2224 7.1e-08
2223 7.4e-08
2222 7.7e-08
2221 7.9e-08
2220 8.2e-08
2219 8.5e-08
2218 8.8e-08
2217 9.2e-08
2216 9.5e-08
2215 9.8e-08
2214  1e-07
2213 1.1e-07
2212 1.1e-07
2211 1.1e-07
2210 1.2e-07
2209 1.2e-07
2208 1.3e-07
2207 1.3e-07
2206 1.4e-07
2205 1.4e-07
2204 1.5e-07
2203 1.5e-07
2202 1.6e-07
2201 1.6e-07
2200 1.7e-07
2199 1.7e-07
2198 1.8e-07
2197 1.9e-07
2196 1.9e-07
2195  2e-07
2194 2.1e-07
2193 2.1e-07
2192 2.2e-07
2191 2.3e-07
2190 2.4e-07
2189 2.5e-07
2188 2.6e-07
2187 2.6e-07
2186 2.7e-07
2185 2.8e-07
2184 2.9e-07
2183  3e-07
2182 3.1e-07
2181 3.3e-07
2180 3.4e-07
2179 3.5e-07
2178 3.6e-07
2177 3.7e-07
2176 3.9e-07
2175  4e-07
2174 4.1e-07
2173 4.3e-07
2172 4.4e-07
2171 4.6e-07
2170 4.8e-07
2169 4.9e-07
2168 5.1e-07
2167 5.3e-07
2166 5.5e-07
2165 5.6e-07
2164 5.8e-07
2163  6e-07
2162 6.3e-07
2161 6.5e-07
2160 6.7e-07
2159 6.9e-07
2158 7.2e-07
2157 7.4e-07
2156 7.7e-07
2155 7.9e-07
2154 8.2e-07
2153 8.5e-07
2152 8.8e-07
2151 9.1e-07
2150 9.4e-07
2149 9.7e-07
2148  1e-06
2147  1e-06
2146 1.1e-06
2145 1.1e-06
2144 1.1e-06
2143 1.2e-06
2142 1.2e-06
2141 1.3e-06
2140 1.3e-06
2139 1.4e-06
2138 1.4e-06
2137 1.4e-06
2136 1.5e-06
2135 1.5e-06
2134 1.6e-06
2133 1.7e-06
2132 1.7e-06
2131 1.8e-06
2130 1.8e-06
2129 1.9e-06
2128 1.9e-06
2127  2e-06
2126 2.1e-06
2125 2.1e-06
2124 2.2e-06
2123 2.3e-06
2122 2.4e-06
2121 2.4e-06
2120 2.5e-06
2119 2.6e-06
2118 2.7e-06
2117 2.8e-06
2116 2.9e-06
2115  3e-06
2114 3.1e-06
2113 3.2e-06
2112 3.3e-06
2111 3.4e-06
2110 3.5e-06
2109 3.6e-06
2108 3.7e-06
2107 3.8e-06
2106  4e-06
2105 4.1e-06
2104 4.2e-06
2103 4.4e-06
2102 4.5e-06
2101 4.7e-06
2100 4.8e-06
2099  5e-06
2098 5.1e-06
2097 5.3e-06
2096 5.5e-06
2095 5.6e-06
2094 5.8e-06
2093  6e-06
2092 6.2e-06
2091 6.4e-06
2090 6.6e-06
2089 6.8e-06
2088  7e-06
2087 7.2e-06
2086 7.5e-06
2085 7.7e-06
2084  8e-06
2083 8.2e-06
2082 8.5e-06
2081 8.7e-06
2080  9e-06
2079 9.3e-06
2078 9.6e-06
2077 9.9e-06
2076  1e-05
2075 1.1e-05
2074 1.1e-05
2073 1.1e-05
2072 1.2e-05
2071 1.2e-05
2070 1.2e-05
2069 1.3e-05
2068 1.3e-05
2067 1.3e-05
2066 1.4e-05
2065 1.4e-05
2064 1.5e-05
2063 1.5e-05
2062 1.6e-05
2061 1.6e-05
2060 1.7e-05
2059 1.7e-05
2058 1.8e-05
2057 1.8e-05
2056 1.9e-05
2055 1.9e-05
2054  2e-05
2053 2.1e-05
2052 2.1e-05
2051 2.2e-05
2050 2.3e-05
2049 2.3e-05
2048 2.4e-05
2047 2.5e-05
2046 2.5e-05
2045 2.6e-05
2044 2.7e-05
2043 2.8e-05
2042 2.9e-05
2041 2.9e-05
2040  3e-05
2039 3.1e-05
2038 3.2e-05
2037 3.3e-05
2036 3.4e-05
2035 3.5e-05
2034 3.6e-05
2033 3.7e-05
2032 3.8e-05
2031  4e-05
2030 4.1e-05
2029 4.2e-05
2028 4.3e-05
2027 4.4e-05
2026 4.6e-05
2025 4.7e-05
2024 4.9e-05
2023  5e-05
2022 5.1e-05
2021 5.3e-05
2020 5.5e-05
2019 5.6e-05
2018 5.8e-05
2017 5.9e-05
2016 6.1e-05
2015 6.3e-05
2014 6.5e-05
2013 6.7e-05
2012 6.9e-05
2011 7.1e-05
2010 7.3e-05
2009 7.5e-05
2008 7.7e-05
2007 7.9e-05
2006 8.1e-05
2005 8.4e-05
2004 8.6e-05
2003 8.9e-05
2002 9.1e-05
2001 9.4e-05
2000 9.6e-05
1999 9.9e-05
1998 0.0001
1997 0.0001
1996 0.00011
1995 0.00011
1994 0.00011
1993 0.00012
1992 0.00012
1991 0.00012
1990 0.00013
1989 0.00013
1988 0.00013
1987 0.00014
1986 0.00014
1985 0.00015
1984 0.00015
1983 0.00015
1982 0.00016
1981 0.00016
1980 0.00017
1979 0.00017
1978 0.00018
1977 0.00018
1976 0.00019
1975 0.00019
1974 0.0002
1973 0.0002
1972 0.00021
1971 0.00021
1970 0.00022
1969 0.00023
1968 0.00023
1967 0.00024
1966 0.00025
1965 0.00025
1964 0.00026
1963 0.00027
1962 0.00027
1961 0.00028
1960 0.00029
1959 0.0003
1958 0.0003
1957 0.00031
1956 0.00032
1955 0.00033
1954 0.00034
1953 0.00035
1952 0.00036
1951 0.00037
1950 0.00038
1949 0.00039
1948 0.0004
1947 0.00041
1946 0.00042
1945 0.00043
1944 0.00044
1943 0.00045
1942 0.00046
1941 0.00048
1940 0.00049
8
2733  1e-17
2732 1.1e-17
2731 1.1e-17
2730 1.2e-17
2729 1.2e-17
2728 1.3e-17
2727 1.4e-17
2726 1.4e-17
2725 1.5e-17
2724 1.6e-17
2723 1.7e-17
2722 1.8e-17
2721 1.9e-17
2720  2e-17
2719 2.1e-17
2718 2.2e-17
2717 2.3e-17
2716 2.4e-17
2715 2.6e-17
2714 2.7e-17
2713 2.9e-17
2712  3e-17
2711 3.2e-17
2710 3.4e-17
2709 3.5e-17
2708 3.7e-17
2707 3.9e-17
2706 4.1e-17
2705 4.4e-17
2704blimps-3.9/examples/processor/distribution/clustal.in.cblks000064400001460000012000000054061062461143200246220ustar00jorjastaff00000400000027ID   clustalxi; BLOCK
AC   clustalxiA; distance from previous block=(20,20)
DE   clustal.in
BL   UNK;  width=27; seqs=10; 99.5%=1080; strength=1888 
MTCH_ARATH           (  20) LPLPGTVYTVCGGPPCQGISGYNRYRN   4
MTCH_ARAAR           (  20) LPLPGTVYSVCGGPPCQGISGYNRFRN   3
MTDM_ARATH           (  20) LPLPGQVDFINGGPPCQGFSGMNRFNQ   3
MET2_ARATH           (  20) LPLPGQVDFINGGPPCQGFSGMNRFSH   3
MTDM_PISAT           (  20) LPLPGQVDFINGGPPCQGFSGMNRFNT   3
MTDM_MOUSE           (  20) LPQKGDVEMLCGGPPCQGFSGMNRFNS   2
MTDM_HUMAN           (  20) LPQKGDVEMLCGGPPCQGFSGMNRFNS   2
MTDM_XENLA           (  20) LPQKGDVEMLCGGPPCQGFSGMNRFNS   2
MTDM_PARLI           (  20) LPQKGDVELLCGGPPCQGFSGMNRFNS   2
MTDM_CHICK           (  20) LPQKGDVEMLCGGPPCQGFSGMNRFNS   2
//
ID   clustalxi; BLOCK
AC   clustalxiB; distance from previous block=(2,2)
DE   clustal.in
BL   UNK;  width=60; seqs=10; 99.5%=2420; strength=1824 
MTCH_ARATH           (  49) APLEDQKNQQLLVFLDIIDFLKPNYVLMENVVDLLRFSKGFLARHAVASFVAMNYQTRLG   9
MTCH_ARAAR           (  49) APLEDKKNQQLLVFLDIIDFLKPSYVLMENVVDLLRFSKGYLARHAVASFVAMNYQTRLG   9
MTDM_ARATH           (  49) SSWSKVQCEMILAFLSFADYFRPRYFLLENVRTFVSFNKGQTFQLTLASLLEMGYQVRFG   6
MET2_ARATH           (  49) GSWSKVQCEMILAFLSFADYFRPKYFLLENVKKFVTYNKGRTFQLTMASLLEMGYQVRFG   7
MTDM_PISAT           (  49) STWSKVQCEMILAFLSFADYFRPRYFLLENVRNFVSFNKGQTFRLTLASLLEMGYQVRFG   5
MTDM_MOUSE           (  49) RTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSYRRSMVLKLTLRCLVRMGYQCTFG   5
MTDM_HUMAN           (  49) RTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFG   4
MTDM_XENLA           (  49) RTYSKFKNSLVVSYLSYCDYYRPKYFLLENVRNFVSFKKSMVLKLTLRCLVRMGYQCTFG   5
MTDM_PARLI           (  49) REYSKFKNSLISSYLSYCDYYRPRFFLLENVRNFVSYKKNMVLKLALRCLIRMGYQCTFG   6
MTDM_CHICK           (  49) RTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFG   4
//
ID   clustalxi; BLOCK
AC   clustalxiC; distance from previous block=(0,0)
DE   clustal.in
BL   UNK;  width=51; seqs=10; 99.5%=2069; strength=1741 
MTCH_ARATH           ( 109) MMAAGSYGLPQLRNRVFLWAAQPSEKLPPYPLPTHEVAKKFNTPKEFKDLQ   7
MTCH_ARAAR           ( 109) MMTAGSYGLPQVRNRVFLWAAQPTEKLPPYPLPTHEVEKKYNTPKEFEDLQ   7
MTDM_ARATH           ( 109) ILEAGAYGVSQSRKRAFIWAAAPEEVLPEWPEPMHVFGVPKLKISLSQGLH   5
MET2_ARATH           ( 109) ILEAGTYGVSQPRKRVIIWAASPEEVLPEWPEPMHVFDNPGSKISLPRGLR   6
MTDM_PISAT           ( 109) ILEAGAFGVSQSRKRAFIWAASPEDVLPEWPEPMHVFSAPELKITLAENVQ   7
MTDM_MOUSE           ( 109) VLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDK   4
MTDM_HUMAN           ( 109) VLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDK   4
MTDM_XENLA           ( 109) VLQAGQYGVAQTRRRAIVLAAAPGEKLPMFPEPLHVFAPRACTLSVVVDEK   4
MTDM_PARLI           ( 109) ILQAGQYGVPQTRRRAIILAAAPGEKLPFYPEPLHVFSSRACSLSVMIGEK   5
MTDM_CHICK           ( 109) VLQAGQYGVAQTRRRAIVLAAAPGEKLPMFPEPLHVFAPRACQLSVVVDDK   4
//
blimps-3.9/examples/processor/distribution/clustal.in.seqs000064400001460000012000000037101062461143000244710ustar00jorjastaff00000400000027>MTCH_ARATH   
---------DGFKSHL----LPLPGTVYTVCGGPPCQGISGYNRYRNNEAPLEDQKNQQL
LVFLDIIDFLKPNYVLMENVVDLLRFSKGFLARHAVASFVAMNYQTRLGMMAAGSYGLPQ
LRNRVFLWAAQPSEKLPPYPLPTHEVAKKFNTPKEFKDLQ--VGRIQMEFLKLDNALTLA

>MTCH_ARAAR   
---------DGFKSHL----LPLPGTVYSVCGGPPCQGISGYNRFRNKQAPLEDKKNQQL
LVFLDIIDFLKPSYVLMENVVDLLRFSKGYLARHAVASFVAMNYQTRLGMMTAGSYGLPQ
VRNRVFLWAAQPTEKLPPYPLPTHEVEKKYNTPKEFEDLQ--VGLIQKELLQLDNALTLA

>MTDM_ARATH   
VSTTEANELAAKLTEEQKSTLPLPGQVDFINGGPPCQGFSGMNRFNQ--SSWSKVQCEMI
LAFLSFADYFRPRYFLLENVRTFVSFNKGQTFQLTLASLLEMGYQVRFGILEAGAYGVSQ
SRKRAFIWAAAPEEVLPEWPEPMHVFGVPKLKISLSQGLHYAAVRSTALG-APFRPITVR

>MET2_ARATH   
VSTVEAAELAAKLDENQKSTLPLPGQVDFINGGPPCQGFSGMNRFSH--GSWSKVQCEMI
LAFLSFADYFRPKYFLLENVKKFVTYNKGRTFQLTMASLLEMGYQVRFGILEAGTYGVSQ
PRKRVIIWAASPEEVLPEWPEPMHVFDNPGSKISLPRGLRYDAGCNTKFG-APFRSITVR

>MTDM_PISAT   
ISTAEAAELASKLDDKDLNSLPLPGQVDFINGGPPCQGFSGMNRFNT--STWSKVQCEMI
LAFLSFADYFRPRYFLLENVRNFVSFNKGQTFRLTLASLLEMGYQVRFGILEAGAFGVSQ
SRKRAFIWAASPEDVLPEWPEPMHVFSAPELKITLAENVQYAAVCSTANG-APLRAITVR

>MTDM_MOUSE   
-------EVTNSLGQR----LPQKGDVEMLCGGPPCQGFSGMNRFNS--RTYSKFKNSLV
VSFLSYCDYYRPRFFLLENVRNFVSYRRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQ
TRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITER

>MTDM_HUMAN   
-------ETTNSRGQR----LPQKGDVEMLCGGPPCQGFSGMNRFNS--RTYSKFKNSLV
VSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQ
TRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVR

>MTDM_XENLA   
-------EKTNSLGQR----LPQKGDVEMLCGGPPCQGFSGMNRFNS--RTYSKFKNSLV
VSYLSYCDYYRPKYFLLENVRNFVSFKKSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQ
TRRRAIVLAAAPGEKLPMFPEPLHVFAPRACTLSVVVDEKKYVSNTTRTNSSLFRTITVR

>MTDM_PARLI   
-------EKTSRTGQK----LPQKGDVELLCGGPPCQGFSGMNRFNS--REYSKFKNSLI
SSYLSYCDYYRPRFFLLENVRNFVSYKKNMVLKLALRCLIRMGYQCTFGILQAGQYGVPQ
TRRRAIILAAAPGEKLPFYPEPLHVFSSRACSLSVMIGEKKIESNNQWCLSAPYRTITVR

>MTDM_CHICK   
-------EKTNSLGQK----LPQKGDVEMLCGGPPCQGFSGMNRFNS--RTYSKFKNSLV
VSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQ
TRRRAIVLAAAPGEKLPMFPEPLHVFAPRACQLSVVVDDKKFVSNITRTYSGPFRTITVR



blimps-3.9/examples/processor/distribution/clustal.in.wblks000064400001460000012000000054111062461143200246420ustar00jorjastaff00000400000027ID   clustalxi; BLOCK
AC   clustalxiA; distance from previous block=(20,20)
DE   clustal.in
BL   UNK;   width=27; seqs=10; 99.5%=1080; strength=1888 
MTCH_ARATH           (  20) LPLPGTVYTVCGGPPCQGISGYNRYRN 100
MTCH_ARAAR           (  20) LPLPGTVYSVCGGPPCQGISGYNRFRN  88
MTDM_ARATH           (  20) LPLPGQVDFINGGPPCQGFSGMNRFNQ  72
MET2_ARATH           (  20) LPLPGQVDFINGGPPCQGFSGMNRFSH  80
MTDM_PISAT           (  20) LPLPGQVDFINGGPPCQGFSGMNRFNT  72
MTDM_MOUSE           (  20) LPQKGDVEMLCGGPPCQGFSGMNRFNS  61
MTDM_HUMAN           (  20) LPQKGDVEMLCGGPPCQGFSGMNRFNS  61
MTDM_XENLA           (  20) LPQKGDVEMLCGGPPCQGFSGMNRFNS  61
MTDM_PARLI           (  20) LPQKGDVELLCGGPPCQGFSGMNRFNS  65
MTDM_CHICK           (  20) LPQKGDVEMLCGGPPCQGFSGMNRFNS  61
//
ID   clustalxi; BLOCK
AC   clustalxiB; distance from previous block=(2,2)
DE   clustal.in
BL   UNK;   width=60; seqs=10; 99.5%=2420; strength=1824 
MTCH_ARATH           (  49) APLEDQKNQQLLVFLDIIDFLKPNYVLMENVVDLLRFSKGFLARHAVASFVAMNYQTRLG 100
MTCH_ARAAR           (  49) APLEDKKNQQLLVFLDIIDFLKPSYVLMENVVDLLRFSKGYLARHAVASFVAMNYQTRLG 100
MTDM_ARATH           (  49) SSWSKVQCEMILAFLSFADYFRPRYFLLENVRTFVSFNKGQTFQLTLASLLEMGYQVRFG  60
MET2_ARATH           (  49) GSWSKVQCEMILAFLSFADYFRPKYFLLENVKKFVTYNKGRTFQLTMASLLEMGYQVRFG  74
MTDM_PISAT           (  49) STWSKVQCEMILAFLSFADYFRPRYFLLENVRNFVSFNKGQTFRLTLASLLEMGYQVRFG  57
MTDM_MOUSE           (  49) RTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSYRRSMVLKLTLRCLVRMGYQCTFG  51
MTDM_HUMAN           (  49) RTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFG  48
MTDM_XENLA           (  49) RTYSKFKNSLVVSYLSYCDYYRPKYFLLENVRNFVSFKKSMVLKLTLRCLVRMGYQCTFG  49
MTDM_PARLI           (  49) REYSKFKNSLISSYLSYCDYYRPRFFLLENVRNFVSYKKNMVLKLALRCLIRMGYQCTFG  62
MTDM_CHICK           (  49) RTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFG  48
//
ID   clustalxi; BLOCK
AC   clustalxiC; distance from previous block=(0,0)
DE   clustal.in
BL   UNK;   width=51; seqs=10; 99.5%=2069; strength=1741 
MTCH_ARATH           ( 109) MMAAGSYGLPQLRNRVFLWAAQPSEKLPPYPLPTHEVAKKFNTPKEFKDLQ  99
MTCH_ARAAR           ( 109) MMTAGSYGLPQVRNRVFLWAAQPTEKLPPYPLPTHEVEKKYNTPKEFEDLQ 100
MTDM_ARATH           ( 109) ILEAGAYGVSQSRKRAFIWAAAPEEVLPEWPEPMHVFGVPKLKISLSQGLH  76
MET2_ARATH           ( 109) ILEAGTYGVSQPRKRVIIWAASPEEVLPEWPEPMHVFDNPGSKISLPRGLR  84
MTDM_PISAT           ( 109) ILEAGAFGVSQSRKRAFIWAASPEDVLPEWPEPMHVFSAPELKITLAENVQ  96
MTDM_MOUSE           ( 109) VLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDK  54
MTDM_HUMAN           ( 109) VLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDK  54
MTDM_XENLA           ( 109) VLQAGQYGVAQTRRRAIVLAAAPGEKLPMFPEPLHVFAPRACTLSVVVDEK  56
MTDM_PARLI           ( 109) ILQAGQYGVPQTRRRAIILAAAPGEKLPFYPEPLHVFSSRACSLSVMIGEK  66
MTDM_CHICK           ( 109) VLQAGQYGVAQTRRRAIVLAAAPGEKLPMFPEPLHVFAPRACQLSVVVDDK  55
//
blimps-3.9/examples/processor/distribution/msf.in.blks000064400001460000012000000257241062461143300236030ustar00jorjastaff00000400000027ID   msfxinx; BLOCK
AC   msfxinxA; distance from previous block=(10,10)
DE   msf.in
BL   UNK motif;  width=13; seqs=33; 99.5%=0; strength=0 
P09254-1             (  10) AGYDICVPYNLYL 0.375409
A37470-1             (  10) AGYDIAMPYTAVL 0.582598
Q00030-2             (  10) AGYDISAQTNATI 0.343065
P28892-1             (  10) AGYDISAPEDATI 0.255653
P10234-1             (  10) AGFDIVVRRPVTV 0.657557
P11365-6             (  10) HKVDLRAASDFLL 1.080913
P06968-1             (  10) AGLDLRACLNDAV 0.455011
P43792-1             (  10) AGLDLRALIDESF 0.456967
S44300-1             (  10) AGLDLRACLDEPL 0.377447
P31625-2             (  10) AGLDLCATSYTVL 0.355910
P07570-2             (  10) AGLDLCSTSHTVL 0.355910
P10271-1             (  10) AGLDLSSQKDLIL 0.333429
P21407-2             (  10) AGLDLCTTTDTIL 0.343284
P10265-1             (  10) AAVDLCTIQAVSL 0.740662
P11204-4             (  10) AGFDLCVPYDIMI 0.307921
P16088-4             (  10) AGYDLLAAKEIHL 0.375645
JQ1162-4             (  10) AGYDLICPQEVSI 0.180589
P16901-4             (  10) AGYDLICPQEVCI 0.246523
P23427-4             (  10) AGYDLICPQEISI 0.174339
P03370-4             (  10) AGYDLICPQEISI 0.174339
P23426-4             (  10) AGYDLICPQEISI 0.174339
P35956-4             (  10) AGYDLICPQEISI 0.174339
P33459-4             (  10) AGYDLICPEEVTI 0.188656
P32208-1             (  10) AGYDLYSAYSYTV 0.316228
P32518-1             (  10) AGYDLSSAAETKV 0.320832
P33317-1             (  10) AGYDIYASQDITI 0.334883
P43058-1             (  10) AGYDLYSAEAATI 0.240091
P33316-1             (  10) AGYDLYSAYDYTI 0.188664
P14597-1             (  10) AGLDLCSAYDCVI 0.263882
P21035-1             (  10) AGYDLYSAYDYTI 0.188664
S26429-1             (  10) AGYDLFSAYDIKV 0.315961
P28893-1             (  10) AGFDLSVLEDREF 0.552338
Q00030-1             (  10) DGRLLVLINNHTV 1.567952
//
ID   msfxinx; BLOCK
AC   msfxinxB; distance from previous block=(7,7)
DE   msf.in
BL   UNK motif;  width=21; seqs=33; 99.5%=0; strength=0 
P09254-1             (  30) NEFIKIVLPIIRDWDLQHPSI 1.307823
A37470-1             (  30) APGENLHVRLPVAYAADAHAA 0.981646
Q00030-2             (  30) EPDESYFVELPIVFSSSNPAV 0.803506
P28892-1             (  30) DPDESHFVDLPIVFANSNPAV 0.905138
P10234-1             (  30) ANGTTVVQPSLRMLHADAGPA 1.461928
P11365-6             (  30) PQMSIQPVPVEPIPSLPLGTM 1.125987
P06968-1             (  30) APGDTTLVPTGLAIHIADPSL 0.535921
P43792-1             (  30) QPGETKLIPTGLSIYIADPNL 0.518314
S44300-1             (  30) EPDETCLISTGLAIYLGHSNV 0.615041
P31625-2             (  30) PEMGVQTLATGVFGPLPPGTV 0.437403
P07570-2             (  30) PEMGPQALSTGIYGPLPPNTF 0.493820
P10271-1             (  30) LEDGVSLVPTLVKGTLPEGTT 0.573429
P21407-2             (  30) TQNSPLTLPVGIYGPLPPQTF 0.850501
P10265-1             (  30) PGEPPQKIPTGVYGPLPEGTV 0.610700
P11204-4             (  30) PVSDTKIIPTDVKIQVPPNSF 0.642461
P16088-4             (  30) LPGEVKVIPTGVKLMLPKGYW 0.370310
JQ1162-4             (  30) PAGQVKKIPIDLRINLRKNQW 0.404432
P16901-4             (  30) PAGQVRKIPINLRINLKEDQW 0.463580
P23427-4             (  30) PAGQVKRIAIDLKINLKKDQW 0.276867
P03370-4             (  30) PAGQVKRIAIDLKINLKKDQW 0.276867
P23426-4             (  30) PAGQVKRIAIDLKINLKKDQW 0.276867
P35956-4             (  30) PAGQVKRIAIDLKINLKKDQW 0.276867
P33459-4             (  30) EPGQVKCIPIELRLNLKKSQW 0.459075
P32208-1             (  30) KPYNRILVRTDICLMIPDKCY 0.848485
P32518-1             (  30) PARGKALVPTDLSIAVPQGTY 0.372379
P33317-1             (  30) PAMGQGMVSTDISFTVPVGTY 0.510945
P43058-1             (  30) PAHGQGLVSTDISIIVPIGTY 0.490660
P33316-1             (  30) PPMEKAVVKTDIQIALPSGCY 0.423147
P14597-1             (  30) PSHCSRVVFTDLLIKPPSGCY 0.819599
P21035-1             (  30) PPGERQLIKTDISMSMPKICY 0.631264
S26429-1             (  30) PARGRALVPTDLVFQFPPGCY 0.471911
P28893-1             (  30) IRGCHYRLPTGLAIAVPRGYV 0.713914
Q00030-1             (  30) SAGEFYSVLTDVGVRVACSSG 1.049214
//
ID   msfxinx; BLOCK
AC   msfxinxC; distance from previous block=(2,2)
DE   msf.in
BL   UNK motif;  width=13; seqs=33; 99.5%=0; strength=0 
P09254-1             (  53) AYIFGRSSKSRSG 0.476064
A37470-1             (  53) PYVFGRSSCNLRG 0.438049
Q00030-2             (  53) PCIFGRSSMNRRG 0.354106
P28892-1             (  53) PCIFGRSSMNRRG 0.354106
P10234-1             (  53) CYVLGRSSLNARG 0.452383
P11365-6             (  53) GLILGRGSASTLQ 0.917253
P06968-1             (  53) AMMLPRSGLGHKH 0.462827
P43792-1             (  53) AVILPRSGLGHKH 0.264911
S44300-1             (  53) ATILPRSGLGHKH 0.320466
P31625-2             (  53) GLLLGRSSASLKG 0.341152
P07570-2             (  53) GLILGRSSITMKG 0.413582
P10271-1             (  53) GLIIGRSSNYKKG 0.464087
P21407-2             (  53) GLILAEPALPSKG 1.287040
P10265-1             (  53) GLILGRSSLNLKG 0.178421
P11204-4             (  53) GWVTGKSSMAKQG 0.526968
P16088-4             (  53) GLIIGKSSIGSKG 0.310227
JQ1162-4             (  53) AMIGTKSSFASKG 0.213468
P16901-4             (  53) AMVGTKSSFASKG 0.244718
P23427-4             (  53) AMIGTKSSFANKG 0.213468
P03370-4             (  53) AMIGTKSSFANKG 0.213468
P23426-4             (  53) AMIGTKSSFANKG 0.213468
P35956-4             (  53) AMIGTKSSFANKG 0.213468
P33459-4             (  53) AMIATKSSMAAKG 0.214790
P32208-1             (  53) GRISPRSGLSLNY 0.455146
P32518-1             (  53) ARIAPRSGLAWKY 0.320791
P33317-1             (  53) GRIAPRSGLAVKN 0.339351
P43058-1             (  53) GRVAPRSGLAVKH 0.231713
P33316-1             (  53) GRVAPRSGLAAKH 0.224137
P14597-1             (  53) GRIAPRSGLAVKH 0.200463
P21035-1             (  53) GRIAPRSGLSLKG 0.187548
S26429-1             (  53) GRIAPRSGLAAKF 0.248442
P28893-1             (  53) GIITPRSSQAKNF 0.566606
Q00030-1             (  53) IVLAQISGLPHVG 1.137316
//
ID   msfxinx; BLOCK
AC   msfxinxD; distance from previous block=(22,22)
DE   msf.in
BL   UNK motif;  width=15; seqs=33; 99.5%=0; strength=0 
P09254-1             (  88) IVCPTAWPAGEHCKF 0.952262
A37470-1             (  88) IVLPTAWPPGEPCRF 0.876336
Q00030-2             (  88) IVLPTRWVTGRTCCF 0.852725
P28892-1             (  88) IVLPTRWVAGRTCCF 0.752725
P10234-1             (  88) LVVPTRWLPGHVCAF 1.137765
P11365-6             (  88) ELWIVNIPQKYQVLC 1.994524
P06968-1             (  88) GLIDSDYQGQLMISV 0.397504
P43792-1             (  88) GLIDSDYQGPLMVSM 0.367920
S44300-1             (  88) GLIDSDYQGPLMVSC 0.367920
P31625-2             (  88) GVIDSDYTGEIKILA 0.304609
P07570-2             (  88) GVIDNDYTGEIKIMA 0.340778
P10271-1             (  88) GVIDSDFQGEIKVMV 0.284538
P21407-2             (  88) GILDNDFEGEIHIIL 0.516967
P10265-1             (  88) SVVDSDYKGEIQLVI 0.691021
P11204-4             (  88) GIIDEGYTGEIQVIC 0.256909
P16088-4             (  88) GVIDEGYRGEIGVIM 0.233782
JQ1162-4             (  88) GIVDSGYQGIIQVVI 0.255096
P16901-4             (  88) GIIDSGYQGIIQVVV 0.234604
P23427-4             (  88) GIIDSGYQGTIQVVI 0.199187
P03370-4             (  88) GIIDSGYQGTIQVVI 0.199187
P23426-4             (  88) GIIDSGYQGTIQVVI 0.199187
P35956-4             (  88) GIIDSGYQGTIQVVI 0.199187
P33459-4             (  88) GIIDSGYQGQIQVIM 0.259835
P32208-1             (  88) GVIDSDYRGEIGIVF 0.196045
P32518-1             (  88) GVIDADYRGPVGVVL 0.257529
P33317-1             (  88) GVVDRDYTGEVKVVL 0.346354
P43058-1             (  88) GVIDADYRGEVKVVL 0.234195
P33316-1             (  88) GVIDEDYRGNVGVVL 0.211695
P14597-1             (  88) GVIDEDYRGNVGVVL 0.211695
P21035-1             (  88) GVIDEDYRGNIGVIL 0.214505
S26429-1             (  88) GVIDPDYRGNVSVVL 0.404288
P28893-1             (  88) GIIDSDFRGHIHIMV 0.429311
Q00030-1             (  88) GIVDSGYRGVVKAVQ 0.619812
//
ID   msfxinx; BLOCK
AC   msfxinxE; distance from previous block=(4,4)
DE   msf.in
BL   UNK motif;  width=10; seqs=33; 99.5%=0; strength=0 
P09254-1             ( 107) LTGDDIRIKT 0.378452
A37470-1             ( 107) VTQEPLVAAA 0.615715
Q00030-2             ( 107) INKYPVYITK 0.303816
P28892-1             ( 107) VNKYPVSITK 0.220482
P10234-1             ( 107) LTGVPVTLEA 0.339937
P11365-6             ( 107) SPKGVFSISK 0.363114
P06968-1             ( 107) RGQDSFTIQP 0.304742
P43792-1             ( 107) RGNEPFKIEV 0.249115
S44300-1             ( 107) RGKEPYTINP 0.330067
P31625-2             ( 107) APNKIIVINA 0.288782
P07570-2             ( 107) AVNNIVTVSQ 0.375393
P10271-1             ( 107) AAKNAVIIHK 0.338736
P21407-2             ( 107) TTKDLVTIPK 0.315201
P10265-1             ( 107) SSIPWSASPR 0.713312
P11204-4             ( 107) IGKSNIKLIE 0.417247
P16088-4             ( 107) VSRKSITLME 0.449695
JQ1162-4             ( 107) SNDEEVIIPQ 0.186919
P16901-4             ( 107) SNDKEVIIPQ 0.181150
P23427-4             ( 107) SNNKEVVIPQ 0.118650
P03370-4             ( 107) SNNKEVVIPQ 0.118650
P23426-4             ( 107) SNNKEVVIPQ 0.118650
P35956-4             ( 107) SNNKEVVIPQ 0.118650
P33459-4             ( 107) SNKIAVVIPQ 0.210958
P32208-1             ( 107) NGCSDFNIKV 0.316949
P32518-1             ( 107) HSEVDFEVKV 0.249285
P33317-1             ( 107) HSQRDFAIKK 0.278742
P43058-1             ( 107) HSEKDFEIKE 0.214212
P33316-1             ( 107) FGKEKFEVKK 0.250801
P14597-1             ( 107) FGNSDFEVKK 0.185997
P21035-1             ( 107) NGKCTFNVNT 0.403312
S26429-1             ( 107) FSESSFNIRR 0.341784
P28893-1             ( 107) SAIADFSVKK 0.323927
Q00030-1             ( 107) ANGVNTVVPP 0.377559
//
ID   msfxinx; BLOCK
AC   msfxinxF; distance from previous block=(53,53)
DE   msf.in
BL   UNK motif;  width=14; seqs=33; 99.5%=0; strength=0 
P09254-1             ( 170) IAFPYAIRGKCGIP 0.843472
A37470-1             ( 170) AAVPPSARGPRGFG 0.488146
Q00030-2             ( 170) HDAPSSARSEGGFG 0.424949
P28892-1             ( 170) REAPSSLRADGGFG 0.471876
P10234-1             ( 170) KALRNYPRGVPDST 0.870522
P11365-6             ( 170) TREKSAGPEIKKMG 1.125366
P06968-1             ( 170) EDFDATDRGEGGFG 0.221333
P43792-1             ( 170) EDFQQTERGEGGFG 0.237435
S44300-1             ( 170) EEFELTERGAGGFG 0.211713
P31625-2             ( 170) GKTINRDRQDKGFG 0.442596
P07570-2             ( 170) DNKVQQPYRGQGSF 1.156968
P10271-1             ( 170) NPVIKEERGSEGFG 0.460445
P21407-2             ( 170) SNFHKPYRGASAPG 0.799525
P10265-1             ( 170) NSEIKRIGGLVSTD 1.075580
P11204-4             ( 170) DENKISQRGDKGFG 0.417818
P16088-4             ( 170) KVVMDSERGDNGYG 0.535039
JQ1162-4             ( 170) GETRKTERGNQGFG 0.132951
P16901-4             ( 170) GETRRTERGNQGFG 0.162866
P23427-4             ( 170) GETRKTERGEQGFG 0.114433
P03370-4             ( 170) GETRKTERGEQGFG 0.114433
P23426-4             ( 170) GETRKTERGEQGFG 0.114433
P35956-4             ( 170) GETRKTERGEQGFG 0.114433
P33459-4             ( 170) GESRKTERGEKGFG 0.211510
P32208-1             ( 170) KCLEDTERGNSGFG 0.218992
P32518-1             ( 170) DDLDSTVRGSGGFG 0.237758
P33317-1             ( 170) DSLEESARGAGGFG 0.226478
P43058-1             ( 170) EELDNTERGEGGFG 0.125502
P33316-1             ( 170) QALDDTERGSGGFG 0.191466
P14597-1             ( 170) NCLDNTDRGDSGFG 0.206629
P21035-1             ( 170) QSLDSTNRGDQGFG 0.212253
S26429-1             ( 170) TQLGETDRGASGFG 0.357804
P28893-1             ( 170) ETLERTRRGTGGFG 0.337223
Q00030-1             ( 170) ETINVTNINLTENG 1.138054
//
blimps-3.9/examples/processor/distribution/msf.in.cblks000064400001460000012000000237601062461143300237440ustar00jorjastaff00000400000027ID   msfxinx; BLOCK
AC   msfxinxA; distance from previous block=(10,10)
DE   msf.in
BL   UNK;  width=13; seqs=33; 99.5%=811; strength=1146 
P09254-1             (  10) AGYDICVPYNLYL   0
A37470-1             (  10) AGYDIAMPYTAVL   1
Q00030-2             (  10) AGYDISAQTNATI   0
P28892-1             (  10) AGYDISAPEDATI   0
P10234-1             (  10) AGFDIVVRRPVTV   1
P11365-6             (  10) HKVDLRAASDFLL   1
P06968-1             (  10) AGLDLRACLNDAV   0
P43792-1             (  10) AGLDLRALIDESF   0
S44300-1             (  10) AGLDLRACLDEPL   0
P31625-2             (  10) AGLDLCATSYTVL   0
P07570-2             (  10) AGLDLCSTSHTVL   0
P10271-1             (  10) AGLDLSSQKDLIL   0
P21407-2             (  10) AGLDLCTTTDTIL   0
P10265-1             (  10) AAVDLCTIQAVSL   1
P11204-4             (  10) AGFDLCVPYDIMI   0
P16088-4             (  10) AGYDLLAAKEIHL   0
JQ1162-4             (  10) AGYDLICPQEVSI   0
P16901-4             (  10) AGYDLICPQEVCI   0
P23427-4             (  10) AGYDLICPQEISI   0
P03370-4             (  10) AGYDLICPQEISI   0
P23426-4             (  10) AGYDLICPQEISI   0
P35956-4             (  10) AGYDLICPQEISI   0
P33459-4             (  10) AGYDLICPEEVTI   0
P32208-1             (  10) AGYDLYSAYSYTV   0
P32518-1             (  10) AGYDLSSAAETKV   0
P33317-1             (  10) AGYDIYASQDITI   0
P43058-1             (  10) AGYDLYSAEAATI   0
P33316-1             (  10) AGYDLYSAYDYTI   0
P14597-1             (  10) AGLDLCSAYDCVI   0
P21035-1             (  10) AGYDLYSAYDYTI   0
S26429-1             (  10) AGYDLFSAYDIKV   0
P28893-1             (  10) AGFDLSVLEDREF   1
Q00030-1             (  10) DGRLLVLINNHTV   2
//
ID   msfxinx; BLOCK
AC   msfxinxB; distance from previous block=(7,7)
DE   msf.in
BL   UNK;  width=21; seqs=33; 99.5%=1272; strength=1135 
P09254-1             (  30) NEFIKIVLPIIRDWDLQHPSI   1
A37470-1             (  30) APGENLHVRLPVAYAADAHAA   1
Q00030-2             (  30) EPDESYFVELPIVFSSSNPAV   1
P28892-1             (  30) DPDESHFVDLPIVFANSNPAV   1
P10234-1             (  30) ANGTTVVQPSLRMLHADAGPA   1
P11365-6             (  30) PQMSIQPVPVEPIPSLPLGTM   1
P06968-1             (  30) APGDTTLVPTGLAIHIADPSL   1
P43792-1             (  30) QPGETKLIPTGLSIYIADPNL   1
S44300-1             (  30) EPDETCLISTGLAIYLGHSNV   1
P31625-2             (  30) PEMGVQTLATGVFGPLPPGTV   0
P07570-2             (  30) PEMGPQALSTGIYGPLPPNTF   0
P10271-1             (  30) LEDGVSLVPTLVKGTLPEGTT   1
P21407-2             (  30) TQNSPLTLPVGIYGPLPPQTF   1
P10265-1             (  30) PGEPPQKIPTGVYGPLPEGTV   1
P11204-4             (  30) PVSDTKIIPTDVKIQVPPNSF   1
P16088-4             (  30) LPGEVKVIPTGVKLMLPKGYW   0
JQ1162-4             (  30) PAGQVKKIPIDLRINLRKNQW   0
P16901-4             (  30) PAGQVRKIPINLRINLKEDQW   0
P23427-4             (  30) PAGQVKRIAIDLKINLKKDQW   0
P03370-4             (  30) PAGQVKRIAIDLKINLKKDQW   0
P23426-4             (  30) PAGQVKRIAIDLKINLKKDQW   0
P35956-4             (  30) PAGQVKRIAIDLKINLKKDQW   0
P33459-4             (  30) EPGQVKCIPIELRLNLKKSQW   0
P32208-1             (  30) KPYNRILVRTDICLMIPDKCY   1
P32518-1             (  30) PARGKALVPTDLSIAVPQGTY   0
P33317-1             (  30) PAMGQGMVSTDISFTVPVGTY   1
P43058-1             (  30) PAHGQGLVSTDISIIVPIGTY   0
P33316-1             (  30) PPMEKAVVKTDIQIALPSGCY   0
P14597-1             (  30) PSHCSRVVFTDLLIKPPSGCY   1
P21035-1             (  30) PPGERQLIKTDISMSMPKICY   1
S26429-1             (  30) PARGRALVPTDLVFQFPPGCY   0
P28893-1             (  30) IRGCHYRLPTGLAIAVPRGYV   1
Q00030-1             (  30) SAGEFYSVLTDVGVRVACSSG   1
//
ID   msfxinx; BLOCK
AC   msfxinxC; distance from previous block=(2,2)
DE   msf.in
BL   UNK;  width=13; seqs=33; 99.5%=832; strength=1182 
P09254-1             (  53) AYIFGRSSKSRSG   0
A37470-1             (  53) PYVFGRSSCNLRG   0
Q00030-2             (  53) PCIFGRSSMNRRG   0
P28892-1             (  53) PCIFGRSSMNRRG   0
P10234-1             (  53) CYVLGRSSLNARG   0
P11365-6             (  53) GLILGRGSASTLQ   1
P06968-1             (  53) AMMLPRSGLGHKH   0
P43792-1             (  53) AVILPRSGLGHKH   0
S44300-1             (  53) ATILPRSGLGHKH   0
P31625-2             (  53) GLLLGRSSASLKG   0
P07570-2             (  53) GLILGRSSITMKG   0
P10271-1             (  53) GLIIGRSSNYKKG   0
P21407-2             (  53) GLILAEPALPSKG   1
P10265-1             (  53) GLILGRSSLNLKG   0
P11204-4             (  53) GWVTGKSSMAKQG   1
P16088-4             (  53) GLIIGKSSIGSKG   0
JQ1162-4             (  53) AMIGTKSSFASKG   0
P16901-4             (  53) AMVGTKSSFASKG   0
P23427-4             (  53) AMIGTKSSFANKG   0
P03370-4             (  53) AMIGTKSSFANKG   0
P23426-4             (  53) AMIGTKSSFANKG   0
P35956-4             (  53) AMIGTKSSFANKG   0
P33459-4             (  53) AMIATKSSMAAKG   0
P32208-1             (  53) GRISPRSGLSLNY   0
P32518-1             (  53) ARIAPRSGLAWKY   0
P33317-1             (  53) GRIAPRSGLAVKN   0
P43058-1             (  53) GRVAPRSGLAVKH   0
P33316-1             (  53) GRVAPRSGLAAKH   0
P14597-1             (  53) GRIAPRSGLAVKH   0
P21035-1             (  53) GRIAPRSGLSLKG   0
S26429-1             (  53) GRIAPRSGLAAKF   0
P28893-1             (  53) GIITPRSSQAKNF   1
Q00030-1             (  53) IVLAQISGLPHVG   1
//
ID   msfxinx; BLOCK
AC   msfxinxD; distance from previous block=(22,22)
DE   msf.in
BL   UNK;  width=15; seqs=33; 99.5%=829; strength=1203 
P09254-1             (  88) IVCPTAWPAGEHCKF   1
A37470-1             (  88) IVLPTAWPPGEPCRF   1
Q00030-2             (  88) IVLPTRWVTGRTCCF   1
P28892-1             (  88) IVLPTRWVAGRTCCF   1
P10234-1             (  88) LVVPTRWLPGHVCAF   1
P11365-6             (  88) ELWIVNIPQKYQVLC   2
P06968-1             (  88) GLIDSDYQGQLMISV   0
P43792-1             (  88) GLIDSDYQGPLMVSM   0
S44300-1             (  88) GLIDSDYQGPLMVSC   0
P31625-2             (  88) GVIDSDYTGEIKILA   0
P07570-2             (  88) GVIDNDYTGEIKIMA   0
P10271-1             (  88) GVIDSDFQGEIKVMV   0
P21407-2             (  88) GILDNDFEGEIHIIL   1
P10265-1             (  88) SVVDSDYKGEIQLVI   1
P11204-4             (  88) GIIDEGYTGEIQVIC   0
P16088-4             (  88) GVIDEGYRGEIGVIM   0
JQ1162-4             (  88) GIVDSGYQGIIQVVI   0
P16901-4             (  88) GIIDSGYQGIIQVVV   0
P23427-4             (  88) GIIDSGYQGTIQVVI   0
P03370-4             (  88) GIIDSGYQGTIQVVI   0
P23426-4             (  88) GIIDSGYQGTIQVVI   0
P35956-4             (  88) GIIDSGYQGTIQVVI   0
P33459-4             (  88) GIIDSGYQGQIQVIM   0
P32208-1             (  88) GVIDSDYRGEIGIVF   0
P32518-1             (  88) GVIDADYRGPVGVVL   0
P33317-1             (  88) GVVDRDYTGEVKVVL   0
P43058-1             (  88) GVIDADYRGEVKVVL   0
P33316-1             (  88) GVIDEDYRGNVGVVL   0
P14597-1             (  88) GVIDEDYRGNVGVVL   0
P21035-1             (  88) GVIDEDYRGNIGVIL   0
S26429-1             (  88) GVIDPDYRGNVSVVL   0
P28893-1             (  88) GIIDSDFRGHIHIMV   0
Q00030-1             (  88) GIVDSGYRGVVKAVQ   1
//
ID   msfxinx; BLOCK
AC   msfxinxE; distance from previous block=(4,4)
DE   msf.in
BL   UNK;  width=10; seqs=33; 99.5%=681; strength=976 
P09254-1             ( 107) LTGDDIRIKT   0
A37470-1             ( 107) VTQEPLVAAA   1
Q00030-2             ( 107) INKYPVYITK   0
P28892-1             ( 107) VNKYPVSITK   0
P10234-1             ( 107) LTGVPVTLEA   0
P11365-6             ( 107) SPKGVFSISK   0
P06968-1             ( 107) RGQDSFTIQP   0
P43792-1             ( 107) RGNEPFKIEV   0
S44300-1             ( 107) RGKEPYTINP   0
P31625-2             ( 107) APNKIIVINA   0
P07570-2             ( 107) AVNNIVTVSQ   0
P10271-1             ( 107) AAKNAVIIHK   0
P21407-2             ( 107) TTKDLVTIPK   0
P10265-1             ( 107) SSIPWSASPR   1
P11204-4             ( 107) IGKSNIKLIE   0
P16088-4             ( 107) VSRKSITLME   0
JQ1162-4             ( 107) SNDEEVIIPQ   0
P16901-4             ( 107) SNDKEVIIPQ   0
P23427-4             ( 107) SNNKEVVIPQ   0
P03370-4             ( 107) SNNKEVVIPQ   0
P23426-4             ( 107) SNNKEVVIPQ   0
P35956-4             ( 107) SNNKEVVIPQ   0
P33459-4             ( 107) SNKIAVVIPQ   0
P32208-1             ( 107) NGCSDFNIKV   0
P32518-1             ( 107) HSEVDFEVKV   0
P33317-1             ( 107) HSQRDFAIKK   0
P43058-1             ( 107) HSEKDFEIKE   0
P33316-1             ( 107) FGKEKFEVKK   0
P14597-1             ( 107) FGNSDFEVKK   0
P21035-1             ( 107) NGKCTFNVNT   0
S26429-1             ( 107) FSESSFNIRR   0
P28893-1             ( 107) SAIADFSVKK   0
Q00030-1             ( 107) ANGVNTVVPP   0
//
ID   msfxinx; BLOCK
AC   msfxinxF; distance from previous block=(53,53)
DE   msf.in
BL   UNK;  width=14; seqs=33; 99.5%=820; strength=1070 
P09254-1             ( 170) IAFPYAIRGKCGIP   1
A37470-1             ( 170) AAVPPSARGPRGFG   0
Q00030-2             ( 170) HDAPSSARSEGGFG   0
P28892-1             ( 170) REAPSSLRADGGFG   0
P10234-1             ( 170) KALRNYPRGVPDST   1
P11365-6             ( 170) TREKSAGPEIKKMG   1
P06968-1             ( 170) EDFDATDRGEGGFG   0
P43792-1             ( 170) EDFQQTERGEGGFG   0
S44300-1             ( 170) EEFELTERGAGGFG   0
P31625-2             ( 170) GKTINRDRQDKGFG   0
P07570-2             ( 170) DNKVQQPYRGQGSF   1
P10271-1             ( 170) NPVIKEERGSEGFG   0
P21407-2             ( 170) SNFHKPYRGASAPG   1
P10265-1             ( 170) NSEIKRIGGLVSTD   1
P11204-4             ( 170) DENKISQRGDKGFG   0
P16088-4             ( 170) KVVMDSERGDNGYG   1
JQ1162-4             ( 170) GETRKTERGNQGFG   0
P16901-4             ( 170) GETRRTERGNQGFG   0
P23427-4             ( 170) GETRKTERGEQGFG   0
P03370-4             ( 170) GETRKTERGEQGFG   0
P23426-4             ( 170) GETRKTERGEQGFG   0
P35956-4             ( 170) GETRKTERGEQGFG   0
P33459-4             ( 170) GESRKTERGEKGFG   0
P32208-1             ( 170) KCLEDTERGNSGFG   0
P32518-1             ( 170) DDLDSTVRGSGGFG   0
P33317-1             ( 170) DSLEESARGAGGFG   0
P43058-1             ( 170) EELDNTERGEGGFG   0
P33316-1             ( 170) QALDDTERGSGGFG   0
P14597-1             ( 170) NCLDNTDRGDSGFG   0
P21035-1             ( 170) QSLDSTNRGDQGFG   0
S26429-1             ( 170) TQLGETDRGASGFG   0
P28893-1             ( 170) ETLERTRRGTGGFG   0
Q00030-1             ( 170) ETINVTNINLTENG   1
//
blimps-3.9/examples/processor/distribution/msf.in.seqs000064400001460000012000000155671062461143300236270ustar00jorjastaff00000400000027>P09254-1   
*****KRQEDAGYDICVPYNLYLKR*****NEFIKIVLPIIRDWDLQHPSI*NAYIFGRS
SKSRSGI*********************IVCPTAWPAGEHCKFYVYNLTGDDIRIKTGDR
LAQVLLIDHNTQ****************************IHLKHNVLSNIAFPYAIRGK
CGIPGVQ*********
>A37470-1   
*TFAPKRDEDAGYDIAMPYTAVL*******APGENLHVRLPVAYAADAHAA*APYVFGRS
SCNLRGL*********************IVLPTAWPPGEPCRFVLRNVTQEPLVAAAGQR
VAQLLLLARRLE*WLPSGLNDREPFPTSPRAAPPAPGAPRLRWRRVADLAAAVPPSARGP
RGFGSTGL********
>Q00030-2   
DYFAPKRDEDAGYDISAQTNATI*******EPDESYFVELPIVFSSSNPAV*TPCIFGRS
SMNRRGL*********************IVLPTRWVTGRTCCFFILNINKYPVYITKGQR
VAQLVLTEDIDEALIPTNVNYNTPFPTYSPTGAVKHNPTPILWKFTEAFDHDAPSSARSE
GGFGST**********
>P28892-1   
*****KRVEDAGYDISAPEDATI*******DPDESHFVDLPIVFANSNPAV*TPCIFGRS
SMNRRGL*********************IVLPTRWVAGRTCCFFILNVNKYPVSITKGQR
VAQLLLTEDIDDALIPPTVNYDNPFPTYSPSESTKAPQSPVLWKFTTDFDREAPSSLRAD
GGFGSTGL********
>P10234-1   
*****KREEDAGFDIVVRRPVTV*P*****ANGTTVVQPSLRMLHADAGPA*ACYVLGRS
SLNARGL*********************LVVPTRWLPGHVCAFVVYNLTGVPVTLEAGAK
VAQLLVAGADALPWIPP***************************DNFHGTKALRNYPRGV
PDSTAEPR********
>P11365-6   
**********HKVDLRAASDFLL*M*****PQMSIQPVPVEPIPSLPLGTM**GLILGRG
SASTLQG****************LVVHPELWIVNIPQKYQVLC***SSPKGVFSISKGDR
IPQLLLL***************************************LPDNTREKSAGPEI
KKMGS***********
>P06968-1   
****YATSGSAGLDLRACLNDAVEL*****APGDTTLVPTGLAIHIADPSL*AAMMLPRS
GLGHKHG**************IVLGNLVGLIDSDYQGQLMISVW**NRGQDSFTIQPGER
IAQMIFVPVVQ*********************************AEFNLVEDFDATDRGE
GGFGHSGR********
>P43792-1   
****YATEGSAGLDLRALIDESFEI*****QPGETKLIPTGLSIYIADPNL*AAVILPRS
GLGHKHG**************IVLGNLVGLIDSDYQGPLMVSMW**NRGNEPFKIEVGDR
IAQLVFVPVVQ*********************************AEFNIVEDFQQTERGE
GGFGHSGK********
>S44300-1   
****YATTGSAGLDLRACLDEPLKI*****EPDETCLISTGLAIYLGHSNV*AATILPRS
GLGHKHG**************IVLGNLVGLIDSDYQGPLMVSCW**NRGKEPYTINPGDR
IAQLVVLPILK*********************************AQFAVVEEFELTERGA
GGFGSSGQ********
>P31625-2   
*****ATRGSAGLDLCATSYTVL*T*****PEMGVQTLATGVFGPLPPGTV**GLLLGRS
SASLKG*****************ILIHPGVIDSDYTGEIKILA***SAPNKIIVINAGQR
IAQLLLVPLV**************************************IQGKTINRDRQD
KGFG************
>P07570-2   
****RATPGSAGLDLCSTSHTVL*T*****PEMGPQALSTGIYGPLPPNTF**GLILGRS
SITMKG*****************LQVYPGVIDNDYTGEIKIMA***KAVNNIVTVSQGNR
IAQLILLPLI**************************************ETDNKVQQPYRG
QGSFGSSDI*******
>P10271-1   
*****GTPGSAGLDLSSQKDLIL*S*****LEDGVSLVPTLVKGTLPEGTT**GLIIGRS
SNYKKG*****************LEVLPGVIDSDFQGEIKVMV***KAAKNAVIIHKGER
IAQLLLLPY*************************************LKLPNPVIKEERGS
EGFG************
>P21407-2   
****RATAGSAGLDLCTTTDTIL*T*****TQNSPLTLPVGIYGPLPPQTF**GLILAEP
ALPSKG*****************IQVLPGILDNDFEGEIHIIL***STTKDLVTIPKGTR
LAQIVILPLQ*************************************QINSNFHKPYRGA
SAPG************
>P10265-1   
*****TTSGSAAVDLCTIQAVSL*L*****PGEPPQKIPTGVYGPLPEGTV**GLILGRS
SLNLKG*****************VQIHTSVVDSDYKGEIQLVI***SSSIPWSASPR*DR
IAQLLLLPY*************************************IKGGNSEIKRIGGL
VSTDP***********
>P11204-4   
*QIKEKRDEDAGFDLCVPYDIMI*******PVSDTKIIPTDVKIQVPPNSF**GWVTGKS
SMAKQG*****************LLINGGIIDEGYTGEIQVICT**NIGKSNIKLIEGQK
FAQLIILQHHS*********************************NSRQPWDENKISQRGD
KGFGSTGVF**WVENI
>P16088-4   
***LDKRSEDAGYDLLAAKEIHL*******LPGEVKVIPTGVKLMLPKGYW**GLIIGKS
SIGSKG*****************LDVLGGVIDEGYRGEIGVIMI**NVSRKSITLMERQK
IAQLIILPCKH*********************************EVLEQGKVVMDSERGD
NGYGSTGVFSSWVDRI
>JQ1162-4   
**IVKKRAEDAGYDLICPQEVSI*******PAGQVKKIPIDLRINLRKNQW**AMIGTKS
SFASKG*****************VFVQGGIVDSGYQGIIQVVIY**NSNDEEVIIPQGRK
FAQLILMPLIH*********************************EELEPWGETRKTERGN
QGFGSTGAY**WIENI
>P16901-4   
**ILPKRAEDAGYDLICPQEVCI*******PAGQVRKIPINLRINLKEDQW**AMVGTKS
SFASKG*****************VFVQGGIIDSGYQGIIQVVVY**NSNDKEVIIPQGRK
FAQLILMPLIH*********************************EDLEAWGETRRTERGN
QGFGSTGAY**WIENI
>P23427-4   
**ILQKRAEDAGYDLICPQEISI*******PAGQVKRIAIDLKINLKKDQW**AMIGTKS
SFANKG*****************VFVQGGIIDSGYQGTIQVVIY**NSNNKEVVIPQGRK
FAQLILMPLIH*********************************EELKPWGETRKTERGE
QGFGSTGMY**WIENI
>P03370-4   
**ILQKRAEDAGYDLICPQEISI*******PAGQVKRIAIDLKINLKKDQW**AMIGTKS
SFANKG*****************VFVQGGIIDSGYQGTIQVVIY**NSNNKEVVIPQGRK
FAQLILMPLIH*********************************EELEPWGETRKTERGE
QGFGSTGMY**WIENI
>P23426-4   
**ILQKRAEDAGYDLICPQEISI*******PAGQVKRIAIDLKINLKKDQW**AMIGTKS
SFANKG*****************VFVQGGIIDSGYQGTIQVVIY**NSNNKEVVIPQGRK
FAQLILMPLIH*********************************EELEPWGETRKTERGE
QGFGSTGMY**WIENI
>P35956-4   
**ILQKRAEDAGYDLICPQEISI*******PAGQVKRIAIDLKINLKKDQW**AMIGTKS
SFANKG*****************VFVQGGIIDSGYQGTIQVVIY**NSNNKEVVIPQGRK
FAQLILMPLIH*********************************EELEPWGETRKTERGE
QGFGSTGMY**WIENI
>P33459-4   
**ILPKREEDAGYDLICPEEVTI*******EPGQVKCIPIELRLNLKKSQW**AMIATKS
SMAAKG*****************VFTQGGIIDSGYQGQIQVIMY**NSNKIAVVIPQGRK
FAQLILMDKKH*********************************GKLEPWGESRKTERGE
KGFGSTGMY**WIENI
>P32208-1   
*****SMSGSAGYDLYSAYSYTV*******KPYNRILVRTDICLMIPDKCY**GRISPRS
GLSLNYN****************IDIGGGVIDSDYRGEIGIVFI**NNGCSDFNIKVGDR
IAQIIFERVEY*********************************PIMEEVKCLEDTERGN
SGFGSSGM********
>P32518-1   
*****ASSLAAGYDLSSAAETKV*******PARGKALVPTDLSIAVPQGTY**ARIAPRS
GLAWKYS****************IDVGAGVIDADYRGPVGVVLF**NHSEVDFEVKVGDR
IAQLIVQKIVT*********************************PEVEQVDDLDSTVRGS
GGFGSTGV********
>P33317-1   
*****GSATAAGYDIYASQDITI*******PAMGQGMVSTDISFTVPVGTY**GRIAPRS
GLAVKNG****************IQTGAGVVDRDYTGEVKVVLF**NHSQRDFAIKKGDR
VAQLILEKIVDD********************************AQIVVVDSLEESARGA
GGFGSTGN********
>P43058-1   
*****GSALAAGYDLYSAEAATI*******PAHGQGLVSTDISIIVPIGTY**GRVAPRS
GLAVKHG****************ISTGAGVIDADYRGEVKVVLF**NHSEKDFEIKEGDR
IAQLVLEQIVNA*******************************DIKEISLEELDNTERGE
GGFGSTGK********
>P33316-1   
*****GSARAAGYDLYSAYDYTI*******PPMEKAVVKTDIQIALPSGCY**GRVAPRS
GLAAKHF****************IDVGAGVIDEDYRGNVGVVLF**NFGKEKFEVKKGDR
IAQLICERIFY*********************************PEIEEAQALDDTERGS
GGFGSTGK********
>P14597-1   
*****GSPGAAGLDLCSAYDCVI*******PSHCSRVVFTDLLIKPPSGCY**GRIAPRS
GLAVKHF****************IDVGAGVIDEDYRGNVGVVLF**NFGNSDFEVKKGDR
IAQLICERISC*********************************PAVQEVNCLDNTDRGD
SGFGSTGS********
>P21035-1   
*****QSPGAAGYDLYSAYDYTI*******PPGERQLIKTDISMSMPKICY**GRIAPRS
GLSLKG*****************IDIGGGVIDEDYRGNIGVILI**NNGKCTFNVNTGDR
IAQLIYQRIYY*********************************PELEEVQSLDSTNRGD
QGFGSTGL********
>S26429-1   
*****ATHGAAGYDLFSAYDIKV*******PARGRALVPTDLVFQFPPGCY**GRIAPRS
GLAAKFF****************IDVGAGVIDPDYRGNVSVVLF**NFSESSFNIRRGDR
VAQLILERIMV*********************************PELSELTQLGETDRGA
SGFGFTGM********
>P28893-1   
*****SSPGSAGFDLSVLEDREF*******IRGCHYRLPTGLAIAVPRGYV**GIITPRS
SQAKNF*******************VSTGIIDSDFRGHIHIMV****SAIADFSVKKNQR
IAQLVVTPCLT********************************QSEVVPYETLERTRRGT
GGFGSSGQ********
>Q00030-1   
*****ARAEADGRLLVLINNHTVELSAGLGSAGEFYSVLTDVGVRVACSSGYAIVLAQIS
GLPHVGREPGNFSNITFTGNLANYYTAYGIVDSGYRGVVKAVQF***ANGVNTVVPPGCM
SLGLVLVKLST***************************************ETINVTNINL
TENGRSPRVNIFY***


blimps-3.9/examples/processor/distribution/msf.in.wblks000064400001460000012000000237661062461143300237760ustar00jorjastaff00000400000027ID   msfxinx; BLOCK
AC   msfxinxA; distance from previous block=(10,10)
DE   msf.in
BL   UNK;   width=13; seqs=33; 99.5%=811; strength=1146 
P09254-1             (  10) AGYDICVPYNLYL  24
A37470-1             (  10) AGYDIAMPYTAVL  37
Q00030-2             (  10) AGYDISAQTNATI  22
P28892-1             (  10) AGYDISAPEDATI  16
P10234-1             (  10) AGFDIVVRRPVTV  42
P11365-6             (  10) HKVDLRAASDFLL  69
P06968-1             (  10) AGLDLRACLNDAV  29
P43792-1             (  10) AGLDLRALIDESF  29
S44300-1             (  10) AGLDLRACLDEPL  24
P31625-2             (  10) AGLDLCATSYTVL  23
P07570-2             (  10) AGLDLCSTSHTVL  23
P10271-1             (  10) AGLDLSSQKDLIL  21
P21407-2             (  10) AGLDLCTTTDTIL  22
P10265-1             (  10) AAVDLCTIQAVSL  47
P11204-4             (  10) AGFDLCVPYDIMI  20
P16088-4             (  10) AGYDLLAAKEIHL  24
JQ1162-4             (  10) AGYDLICPQEVSI  12
P16901-4             (  10) AGYDLICPQEVCI  16
P23427-4             (  10) AGYDLICPQEISI  11
P03370-4             (  10) AGYDLICPQEISI  11
P23426-4             (  10) AGYDLICPQEISI  11
P35956-4             (  10) AGYDLICPQEISI  11
P33459-4             (  10) AGYDLICPEEVTI  12
P32208-1             (  10) AGYDLYSAYSYTV  20
P32518-1             (  10) AGYDLSSAAETKV  20
P33317-1             (  10) AGYDIYASQDITI  21
P43058-1             (  10) AGYDLYSAEAATI  15
P33316-1             (  10) AGYDLYSAYDYTI  12
P14597-1             (  10) AGLDLCSAYDCVI  17
P21035-1             (  10) AGYDLYSAYDYTI  12
S26429-1             (  10) AGYDLFSAYDIKV  20
P28893-1             (  10) AGFDLSVLEDREF  35
Q00030-1             (  10) DGRLLVLINNHTV 100
//
ID   msfxinx; BLOCK
AC   msfxinxB; distance from previous block=(7,7)
DE   msf.in
BL   UNK;   width=21; seqs=33; 99.5%=1272; strength=1135 
P09254-1             (  30) NEFIKIVLPIIRDWDLQHPSI  89
A37470-1             (  30) APGENLHVRLPVAYAADAHAA  67
Q00030-2             (  30) EPDESYFVELPIVFSSSNPAV  55
P28892-1             (  30) DPDESHFVDLPIVFANSNPAV  62
P10234-1             (  30) ANGTTVVQPSLRMLHADAGPA 100
P11365-6             (  30) PQMSIQPVPVEPIPSLPLGTM  77
P06968-1             (  30) APGDTTLVPTGLAIHIADPSL  37
P43792-1             (  30) QPGETKLIPTGLSIYIADPNL  35
S44300-1             (  30) EPDETCLISTGLAIYLGHSNV  42
P31625-2             (  30) PEMGVQTLATGVFGPLPPGTV  30
P07570-2             (  30) PEMGPQALSTGIYGPLPPNTF  34
P10271-1             (  30) LEDGVSLVPTLVKGTLPEGTT  39
P21407-2             (  30) TQNSPLTLPVGIYGPLPPQTF  58
P10265-1             (  30) PGEPPQKIPTGVYGPLPEGTV  42
P11204-4             (  30) PVSDTKIIPTDVKIQVPPNSF  44
P16088-4             (  30) LPGEVKVIPTGVKLMLPKGYW  25
JQ1162-4             (  30) PAGQVKKIPIDLRINLRKNQW  28
P16901-4             (  30) PAGQVRKIPINLRINLKEDQW  32
P23427-4             (  30) PAGQVKRIAIDLKINLKKDQW  19
P03370-4             (  30) PAGQVKRIAIDLKINLKKDQW  19
P23426-4             (  30) PAGQVKRIAIDLKINLKKDQW  19
P35956-4             (  30) PAGQVKRIAIDLKINLKKDQW  19
P33459-4             (  30) EPGQVKCIPIELRLNLKKSQW  31
P32208-1             (  30) KPYNRILVRTDICLMIPDKCY  58
P32518-1             (  30) PARGKALVPTDLSIAVPQGTY  25
P33317-1             (  30) PAMGQGMVSTDISFTVPVGTY  35
P43058-1             (  30) PAHGQGLVSTDISIIVPIGTY  34
P33316-1             (  30) PPMEKAVVKTDIQIALPSGCY  29
P14597-1             (  30) PSHCSRVVFTDLLIKPPSGCY  56
P21035-1             (  30) PPGERQLIKTDISMSMPKICY  43
S26429-1             (  30) PARGRALVPTDLVFQFPPGCY  32
P28893-1             (  30) IRGCHYRLPTGLAIAVPRGYV  49
Q00030-1             (  30) SAGEFYSVLTDVGVRVACSSG  72
//
ID   msfxinx; BLOCK
AC   msfxinxC; distance from previous block=(2,2)
DE   msf.in
BL   UNK;   width=13; seqs=33; 99.5%=832; strength=1182 
P09254-1             (  53) AYIFGRSSKSRSG  37
A37470-1             (  53) PYVFGRSSCNLRG  34
Q00030-2             (  53) PCIFGRSSMNRRG  28
P28892-1             (  53) PCIFGRSSMNRRG  28
P10234-1             (  53) CYVLGRSSLNARG  35
P11365-6             (  53) GLILGRGSASTLQ  71
P06968-1             (  53) AMMLPRSGLGHKH  36
P43792-1             (  53) AVILPRSGLGHKH  21
S44300-1             (  53) ATILPRSGLGHKH  25
P31625-2             (  53) GLLLGRSSASLKG  27
P07570-2             (  53) GLILGRSSITMKG  32
P10271-1             (  53) GLIIGRSSNYKKG  36
P21407-2             (  53) GLILAEPALPSKG 100
P10265-1             (  53) GLILGRSSLNLKG  14
P11204-4             (  53) GWVTGKSSMAKQG  41
P16088-4             (  53) GLIIGKSSIGSKG  24
JQ1162-4             (  53) AMIGTKSSFASKG  17
P16901-4             (  53) AMVGTKSSFASKG  19
P23427-4             (  53) AMIGTKSSFANKG  17
P03370-4             (  53) AMIGTKSSFANKG  17
P23426-4             (  53) AMIGTKSSFANKG  17
P35956-4             (  53) AMIGTKSSFANKG  17
P33459-4             (  53) AMIATKSSMAAKG  17
P32208-1             (  53) GRISPRSGLSLNY  35
P32518-1             (  53) ARIAPRSGLAWKY  25
P33317-1             (  53) GRIAPRSGLAVKN  26
P43058-1             (  53) GRVAPRSGLAVKH  18
P33316-1             (  53) GRVAPRSGLAAKH  17
P14597-1             (  53) GRIAPRSGLAVKH  16
P21035-1             (  53) GRIAPRSGLSLKG  15
S26429-1             (  53) GRIAPRSGLAAKF  19
P28893-1             (  53) GIITPRSSQAKNF  44
Q00030-1             (  53) IVLAQISGLPHVG  88
//
ID   msfxinx; BLOCK
AC   msfxinxD; distance from previous block=(22,22)
DE   msf.in
BL   UNK;   width=15; seqs=33; 99.5%=829; strength=1203 
P09254-1             (  88) IVCPTAWPAGEHCKF  48
A37470-1             (  88) IVLPTAWPPGEPCRF  44
Q00030-2             (  88) IVLPTRWVTGRTCCF  43
P28892-1             (  88) IVLPTRWVAGRTCCF  38
P10234-1             (  88) LVVPTRWLPGHVCAF  57
P11365-6             (  88) ELWIVNIPQKYQVLC 100
P06968-1             (  88) GLIDSDYQGQLMISV  20
P43792-1             (  88) GLIDSDYQGPLMVSM  18
S44300-1             (  88) GLIDSDYQGPLMVSC  18
P31625-2             (  88) GVIDSDYTGEIKILA  15
P07570-2             (  88) GVIDNDYTGEIKIMA  17
P10271-1             (  88) GVIDSDFQGEIKVMV  14
P21407-2             (  88) GILDNDFEGEIHIIL  26
P10265-1             (  88) SVVDSDYKGEIQLVI  35
P11204-4             (  88) GIIDEGYTGEIQVIC  13
P16088-4             (  88) GVIDEGYRGEIGVIM  12
JQ1162-4             (  88) GIVDSGYQGIIQVVI  13
P16901-4             (  88) GIIDSGYQGIIQVVV  12
P23427-4             (  88) GIIDSGYQGTIQVVI  10
P03370-4             (  88) GIIDSGYQGTIQVVI  10
P23426-4             (  88) GIIDSGYQGTIQVVI  10
P35956-4             (  88) GIIDSGYQGTIQVVI  10
P33459-4             (  88) GIIDSGYQGQIQVIM  13
P32208-1             (  88) GVIDSDYRGEIGIVF  10
P32518-1             (  88) GVIDADYRGPVGVVL  13
P33317-1             (  88) GVVDRDYTGEVKVVL  17
P43058-1             (  88) GVIDADYRGEVKVVL  12
P33316-1             (  88) GVIDEDYRGNVGVVL  11
P14597-1             (  88) GVIDEDYRGNVGVVL  11
P21035-1             (  88) GVIDEDYRGNIGVIL  11
S26429-1             (  88) GVIDPDYRGNVSVVL  20
P28893-1             (  88) GIIDSDFRGHIHIMV  22
Q00030-1             (  88) GIVDSGYRGVVKAVQ  31
//
ID   msfxinx; BLOCK
AC   msfxinxE; distance from previous block=(4,4)
DE   msf.in
BL   UNK;   width=10; seqs=33; 99.5%=681; strength=976 
P09254-1             ( 107) LTGDDIRIKT  53
A37470-1             ( 107) VTQEPLVAAA  86
Q00030-2             ( 107) INKYPVYITK  43
P28892-1             ( 107) VNKYPVSITK  31
P10234-1             ( 107) LTGVPVTLEA  48
P11365-6             ( 107) SPKGVFSISK  51
P06968-1             ( 107) RGQDSFTIQP  43
P43792-1             ( 107) RGNEPFKIEV  35
S44300-1             ( 107) RGKEPYTINP  46
P31625-2             ( 107) APNKIIVINA  40
P07570-2             ( 107) AVNNIVTVSQ  53
P10271-1             ( 107) AAKNAVIIHK  47
P21407-2             ( 107) TTKDLVTIPK  44
P10265-1             ( 107) SSIPWSASPR 100
P11204-4             ( 107) IGKSNIKLIE  58
P16088-4             ( 107) VSRKSITLME  63
JQ1162-4             ( 107) SNDEEVIIPQ  26
P16901-4             ( 107) SNDKEVIIPQ  25
P23427-4             ( 107) SNNKEVVIPQ  17
P03370-4             ( 107) SNNKEVVIPQ  17
P23426-4             ( 107) SNNKEVVIPQ  17
P35956-4             ( 107) SNNKEVVIPQ  17
P33459-4             ( 107) SNKIAVVIPQ  30
P32208-1             ( 107) NGCSDFNIKV  44
P32518-1             ( 107) HSEVDFEVKV  35
P33317-1             ( 107) HSQRDFAIKK  39
P43058-1             ( 107) HSEKDFEIKE  30
P33316-1             ( 107) FGKEKFEVKK  35
P14597-1             ( 107) FGNSDFEVKK  26
P21035-1             ( 107) NGKCTFNVNT  57
S26429-1             ( 107) FSESSFNIRR  48
P28893-1             ( 107) SAIADFSVKK  45
Q00030-1             ( 107) ANGVNTVVPP  53
//
ID   msfxinx; BLOCK
AC   msfxinxF; distance from previous block=(53,53)
DE   msf.in
BL   UNK;   width=14; seqs=33; 99.5%=820; strength=1070 
P09254-1             ( 170) IAFPYAIRGKCGIP  73
A37470-1             ( 170) AAVPPSARGPRGFG  42
Q00030-2             ( 170) HDAPSSARSEGGFG  37
P28892-1             ( 170) REAPSSLRADGGFG  41
P10234-1             ( 170) KALRNYPRGVPDST  75
P11365-6             ( 170) TREKSAGPEIKKMG  97
P06968-1             ( 170) EDFDATDRGEGGFG  19
P43792-1             ( 170) EDFQQTERGEGGFG  21
S44300-1             ( 170) EEFELTERGAGGFG  18
P31625-2             ( 170) GKTINRDRQDKGFG  38
P07570-2             ( 170) DNKVQQPYRGQGSF 100
P10271-1             ( 170) NPVIKEERGSEGFG  40
P21407-2             ( 170) SNFHKPYRGASAPG  69
P10265-1             ( 170) NSEIKRIGGLVSTD  93
P11204-4             ( 170) DENKISQRGDKGFG  36
P16088-4             ( 170) KVVMDSERGDNGYG  46
JQ1162-4             ( 170) GETRKTERGNQGFG  11
P16901-4             ( 170) GETRRTERGNQGFG  14
P23427-4             ( 170) GETRKTERGEQGFG  10
P03370-4             ( 170) GETRKTERGEQGFG  10
P23426-4             ( 170) GETRKTERGEQGFG  10
P35956-4             ( 170) GETRKTERGEQGFG  10
P33459-4             ( 170) GESRKTERGEKGFG  18
P32208-1             ( 170) KCLEDTERGNSGFG  19
P32518-1             ( 170) DDLDSTVRGSGGFG  21
P33317-1             ( 170) DSLEESARGAGGFG  20
P43058-1             ( 170) EELDNTERGEGGFG  11
P33316-1             ( 170) QALDDTERGSGGFG  17
P14597-1             ( 170) NCLDNTDRGDSGFG  18
P21035-1             ( 170) QSLDSTNRGDQGFG  18
S26429-1             ( 170) TQLGETDRGASGFG  31
P28893-1             ( 170) ETLERTRRGTGGFG  29
Q00030-1             ( 170) ETINVTNINLTENG  98
//
blimps-3.9/examples/processor/test.csh000075500001460000012000000002411062461140400204570ustar00jorjastaff00000400000027#!/bin/csh
#
set ins = (*.in)
foreach in ($ins)
        ./process.csh $in
        echo "Checking $in..."
        diff $in.wblks distribution/$in.wblks
end

exit
blimps-3.9/examples/protomat/000075500001460000012000000000001043043306600166305ustar00jorjastaff00000400000027blimps-3.9/examples/protomat/README000064400001460000012000000010660733525425400175250ustar00jorjastaff00000400000027	Sample files for protomat (Block Maker)



S. Henikoff, J. G. Henikoff, W. J. Alford & S. Pietrokovski, "Automated 
construction and graphical presentation of protein blocks from unaligned 
sequences", Gene-COMBIS, Gene 163 (1995) GC 17-26. 


Protomat uses Ham Smith's "motif" algorithm as implemented in Block Maker:
http://blocks.fhcrc.org/blockmkr/make_blocks.html

protomat.csh runs the protomat system to construct blocks from an
input of of protein sequences in fasta format. Example is:
	protomat.csh lipo.pros

Compare results with files in distribution/

blimps-3.9/examples/protomat/calibrate.csh000075500001460000012000000023750772350633100212760ustar00jorjastaff00000400000027#!/bin/csh
#		Theoretical calibration
#		Create blks_final/ first
#
unalias rm
unalias mv
unalias cp

set docs = /howard/servers/blimps/blimps-3.5/docs
set bin = /howard/servers/blimps/blimps-3.5/bin
#	Use a .frq where the 20aas add up to exactly 1.00000
set frq = $docs/default.amino.frq

#	SWISS 38 sequences & residues
set NSEQ = 80000
set NRES = 29085965

rm pssmdist.dat
set ps = (process.PRa process.PRb bad.PR)
foreach p ($ps)
 set entries = (`awk '{ print $1 }' $p`)
 foreach ipb ($entries)

   set blks = blks_add/$ipb.blks
   set new = blks_final/$ipb.blks
   set mats = $ipb.mats
   set obsf = $ipb.obsf

   #       Make matrices and observed frequency files:
   $bin/blk2pssm $blks $mats B 3
   $bin/blk2pssm $blks $obsf B 21
#
#		writes pssmdist.dat
   $bin/pssmdist $mats $obsf $frq $NSEQ $NRES >& /dev/null
   $bin/pssmBL pssmdist.dat $blks $ipb.temp
   cat pssmdist.dat >> pssmdist.$p
   rm pssmdist.dat $ipb.cf $mats $obsf >& /dev/null

#	800seqs is made by addseqs.pl
   set flag = `grep -c $ipb 800seqs`
   if (flag == 0) then
      $bin/blweight $ipb.temp $ipb.c80 C80 M >& /dev/null
      $bin/blweight $ipb.c80 $new P M >& /dev/null
      rm $ipb.c80
   else
      $bin/blweight $ipb.temp $new P M >& /dev/null
   endif
   rm $ipb.temp

 end
end

exit(0)
blimps-3.9/examples/protomat/lipo.pros000064400001460000012000000023430625733061200205070ustar00jorjastaff00000400000027
>BBP_PIEBR BILIN-BINDING PROTEIN (BBP) 
NVYHDGACPE VKPVDNFDWS NYHGKWWEVA KYPNSVEKYG KCGWAEYTPE GKSVKVSNYH
VIHGKEYFIE GTAYPVGDSK IGKIYHKLTY GGVTKENVFN VLSTDNKNYI IGYYCKYDED
KKGHQDFVWV LSRSKVLTGE AKTAVENYLI GSPVVDSQKL VYSDFSEAAC KVN

>ICYA_MANSE INSECTICYANIN A FORM (BLUE BILIPROTEIN) 
GDIFYPGYCP DVKPVNDFDL SAFAGAWHEI AKLPLENENQ GKCTIAEYKY DGKKASVYNS
FVSNGVKEYM EGDLEIAPDA KYTKQGKYVM TFKFGQRVVN LVPWVLATDY KNYAINYNCD
YHPDKKAHSI HAWILSKSKV LEGNTKEVVD NVLKTFSHLI DASKFISNDF SEAACQYSTT
YSLTGPDRH

>LACB_BOVIN BETA-LACTOGLOBULIN PRECURSOR (BETA-LG) 
MKCLLLALAL TCGAQALIVT QTMKGLDIQK VAGTWYSLAM AASDISLLDA QSAPLRVYVE
ELKPTPEGDL EILLQKWENG ECAQKKIIAE KTKIPAVFKI DALNENKVLV LDTDYKKYLL
FCMENSAEPE QSLACQCLVR TPEVDDEALE KFDKALKALP MHIRLSFNPT QLEEQCHI

>MUP2_MOUSE MAJOR URINARY PROTEIN 2 PRECURSOR (MUP 2) 
MKMLLLLCLG LTLVCVHAEE ASSTGRNFNV EKINGEWHTI ILASDKREKI EDNGNFRLFL
EQIHVLEKSL VLKFHTVRDE ECSELSMVAD KTEKAGEYSV TYDGFNTFTI PKTDYDNFLM
AHLINEKDGE TFQLMGLYGR EPDLSSDIKE RFAKLCEEHG ILRENIIDLS NANRCLQARE

>RETB_BOVIN PLASMA RETINOL-BINDING PROTEIN (PRBP) 
ERDCRVSSFR VKENFDKARF AGTWYAMAKK DPEGLFLQDN IVAEFSVDEN GHMSATAKGR
VRLLNNWDVC ADMVGTFTDT EDPAKFKMKY WGVASFLQKG NDDHWIIDTD YETFAVQYSC
RLLNLDGTCA DSYSFVFARD PSGFSPEVQK IVRQRQEELC LARQYRLIPH NGYCDGKSER
NIL
blimps-3.9/examples/protomat/protomat.csh000075500001460000012000000060131041506107000211720ustar00jorjastaff00000400000027#!/bin/csh

#    protomat.csh 
#	Output files written with same prefix as input file:
#		.out	blocks in "pretty" format
#		.mblks	blocks 
#		.mcob	cobbler sequence
#		.mmap	block map
#		.mmast	PSSM for mast

setenv BLIMPS_DIR ../..
set bindir = ../../bin
set path = ($bindir $path)
#       SWISS 38 sequences & residues for calibrate step
set NSEQ = 80000
set NRES = 29085965
unalias rm
unalias mv
unalias cp
limit coredumpsize 1k
limit datasize 32m

set pros = $1
set r = $pros:r
set frq = $BLIMPS_DIR/docs/default.amino.frq

#  makelis reads $prefix.in and writes $prefix.lis, .pros, .seqlen, .err, .warn
#$bindir/makelis $prefix $return

#	Find out how many sequences there are
set nseq = (`grep -c '^>' $pros`)
if ( $nseq > 250 ) then
   echo -n "ERROR: Your input has $nseq sequences which" >> $r.out
   echo " exceed's Block Maker's limit of 250 $nseq sequences" >> $r.out
   exit(-1)
endif

#	Make blocks from the proteins (motifj executes motomat)
#	NOTE: motifj writes $r.motifj.pros with MINIMUM seq len marked for gibbs
echo "              **BLOCKS from MOTIF**" >> $r.out
echo " " >> $r.out
#	For dups:  motifj 4 -$pros 0 dups 17 (0 seqs => n/2 to start)
$bindir/motifj 4 -$r.pros >& /dev/null
#  Run motomat again so sequences are NOT clumped (users want original order)
$bindir/motomat $r.mot 1 1 -10 >& /dev/null

if ( -e $r.blks ) then
   # Calibrate blocks for blimps searching
   #	Compute searching PSSMs
   $bindir/blk2pssm $r.blks $r.mats B 3 >& /dev/null
   #	Compute frequency PSSMs for true positive distribution
   $bindir/blk2pssm $r.blks $r.obsf B 21 >& /dev/null
   #    Calculate theoretical score distribution, writes pssmdist.dat
   $bindir/pssmdist $r.mats $r.obsf $frq $NSEQ $NRES >& /dev/null
   #    Insert blimps scoring info in blocks on BL line
   $bindir/pssmBL pssmdist.dat $r.blks $r.cblks >& /dev/null
   rm pssmdist.dat $r.mats $r.obsf >& /dev/null

   # Add position-specific sequence weights to blocks
   $bindir/blweight $r.cblks $r.mblks P M >& /dev/null
   #	Produce a "multiple alignment"
   $bindir/blalign $r.mblks >> $r.out
   #	Make cobbler sequence = $r.mcob
   echo "TY	2"	     > $r.cf
   echo "BL	$r.mblks"   >> $r.cf
   echo "DB	$r.pros"    >> $r.cf
   echo "OU	$r.mcob"    >> $r.cf
   echo "SU	$BLIMPS_DIR/docs/default.iij" >> $r.cf
   $bindir/cobbler $r.cf >& /dev/null
   #		Show the cobbler sequence now
   echo "" >> $r.out
   echo "" >> $r.out
   echo "      **COBBLER sequence from MOTIF**" >> $r.out
   cat $r.mcob | tr '\015' ' ' >> $r.out
else
   echo "ERROR: No blocks produced by MOTIF" >> $r.out
endif
#
#
#
#---------------------------------------------------------------------------
#	Format PSSMs for MAST searches & make map files
if (-e $r.mblks) then
   $bindir/blk2pssm $r.mblks $r.mmast M >& /dev/null
   #	Make block map files
   $bindir/makeblockmap $r.mblks $r.mmap >& /dev/null
endif

#---------------------------------------------------------------------------

#   	Clean up
rm motomat.err $r.mot $r.blks $r.cblks $r.cf $r.motifj.pros >& /dev/null
exit(0)
blimps-3.9/examples/protomat/distribution/000075500001460000012000000000001041506223500213465ustar00jorjastaff00000400000027blimps-3.9/examples/protomat/distribution/lipo.mblks000064400001460000012000000013331062461167300233530ustar00jorjastaff00000400000027ID   none; BLOCK
AC   lipoxxxA; distance from previous block=(13,26)
DE   none
BL   DWA;   width=14; seqs=5; 99.5%=668; strength=1305 
BBP_PIEBR            (  16) NFDWSNYHGKWWEV  93
ICYA_MANSE           (  17) DFDLSAFAGAWHEI  80
LACB_BOVIN           (  25) GLDIQKVAGTWYSL 100
MUP2_MOUSE           (  27) NFNVEKINGEWHTI 100
RETB_BOVIN           (  14) NFDKARFAGTWYAM  81
//
ID   none; BLOCK
AC   lipoxxxB; distance from previous block=(69,78)
DE   none
BL   TDY;   width=11; seqs=5; 99.5%=656; strength=1309 
BBP_PIEBR            ( 101) VLSTDNKNYII  89
ICYA_MANSE           ( 105) VLATDYKNYAI  68
LACB_BOVIN           ( 110) VLDTDYKKYLL  76
MUP2_MOUSE           ( 110) IPKTDYDNFLM  96
RETB_BOVIN           ( 106) IIDTDYETFAV 100
//
blimps-3.9/examples/protomat/distribution/lipo.mcob000064400001460000012000000004011062461167300231560ustar00jorjastaff00000400000027>lipoxxx ICYA_MANSE from 1 to 189 with embedded consensus blocks
gdifypgycpdvkpvnNFDVSKFAGTWYEIaklplenenqgkctiaeykydgkkasvynsfvsngvkeymegdleiapda
kytkqgkyvmtfkfgqrvvnlvpwVLDTDYKNYLInyncdyhpdkkahsihawilskskvlegntkevvdnvlktfshli
daskfisndfseaacqysttysltgpdrh
blimps-3.9/examples/protomat/distribution/lipo.mmap000064400001460000012000000003141062461167300231730ustar00jorjastaff00000400000027>lipoxxx 2 5 120 none
none
BBP_PIEBR 111 2
A 16 29
B 101 111
ICYA_MANSE 115 2
A 17 30
B 105 115
LACB_BOVIN 120 2
A 25 38
B 110 120
MUP2_MOUSE 120 2
A 27 40
B 110 120
RETB_BOVIN 116 2
A 14 27
B 106 116
//
blimps-3.9/examples/protomat/distribution/lipo.mmast000064400001460000012000000101021062461167300233560ustar00jorjastaff00000400000027ALPHABET= ARNDCQEGHILKMFPSTWYVBZX
log-odds matrix: alength= 23 w= 14
-3.082 -2.709  8.415  4.228 -4.167 -2.560 -2.085  3.916 -0.748 -5.293 -6.068 -2.077 -4.731 -4.927 -5.179 -1.770 -2.601 -5.817 -4.900 -5.248  6.142 -2.271 -1.881 
-5.013 -5.892 -6.084 -6.767 -3.557 -7.071 -6.851 -6.355 -3.393 -0.437  3.095 -6.276 -0.599  10.665 -8.203 -6.226 -5.065 -1.245  1.853 -1.840 -6.454 -6.937 -3.422 
-4.429 -3.742  5.440  9.555 -5.353 -2.936 -0.580 -3.199 -1.958 -5.658 -6.785 -2.685 -5.565 -5.821 -5.361 -2.752 -3.548 -7.003 -5.959 -5.937  7.674 -1.503 -2.724 
-2.646 -2.332 -4.264 -4.767 -1.935 -3.401 -3.992 -4.861 -3.389  4.116  2.254  1.793  0.219 -0.526 -5.797 -4.317 -2.727  9.658 -1.090  3.382 -4.537 -3.761 -1.750 
 2.284 -1.356 -1.016 -0.842 -2.011  4.224  3.361 -1.980 -1.041 -3.648 -4.054 -0.455 -2.501 -4.242 -3.594  3.927 -1.038 -4.748 -3.493 -2.784 -0.921  3.699 -0.772 
 1.538  4.068  4.186 -1.543 -3.142 -0.623 -1.314 -2.299 -0.999 -3.822 -4.132  5.737 -2.909 -4.547 -4.000 -1.614 -2.319 -4.975 -3.723 -3.351  1.077 -1.044 -1.057 
-3.177 -4.888 -5.031 -5.695 -2.202 -5.316 -5.590 -5.634 -1.625  4.207  0.196 -4.775 -0.227  7.313 -6.570 -4.947 -3.253 -0.606  5.886  3.477 -5.391 -5.483 -2.492 
 5.634 -2.746  4.543 -2.100 -1.745 -2.528 -2.666 -1.473  7.146 -3.284 -3.978 -2.169 -2.996 -3.701 -4.206 -1.112 -2.360 -4.883 -2.294 -2.384  0.938 -2.612 -1.321 
-2.918 -6.584 -3.540 -4.925 -5.191 -6.282 -6.866  10.244 -5.214 -7.641 -8.092 -5.346 -6.946 -6.904 -7.247 -4.384 -5.921 -6.840 -7.731 -7.281 -4.292 -6.637 -4.428 
 1.876 -0.966 -1.495 -1.316 -1.948 -0.927  3.031 -2.681 -1.923 -2.429 -3.318  3.167 -2.374 -3.940 -3.576 -0.700  4.840 -4.656 -3.642 -1.784 -1.398  1.481 -0.752 
-7.025 -6.625 -7.647 -8.389 -6.724 -7.237 -7.388 -6.673 -4.713 -5.596 -5.380 -7.056 -4.901 -1.192 -11.203 -7.906 -7.078  17.493  0.246 -6.324 -8.050 -7.329 -5.796 
-4.179 -3.127 -2.526 -4.349 -4.572 -2.993 -3.522 -4.782  9.886 -3.515 -3.602 -3.403 -2.749  1.581 -6.398 -4.444 -4.670  10.173  8.358 -4.081 -3.516 -3.315 -2.595 
 2.148 -2.021 -1.254 -0.493 -1.906 -0.737  4.769 -2.347 -1.534 -3.014 -3.760 -0.920 -2.673 -3.957 -3.551  2.578  3.135 -4.706 -3.681 -2.203 -0.841  2.613 -0.769 
-2.642 -4.617 -5.400 -5.710 -1.245 -4.652 -5.643 -5.846 -4.356  6.117  3.636 -4.324  5.522 -0.402 -6.155 -4.897 -2.554 -4.033 -2.697  4.171 -5.568 -5.255 -2.471 
log-odds matrix: alength= 23 w= 11
-2.858 -5.934 -6.257 -6.457 -1.774 -6.037 -6.539 -6.654 -5.966  7.245  0.292 -5.412 -0.164 -1.793 -6.812 -5.559 -2.877 -5.381 -3.690  7.040 -6.365 -6.342 -3.494 
-3.289 -4.800 -5.568 -5.586 -2.046 -5.110 -5.542 -5.848 -4.567  4.523  5.455 -4.323  0.814 -0.935  4.636 -5.118 -3.392 -4.775 -3.353  0.614 -5.578 -5.373 -2.166 
 1.571 -1.225 -0.203  6.416 -2.686 -1.558 -0.446 -2.062 -1.785 -3.848 -4.649  3.283 -3.417 -4.567 -3.793  2.130 -1.775 -5.469 -4.314 -3.438  3.389 -0.882 -1.007 
-3.221 -4.694 -3.093 -4.470 -3.038 -4.639 -5.001 -5.120 -5.116 -3.156 -4.493 -4.064 -3.760 -5.261 -5.605 -1.822  10.254 -6.443 -5.579 -2.638 -3.840 -4.860 -3.098 
-5.712 -5.444 -1.084  11.192 -6.789 -4.302 -1.364 -4.807 -3.813 -6.907 -8.147 -4.121 -7.001 -7.257 -6.513 -4.304 -5.154 -8.439 -7.574 -7.287  5.579 -2.515 -4.101 
-4.477 -3.960  4.468 -3.900 -4.604 -3.952 -4.598 -5.024  1.103 -3.234 -3.540 -3.834 -3.121  2.531 -6.578 -4.308 -4.288  0.707  11.259 -3.601 -0.073 -4.345 -2.632 
-2.850  0.379 -0.956  4.683 -4.692 -0.248  3.902 -3.501 -1.456 -4.645 -5.034  6.652 -3.635 -5.298 -4.106 -2.434 -3.088 -5.472 -4.342 -4.534  2.105  2.277 -1.526 
-2.910 -1.144  8.285 -0.324 -3.367 -1.761 -2.144 -2.246 -0.715 -3.805 -4.699  2.887 -3.496 -4.486 -4.593 -1.150  3.421 -5.463 -4.147 -3.559  3.612 -1.994 -1.428 
-4.864 -5.158 -5.295 -6.428 -4.318 -5.578 -5.921 -6.239 -0.085 -1.959 -1.876 -5.293 -2.093  8.976 -7.525 -5.680 -5.116  0.670  9.980 -2.869 -5.910 -5.787 -3.361 
 4.224 -4.361 -4.964 -5.144 -1.150 -4.438 -4.787 -3.359 -4.076  4.071  4.446 -3.756  0.401 -1.286 -5.168 -2.895 -2.749 -4.502 -3.291  0.692 -5.062 -4.650 -1.641 
-2.561 -4.524 -5.315 -5.656 -1.225 -4.494 -5.538 -5.766 -4.250  5.935  3.307 -4.233  6.143 -0.451 -6.117 -4.783 -2.494 -4.011 -2.679  4.356 -5.500 -5.129 -2.440 
blimps-3.9/examples/protomat/distribution/lipo.out000064400001460000012000000014141062461167300230520ustar00jorjastaff00000400000027              **BLOCKS from MOTIF**
 
>lipoxxx none
5 sequences are included in 2 blocks

            lipoxxxA, width = 14lipoxxxB, width = 11     
           BBP_PIEBR    16 NFDWSNYHGKWWEV (  71)   101 VLSTDNKNYII
          ICYA_MANSE    17 DFDLSAFAGAWHEI (  74)   105 VLATDYKNYAI
          LACB_BOVIN    25 GLDIQKVAGTWYSL (  71)   110 VLDTDYKKYLL
          MUP2_MOUSE    27 NFNVEKINGEWHTI (  69)   110 IPKTDYDNFLM
          RETB_BOVIN    14 NFDKARFAGTWYAM (  78)   106 IIDTDYETFAV


      **COBBLER sequence from MOTIF**
>lipoxxx ICYA_MANSE from 1 to 189 with embedded consensus blocks
gdifypgycpdvkpvnNFDVSKFAGTWYEIaklplenenqgkctiaeykydgkkasvynsfvsngvkeymegdleiapda
kytkqgkyvmtfkfgqrvvnlvpwVLDTDYKNYLInyncdyhpdkkahsihawilskskvlegntkevvdnvlktfshli
daskfisndfseaacqysttysltgpdrh
blimps-3.9/include/000075500001460000012000000000001041505630000145635ustar00jorjastaff00000400000027blimps-3.9/include/aabet.h000064400001460000012000000061650774312245700160410ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* aabet.h: Definitions for amino acids */
/* Modified by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef __AABET_H__
#define __AABET_H__

#define AAID_MIN	1	/* Smallest letter value in binary alphabet */
#define AAID_MAX	24	/* Maximum letter value in binary alphabet */
#define AAID_CNT	24	/* Number of letters in alphabet */
#define AAID_NAR	(AAID_MAX+1)
#define AAID_IGNORE	(AAID_MAX+3)

#define NA AAID_NAR		/* Not A residue */
#define EL (NA+1)		/* End of Line */
#define ES (NA+2)		/* End of Sequence */
#define IC AAID_IGNORE	/* Ignore this Character */

#define UNKNOWN_AA_CHR	'X'
#define STOP_AA_CHR	'*'
#define GAP_AA_CHR '-'

/* Alpha chars that are not codes are treated as wildcard place holders */
/* (unknown amino acids) */
#define UN 23			/* 23 = 'X' an unknown aa */


EXTERN int aa_atob[1<
#include 
*/
#include  /* defines CHAR_BIT for aabet.h and ntbet.h */

/* EXTERN should be defined in the main program module only */
#ifndef EXTERN
#define EXTERN	extern
#ifndef INITIAL
#define INITIAL(x)
#endif
#else
#ifndef INITIAL
#define INITIAL(x) = x
#endif
#ifndef INIT
#define INIT
#endif
#endif

/* much deleted here */

/* added */
#define PROTO(x) () 


#endif /* __BLAST_H__ */




/* Change log information follows. */
/* $Log: blastapp.h,v $
 * Revision 2.2010  1995/07/28  23:47:14  billa
 * Added new convert method and pattern matching and minor updates merged.
 *
 * Revision 2.2001  1994/05/18  19:17:57  billa
 * Removed global.c and moved Buffer variable to strutil.[ch].
 *
 * Revision 2.2000  1994/05/10  18:39:13  billa
 * System version 2.2 A [2.2000]
 * Goofed on dev. version.
 *
 * Revision 2.1100  1994/05/10  18:27:07  billa
 * System version 2.2 A [2.1100].
 * Created blimps library and fixed up minor bugs.  No major changes to the
 * program.
 *
 * Revision 2.1025  1994/05/10  00:51:47  billa
 * Added SCCS patterns to trick the what command into printing out the RCS
 * identifying patterns.
 *
 * Revision 2.1020  1994/04/27  21:59:11  billa
 * After library creation.  In testing phase.
 *
 * Revision 2.1015  1994/04/26  03:15:34  billa
 * Pre-library checkin.
 *
 * Revision 2.1011  1994/04/26  03:14:16  billa
 * Pre-library checkin.
 *
 * Revision 2.1010  1994/04/26  00:28:18  billa
 * Cleaned up warnings from gcc switches.
 *
 * Revision 2.1000  1994/03/09  22:23:59  billa
 * System version 2.1 A [2.1000]
 * Added reading and scoring of precomputed site specific scoring matricies.
 * Reconfigured files.[ch] into files.[ch] and config.[ch].
 *
 * Revision 2.0  1993/12/06  19:31:18  billa
 * System version 2.0 A [2.0000].
 * Changed source to remove some warnings.  Added sequence weights to the
 * blocks.  Added a conversion method to use the weights.  Made the method
 * the default.  Added some ifndef's in preparation of creating a library
 * of functions.  Added the ability to choose the genetic code to use for
 * translation.  Added the ability to read a flat file as a sequence if the
 * other types sequences fail to match.  Added some defines for strdup().
 *
 * Revision 1.1120  1993/12/02  03:44:22  billa
 * Development version 1.1120.  Right after copyright/license info added.
 *
 * Revision 1.1101  1993/12/02  03:37:12  billa
 * Added the copyright notice to the top of the file.
 *
 * Revision 1.1100  1993/09/09  17:23:19  billa
 * System version 1.1 B [1.1100].
 *
 * Revision 1.1000  1993/08/27  17:01:31  billa
 * System version 1.1 A, development version 1.1000.
 * Added the function reclaim_space() and the macro CheckMem(A) to handle
 * the situation when there is no more memory to allocate.
 *
 * Revision 1.0  1993/08/14  00:50:52  billa
 * System version 1.00
 *
 * Revision 0.110  1993/08/10  02:50:53  billa
 * System version update.  Added convert.[ch], scoring.[ch] and version.[ch].
 *
 * Revision 0.105  1993/08/04  19:53:40  billa
 * System version 0.105.  Post file structure reorganization.
 *
 * Revision 0.100  1993/08/03  00:48:46  billa
 * System version 0.100.  Pre file structure reorganization.
 *
 * Revision 0.11  1993/07/16  22:16:00  billa
 * Added RCS information.  Added PROTO definition.
 * 
 */






                                                                        *
*                             COPYRIGHT NOTICE                            *
*                                                                         *
* This software/database is categorized as "United States Government      *
* Work" under the terms of the United States Copblimps-3.9/include/blocks.h000064400001460000012000000117400774312246000162270ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* blocks.h: declaration of blocks data type and basic block operations */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef BLOCKS_H_
#define BLOCKS_H_

#define MINAC 7			/* min & max possible AC lengths */
#define MAXAC 10

#include 
#include 

/*
 * Exported variables and data structures
 */


/* 
 * Sequence, Cluster, and Block data types
 */


struct cluster_struct {
  int      num_sequences;	   /* number of sequences in the block */
  Sequence *sequences;		   /* the array of Sequences of the cluster */
};
typedef struct cluster_struct Cluster;

struct block_struct {
  char     id[SMALL_BUFF_LENGTH];  /* Block ID string */
  char     ac[SMALL_BUFF_LENGTH];  /* Block AC string */
  char     de[SMALL_BUFF_LENGTH];  /* Block DE string */
  char     bl[SMALL_BUFF_LENGTH];  /* Block BL string */
  char     number[SMALL_BUFF_LENGTH]; /* AC:  block number IPR123456A  */
  char     family[SMALL_BUFF_LENGTH]; /* AC: block family IPR123456 */
  char     motif[20];		   /* BL: motif */
  int      width;		   /* BL: block width */
  int      percentile;		   /* BL: 99.5% score */
  int      strength;		   /* BL: strength (median TP score) */
  int      max_sequences;          /* max number of sequences in the block */
  int      num_sequences;          /* number of sequences in the block */
  int      max_clusters;	   /* max number of clusters in the block */
  int      num_clusters;	   /* number of clusters in the block */
  int      min_prev;               /* AC: min distance from previous block */
  int      max_prev;	           /* AC: max distance from previous block */
  int undefined;		/* for future use */
  double undefined_dbl;		/* for future use */
  void *undefined_ptr;		/* for future use */
  Cluster  *clusters;		   /* the array of Clusters of the block */
  Sequence *sequences;		   /* the array of Sequences of the block */
  Residue  **residues;		   /* the 2-d array of residues [seq][pos] */
};
typedef struct block_struct Block;


/*
 * Exported functions
 */

/*
 * read_a_block
 *   reads a block from the data base and returns a pointer to the new
 *   block data structure
 *   Parameters:  
 *     FILE *bfp: the file pointer the the blocks database/file
 *   Error codes: NULL if a block was not read
 */

extern Block *read_a_block ();
extern Block *read_a_block_faster ();
extern Boolean read_to_block();


/*
 * block_comparison
 *   Compares two blocks.   It compares by the value in the id
 *   field if it exists.
 *   Parameters:
 *     BlockListEntry a, b: the entries to compare
 *   Return codes:  a return value < 0 if a < b, a return value = 0 if a == b,
 *                  and a return value > 0 if a > b
 *   Error codes: none
 */

extern int block_comparison();


/* 
 * free_block
 *   Frees the block and the sub elements.
 *   Parameters: 
 *     Score *score: the score to free
 *   Return code: none
 *   Error code: none
 */
extern void free_block() ;

extern int read_block_header();
extern void read_block_body();
extern void next_cluster();

/* 
 * resize_block_sequences
 *   Increases the memory for the storage of the sequences of a block.
 *   Parameter:
 *     Block *block: the block to resize
 *   Error codes: none
 */
extern void resize_block_sequences();

extern void resize_block_clusters();

/*
 * print_block
 *   Prints a block data structure.  Primarily for debugging purposes.
 *   Parameters: 
 *     Block *block:  the block to print
 *   Error Codes: none
 */

extern void print_block();

/*
 * ouput_block
 *   Outputs a block data structure to the given file. 
 *   Parameters: 
 *     Block *block:  the block to print
 *     FILE  *obfp:   the ouput block file pointer
 *   Error Codes: none
 */

extern void output_block();

/*
 * ouput_block_s
 *   Outputs a block data structure to the given file with the 
 *   specified style of data.
 *   Parameters: 
 *     Block *block:  the block to print
 *     FILE  *obfp:   the ouput block file pointer
 *     int    style:   the kind of output (INT_OUTPUT, FLOAT_OUTPUT)
 *   Error Codes: none
 */

extern void output_block_s();

/*
 *  new_block
 *    Creates a new empty Block structrue
 *    Parameters:
 *      ncols:  Number of columns = sequence length
 *      nrows:	Number of rows = number of sequences
 */

extern Block *new_block();






#endif /*  BLOCKS_H_ */

/* Change log information follows. */
/* 
 * Changes since 3.3.2:
  12/15/99  Added double undefined_dbl field.
  12/17/99  Added family field, MINAC, MAXAC
 * Changes since 3.2.5:
   2/11/99  Added min_prev & max_prev fields to the blocks structure;
		rename block->sequence_length to block_width.
 * Changes since 3.2.2:
   1/29/98  Added resize_block_clusters(), etc.
 * Changes since 3.2:
   4/16/97  Added resize_block_sequences()
 * Changes since 3.1:
   2/14/97  Added new_block().
 *
 */

blimps-3.9/include/blocksprogs.h000064400001460000012000000006620774312246000173030ustar00jorjastaff00000400000027/*	system headers */
#include 
#include 
#include 
#include 
#include 
#include 
/*	blimps library headers */
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
blimps-3.9/include/convert.h000064400001460000012000000121040774312246000164250ustar00jorjastaff00000400000027
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* convert.h: functions for different methods of converting a block into a */
/*            matrix */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef CONVERT_H_
#define CONVERT_H_

/*    Defaults for Altschul's substitution probability pseudo-count
	conversion method (3)  */
#define LOCAL_QIJ_FILE "default.qij"
#define LOCAL_QIJ_RTOT 5.0
#define AAS 21

/*
 * Exported variables and data structures
 */
extern double RTot;		/* total number of pseudo-counts */

struct float_qij {		/* qij matrix and marginal frequencies */
  double value[AAS][AAS];
  double marg[AAS];
};
extern struct float_qij *Qij;

struct pb_counts {		/* for pb_weights() */
  double diffaas;		/* # of different aas in position */
  double naas[MATRIX_AA_WIDTH]; /* # of each aa in position */
};

/* Pauline Ng's definitions (renamed) */

/* Dirichlet stuff */
#define MAXDIRI 40 /* max # of Dirichlet components (was MAXCOMP) */
/* Dirichlet mixtures  (was struct dirichlet) */
struct diri {   
   int ncomp;           /* number of components */
   double q[MAXDIRI];
   double altot[MAXDIRI];
   double alpha[MAXDIRI][AAS];
   double alpha_normalized[MAXDIRI][AAS]; /* Pauline, relative freq. of amino
                                        acid to component (normalized against
                                        component length*/
   double frequency_to_background_ratio[MAXDIRI][AAS];
                                /* frequency to background ratio as calculated
                                in TableII of Sjolander's 1996 CABIOS paper*/
};

#define SIFT_TOLERANCE .05	/* was TOLERANCE_PROB_THRESHOLD */

/*
 * Exported functions
 */
extern struct float_qij *load_qij();
extern void pb_weights();
extern void normalize();


/*
 * block_to_matrix
 *   converts a block into a matrix (possition specific matrix?) according
 *   to the rule specified in BlockToMatrixConversionType.  The block field
 *   of the matrix is set in this function.
 *   Parameters:
 *     Block *block: the block to convert
 *   Return codes: Returns the pointer to the new Matrix.
 *   Error codes:
 */

extern Matrix *block_to_matrix();







/*
 * original_conversion_method
 *   The original conversion method.  This is done by weighted average of the 
 *   clusters.  This follows the method in patmat.
 *   Parameters:
 *     Block *block:   the block to be converted
 *     Matrix *matrix: where the resulting matrix will be put
 *   Error codes: none
 */

extern void original_conversion_method();


/*
 * original_conversion_method_cleaned_up
 *   The original conversion method.  This is done by weighted average of the 
 *   clusters.  This follows the method in patmat but has been written in
 *   a more legible manner and has the following changes:
 *     no more reliance on flag values for B, Z, and X
 *     X, '-', '*', & non-code scores are read straight from the frequencies
 *     the frequencies for B and Z are ignored, when a B or Z is encountered
 *       it is partitioned between D & N or E & Q.
 *     the matrix scores for B and Z are computed from the matrix scores of 
 *       D & N and E & Q.
 *   Parameters:
 *     Block *block:   the block to be converted
 *     Matrix *matrix: where the resulting matrix will be put
 *   Error codes: none
 */
extern void original_conversion_method_cleaned_up();

/*
 * pre_weighted_conversion_method
 *   This conversion method uses the pre-weighted sequence scores and
 *   uses the basic matrix construction method.  This method has the
 *   following properties:
 *     X, '-', '*', & non-code scores are read straight from the frequencies
 *     the frequencies for B and Z are ignored, when a B or Z is encountered
 *       it is partitioned between D & N or E & Q.
 *     the matrix scores for B and Z are computed from the matrix scores of 
 *       D & N and E & Q.
 *   Parameters:
 *     Block *block:   the block to be converted
 *     Matrix *matrix: where the resulting matrix will be put
 *   Error codes: none
 */
extern void pre_weighted_conversion_method();

extern void pb_weights();

extern void altschul_data_dependent_conversion_method();
extern void gribskov_conversion_method();

/* Pauline's routines (renamed) */
extern void SIFT_conversion_method();
extern void SIFT_pssm();			/* SIFT_alts() */
extern struct diri *load_diri();		/* load_diri_file() */
extern void counts_nogaps();			/* counts_no_gaps */
extern double similarity_dependent_scale();	/* ..._0() */
extern void pseudo_diri();			/* pseudo_diric() */
extern int find_max_aa_col();			/* ..._in_col() */
extern int find_max_aa_pssm();			/* ..._in_pssm() */
extern double add_logs();			/* add_logs() */


#endif /*  CONVERT_H_ */

/* Change log information follows. 
    Changes since version 3.4:
Made normalize() external
12/29/00 Added Pauline's SIFT stuff.
    Changes for version 3.0.1:
    5/23/96 Added gribskov_conversion_method()
    Changes for version 3.0.0:
    9/16/95 Added pb_weights() routine.  JGH
 *  9/9/95 Added LOCAL_QIJ_FILE & LOCAL_QIJ_RTOT   JGH
*/
blimps-3.9/include/errors.h000064400001460000012000000064500774312246000162700ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* errors.h: error reporting functions */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef ERRORS_H_
#define ERRORS_H_

/*
 * Exported variables and data structures
 */

#define INFO_ERR_LVL    1	/* General information. */
#define WARNING_ERR_LVL 2	/* Probable user error. */
				/* Generally recoverable. */
#define SERIOUS_ERR_LVL 3	/* Probable user error. */
				/* Difficult to recover from. */
#define PROGRAM_ERR_LVL 4	/* Programing error, problem should have */
				/* been caught before it arose. */
				/* Recoverability varies. */
#define FATAL_ERR_LVL   5	/* Various causes, user or programmer. */
				/* Unable to recover from. */
				/* Exits program with FATAL_ERR_LVL value. */




extern char ErrorBuffer[LARGE_BUFF_LENGTH];
extern int  ErrorLevelReport;


/*
 * Exported functions
 */

/*
 * set_error_file_name
 *   Sets the name of the error output file to use.
 *   Parameters:
 *     char *error_file: the name of the file.
 *   Error codes: None
 */

extern void set_error_file_name();


/*
 * ErrorReport
 *   ErrorReport prints out the error message in the ErrorBuffer to stderr and
 *   the ErrorFile if it can be opened.
 *   Note: The error message must be placed in ErrorBuffer before ErrorReport
 *         is called.
 *   Parameters:
 *     int err_level:  The error level reporting at.  If the error level is
 *                     >= FATAL_ERR_LVL, exit() is called with the error level.
 *   Error codes: None
 */

extern void ErrorReport();


/*
 * ABRT_signal_handler
 *   Catches the SIGABRT signal and announces the probable cause that was
 *   seen in testing.  It appears that when there is very little memory
 *   left free() has a hard time deallocating memory.  I'm guessing that it
 *   is when it is trying to put the free memory block into a list, the
 *   error that occurs is: "getfreehdr: out of memory".  The error seems to
 *   have only occured in the function call free() after many small blocks
 *   of memory have been freed.  It probably cannot handle as many free 
 *   blocks of memory as it is getting.
 *   NOTE: The memory recover functions "should" work.  The only
 *     problem appears to be in the function free().  The function is
 *     always called with a valid pointer to a busy block, allocated
 *     previously by a malloc function, when the error occurs.  And for
 *     about 10 calls before the error the pointer is OK too.  The
 *     problem I'm having with free() may be particular to this
 *     development system (SunOS Release 4.1.3) or I might have done
 *     something that causes this side effect.
 *   NOTE: The function recover_memory() in memory.c handles the recovery
 *     of memory when there is no more allocatable memory.  See the macro
 *     CheckMem(A) in memory.h to see how the function is called.
 *   Parameters: none
 *   Error codes: none, aborts the program.
 */

extern void ABRT_signal_handler();

#endif /*  ERRORS_H_ */

/* Change log information follows. */
/*
 * Revision 0.20  1993/06/23  16:46:49  billa
 * creation, error reporting to stderr and to the error file from
 * ErrorReport()
 *
 */



blimps-3.9/include/files.h000064400001460000012000000113440774312246000160540ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* files.h: access to configuration and database files */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef FILES_H_
#define FILES_H_

/*
 * Exported variables and data structures
 */

#define BLOCK_FILES    0
#define MATRIX_FILES   1
#define DATABASE_FILES 2
#define FREQUENCY_FILE 3
#define SEQUENCE_FILES 4
#define PATTERN_FILES 5



extern char ExportMatrixFile[SMALL_BUFF_LENGTH];
extern char OutputFile[SMALL_BUFF_LENGTH];

/* NOTE: The file lists are here only so that config.c has access to */
/*       the file_list struct.  When reading in the config file it is */
/*       necessary to handle the file lists directly.  The code should */
/*       be rewritten so that this is not necessary. */

struct file_list {
  FILE *fp;			/* pointer to the currently open file */
  int db_type;			/* the type of database this is */
  int seq_type;			/* the sequence type of the database, if */
				/* this is a seq. database. */
  int num_files;		/* the number of files in the list */
  int max_files;		/* the current maximum number of files */
				/* allowed in the list.  Can grow. */
  int cur_file;			/* the current position in the file list */
  char **file_names;		/* the array of strings of the file names */
};
typedef struct file_list FileList;

extern FileList BlockFiles;
extern FileList MatrixFiles;
extern FileList DatabaseFiles;
extern FileList FrequencyFile;	/* Note: should be only one in the list */
extern FileList SequenceFiles; 
extern FileList PatternFiles; 




/*
 * Exported functions
 */


/*
 * insert_file
 *   insert_file inserts the file_name into the file_group list
 *   Parameters:
 *     char *file_name: the name of the file
 *     int file_group: the group to get a file pointer for.
 *   Return codes: none
 *   Error codes:
 */

extern void insert_file();


/*
 * get_file
 *   get_file retrieves the file pointer of the requested group.
 *   Parameters:
 *     int file_group: the group to get a file pointer for.
 *   Return codes: Returns the file pointer to the requested file group
 *   Error codes:
 */

extern FILE *get_file();


/*
 * rewind_file
 *   rewind_file sets/resets the file pointer of the specified group back to
 *   the first file, first character.
 *   Parameters:
 *     int file_group: the group rewind.
 *   Return codes: none
 *   Error codes:
 */

extern void rewind_file();


/*
 * get_current_file_name
 *   Returns a pointer to the string of the current file name.
 *   Parameters:
 *     int file_group: the group rewind.
 *   Return codes: a string of the filename
 *   Error codes:  NULL if there is no filename
 */

extern char *get_current_file_name();


/*
 * get_file_name
 *   Returns a string of the requested file name.  (this is a copy)
 *   Parameters:
 *     int file_num:   which file to return (0..num_files);
 *     int file_group: the file group for the name
 *   Return codes: a string of the filename
 *   Error codes:  NULL if there is no filename
 */

char *get_file_name();


/*
 * number_of_files
 *   Returns the number of files in the file group.
 *   Parameters: 
 *     int file_group: the group rewind.
 *   Return codes: the number of files in the file group.
 *   Error codes:  -1 if the file group is unknown
 */

extern int number_of_files();

extern void file_assign();

/*
 * get_sequence_db_seq_type
 *   Returns the type of sequences of the databases.  
 *   NOTE: this assumes that all the sequences in a database file are
 *         of the same type, and that all of the database files are of
 *         the same type.
 *   NOTE: SequenceFiles.db_type is set only at the end of reading the 
 *         configuration file.
 *   Parameters: none
 *   Return codes: the different sequence types
 *   Error codes:  none
 */

extern int get_sequence_db_seq_type();


/*
 * get_sequence_db_db_type
 *   Returns the kind of the database of the seqeuence database file 
 *   currently being read.  
 *   NOTE: SequenceFiles.db_type is set each time a new sequence file is
 *         opened.
 *   Parameters: none
 *   Return codes: the different sequence db types
 *   Error codes:  none
 */

extern int get_sequence_db_db_type();




/*
 * Other functions
 */


/*
 * close_file
 *   closes the selected file group.
 *   Parameters: 
 *     int file_group: the group rewind.
 *   Return codes: none
 *   Error codes:
 *   Note: right now this function is identical to rewind_file() except it
 *         does not set the current file to the beginning.
 */

extern void close_file();




#endif /*  FILES_H_ */

/* Change log information follows. */
/* Changes since version 3.0.0:
*/
blimps-3.9/include/frequency.h000064400001460000012000000031740774312246000167550ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* frequency.h: hardcoded amino acid frequency information for matricies */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef FREQUENCY_H_
#define FREQUENCY_H_

/* the default files with the amino acid frequencies */
#define LOCAL_AMINO_FREQUENCY_FILE   "default.amino.frq" 
#define LOCAL_CODON_FREQUENCY_FILE   "default.codon.frq" 


/*
 * Exported variables and data structures
 */


extern double frequency[MATRIX_AA_WIDTH];

extern double Codon_Usage[64];


/*
 * Exported functions
 */

/*
 * load_frequencies
 *   reads in the frequencies if there is a frequency file.
 *   Parameters:
 *     char *fname: The frequency file filename
 *   Return codes: TRUE if there was a frequency file, FALSE if not.
 *   Creates the global array frequency[]
 */

extern Boolean load_frequencies();


/*
 *  load_codons
 *    reads in the codon usages if there is a codon usage file.
 *    Parameters:
 *      FILE *ffp:  The codon usage file.
 *    Creates the global array Codon_Usage[]
 */

extern Boolean load_codons();

/*
 *  frq_qij
 *    Calls load_frequencies() and load_Qij to initialize the
 *    global variables frequency[], Qij, RTot
 */
extern void frq_qij();

#endif /*  FREQUENCY_H_ */
/* Change log information follows. */
/*
   Changes since 3.1:
   2/14/97 Added Codon_Usage[] and load_codons()
 * Revision 2.2011  1995/07/29  02:34:27  billa
 * Made load_frequencies more portable.
 *
 *
 */
blimps-3.9/include/gcode.h000064400001460000012000000103401041505644500160250ustar00jorjastaff00000400000027/* (C) Copyright 1993-2006, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* gcode.h: Definitions for the translation of nucleotides to amino acids */
/* Modified by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef __GCODE_H__
#define __GCODE_H__

typedef struct {
	char	*name;
	char	*code;
	char	*inits;
	} GeneticCode, *GeneticCodePtr;

#define CODON_LEN	3	/* No. of nucleotides per codon */

#define NUMBER_OF_GENETIC_CODES 17
EXTERN GeneticCode gcodes[NUMBER_OF_GENETIC_CODES]
#ifdef INIT
= {
"Standard",
"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0001000000000000000100000000000000010000000000000000000000000000",

"Vertebrate Mitochondrial",
"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG",
"0000000000000000000000000000000011110000000000000001000000000000",

"Yeast Mitochondrial",
"FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000110000000000000000000000000000",

"Mold Mitochondrial and Mycoplasma",
"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0011000000000000000100000000000011110000000000000001000000000000",

"Invertebrate Mitochondrial",
"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG",
"0001000000000000000000000000000011110000000000000001000000000000",

"Ciliate Nuclear",
"FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000",

"Echinoderm Mitochondrial",
"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000001000000000000",

"Euplotid Nuclear" ,
"FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000",

"Bacterial and Plant Plastid" ,
"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0001000000000000000100000000000011110000000000000001000000000000",

"Alternative Yeast Nuclear" ,
"FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000100000000000000010000000000000000000000000000",

"Ascidian Mitochondrial" ,
"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000",

"Flatworm Mitochondrial" ,
"FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000",

"Blepharisma Macronuclear" ,
"FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000",

"Chlorophycean Mitochondrial" ,
"FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000",

"Trematode Mitochondrial" ,
"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000001000000000000",

"Scenedesmus obliquus mitochondrial" ,
"FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000",

"Thraustochytrium mitochondrial code" ,
"FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000010010000000000000001000000000000"
}
#endif
	;


void init_gcode PROTO((GeneticCodePtr, unsigned char [64], unsigned char [64]));
unsigned char codon2aa PROTO((unsigned char *, unsigned, unsigned, unsigned));
void aa2codon PROTO((unsigned char *));

#endif /* !__GCODE_H__ */




/* Change log information follows. */
/* 
   Changes since version 3.6:
   10/14/04 fixed gcodes table (missing commas!)
   Changes since version 3.4:
   8/ 8/01  Updated from ncbi/data/gc.prt
   Changes since version 3.1:
   1/20/97  Added aa2codon()
 */
/*  Old codes
"Protozoan Mitochondrial",
"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0011000000000000000100000000000000010000000000000000000000000000",

"Plant Mitochondrial",
"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRWIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000",
*/
h: Definitions for the translation of nucleotides to amino acids */
/* Modified by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef __GCODE_H__
#define __GCODE_H__

typedef struct {
	char	*name;
	char	*code;
	char	*inits;
	} GeneticCode, *GeneticCodePtr;

blimps-3.9/include/global.h000064400001460000012000000024400774312246000162070ustar00jorjastaff00000400000027/* (C) Copyright 1993-9, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* global.h: basic global defines and variable declarations used in *
 *           all blimps modules                                     */
/* Put system headers here */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef GLOBAL_H_
#define GLOBAL_H_

/*	system headers used by all modules */
#include 
#include 
#include 
#include 
#include 
#include 

/*
 * Exported variables and data structures
 */


/*
 * Boolean type and values 
 */
typedef int Boolean;

#ifndef TRUE
#define TRUE  1
#endif
#ifndef FALSE
#define FALSE 0
#endif



/* 
 * min and max and round
 */
#define max(A, B) ((A) > (B) ? (A) : (B))
#define min(A, B) ((A) < (B) ? (A) : (B))
#define round(x) ((x >= 0.0) ? (int) (x+0.5) : (int) (x-0.5))


/*	blimps library headers used by all modules */
#include 
#include 
#include 
#include 

#endif /*  GLOBAL_H_ */

/* Change log information follows. */
/* Changes since version 3.0.0:
12/ 6/99 Put common system & blimps headers here.
*/
blimps-3.9/include/license.h000064400001460000012000000150551041505653700164000ustar00jorjastaff00000400000027/* (C) Copyright 1993-2006, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in this file. */

/* license.h: Copyright information */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

/* licence stuff here */

#ifndef LICENSE_H_
#define LICENSE_H_

/* this information is copied from the LICENSE file that is */
/* distributed with the source code. */

/* FHCRC information */
/*
                      FHCRC NONCOMMERCIAL LICENSE
                Fred Hutchinson Cancer Research Center
                         1100 Fairview AV North
                          Seattle, WA  98109


This license may be copied and distributed but may not be modified in any way.

                               RECITALS:

      A.  Fred Hutchinson Cancer Research Center is a nonprofit
corporation dedicated to investigating the nature and causes of cancer
and methods of cancer prevention and treatment and for conducting
education in all phases of cancer research.

      B.  This license is designed to permit certain activities with
respect to any computer programs to which it applies on the terms
stated in this license.

                         TERMS AND CONDITIONS:

      1.   Definitions.

      "Program" means the computer software and associated
documentation in whatever form or format including source and object
code.

      "Derivative Work" means any modification, addition, upgrade,
update or improvement of the Program and any other work constituting a
derivative work under the copyright laws.

      "Licensee" means licensee of the Program under this license.

      "FHCRC" means Fred Hutchinson Cancer Research Center.

      2.  License, Copy, Distribute and Create Derivative Work.  FHCRC
hereby grants Licensee and Licensee accepts, subject to the terms and
conditions of this Agreement, a nonexclusive, royalty-free license to
use, copy and sublicense the Program and prepare and sublicense
Derivative Works.  This license is expressly limited as follows:

           a.  All copies of the Program must conspicuously show an
appropriate copyright notice and disclaimer of warranty and must
expressly refer to this license.  In addition, Derivative Works must
conspicuously state that the Program has been modified and the date of
any modification.

           b.  Licensee may not charge any fee or royalty for copies
of the Program or Derivative Work.  Licensee is authorized to
sublicense the Program and any Derivative Work to third parties on a
royalty-free basis subject to the terms of this license but may not
otherwise distribute the Program or any Derivative Work.
Notwithstanding the foregoing, Licensee may be reimbursed for any
actual expenses it incurs in reproducing or delivering a copy of the
Program or any Derivative Work.

           c.  This license does not apply to a work written entirely
by Licensee.

           d.  Licensee agrees to make available to any person to whom
it sublicenses this Program or a Derivative Work source code and
object code for the Program or Derivative Work.

           e.  Licensee may not impose any terms in addition to the
terms of this license on any third party to whom it distributes the
Program, any Derivative Work or any copy thereof.

      3.  Reservation of Rights to FHCRC.  FHCRC hereby reserves to
itself all rights of any nature whatsoever with respect to the
Program.  Any Derivative Work created by FHCRC or its employees or
agents is not subject to the terms of this license.

      4.  Termination of license.  This license precludes any copying,
modification, sublicensing or other distribution of any Program or
Derivative Work except as expressly permitted under this license.
Violation of the terms of this license by Licensee will be deemed an
automatic termination of Licensee's rights under this license;
provided, however, that sublicenses derived from Licensee will remain
in full force and effect provided that any such sublicensees do not
breach the terms of this license.

      5.  Acceptance of Terms of License.  Licensee agrees that by
copying or distributing this Program or by creating, copying or
distributing any Derivative Work, Licensee has agreed to the terms of
this license.

      6.  Limitation of Remedies and Indemnity.  Because this Program
is licensed on a royalty-free basis, FHCRC and any person distributing
this Program or any Derivative Work expressly disclaim all warranties
express or implied including, without limitation, any implied warranty
of merchantability or fitness for a particular purpose.  Neither FHCRC
nor any other party distributing the Program or any Derivative Work
will be liable for any damages arising from or related to the use of
the Program or such Derivative Work, including, without limitation,
incidental or consequential damages caused by the use or inability to
use the Program or loss or damage to data.

      Licensee agrees to indemnify, defend and hold FHCRC harmless
from and against any claims, causes of action, damages, liabilities
and expenses, including without limitation attorney's fees, arising
from or related to Licensee's use, copying or distribution of the
Program or any Derivative Work.

      7.  Severability.  If any provision of this license is held
invalid under any applicable law or for any other reason, such
invalidity shall not effect any other provision of this license that
can be given effect without the invalid provision.

      8.  Notice.  Persons wishing to communicate with FHCRC
concerning this license or the Program should address their
communications as follows:

      Fred Hutchinson Cancer Research Center
      Attn:  Dr. Steven Henikoff
      1124 Columbia Street, MS A1-162
      Seattle, WA  98104
*/


/* skiplist information */
/*
The skiplist code is under the GNU License.  A copy of the GNU
General Public License is available for anonymous ftp at
prep.ai.mit.edu in the file /pub/gnu/COPYING-1.0 .

The skiplist package was written by Dominic Giampaolo
.  The package is available by ftp from
homeboy.wpi.edu in pub/skiplist.tar.Z .

The code is based off of code by William Pugh.  The paper by William
Pugh describing skiplists can be found in:
William Pugh, "Skip lists: a probabilistic alternative to balanced trees.",
Communications of the ACM.  vol.33, no.6.  pp. 668-76.  June 1990.
*/




#endif /*  LICENSE_H_ */

/* Change log information follows */
/* 
 * Revision 1.1101  1993/11/23  18:06:16  billa
 * Updated the license information.
 *
 * Revision 0.1  1993/06/17  23:57:16  billa
 * creation
 *
 */



blimps-3.9/include/matrix.h000064400001460000012000000114500774312246000162540ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* matrix.h: Matrix datatype and matrix manipulation functions */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef MATRIX_H_
#define MATRIX_H_

#include 

/*
 * Exported variables and data structures
 */

typedef double MatType;		/* so we can easily change to double if */
				/* needed.  NOTE:  read_matrix_body will */
				/* need to be changed to reflect any changes */
				/* to the type of MatType. */
				/* and convert.c it rounds values to an int */
				/* before storing */
				/* WARNING!!! in convert.c there is a LOT of */
				/* rounding! (and I mean a LOT). */

#define NUMBER_WIDTH 20
#define DESC_WIDTH   80

#define MATRIX_AA_WIDTH     26	/* 20 aa, 3 ambig, 1 stop, 1 gap, and */
				/* 1 for non-codes J, O, U. */
				/* the +2 to account for the gap and */
                                /* codes that are not defined ( - and */
				/* J, O, U ) */

struct matrix_struct {
  Block *block;			/* the block that this matrix is from */
  char id[SMALL_BUFF_LENGTH];	/* Matrix ID string */
  char ac[SMALL_BUFF_LENGTH];	/* Matrix AC string */
  char de[DESC_WIDTH];		/* Matrix DE string */
  char ma[SMALL_BUFF_LENGTH];	/* Matrix MA string */
  char number[NUMBER_WIDTH];	/* the number of this matrix */
  char motif[20];		/* motif */
  int width;			/* the length of the sequence/matrix */
  int num_sequences;		/* the number of sequences that were in the */
				/* generating data. */
  int percentile;		/* the block/matrix percentile */
  int strength;			/* the block/matrix strength */
  int max_length;		/* max length when reading in */
  Pattern **patterns;		/* the patterns for this PSSM, an array 
				   of ptrs to Patterns, NULL */
  int undefined;		/* for future use */
  void *undefined_ptr;		/* for future use */
  MatType *weights[MATRIX_AA_WIDTH]; /* the weight matrix */
};
typedef struct matrix_struct Matrix;



/*
 * Exported functions
 */

/*
 * read_a_matrix
 *   reads a matrix from the data base and returns a pointer to the new
 *   matrix data structure
 *   Parameters: 
 *     FILE *mfp: a pointer to the database file with the matrix.
 *   Error codes: NULL if a matrix was not read
 */

extern Matrix *read_a_matrix ();


/*
 * matrix_comparison
 *   Compares two matricies.   It compares by the value in the block->id
 *   field if it exists.
 *   Parameters:
 *     MatrixListEntry a, b: the entries to compare
 *   Return codes:  a return value < 0 if a < b, a return value = 0 if a == b,
 *                  and a return value > 0 if a > b
 *   Error codes: none
 */

extern int matrix_comparison();


/*
 * new_matrix
 *   allocates space for a matrix of length len, sets up the data structure
 *   and returns a pointer to the Matrix.
 *   Parameters:
 *     int len: the length of the sequence/matrix
 *   Error codes:
 */

extern Matrix *new_matrix();


/* 
 * free_matrix
 *   Deletes the matrix and the sub elements.
 *   Parameters: 
 *     Matrix *matrix: the matrix to free
 *   Return code: none
 *   Error code: none
 */

extern void free_matrix();


/*
 * print_matrix
 *   Prints a Matrix data structure.  Primarily for debugging purposes.
 *   Parameters: 
 *     Matrix *matrix:  the matrix to print
 *   Error Codes: none
 */

extern void print_matrix();


/* 
 * output_matrix
 *   Outputs a matrix data structure to the given file.
 *   Parameters: 
 *     Matrix *matrix: the matrix to output
 *     FILE   *omfp:   the output matrix file pointer
 *   Return code: none
 *   Error code: none
 */

extern void output_matrix();


/* 
 * output_matrix_s
 *   Outputs a matrix data structure to the given file with the 
 *   specified style of data.
 *   Parameters: 
 *     Matrix *matrix: the matrix to output
 *     FILE   *omfp:   the output matrix file pointer
 *     int    style:   the kind of output (INT_OUTPUT, FLOAT_OUTPUT)
 *   Return code: none
 *   Error code: none
 */

extern void output_matrix_s();

/* 
 * output_matrix_st
 *   Outputs a matrix data structure to the given file with the 
 *   specified style of data. Optionally only outputs ACTG.
 *   Parameters: 
 *     Matrix *matrix: the matrix to output
 *     FILE   *omfp:   the output matrix file pointer
 *     int    style:   the kind of output (INT_OUTPUT, FLOAT_OUTPUT)
 *     int    type:    the type of matrix (AA_SEQ, NA_SEQ)
 *   Return code: none
 *   Error code: none
 */

extern void output_matrix_st();




#endif /*  MATRIX_H_ */

/* Change log information follows. */
/*
  Changes since 3.2.5:
  2/11/99  Renamed Matrix->length to Matrix->width.
  Changes since 3.1:
  2/14/97  Added output_matrix_st().
  Changes since 3.0.0:
  3/25/96   Changed MatType from int to double.   JGH
*/
blimps-3.9/include/memory.h000064400001460000012000000114030774312246000162560ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* memory.h: Memory management functions and macros. */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef MEMORY_H_
#define MEMORY_H_

/*
 * Exported variables and data structures
 */

#define REPORT_DECREASE_AMOUNT  1  /* amount to decrease NumberToReport by */
				   /* if there is not enough room */
				   /* NOTE: MUST be greater than zero */


/*
 * Exported macros
 */

/********************************************************************
 * This macro is supposed to enclose malloc, calloc, and realloc 
 * assignments.  For example:                             
 * CheckMem(                                              
 *          new_block = (Block *) malloc(sizeof(Block))   
 *          );                                            
 * 
 * Note that if using around a realloc you should be assigning the new 
 * memory pointer to a temporary variable so that you do not loose the 
 * original pointer to memory if the CheckMem macro has to loop.
 * For example:                          
 *  Residue *tmp_ptr;  
 *  ...  
 *  CheckMem(                                                        
 *           tmp_ptr = (Residue *) realloc(seq->sequence,            
 *                                         seq->max_length *   
 *                                         sizeof(Residue))    
 *           );                                                      
 *  seq->sequence = tmp_ptr;
 * 
 ********************************************************************/

#ifndef NO_RECLAIM
#define CheckMem(A)		           \
{                                          \
  while(((A) == NULL) &&                   \
	((reclaim_space()) ?               \
	 TRUE :                            \
	 (sprintf(ErrorBuffer,             \
		 "Unable to recover enough memory to continue.  Aborting.\n"),\
	  ErrorReport(FATAL_ERR_LVL),      \
	  FALSE)                           \
	 )                                 \
	);                                 \
}
#else
#define CheckMem(A)                        \
{                                          \
  while(((A) == NULL) &&                   \
        (sprintf(ErrorBuffer,              \
                 "Unable to allocate memory.  Aborting.\n"),\
         ErrorReport(FATAL_ERR_LVL),       \
         FALSE)                            \
        );                                 \
}
#endif /* NO_RECLAIM */


/*
 * Exported functions
 */

/*
 * reclaim_space
 *   Tries to reclaim some of the allocated memory.  It tries to
 *   reclaim the memory from the various lists that are used by
 *   decreasing the elements that can be stored in the lists.
 *   NOTE: This function assumes that the searching has already begun.
 *         If that is not the case it will report that it was unable
 *         to get space because the list size and the NumberToReport
 *         will likely be zero.  This doesn't really matter much
 *         because if we have to reclaim space that early in the run, 
 *         there are problems.
 *   NOTE: Because of the SavedNodes list in the skiplist package many
 *         calls to reclaim_space may be needed before the free lists
 *         are filled and actual memory is freed.  This is not that
 *         big of a problem, considering that a balance will be
 *         reached with the nodes in the free lists.  The only time
 *         this would cause the Scores list size to reduce to zero is
 *         if there is so little memory that there can be only about
 *         20 scores in the list.  That amount of memory is about 100
 *         Kbytes. 
 *   Parameters: none
 *   Return codes: TRUE if it was able to get free some space, FALSE
 *                 if not.
 *   Error codes:  FALSE if it unable to get space.
 */

#ifndef NO_RECLAIM
extern Boolean reclaim_space();
#endif /* NO_RECLAIM */


/*
 * init_reclaim_space
 *   Sets up the reclaim_space function to call the passed function.
 *   Parameters:
 *     Boolean (*rec_func)(): The reclaiming function.
 *   Return codes: none.
 *   Error codes: none.
 */

extern void init_reclaim_space();


#endif /*  MEMORY_H_ */




/* Change log information follows. */
/* 
 * Revision 2.1021  1994/05/09  20:22:18  billa
 * Made the reclaim_space() function call the programmer supplied memory
 * recovery function rather than using the blimps specific code.
 *
 * Revision 2.1017  1994/04/27  02:29:29  billa
 * Removed RECLAIM_SPACE define.
 *
 * Revision 1.1000  1993/08/27  16:56:34  billa
 * Creation.  Added the function reclaim_space() and the macro CheckMem(A)
 * to handle the situation when there is no more memory to allocate.
 *
 */



 * assignments.  For example:                             
 * CheckMem(                                              
 *          new_block = (Block *) malloc(sizeof(Block))   
 *          );                                            
 * 
 * Note that blimps-3.9/include/ntbet.h000064400001460000012000000171110774312246000160640ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* ntbet.h: Definitions for nucleotides */
/* Modified by: Bill Alford */
/* Change log information is at the end of the file. */


#ifndef __NTBET_H__
#define __NTBET_H__

#define NUCID_MIN	0
#define NUCID_MAX	15
#define NUCID_CNT	16
#define NUCID_NAR	(NUCID_MAX+1)
#define NUCID_IGNORE	(NUCID_MAX+3)

#define NA NUCID_NAR	/* Not A Residue */
#define EL (NA+1)		/* End of Line */
#define ES (NA+2)		/* End of Sequence */
#define IC NUCID_IGNORE	/* Ignore this Character */
#define UNKNOWN_NT_CHR	'N'
#define GAP_NT_CHR '-'

/* Alpha chars that are not codes are treated as wildcard place holders */
/* (unknown nucleotides) */
#define UN 14			/* 14 = 'N' an unknown nt */


/*********************************************
*
*  ASCII-to-binary and binary-to-ASCII
*  translation tables
*
*********************************************/

EXTERN int nt_atob[1<>8)%nt_bdegen[c].ndegen] \
	: ((rnd_gen()>>8) % 4) )

/* Generate an appropriate random ASCII nucleotide from the list ACGT */
#define RANDOM_ANUC(c)	(nt_atob[c] < nt_atob['-'] ? \
	nt_adegen[nt_atob[c]].list[(rnd_gen()>>8)%nt_adegen[nt_atob[c]].ndegen] \
	: nt_btoa[((rnd_gen()>>8) % 4)] )

#undef NA
#undef EL
#undef ES
#undef IC

#undef UN

EXTERN double	ntfq[4]
#ifdef INIT
	= { 0.25, 0.25, 0.25, 0.25 }
#endif
	;

#endif /* __NTBET_H__ */




/* Change log information follows. */
/* 
 * Revision 0.52  1993/07/27  20:46:50  billa
 * Modified nt_atob so that alphabetic characters that are not codes are
 * treated as unknown nucleotides for placeholdings.  Also made it closer
 * to IUB codes by removing 'P' = 'R' and 'Q' = 'Y', 'P' and 'Q' are
 * treated as just mentioned above.  To take into account GCG codes, made
 * the representation of 'X' be equivalent to 'N' (this false under the
 * first sentence too).  The changes to nt_atob are:
 *      'P' gets the same binary representation as 'N', not 'R' as before
 *      'Q' gets the same binary representation as 'N', not 'Y' as before
 *      'E', 'F', 'I', 'J', 'L', 'O', 'Z' get the same binary
 *              representation as 'N'
 *      'X' gets the same binary representation as 'N'
 * Commented out the n4 information (nt_n4toa, nt_aton4).  This was
 * not used.
 * Modified nt_arevcomp so that 'P' and 'Q' are not treated as possible
 * codes and 'X' is treated as a any nucleotide ('N') as in GCG.  The
 * other alphabetic characters that are not codes are considered to be
 * NANT, as before.  The changes to nt_arevcomp are:
 *      revcomp of 'P' changed to NANT ('?') from 'Y'
 *      revcomp of 'Q' changed to NANT from 'R'
 *      revcomp of 'X' changed to 'N' from NANT
 *
 */
blimps-3.9/include/options.h000064400001460000012000000064300774312246000164450ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* options.h: */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef OPTIONS_H_
#define OPTIONS_H_

extern char **OptionsARGV;	/* Global options/arguments for */
extern int OptionsARGC;		/* sub-algorithms*/


/* 
 * get_option_args
 *  This retrieves the desired option arguments from the OptionsARGV
 *  array.  This is the function to use to retrieve options for any of
 *  the sub-algorithms (algorithms that are optional and not used
 *  generally).
 *  The options/arguments are accessed from the returned pointer.
 *  NOTE: there is no argument quoting yet.  All arguments are
 *    whitespace delimited.
 *  To identify which algorithm a set of arguments belongs to the
 *  arguments need to be prefixed and postfixed with a key.  For
 *  example (the colon is needed):
 *    OP Alt: arg0 arg1 arg2 arg3 :Alt
 *
 *  NOTE: The key is case INsensitive.  Also, if there is no
 *    terminating key the rest of the arguments are included in the
 *    returned argc.
 *  In the above example the returned value for argc would be 4 and
 *  the argv vector would start at arg0.
 *  WARNING: all of the following arguments after the key region are
 *    STILL accessible.  Only the address of the first arg is set.  No
 *    memory is duplicated.
 *  IMPORTANT NOTE: This does NOT follow the standard argc/argv
 *    conventions in main().  The argv[0] is the first ARGUMENT.
 *  Parameters:
 *    char *key:        the key (case INsensitive)
 *    int *argc_ptr:    a pointer to where to place argc.
 *    char ***argv_ptr: a pointer to where to place the argv address.
 *                      (remember argv is accessed as an array of char
 *                      ptrs.  An array of char ptrs is of type char **.  
 *                      so this is just a pointer to the place to put
 *                      the "array")
 *  Return Codes: returns TRUE if it can find the key region, FALSE
 *                otherwise
 *  Error Codes:  See above and argc is set to -1 and argv is set to NULL
 *
 *  Calling example:
 *    int argc;
 *    char **argv;  -- this can NOT be an array
 *    int result;
 *
 *    result = get_option_args("mykey", & argc, & argv); -- pass the addresses!
 *    if (result == TRUE) {
 *      printf("Got them\n");
 *    }
 *    else {
 *      printf("Could not find the args\n");
 *      -- error handling stuff here -- 
 *    }
 */

extern Boolean get_option_args();


/* 
 * insert_into_options
 *   Inserts the tokens in string into the options array for later
 *   retreival. 
 *   NOTE, get_token() is the function called to parse the tokens.  If
 *     a parse is in progress just pass in NULL, this will get passed
 *     to get_token() the first time, retreiving the next token.
 *   Parameters:
 *     char  *string: the string of tokens whitespace delimited
 *   Return codes: none
 *   Error codes: none
 */

extern void insert_into_options();


#endif /*  OPTIONS_H_ */

/* Change log information follows. */
/* $Log: options.h,v $
 * Revision 2.2010  1995/07/28  23:47:14  billa
 * Added new convert method and pattern matching and minor updates merged.
 * */
blimps-3.9/include/output.h000064400001460000012000000001550774312246000163100ustar00jorjastaff00000400000027


#ifndef OUTPUT_H_
#define OUTPUT_H_

#define INT_OUTPUT 0
#define FLOAT_OUTPUT 1


#endif /* OUTPUT_H_ */
blimps-3.9/include/pattern.h000064400001460000012000000026520774312246000164310ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* pattern.h:  */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef PATTERN_H_
#define PATTERN_H_

/*
 * Exported variables and data structures
 */

extern Boolean UsePatterns;  /* initially FALSE */

typedef struct pattern_residue_struct PatternResidue;
struct pattern_residue_struct {
  int offset;			/* the offset from the current position,
				   the current position is the previous 
				   PatternResidue or the starting location */
  int num_residues;		/* the number of residues */
  char *residues;		/* the residues */
  PatternResidue *next; /* the next pattern res. in the list */
};


struct pattern_struct {
  int beg_offset;		/* the offset from here to the beginning of
				   the sequence */
  int num_residues;		/* the number of sub residues */
  PatternResidue *pat;		/* the list of residues in the pattern */
};
typedef struct pattern_struct Pattern;




extern void scan_patterns();

extern Boolean pattern_matches();

extern int residue_compare_function();

#endif /*  PATTERN_H_ */

/* Change log information follows. */
/* $Log: pattern.h,v $
 * Revision 2.2010  1995/07/28  23:47:14  billa
 * Added new convert method and pattern matching and minor updates merged.
 *
 */

blimps-3.9/include/protomat.h000064400001460000012000000266251054326052000166170ustar00jorjastaff00000400000027/*------------------------------------------------------------------------*/
/*(C) Copyright 1991-2006, Fred Hutchinson Cancer Research Center         */
/*      motifj.h  Header file for PROTOMAT programs                       */
/* NOTE for Silicon Graphics users:  The type of scores in
       struct score should be changed from char to int to get correct
       processing (but not for SUN!)                                      */
/*------------------------------------------------------------------------*/
/*  6/29/90 J. Henikoff
    1/28/99 Increased SNAMELEN from 11 to 18; IDLEN from 10 to 12
    2/21/00 Added id->full_entry to struct db_id
    8/20/01 Increased MAXSEQS and MAXFREQ from 400 to 600
    1/ 2/06 Increase MAXSEQS and MAXFREQ from 600 to 1000
   12/23/06 Increased SNAMELEN from 18 to 20
--------------------------------------------------------------------------*/
#include 
#include 
#include 

#define VERSION		   8		/*  motifj version number */
#define YES                1
#define NO                 0
#define ESC               27
#define CR                13
#define LF                10
#define UMIN(x, y)	  ( (xy) ? x : y)   /* UNIX max macro */
/*   INDEX & INDEXCOL compute the sequential indices for the lower half of an
     nxn symmetric matrix given row & column coordinates.  Lower half has
     n(n-1)/2 entries; col=0,n-2 and row=col+1,n-1; col has n-col-1 rows.
     Index runs from 0 to n(n-1)/2 - 1 down columns with
     (index=0)==(col=0,row=1) and (index=n(n-1)/2-1)==(col=n-2,row=n-1).  */
#define INDEXCOL(n, col)    ( col*n - (col*(col+1))/2 )
#define INDEXCOLROW(n, col, row)  ( col*n - (col*(col+3))/2 - 1 + row )

#define randomize()       srand((unsigned)time(NULL))  /* Seed rand() */

#define MAX_DISTANCE  	  24	/* Max spacing between aminos of motif */
#define MIN_DISTANCE      1     /* Min distance specification */
#define MAXSEQS	  	  1000  /* Max number of sequences to be analyzed */
#define MINSEQS           2     /* Min number of sequences to be analyzed */
#define MAXFREQ           1000  /* Max occurences of motif in all seqs */
#define MAX_LENGTH	  5500  /* Max length of each sequence */
#define MIN_DOMAIN_WIDTH  10	/* Minimum width */
#define MAX_DOMAIN_WIDTH  55	/* Maximum width */
#define MAX_MERGE_WIDTH   55	/* Max. width of merged blocks */
#define RELEVANT_MOTIFS   50	/* Only top scoring motifs are retained */
#define MAX_MOTIFS	  100	/* Buffer motifs before discarding */
#define MINSCORE          1     /* Min block trimming column score (0-2500)*/
#define CLTHRES            80   /* Clustering identity percentage (0-100)*/
#define DROPSCORE         -10   /* Default std devs *10 for dropping block */
#define MOTAUTO4            3   /* max. # motifs for run type 4  */
#define MOTAUTO3	    6   /* min. # motifs for run type 3 */
#define MAXBLK             15   /* max # blocks for shotgun assembly */
#define MAXTITLE	   75   /* max sequence title length */

#define PROTEIN_SUBDIRECTORY "pros/"  /* Subdirectory containing proteins */
#define PROTEIN_EXTENSION    ".pro"    /* Extension for all protein files */
#define READ                 "r"       /* Code to read disk files */
#define SNAMELEN              20       /* Max length of sequence name */
#define IDLEN                 12       /* Max length of db id */
#define FNAMELEN              80       /* Max length of file name */
#define MAXLINE               480      /* Max line length for ASCII file */
#define MATSIZE               21       /* Scoring matrix dimension */
#define HIGHPASS              4	       /* Default high pass filter value */

#define round(x) ((x >= 0.0) ? (int) (x+0.5) : (int) (x-0.5))

/* Declare new data types */
typedef unsigned char *aa_type[20][20][MAX_DISTANCE];

/* Structure to store information about each motif: */
/*  NOTE: integer fields defined as unsigned char to save space;
	  they must not exceed 255 in value */
struct motif_struct {
  unsigned char aa1, aa2, aa3, distance1, distance2;
  /*  freq is the number of sequences with this motif */
  int freq, dups;
  /*   seq_no[freq] lists the sequence numbers that have the motif,
       pos[freq] lists the offset of the motif in the corresponding
       sequences; so pos[x] is the offset into sequence # seq_no[x], 
       NOT into sequence # x */
  int seq_no[MAXFREQ], pos[MAXFREQ];
  int score, scores[MAX_DOMAIN_WIDTH], domain, mots;
  char group, sub_group;
  };

/* Structure to store information about groups for motif map routine: */
struct group_struct {
  int group_no, sub_no, position;
  };

/*-------------------------------------------------------------------*/
/*  merged_motif is an array of motifs.  Each entry is one or more   */
/*    motifs.  Each can be thought of as a block of sequences aligned*/
/*    around all the motifs.                                         */
/*-------------------------------------------------------------------*/
struct merged_motif {
	int dropped;			/* YES if dropped */
	char aa[3];			/* Amino acid motif */
	int nmotif;			/* number of motifs, >= 0  */
					/* 0 => merged (inactive) */
	int nident;			/* number of identities */
					/* ..occurs >=SIGNIF in a col. */
	int max_score;			/* max. score of merged motifs */
	int domain;			/* displacement of merged motif blocks */
					/* block width = domain+1 */
	int distance;			/* width of motifs within block */
	int dups;			/* total # dups in all seqs */
	int loffset;			/* 1st position of motif within block*/
	int leftpos[MAXSEQS];		/* leftmost position of motif   */
					/*... for each sequence*/
	int cluster[MAXSEQS];		/* cluster number for each seq */
	int scores[MAX_MERGE_WIDTH];	/* column scores */
	int t_loffset;			/* 1st position of motif within */
					/*  trimmed block */
	int t_domain;			/* trimmed block width=t_domain+1*/
	int t_score;			/* score over trimmed block */
	int position[MAXSEQS];		/* position of block within each seq*/
	int maxpos;			/* max position in any seq */
	int minpos;			/* min position in any seq */
	int in_degree;			/* in-degree of block in DAG */
	int out_degree;			/* out-degree of block in DAG */
};

/*------------------------------------------------------------------------*/
/*   sequences contains all information about the sequences.              */
/*------------------------------------------------------------------------*/
struct sequences {
	int num;		/* number of sequences */
	int totlen;		/* total length of all sequences */
	int *len;		/* lengths of each sequence */
	int *offlen;		/* offset to start of each sequence */
	char *name;		/* 10 char name of each sequence */
	char *seq;		/* sequence bases */
};

/*------------------------------------------------------------------------*/
/*   aux_seq is a list of blocks ordered left to right within a sequence  */
/*  Each sequence has the same number of blocks, but the blocks may be
     arranged in different orders in each sequence.                       */
/*------------------------------------------------------------------------*/
struct aux_seq {
	int block[RELEVANT_MOTIFS];	/* index of block in each position*/
};

struct temp {			/* temporary structure for sorting */
	int value;
	int index;
	int flag;
};
struct dtemp {			/* temporary structure for sorting */
	double value;
	int index;
};

/*-----------------------------------------------------------------------*/
/*    Structure for pairs of sequences.                                  */
/*     pair should be allocated as an array, & the number of the         */
/*     sequences forming the pair inferred from the array index.         */
/*-----------------------------------------------------------------------*/
struct pair {
	int score;		/* # of identities within trimmed block */
	int cluster;		/* cluster # for this pair */
};

/*-----------------------------------------------------------------------*/
/*  block_list is a list of blocks in an order that is consistent among
    all sequences;  it implies a partial multiple alignment.
    The next_block list is a list of all blocks, some of which may
    overlap.  The doubly linked next_best/prev_best list is a subset
    consisting of the best non-overlapping blocks in the list.           */
/*-----------------------------------------------------------------------*/
struct block_list {
	int b;			/* index of block (merged_motif) */
	int minprev;		/* min. distance from previous block */
	int maxprev;		/* max. distance from previous block */
	struct block_list *next_block;  /* all blocks in the list  */
	struct block_list *next_best;   /* best blocks in the list */
	struct block_list *prev_best;
};

/*------------------------------------------------------------------------*/
/*  path is a list of all possible paths through the blocks in all seqs.
     The first_block list includes all blocks, including those that
     possible overlap.  The first_best list includes the best sub-path
     of non-overlapping blocks.                                           */
/*------------------------------------------------------------------------*/
struct path {
	int nblocks;		/* # of blocks in path */
	int nbest;		/* # of blocks in best sub-path */
	int naas;		/* # of AAs in best sub-path */
	unsigned long totscore;	/* sum of scores of blocks in best sub-path*/
	int totmotif;		/* # motifs in best sub-path*/
	int totident;		/* # conserved residues in best sub_path */
	int nseqs;		/* # seqs in best sub-path */
	int seqs[MAXSEQS];	/* YES if path holds for sequence */
	struct block_list *first_block;  /* first block in path */
	struct block_list *first_best;	 /* first block in best sub-path*/

	struct path *next_path;
};

/*----------------------------------------------------------------------*/
/*  Ajacency matrix representation of distances between blocks in
    all sequences.                                                      */
/*----------------------------------------------------------------------*/
struct matrix {
	int npos;		/* # of seqs with positive diff in cell */
	int maxdiff;		/* maximum positive difference in cell  */
/*	int dist[MAXSEQS];	 distance from row to col for seq s */
	int mark;		/* all-purpose flag */
};

struct follow_data {
	struct path *path;
	int mark[RELEVANT_MOTIFS][RELEVANT_MOTIFS];
};

/* -------- Scoring matrix structure ----------------------------------*/
struct score {
	char scores[MATSIZE][MATSIZE];	/* valid range -127 to +128 */
	int highpass;			/* high pass filter value */
};

/*-Structure to split up a file name of the form \.ext -*/
struct split_name {
	int dir_len, file_len, name_len;
};
/*------ Structure to hold the contents of a .lis or .lst file ------*/
struct db_id {
   char entry[SNAMELEN+1];	/* sequence name */
   char full_entry[2*SNAMELEN];	/* enhanced sequence name */
   char ps[2];			/* PS type=T, F or P */
   char info[FNAMELEN];		/* additional text info */
   int len;			/* sequence length */
   int frag;			/* YES if seq is a fragment */
   int lst;			/* seq in .lst file */
   int found;			/* seq found in database */
   int block;			/* seq found in block */
   int search;			/* used by excluded.c => use seq for search*/
   int rank;			/* used by matodat.c, fastodat.c */
   int score;			/* used by matodat.c, fastodat.c */
   double pvalue;		/* P-value */
   struct db_id *next;
   struct db_id *prior;
};

struct db_id *makedbid();
struct db_id *check_entry();
int get_ids();

struct split_name *split_names();

char *dir_unix();
int kr_atoi();
void kr_itoa();

void getscore();

char *num_to_aachar();
int aachar_to_num();
void pr_num_to_aa();
void pr_num_to_aa_space();

blimps-3.9/include/residues.h000064400001460000012000000012400774312246000165670ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* residues.h: Definitions for nucleotides and amino acids and translations */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef RESIDUES_H_
#define RESIDUES_H_
 
#include 
#include 
#include 
#include 
#include 

#endif /*  RESIDUES_H_ */
 
/* Change log information follows. */
/* 
 *
 * Revision 0.10  1993/07/16  21:56:28  billa
 * entry into system
 *
 */



blimps-3.9/include/sequences.h000064400001460000012000000226640774312246000167540ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* sequences.h: sequence manipulation functions */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef SEQUENCES_H_
#define SEQUENCES_H_

/*
 * Exported variables and data structures
 */

#define AA_SEQ 0	/* Amino acid sequence designator */
#define NA_SEQ 1	/* Nucleic acid sequence designator */
#define UNKNOWN_SEQ 2	/* Unknown sequence designator */

#define NA_FREQ 0.85	/* the percent of 'A', 'C', 'G'. & 'T' in */
			/* the sequence to consider it a NA_SEQ */

/* the Residue type */
typedef unsigned char Residue;

struct sequence_struct {
  char name[SMALL_BUFF_LENGTH];	   /* the name of the sequence */
  char info[SMALL_BUFF_LENGTH];	   /* the info line of the sequence */
  int position;			   /* the position of the subsequence (if */
				   /* is one) in the sequence */
  int length;			   /* the length of the sequence */
  int max_length;		   /* the maximum length of memory allocated */
  int type;			   /* type of sequence: AA_SEQ or NA_SEQ */
  double weight;		   /* the weight of the sequence if the */
				   /* sequence is in a block */
  int undefined;		   /* for future use */
  double undefined_dbl;		   /* for future use */
  void *undefined_ptr;		   /* for future use */
  Residue *sequence;		   /* the sequence of either protein or DNA */
};
typedef struct sequence_struct Sequence; 




/* Sequence Database types */
/*--------Sequence database format structure -------------------------*/
#define MAXDB   10		/* Max. # database formats */
#define GB       0		/* GenBank type */
#define PIR      1		/* PIR type */
#define EMBL     2		/* EMBL type.  SwissProt is the same. */
#define GCG      3		/* plain GCG type */
#define GCG_GB   4		/* GCG with GenBank header */
#define GCG_PIR  5		/* GCG with PIR header */
#define GCG_EMBL 6		/* GCG with EMBL/SwissProt header */
#define FASTA    7		/* FASTA type */
#define UNI      8  		/* UNIVERSAL type */
#define FLAT     9		/* FLAT, no title, just sequence */
/*#define VMS 3*/ 		/* PIR/VMS type */
/* NOTE: VMS must be the the last type and UNI must be just before it.  See */
/*       the code in type_dbs for the reason */
/* NOTE: Fasta and Universa (and VMS) formats are very similar.  The */
/*       only difference between Fasta and Universa is that there is a */
/*       '*' at the end of the Universa format.  The reason for the */
/*       Universa format is that there was a time when patmat needed */
/*       the '*' end-of-sequence delimiter.  There is no longer a */
/*       need with blimps, but the universa format handling is being */
/*       kept around for backward compatibility. */
/* NOTE: The GCG formats consists of a header file of the format of the */
/*       originating database and the sequence protion in the GCG */
/*       format.  This obviously can lead to confusion, especially */
/*       since the characters in the second line of the GCG sequence */
/*       format will signal that the sequence is an amino acid */
/*       sequence (bad when the GCG sequence is from a DNA database). */
/* NOTE: The plain GCG format is a kludge.  There is code to handle */
/*       it, but since it is one of the formats that does not have an */
/*       end delimiter there is the possibility that there will be */
/*       junk added to the sequence if there is more than one */
/*       sequence in the file. */

struct db_info {		/* Sequence Database format info */
   char *type;
   char *start;
   char *desc;
   char *seq;
   char *end;
   int title_offset;
   int seq_offset;
};

extern struct db_info DbInfo[MAXDB]; 



/*
 * Exported functions
 */

/*
 * read_a_sequence
 *   reads a sequence from the data base and returns a pointer to the new
 *   Sequence data structure
 *   Parameters:
 *     FILE *sfp: the sequence file pointer 
 *     int db:    the database type of the file
 *     int type:  the type of sequences in the file 
 *   Error codes: Returns NULL if there was no sequence to read.
 */

extern Sequence *read_a_sequence();

/*
 * read_sequence
 *   read_sequence reads from the string the sequence of the given type into
 *   the passed in Sequence data structure
 *   Parameters:
 *     Sequence *seq: the Sequence data structure to put the data in
 *     int seq_type:  the type of sequence (amino acid or nucleic acid)
 *     int start_pos: the position in the sequence to start entering the data
 *     char *str:     the string that has the sequence (NULL terminated)
 *   Note: The entire string up to the NULL character is considered the 
 *         sequence.
 *   Preconditions: seq.length must have a the value of the size allocated to 
 *                  the residues
 *   Postconditions: the residues from start_pos to either seq.length or
 *                   return value + start_pos in the seq.sequence have been
 *                   updated to the residues passed in by the string
 *                   seq.type is set to seq_type
 *   Return codes: returns the number of residues added to the sequence
 *   Error codes: returns the negative value of the number of residues left
 *                over after the sequence has been filled.  
 *   Note: A return value of zero is means that no residues were 
 *         added to the sequence.
 */

extern int read_sequence();

/*
 * sequence_type
 *   tries to guess the type of the sequence passed in the string.
 *   Note: if the sequence can not be matched to an NA_SEQ, it falls through
 *         to being a AA_SEQ.
 *   Parameters:
 *     char *str: the sequence string, no more than SMALL_BUFF_LENGTH long
 *   Return Codes: Returns either AA_SEQ or NA_SEQ depending on
 *                 if the sequence is an Amino Acid or Nucleic Acid.
 *   Error Codes: none
 */

extern int sequence_type();


/*
 * sequence_comparison
 *   Compares two sequences.   It compares by the value in the name
 *   field if it exists.
 *   Parameters:
 *     SequenceListEntry a, b: the entries to compare
 *   Return codes:  a return value < 0 if a < b, a return value = 0 if a == b,
 *                  and a return value > 0 if a > b
 *   Error codes: none
 */

extern int sequence_comparison();

/* 
 * free_sequence
 *   Deletes the sequence and the sub elements.
 *   Parameters: 
 *     Sequence *sequence: the sequence to free
 *   Return code: none
 *   Error code: none
 */

extern void free_sequence();



/*
 * translate_sequence
 *   Given a frame (1, 2, 3, -1, -2, or -3), translates the DNA sequence 
 *   (NA_SEQ) into an amino acid sequence.
 *   Parameters:
 *     Sequence *seq: the DNA sequence
 *     int frame:     the frame to read
 *     unsigned char gcode[64]:    the genetic code (forward).  
 *                                   for frames 1, 2, 3
 *     unsigned char revgcode[64]: the genetic code (reverse complement)
 *                                   for frames -1, -2, -3
 *   Return code: a pointer to the new translated sequence
 *   Error codes: returns the original sequence if the sequence is not a
 *                NA_SEQ or the translation frame is incorrect.
 */

extern Sequence *translate_sequence();

/*  untranslate an amino acid sequence to a degenerate DNA sequence  */
extern Sequence *untranslate_sequence();


/* NOTE: These should only be used in config.c when determining the */
/*       database types.  These should be used to set the values in the */
/*       file lists. */

/* 
 * type_dbs
 *   Figures out the type of the database to be read.
 *   This is from motomisc.c used in the universa conversion program.
 *   Parameters:
 *     FILE *fin:            the database file
 *     struct db_info dbs[]: the information of the structure of the db's
 *   Return codes: the type of database the file is.
 *   Error code: the database number -1 is returned if the type of database
 *               cannot be figured out
 */
extern int type_dbs();


/*
 * seq_type_dbs
 *   Finds the type or the database given.
 *   Parameters:
 *     FILE *fin:            the database file
 *     struct db_info dbs[]: the information of the structure of the db's
 *     int db:               the number of this database (indexes into dbs)
 *   Return codes: Returns the type of sequence of the first entry in the 
 *                 database.  This assumes that the entire database is of this
 *                 type.
 *   Error codes: none
 */

extern int seq_type_dbs();

/*
 * print_sequence
 *   Prints a Sequence data structure.  Primarily for debugging purposes.
 *   Parameters: 
 *     Sequence *seq:  the sequence to print
 *   Error Codes: none
 */

extern void print_sequence();

/*
 * output_sequence
 *   Outputs a Sequence data structure to the given file.
 *   Parameters: 
 *     Sequence *seq:  the sequence to print
 *     FILE *osfp:     the output sequence file pointer
 *   Error Codes: none
 */

extern void output_sequence();


/*
 * resize_sequence
 *   Adds more memory for the storage of the residues of a sequence.
 *   Parameter:
 *     Sequence *seq: the sequence to resize
 *   Error codes: none
 */

extern void resize_sequence();

#endif /*  SEQUENCES_H_ */

/* Change log information follows. */
/*
   Changes since version 3.3.2:
   12/15/99 Added double undefined_dbl field.
   Changes since version 3.2:
   11/24/97 Made resize_sequence() external.
   Changes since version 3.1:
   1/20/97  Added untranslate_sequence()
   Changes since version 2.x:
   3/20/96  Lowered NA_FREQ from 0.90 to 0.85 after user complaints. JGH
 *
 */

blimps-3.9/include/skiplist.h000064400001460000012000000127220774312246000166150ustar00jorjastaff00000400000027/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* skiplist.h: This header file contains the definitions for use with the */
/*             generic SkipList package. */
/* Change log information is at the end of the file. */
/* most of this file is untouched from the distribution I started from, Bill */

/* This header file contains the definitions for use with the generic
 * SkipList package.
 *
 *      -- THIS CODE IS UNDER THE GNU COPYLEFT --
 *
 *    Dominic Giampaolo (nick@maxine.wpi.edu) 
 */

#ifndef SKIPLIST_H
#define SKIPLIST_H


/* RAND_MAX should be defined if you are using an ANSI compiler system,
 * but alas it isn't always.  You should define it to be the correct
 * value for whatever your library rand() function returns.
 *
 * Under unix (mach, bsd, etc), that's 2^31 - 1.  On my Amiga at home 
 * it's 2^15 - 1.  It would be wise to verify what your compiler uses
 * for RAND_MAX (the maximum value returned from rand()) because otherwise
 * the code will _not_ work.
 */
#ifndef RAND_MAX
#define RAND_MAX (0x7fffffff)
#endif


#define ALLOW_DUPLICATES  1   /* allow or disallow duplicates in a list */
#define NO_DUPLICATES	  0
#define DUPLICATE_ITEM	 -1   /* ret val from InsertSL if dups not allowed */


/* typedef's */
typedef struct SLNodeStruct *SLNode;

struct SLNodeStruct
{
  void	 *key;
  SLNode  forward[1]; /* variable sized array of forward pointers */
};

typedef struct _SkipList
{
  struct SLNodeStruct *header;	   /* pointer to header */

  int  (*compare)();
  void (*freeitem)();

  int flags;
  int level;			   /* max index+1 of the forward array */

  int count;                       /* number of elements in the list */
} *SkipList;



/* protos */
SkipList   NewSL();
void	   FreeSL();
int	   InsertSL();
int	   DeleteSL();		/* delete the matching key. */
				/* Only deletes the first one if duplicates. */
void	  *SearchSL();
void	   DoForSL();
void       DoForRangeSL();

int        NumInSL();

void      *Nth(); /* returns the Nth element in the list. */
		  /* Counting starts at 0. */

int LowerSavedNodesLevel();	/* function to lower the amount of nodes */
				/* saved in the SavedNodes list.  Returns */
				/* the new level of saving. */

/* These defines are to be used as return values from the function
 * you pass to DoForSL().  They can be or'ed together to do multiple
 * things (like delete a node and then quit going through the list).
 */
#define  SL_CONTINUE  0x00
#define  SL_DELETE    0x01
#define  SL_QUIT      0x02

#endif	/* SKIPLIST_H */


/* added by Bill Alford */
/* Change log information follows. */
/* $Log: skiplist.h,v $
 * Revision 2.2010  1995/07/28  23:47:14  billa
 * Added new convert method and pattern matching and minor updates merged.
 *
 * Revision 2.2000  1994/05/10  18:39:13  billa
 * System version 2.2 A [2.2000]
 * Goofed on dev. version.
 *
 * Revision 2.1100  1994/05/10  18:27:07  billa
 * System version 2.2 A [2.1100].
 * Created blimps library and fixed up minor bugs.  No major changes to the
 * program.
 *
 * Revision 2.1025  1994/05/10  00:51:47  billa
 * Added SCCS patterns to trick the what command into printing out the RCS
 * identifying patterns.
 *
 * Revision 2.1020  1994/04/27  21:59:11  billa
 * After library creation.  In testing phase.
 *
 * Revision 2.1015  1994/04/26  03:15:34  billa
 * Pre-library checkin.
 *
 * Revision 2.1010  1994/04/26  00:28:18  billa
 * Cleaned up warnings from gcc switches.
 *
 * Revision 2.1000  1994/03/09  22:23:59  billa
 * System version 2.1 A [2.1000]
 * Added reading and scoring of precomputed site specific scoring matricies.
 * Reconfigured files.[ch] into files.[ch] and config.[ch].
 *
 * Revision 2.0  1993/12/06  19:31:18  billa
 * System version 2.0 A [2.0000].
 * Changed source to remove some warnings.  Added sequence weights to the
 * blocks.  Added a conversion method to use the weights.  Made the method
 * the default.  Added some ifndef's in preparation of creating a library
 * of functions.  Added the ability to choose the genetic code to use for
 * translation.  Added the ability to read a flat file as a sequence if the
 * other types sequences fail to match.  Added some defines for strdup().
 *
 * Revision 1.1120  1993/12/02  03:44:22  billa
 * Development version 1.1120.  Right after copyright/license info added.
 *
 * Revision 1.1101  1993/12/02  03:37:12  billa
 * Added the copyright notice to the top of the file.
 *
 * Revision 1.1100  1993/09/09  17:23:19  billa
 * System version 1.1 B [1.1100].
 *
 * Revision 1.1000  1993/08/27  17:01:31  billa
 * System version 1.1 A, development version 1.1000.
 * Added the function reclaim_space() and the macro CheckMem(A) to handle
 * the situation when there is no more memory to allocate.
 *
 * Revision 1.0  1993/08/14  00:50:52  billa
 * System version 1.00
 *
 * Revision 0.110  1993/08/10  02:50:53  billa
 * System version update.  Added convert.[ch], scoring.[ch] and version.[ch].
 *
 * Revision 0.105  1993/08/04  19:53:40  billa
 * System version 0.105.  Post file structure reorganization.
 *
 * Revision 0.100  1993/08/03  00:48:46  billa
 * System version 0.100.  Pre file structure reorganization.
 *
 * Revision 0.51  1993/07/02  00:55:15  billa
 * un-ANSIfied the prototypes.  Removed the argument declarations to be
 * backward compatible.
 *
 * Revision 0.50  1993/07/02  00:36:31  billa
 * Entry into the system.  Addition of skiplists to the system.
 *
 */






blimps-3.9/include/strutil.h000064400001460000012000000053220774312246000164570ustar00jorjastaff00000400000027/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* strutil.h: general string utilities */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef STRUTIL_H_
#define STRUTIL_H_

/*
 * Exported variables and data structures
 */

#define EXTRA_LARGE_BUFF 1000
#define LARGE_BUFF_LENGTH 500	/* The length of large buffers */
#define SMALL_BUFF_LENGTH 100	/* The length of small buffers and */
				/* predeclared strings */
extern char Buffer[LARGE_BUFF_LENGTH];


/*
 * Exported functions
 */

/* 
 * blank_line
 *  returns TRUE if the passed string is only whitespace
 *  Parameters:
 *    char* s: the string to check
 *  Return codes:
 *    TRUE if the line only has whitespace characters, FALSE otherwise.
 *  Error Codes:
 */

extern Boolean blank_line();


/*
 * eat_whitespace
 *   Eats the whitespace at the beginning of the string s1 and returns a 
 *   pointer to the first non whitespace character.  The whitespace characters
 *   are: space, tab, and newline.
 *   Parameters:
 *     char *s : input string
 *   Return Value: the return value is the pointer to the first non-whitespace
 *                 character
 *   Error codes:
 */

extern char *eat_whitespace();


/*
 * remove_trailing_whitespace
 *   Removes trailing whitespace by scanning back from the end of the string
 *   and replacing the leftmost trailing whitespace character with a NULL.
 *   Whitespace characters are: space, tab, newline and carriage return.
 *   NOTE: this is destructive
 *   Parameters:
 *     char *s : input string
 *   Return Value: returns its first argument
 *   Error codes:
 */

extern char *remove_trailing_whitespace();


/*
 * get_token
 *   get_token returns a pointer to a token delimited by whitespace.  The
 *   first call with a string returns the first token.  Subsequent calls (with
 *   the string as NULL) returns pointers to the following tokens.  A NULL
 *   is placed following the token.
 *   Note: get_token must be called with a non-null string pointer the first
 *         time or the behavior is ambiguous.
 *   Whitespace is: space, tab, newline, carriage return
 *   Parameters: 
 *     char *s: the string of tokens
 *   Return Value: the pointer to the token, NULL when there are no more tokens
 *   Error codes:
 *   Notes: get_token() wraps strtok() because the separators will always be 
 *          whitespace and strtok() is cryptic and easy to forget. (for me).
 */

extern char *get_token();




#endif  /* STRUTIL_H_ */

/* Change log information follows. */
/* 
 Changes since version 3.4:
12/23/00 Added EXTRA_LARGE_BUFF
 *
 */
blimps-3.9/include/version.h000064400001460000012000000074211041505636300164360ustar00jorjastaff00000400000027/* (C) Copyright 1993-2006, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */

/* version.h: Header file to version.c. keeps track of the system */
/*            version level. */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */

#ifndef VERSION_H_
#define VERSION_H_

/*  Remember to put the DEVELOPMENT VERSION string in the VERSION define */
#define VERSION "3.8"
#define VERSION_DATE "2006/04"

#ifndef VERSION_FROM_MAKE
#define VERSION_FROM_MAKE ""
#endif


/****
Versions are now as follows:
major_release.minor_release.updates

Major releases, minor releases, and updates are described as below.

*****/
/**************************************************************************
A NOTE ABOUT VERSIONS:

The plan for the difference between versions:
  Major release:  
    A major release would be something like a reconstruction of the
    interface.  New file formats or configuration keys that are
    necessary in order to run.  Also changes to the program structure
    should be limited to a major release.  An example would be
    changing the way the frequency file is laid out.

    ex. system: 1.x c    --> 2.0 A
        dev.    1.xxxyzz --> 2.0

  Minor release:  
    A minor release would be something like an important enhancement
    to a file format or a configuration that could change the
    performance (but not the output) of the program, enhancements to
    the program that do not change the data, but make the program
    better.  An example would be memory management code or new
    names to the configuration file or reading of a matrix database/file.

    ex. system: 1.2 c    --> 1.3 A
        dev.    1.2yzz   --> 1.3000

  Updates:     
    An update would be something that would not get in the way of
    earlier file formats and that could be used by earlier versions of
    this minor release.  Nothing that changes the way the program is
    called.  Examples of updates would be new conversion and scoring
    routines added or a new configuration key that will change the way
    data is output (eg. outputs a matrix) or the ability to read a new
    sequence database format.  Note that reading a new block format
    would be a minor release because there is only one block database
    and it is key to the way the program behaves.  Also note that
    something like being able to read a new sequence database format
    is more suited to an update since there are many different formats
    and external to the program they can be converted to one that
    blimps can already read.  Updates are also for bug fixes.
   
    ex. system: 1.2 B    --> 1.2 C
        dev.    1.22yy   --> 1.2300

**************************************************************************/



/*
 * Exported variables and data structures
 */

/*
 * Exported functions
 */


/*
 * version_strings
 *   Enters the strings to be used by the version output function 
 *   (print_version).
 *   Parameters:
 *     char *program_string:   the name of the program
 *     char *version_string:   the RCS revision number 
 *     char *version_info:     additional version info
 *     char *date_string:      the RCS date
 *     char *copyright_string: the copyright info
 *   Error codes: none
 */

extern void version_strings();


/*
 * print_version
 *   Prints the version of the current release.  
 *   NOTE: version.c must be checked in each time a change is made so that
 *         the version info will be correct
 *   Parameters:
 *     FILE *fp: the file to print the verson info, typically stdout and the
 *               output file
 *   Error codes: none
 */

extern void print_version();


#endif /*  VERSION_H_ */

/* Change log information follows. */
blimps-3.9/lib/000075500001460000012000000000001062462473700137275ustar00jorjastaff00000400000027blimps-3.9/lib/Sun_sparc/000075500001460000012000000000001062460505200156515ustar00jorjastaff00000400000027blimps-3.9/lib/Sun_sparc/libblimps.a000064400001460000012000010225001054326153600177750ustar00jorjastaff00000400000027!
/               1166893918  0     0     0       3884      `
pppppp000000000000000000dddddxxxxxxxxxxxxxxxxxxxxxxeTeTeTeTeTeTeTeTeTeTeTeTeTeTDDDDDPPPPPPPPKKWWWWWWWWWWWWWڬڬڬڬRDRDRDRDRDRDRDRDRDRD`````z z z z z z scan_patternsresidue_compare_functionpattern_matchesUsePatternsListInitializedPatternsinsert_fileget_filerewind_fileget_current_file_nameget_file_namenumber_of_filesclose_fileget_sequence_db_seq_typeget_sequence_db_db_typeErrorFilePatternFilesSequenceFilesFrequencyFileDatabaseFilesMatrixFilesBlockFilesOutputFileExportMatrixFileload_frequenciesload_codonsfrq_qijCodon_Usagefrequencyblock_to_matrixoriginal_conversion_method_cleaned_uppre_weighted_conversion_methodfree_work_pssmmake_gribsload_qijnormalizealtschul_data_dependent_conversion_methodgribskov_conversion_methodpb_weightsoriginal_conversion_methodSIFT_conversion_methodSIFT_pssmload_diricounts_nogapssimilarity_dependent_scalepseudo_dirifind_max_aa_colfind_max_aa_pssmadd_logsQijRTotread_a_blockread_block_headerread_block_bodynext_clusterresize_block_sequencesresize_block_clustersfree_blockblock_comparisonprint_blockoutput_blockoutput_block_snew_blockread_to_blockread_a_block_fasterset_error_file_nameErrorReportABRT_signal_handlerErrorLevelReportErrorBufferinit_gcodecodon2aaaa2codonread_a_matrixnew_matrixfree_matrixmatrix_comparisonprint_matrixoutput_matrixoutput_matrix_soutput_matrix_streclaim_spaceinit_reclaim_spaceread_a_sequenceresize_sequencesequence_typeread_sequencefree_sequencetranslate_sequencesequence_comparisontype_dbsseq_type_dbsprint_sequenceoutput_sequenceuntranslate_sequenceDbInfoblank_lineeat_whitespaceremove_trailing_whitespaceget_tokenBufferLowerSavedNodesLevelNewSLFreeSLInsertSLDeleteSLSearchSLDoForSLDoForRangeSLNumInSLNthSLNodesToSaveInitializedSaveListSavedNodesversion_stringsprint_versionget_option_argsinsert_into_optionsOptionsARGVOptionsARGCblimps_reclaim_spaceread_config_fileinitialize_listsinsert_in_score_listlimit_Scores_list_sizeenter_score_into_print_scoresMinScoreOfListSequencesBlocksMatricesPrintScoresScoresscore_and_enterscore_comparisonneg_score_comparisonfree_scoreoutput_scoresdefault_scoring_methodprint_histogramAlignments_DoneScores_DoneDoHistogramhistogramPASCAL_MAINmy_labsmy_memmovemy_memcpymy_memcmpmy_memsetmy_touppermy_toloweripowstrsubstrpos2strcicmpstrltrimstrrtrimstrrptstrpadstrmovestrdeletestrinsertP_peekP_eofP_eolnP_readpaocP_readlnpaocP_maxposP_trimnamememavailmaxavailP_setunionP_setintP_setdiffP_setxorP_insetP_addsetP_addsetrP_remsetP_setequalP_subsetP_setcpyP_expsetP_packsetP_getcmdlineTimeStampVAXdateVAXtimeP_sun_argv_OutMem_CaseCheck_NilCheck_ShowEscape_Escape_EscIOEXCP_LINE__MallocTemp____top_jbP_ioresultP_escapecodeP_argcP_argvgetwordmakewordfmakewordx2cunescape_urlplustospacerindgetlinesend_fdindescape_shell_cmdnum_to_aacharaachar_to_numpr_num_to_aapr_num_to_aa_spacegetscorekr_atoikr_itoasplit_namesdir_unixmakedbidget_idscheck_entrybl60_highpassbl60_matrixbl62_highpassbl62_matrixpattern.o/      1166893898  102   10    100644  8404      `
ELF4(
.shstrtab.text.bss.data.rodata.rodata1.stab.indexstr.stab.index.symtab.strtab.rela.text.comment㿈#\3`2@!&!@ x@@7@O x	`7@ @ `@+  1@ &  & @`@E-!@@8
@4M /@ AO `/@4 @O `CH@@ @N ;@@.\@!2  2?`!@@
"OM@ O2HT#`@ @  @@\! !!@@0 @,L `A@L`C@@@ @H`;@@(@H#`1!@@ "OL @ Oɐ79\ @@ &1#d @ #h H+!@h@
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@ 
@ @@@O `@`@ L`@}  x@rX@p[H?L`` ]@H ]2O( @@@O @`@ @@& @O@`@  & & @& @ /*` @@
 @O @@  @@
%@O @@ %%%L`+. @L```Ox@@@ -@$@ @ & $@$@@ @`#%`& @O@& H&#l&@hG!`#l`#`@ Ӑ3` @	% @! ``@!؀㿠`@5 `@@^&@] `@ ``@I`
M@0 3? \2@G $@D  3 ``@K@N"@8 &O` `@.5 ̠ `@@"@ ``@``@M L"H` $@ ` @NL@`@&O` ``2O`  `@"@ #@`@㿠@ `@   2O 9 @Unable to recover enough memory to continue.  Aborting.
Unable to find pattern for PSSM %s
pat_file != NULLpattern.cUnable to recover enough memory to continue.  Aborting.
NumInSL(residue_list) == 0pattern.c0pattern.cNumInSL(residue_list) == 0pattern.cUnable to recover enough memory to continue.  Aborting.
NumInSL(residue_list) == 0pattern.cUnable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
0pattern.c%d: (null)
%d: ;
(%d, [%s]) pattern.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  pattern.c<M4
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!@ @ ?`L\l|㿠 @. `%  ' )  +` - / 35`@@   @#!`@ @   "@' @' ``get_file_list(): Unknown file group %d.insert_file(): Bad file list, not entering filename "%s"               into a file list
Unable to recover enough memory to continue.  Aborting.
Already have a frequency file: %sThe file %s will be ignored.
Unable to recover enough memory to continue.  Aborting.
get_file(): Bad file list, unable to open a file
rUnable to open block file: %s
Unable to open matrix file: %s
Unable to open database file: %s
Unable to open frequency file: %s
Unable to read sequence file: %s
Unable to read pattern file: %s
get_file(): Unknown file group            Unable to open a file
rUnknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Assuming there is no title and just sequence.
Unable to read sequence file: %s to determine the type of database
Unable to open block file: %s
Unable to open matrix file: %s
Unable to open database file: %s
Unable to open frequency file: %s
Unable to read sequence file: %sUnable to read pattern file: %sget_file(): Unknown file group            Unable to open a file
rewind_file(): Bad file group, unable to rewind file list
get_current_file_name(): Bad file group, unable to return a file name
get_current_file_name(): No files in the file group                         Unable to return a file name
get_file_name(): Bad file group, unable to return a file name
get_file_name(): No files in the file group                 Unable to return a file name
get_file_name(): Requested file out of the range of the files                 in the file group                 Unable to return a file name
number_of_files(): Bad file group, unable to report number of files
close_file() : Bad file group, unable to rewind file list
files.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  files.c	<K4	,ChHZq	0
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/-@8@@5 8&3@`@;@&@`9? rload_frequencies: Unable to open frequency file: %sload_frequencies: Read a frequency of value of %f for: %c
load_frequencies: Read a frequency of value of %f for: not a residue
load_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisfield has no effect.
%lg%lgUnable to open codon usage fileload_codons: Setting all codon usages to 1.
load_codons: Read a codon usage value of %f for: %c
BLIMPS_DIR%s/docs/default.amino.frq%s/docs/default.qijdefault.amino.frqdefault.qijrfrequency.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  frequency.c
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=@;ș;9[3 @30  N;[2@2 ȁ@;;[3 3@;`H;`[`3`@3p ȁ@BLOCKBLOCKMATRIX; MATRIXInvalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
A ,
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All weights in the block were less than or equal to zero.Computing position-based sequence weights.
convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
pb_weights:%d ignored for %s
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
rdirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

 	

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Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ID   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   CC   none; BLOCKError in block file format.  No ID line.
AC   block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:%s
CC   CC   none; distance from previous block=( , )Error in block file format.  No AC line.
DE   noneError in block file format.  Invalid DE line:%s
CC   CC   noneError in block file format.  No DE line.
BL   motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:%s
Error in block file format.  No BL line.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
Error reading sequence %s in block %s,not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgID   Unable to recover enough memory to continue.  Aborting.
Number of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Allocating more space for clusters in block %s.
Unable to recover enough memory to continue.  Aborting.
--- block ---
ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	%cNA) 	%c] 	%c

--- ----- ---
Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
width= width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s
%-20s (%4d) %c %3d
 %f
//
Unable to recover enough memory to continue.  Aborting.
idacde ; width=%d; seqs=%d; Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
ID   AC   Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
//ID   (%s (%d) %s %sError in block %s: seq %s
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Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
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seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in matrix file format.  No MA line.Attempting to set values to be able to continue.The first column of the matrix will be missed.
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GenBankLOCUSDEFINITIONORIGIN//PIRENTRYTITLESEQUENCE///EMBL/SwissProtID   DE   SQ//GCGGCG-GenBankLOCUSDEFINITIONORIGINLOCUSGCG-PIRENTRYTITLESEQUENCEENTRYGCG-EMBLIDDESQIDFasta>>>Universa>>*Flat-file, no titleUnable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..UnknownUnknownLength:Check:..UNKNOWN%s  Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
read_sequence(): Unknown sequence type,                 asumming amino acid sequence
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
Length:Check:..Deciding if this is a GCG sequence database format of %s.Length:Check:..Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.Could not figure out database format.
Decided on %s database format.
Length:Check:..Length:Check:..>--- sequence ---
%s
>%s 	( %d:%d, AA) 	
%cNA) 	
%c] 	
%c
>--- -------- ---
>%s  %s
%c
%c

%c
untranslate_sequence(): Not an amino acid sequence, not untranslating.                      Returning the original sequence.
Unable to recover enough memory to continue.  Aborting.
Unable to recover enough memory to continue.  Aborting.
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	cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/124sd$3-<4ACX$O|W_,
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options.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  options.c<M4.,><|R^jq}options.cBbss.bssDdata.dataDrodata.rodataget_option_argsinsert_into_optionsOptionsARGVOptionsARGCstrlenstrncasecmpmallocreclaim_spacesprintfErrorReportget_tokenreallocstrdupfreeErrorBuffer		$8@LH\p	t		x			<		x		<	x0HPXt	x								 	$4L`lt08LThp,4HPxcg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/124lXX`$`)-<$H
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Unable to recover memory.
Decreasing the NumberToReport from saving all (%d currently) to %d.Ran out of memory (1), fewer scores will be reported.
Decreasing the number of saved nodes in the list.The saved nodes level of the list has been reduced to %d.The list saved nodes cannot be reduced any more.
The saved nodes level of the list has been reduced to %d.
Decreasing the number of saved nodes in the list.The saved nodes level of the list has been reduced to %d.The list saved nodes cannot be reduced any more.
The saved nodes level of the list has been reduced to %d.
Decreasing the NumberToReport from %d to %d.Ran out of memory (2), fewer scores will be reported.
blimps_reclaim_space(): NumInSL(Scores) is greater than NumberToReport.                 NumInSL(Scores) is supposed to be maintained                 less than or equal to the NumberToReport.                 NumberToReport = %d, NumInSL(Scores) = %d.                 Ran out of memory, removing the excess scores                 in the Scores list.
blimps-mem.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  blimps-mem.c<P4"1CWnxblimps-mem.cBbss.bssDdata.dataDrodata.rodataCallsWhenToReduceNumberOfTimesCalled___const_seg_900000105blimps_reclaim_spacelimit_Scores_list_sizeNumInSLsprintfErrorReportDoForSLLowerSavedNodesLevelScoresNumberToReportErrorBuffer		 ,48<	@X	\	`dhl			``		$	(,08L	TX\h	lpt|	X	<<			xx	 $,8	<@DPX	X`	dhlt	X|X					H	H $	(	48<H	LPT`dhpx|cg: Sun Compiler Common 7.1 2003/03/12@(#)stdlib.h	1.48	00/04/13 SMI@(#)stdlib_iso.h	1.3	01/03/09 SMI@(#)feature_tests.h	1.18	99/07/26 SMI@(#)isa_defs.h	1.20	99/05/04 SMI@(#)stdio.h	1.79	01/04/16 SMI@(#)stdio_iso.h	1.2	99/10/25 SMI@(#)va_list.h	1.13	01/02/08 SMI@(#)stdio_tag.h	1.3	98/04/20 SMI@(#)stdio_impl.h	1.13	01/11/16 SMI@(#)string.h	1.24	99/08/10 SMI@(#)string_iso.h	1.2	99/11/09 SMI@(#)stddef.h	1.16	99/08/10 SMI@(#)stddef_iso.h	1.1	99/08/09 SMI@(#)ctype.h	1.33	99/08/10 SMI@(#)ctype_iso.h	1.1	99/08/09 SMI@(#)malloc.h	1.11	97/08/23 SMI@(#)types.h	1.75	04/01/06 SMI@(#)machtypes.h	1.13	99/05/04 SMI@(#)int_types.h	1.6	97/08/20 SMI@(#)select.h	1.17	01/08/15 SMI@(#)time.h	2.72	05/01/24 SMI@(#)time.h	1.39	99/08/10 SMI@(#)time_iso.h	1.1	99/08/09 SMI@(#)time_impl.h	1.7	01/09/06 SMIacomp: Sun C 5.5 2003/03/12iropt: Sun Compiler Common 7.1 2003/03/12cg: Sun Compiler Common 7.1 2003/03/124l((0$0&-V<	t$H	
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MA field already used.  Cannot have both the BL and the MAfields.  Ignoring the BL line.
Using the PAttern switch causes the REpeats switch to be ignored.Alignments reported will include repeats.
%d%d%dTRUEYESTY0BL field already used.  Cannot have both the MA and the BLfields.  Ignoring the MA line.
%dTRUEYESTY0%dOld style configuration file.New style does not use the SE field.
MATRIXBLOCKUnknown search type: %s
%dTRUEYESTY0DNAAA.err.errrConfiguration file "%s" not found.  Exiting
Old style configuration file.New style uses the ST field instead of P4.
Old style configuration file.New style uses the RE field instead of P5.
Old style configuration file.New style uses the NU field instead of P9.
No block file (BL) or sequence file (SQ) given, aborting.
No sequence file (SQ) or block file (BL) given, aborting.
Configuration file has SQ, BL, and DB entries.Unable to determine the type of search.Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
Missing either the BL or SQ field, aborting.
Configuration file has SQ and BL entries.Unable to determine the type of search.Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
No sequence files given for the sequence database, aborting.
No DB field given, assuming data is in the SQ field.
No block file given (BL field), aborting.
No block files given for the block database, aborting.
No DB field given, assuming data is in the BL field.
No sequence file given (SQ field), aborting.
Unknown search type given, assuming SQ vs BL search.
read_config_file_end(): SearchType variable corrupted.                        Should never have reached this part of the program.                        Possible memory problems.                        The rest of the run may be invalid.                        Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
rUnknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Assuming there is no title and just sequence.
Unable to read sequence file: %s to determine the type of database
config.cV=10.0;DBG_GEN=4.14.14;cd;backend;raw;Xa;O;R=Sun C 5.5 2003/03/12/d0/local/blimps-3.9/blimps; /opt/SUNWspro/prod/bin/cc -xO5 -xarch=native -xmemalign=8s -xlibmil -fns -fsimple=1 -fsingle -xdepend=yes -xbuiltin=%all -xprefetch=auto,explicit -I../include -c  config.c
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Invalid matrix-sequence scoring method specified, %d.Setting the method to the default value and using thedefault scoring method.
No pattern for matrix %s, Scoring the entire matrix
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--- score ---
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--- ----- ---
S:% 6d	P:% 6d	F:% 6d
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Unknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Assuming there is no title and just sequence.
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Unable to read sequence file: %s
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get_file_name(): No files in the file groupget_file_name(): Bad file group, unable to return a file name
number_of_files(): Bad file group, unable to report number of files
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@HPX`8s_)cs_)L5The file %s will be ignored.
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load_frequencies: The value for the non-amino acid will be the last weight seen.load_frequencies: Currently the program ignores non-residue characters so thisload_frequencies: The non-amino acid codes U and J weights are differentload_frequencies: The non-amino acid codes O and U weights are differentload_frequencies: The non-amino acid codes J and O weights are differentload_frequencies: Unable to open frequency file: %sload_codons: Read a codon usage value of %f for: %c
Unable to open codon usage fileload_codons: Setting all codon usages to 1.
GCC: (GNU) 3.4.3 (csl-sol210-3_4-branch+sol_rpath).symtab.strtab.shstrtab.rel.text.data.bss.rodata.str1.1.rodata.str1.4.comment4		%+02g?2LN
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dirichlet(): Cannot open dirichlet file %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
Invalid block to matrix conversion method specified, %d.Using the default conversion method of Altschul's data-dependent method.
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Caught the SIGABRT (6) signal error.In testing, this signal occured when all the availablememory was filled and when trying to free memory to continue,by using free(), after many small blocks had been freed.If that is the case, try setting the number of scores toreport to a lower value than at the point memory was filled. Sorry for the inconvienience, but the memory recoveryfunctions "should" have worked.  See the errors.c source code for programming details.
Aborting due to the SIGABRT signal.
GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2).symtab.strtab.shstrtab.rel.text.data.bss.rodata.str1.1.rodata.str1.4.note.GNU-stack.comment4		@
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read_sequence(): Unknown sequence type,                 asumming amino acid sequence
Ran out of room for sequence %s.  Allocating more space.
Unable to recover enough memory to continue.  Aborting.
translate_sequence(): Not a nucleic acid sequence, not translating.                      Returning the original sequence.
translate_sequence(): Unknown translation frame: %d.Decided on %s database format.
Could not figure out database format.
Deciding if this is a GCG sequence database format of %s.Decided it is a GCG database format of %s.type_dbs(): Unknown database format for GCG type.            Not all of the database formats were handled.
Decided it is not a GCG database format of %s.untranslate_sequence(): Not an amino acid sequence, not untranslating.333333?GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2).symtab.strtab.shstrtab.rel.text.rel.data.bss.rodata.str1.1.rodata.str1.4.rodata.cst8.note.GNU-stack.comment4	)8	) %	T2/  42 C28RX _` o` - x8#
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Unable to recover enough memory to continue.  Aborting.
>?Nthsl.cp->key != ((void *)0)GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2).symtab.strtab.shstrtab.rel.text.data.bss.rodata.str1.4.rodata.cst4.rodata.rodata.str1.1.note.GNU-stack.comment4	p%+029?L	T2	c#	s#	-P	|P
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 ,[sl.cNewNodeOfLevelFreeSLNodeSetSavedNodesLevel__PRETTY_FUNCTION__.0InitializedSaveListSLNodesToSaveSavedNodesmallocreclaim_spaceErrorBufferErrorReportfreeLowerSavedNodesLevelNewSLtimesrandFreeSLInsertSLrandDeleteSLSearchSLDoForSLDoForRangeSLNumInSLNth__assert_fail-;JO_r{<Vv| %2@Y@9"o
y~$Xversion.o/      1179854216  502   503   100644  1628      `
ELF4(UWVSE]u}EjduhjdShjdVhjdWhEEdEEe[^_USS=]u2=uJhhhhhh hSXZhS]ÐQhhhhhh%s   Version %s  %s%s
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GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2).symtab.strtab.shstrtab.rel.text.data.bss.rodata.str1.1.note.GNU-stack.comment4	t	%8+@ 02@4?tOt-X0
	dd%d3d?dJdZzjr|version.cTitleStringProgramStringVersionStringVersionInfoDateStringCopyrightStringversion_stringsstrncpyprint_versionsprintffprintf#.3>CNSgvoptions.o/      1179854217  502   503   100644  2308      `
ELF4(UWVS}1ыEy1ۉU;]}'uQWu4u	<8:t"C;]|ڋEUe[^1_;]]5}'ERW@uPuU::tC;]|+]UCUDUe[^_ÐUWVSEEEjEu!ujEEE(}܅jEuU9U|Nvuuu$uj]EEuMUu!uj}E;EuEu3۾EPu$uj1;M}i5]A;M|UMMe[^_EP5uuo5UMMe[^_Unable to recover enough memory to continue.  Aborting.
GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2).symtab.strtab.shstrtab.rel.text.data.bss.rodata.str1.4.note.GNU-stack.comment4 	H	%T+T02T9?O-XP
	#3?PS_ftoptions.cOptionsARGCOptionsARGVget_option_argsstrncasecmpinsert_into_optionsErrorBuffermallocreclaim_spaceErrorReportget_tokenrealloc__strdupfree	@~	
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Decreasing the NumberToReport from %d to %d.Ran out of memory (2), fewer scores will be reported.
Decreasing the NumberToReport from saving all (%d currently) to %d.Ran out of memory (1), fewer scores will be reported.
blimps_reclaim_space(): NumInSL(Scores) is greater than NumberToReport.                 NumInSL(Scores) is supposed to be maintained                 less than or equal to the NumberToReport.                 NumberToReport = %d, NumInSL(Scores) = %d.                 Ran out of memory, removing the excess scores                 in the Scores list.
Decreasing the number of saved nodes in the list.The saved nodes level of the list has been reduced to %d.
The saved nodes level of the list has been reduced to %d.The list saved nodes cannot be reduced any more.
Unable to recover memory.
>?GCC: (GNU) 3.4.5 20051201 (Red Hat 3.4.5-2).symtab.strtab.shstrtab.rel.text.data.bss.rodata.str1.4.rodata.str1.1.rodata.cst4.rodata.cst8.note.GNU-stack.comment4	%+02*?2>N\[`hhxh-H


	 	
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ELF4(UPhh$UjhhPÉUSjhP t_hStJhSt5hSt ыDPt0u{t]]ÉUjhhP|t~
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fjjLh\S$f$$jShS$5h0t^hP	55h5X5e[^_R0hlh$f$X5e[^_Éj$u!kvƹufjƹ$jhƹufjƹ$*h>SuQShDh$vUnknown configuration file key: %s
read_config_file_end(): SearchType variable corrupted.                        Should never have reached this part of the program.                        Possible memory problems.                        The rest of the run may be invalid.                        Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
Unable to read sequence file: %s to determine the type of database
Unknown search type given, assuming SQ vs BL search.
No sequence files given for the sequence database, aborting.
Unknown sequence format.  Known formats are:Fasta, GenBank, PIR, Swiss Prot, and GCG.Assuming there is no title and just sequence.
No block files given for the block database, aborting.
No block file given (BL field), aborting.
No sequence file given (SQ field), aborting.
No DB field given, assuming data is in the SQ field.
No DB field given, assuming data is in the BL field.
Missing either the BL or SQ field, aborting.
Configuration file has SQ, BL, and DB entries.Unable to determine the type of search.Assuming SQ vs BL search.  Setting SearchType to UNKNOWN.
Configuration file has SQ and BL entries.No block file (BL) or sequence file (SQ) given, aborting.
No sequence file (SQ) or block file (BL) given, aborting.
New style uses the ST field instead of P4.
MA field already used.  Cannot have both the BL and the MAfields.  Ignoring the BL line.
Configuration file "%s" not found.  Exiting
Using the PAttern switch causes the REpeats switch to be ignored.Alignments reported will include repeats.
New style does not use the SE field.
BL field already used.  Cannot have both the MA and the BLfields.  Ignoring the MA line.
New style uses the RE field instead of P5.
New style uses the NU field instead of P9.
%dTRUEYESTYrOld style configuration file.DNAAAMATRIXBLOCKUnknown search type: %s
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All weights in the block were less than or equal to zero.Computing position-based sequence weights.
Unable to recover enough memory to continue.  Aborting.
 ,
.+-0123456789convert: Block is too wide, unable to continue (max=%d).
Qij matrix missing, unable to continue.
BLIMPS_DIR%s/docs/default.sijdefault.sijgribskov_conversion_method: default.sij matrix missing, Cannot continue.
pb_weights:%d ignored for %s
%s/docs/default.diri%s/docs/default.rankdefault.diridefault.rankrSIFT_pssm(): Cannot open %s
SIFT_pssm(): Amino acid %c at pos %d in your original sequence was not allowed by the prediction.
dirichlet(): Cannot open dirichlet file %s
dirichlet(): OUT OF MEMORY
Mixture=Alpha==	

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}N |B}h=k|
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4}N |B}h=k|
}N |B}h=k|	}N |B}h=k|	}N |B}h=k|	}N |B}h=k|	}N |B}h=k|	}N |B}h=k|	p}N |B}h=k|	T}N |B}h=k|	8}N |B}h=k|	}N |B}h=k|	}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|t}N |B}h=k|X}N |B}h=k|<}N |B}h=k| }N Unable to recover enough memory to continue.  Aborting.
ID   AC   DE   BL   ; MATRIXMATRIX on ID line; not a BLOCKnone; BLOCKError in block file format.  Invalid ID line:%s
CC   Error in block file format.  No ID line.
block=(block=(%d,%d);none; distance from previous block=( , )Error in block file format.  Invalid AC line:Error in block file format.  No AC line.
noneError in block file format.  Invalid DE line:Error in block file format.  No DE line.
motif%swidth=width=%d;No width field for block %sSetting width to zero
seqs=seqs=%d99.5%=99.5%%=%d;strength=strength=%dError in block file format.  Invalid BL line:Error in block file format.  No BL line.
No space allocated for sequence %s in block %s.Allocating more space
(%d)%d)Error reading sequence %s in block %s,%d more residues in the sequence than the expected %d.Resetting block width to %d.
not enough residues to fill the sequence.Filling the rest of the sequence with blanks.
next_cluster(): Unknown sequence type, assuming an amino acid sequence.
next_cluster(): Error reading sequence %s in block %s,                Undocumented return value, %d, from read_sequence().
%lgNumber of sequences in block %s read from file as %d but is %d
Allocating more space for sequences in block %s.
Allocating more space for clusters in block %s.
--- block ---ID	%s
AC	%s
DE	%s
BL	%s
motif:	%s
width=%d; 99.5%%=%d; strength=%d;
num sequences: %d	num clusters: %d
%s 	( %d:%d, AA) 	NA) 	??) 	--- ----- ---Unknown output type: %d, using integer output
ID   %s
AC   %s
DE   %s
 width=%d; seqs=%d; 99.5%%=%d; strength=%d BL   %s%-20s (%4d)  %3d
 %f
//
idacde ; width=%d; seqs=%d; //%s (%d) %s %sError in block %s: seq %s
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#1/20           1179848163  501   20    100644  5180      `
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Unable to recover memory.
Decreasing the NumberToReport from saving all (%d currently) to %d.Ran out of memory (1), fewer scores will be reported.
Decreasing the number of saved nodes in the list.The saved nodes level of the list has been reduced to %d.The list saved nodes cannot be reduced any more.
The saved nodes level of the list has been reduced to %d.
Decreasing the NumberToReport from %d to %d.Ran out of memory (2), fewer scores will be reported.
blimps_reclaim_space(): NumInSL(Scores) is greater than NumberToReport.                 NumInSL(Scores) is supposed to be maintained                 less than or equal to the NumberToReport.                 NumberToReport = %d, NumInSL(Scores) = %d.                 Ran out of memory, removing the excess scores                 in the Scores list.
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#1/12           1179848164  501   20    100644  2764      `
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#1/12           1179848164  501   20    100644  6172      `
scores.o8 
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!H|B}h=k|x}N |B}h=k|\}N |B}h=k|@}N |B}h=k|$}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k|}N |B}h=k||}N |B}h=k|`}N |B}h=k|D}N |B}h=k|(}N |B}h=k|}N |B}h=k|}N default_scoring_method(): matrix %s has length <= 0default_scoring_method(): sequence %s has length (amino acids) <= 0default_scoring_method(): Not scoring the sequence.
enter_score(): Error placing matrix score into list
Unable to recover enough memory to continue.  Aborting.
Histogram:
   %5d - %-5d : %d
   %5d -       : %d
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#1/12           1179848165  501   20    100644  13940     `
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#1/12           1179848165  501   20    100644  3004      `
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#1/20           1179848166  501   20    100644  13748     `
protomat.o| __text__TEXTT__picsymbolstub1__TEXT-d` __data__DATA}__cstring__TEXT(__const__TEXTP__la_symbol_ptr__DATAX`0d__nl_symbol_ptr__DATAP01*3P1$18c|+B}H|AAd8/;pH%/AP<x8$;pH|dxxH}xH|ao|t//A<x8(Hp|t/Ax8a@H5xH;@|C8;a<8,xcxHxH}|}y@HcxHM/@<x8c8HH$<x8cPH<8cpHp8!xa|N |8`!He89`9 9@c?#Cccc=X8!P|N |@&|АAB!|~x|#x;`; :: HH@|t/A8/>A08a@8/HE/@8a@8\H1/@8a@8:H||y@K<|zx88a@;{H/(|}x@;(8z8@xHY/|]@;Cx8@xH59 8@@<9`||t/|@/@9 H}zx8BA<8a@8H~x/A:<8a@8H/A:<8a@8Hy/A:<8a@8H]|cyA<;=88xHa<>x88H/@:<8a@8H
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Could not open %s, using default BLOSUM scoring matrix
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/@87A/A/AcxHu|`Ph|\Pblimps-3.9/lib/OSX/README000064400001460000012000000012011062461237000152400ustar00jorjastaff00000400000027Darwin 8.9.0 Darwin Kernel Version 8.9.0: Thu Feb 22 20:54:07 PST 2007; root:xnu-792.17.14~1/RELEASE_PPC Power Macintosh powerpc

gcc -v:
Using built-in specs.
Target: powerpc-apple-darwin8
Configured with: /private/var/tmp/gcc/gcc-5363.obj~28/src/configure --disable-checking -enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib --build=powerpc-apple-darwin8 --host=powerpc-apple-darwin8 --target=powerpc-apple-darwin8
Thread model: posix
gcc version 4.0.1 (Apple Computer, Inc. build 5363)
blimps-3.9/protomat/000075500001460000012000000000001062462131100150075ustar00jorjastaff00000400000027blimps-3.9/protomat/motifj.h000064400001460000012000000301661062461257200164670ustar00jorjastaff00000400000027/*------------------------------------------------------------------------*/
/*(C) Copyright 1991-2006, Fred Hutchinson Cancer Research Center         */
/*      motifj.h  Header file for PROTOMAT programs                       */
/* NOTE for Silicon Graphics users:  The type of scores in
       struct score should be changed from char to int to get correct
       processing (but not for SUN!)                                      */
/*------------------------------------------------------------------------*/
/*  6/29/90 J. Henikoff
    1/28/99 Increased SNAMELEN from 11 to 18; IDLEN from 10 to 12
   12/17/99 Added ctype.h, MINAC, MAXAC
    2/21/00 Added id->full_entry to struct db_id
   >>>>>>>>>>>>>>>>>>>> Blimps 3.4, Blocks 12.0  <<<<<<<<<<<<<<<<<<<<<<
    8/11/00 Added acc to struct db_info
    3/10/01 Increased MAXSEQS from 400 to 600, but still not enough for
		struct best_block in blksort
   12/25/04 Increased MAXSEQS from 600 to 1000
    1/ 2/06 Increased MAXLINE from 240 to 480
    1/ 3/06 Increased SNAMELEN from 18 to 20 (Q9WUM8_MOUSE|Q9WUM8=19)
--------------------------------------------------------------------------*/
#include 
#include 
#include 
#include 
#include 

#define VERSION		   8		/*  motifj version number */
#define YES                1
#define NO                 0
#define ESC               27
#define CR                13
#define LF                10
#define UMIN(x, y)	  ( (xy) ? x : y)   /* UNIX max macro */
/*   INDEX & INDEXCOL compute the sequential indices for the lower half of an
     nxn symmetric matrix given row & column coordinates.  Lower half has
     n(n-1)/2 entries; col=0,n-2 and row=col+1,n-1; col has n-col-1 rows.
     Index runs from 0 to n(n-1)/2 - 1 down columns with
     (index=0)==(col=0,row=1) and (index=n(n-1)/2-1)==(col=n-2,row=n-1).  */
#define INDEXCOL(n, col)    ( col*n - (col*(col+1))/2 )
#define INDEXCOLROW(n, col, row)  ( col*n - (col*(col+3))/2 - 1 + row )

#define randomize()       srand((unsigned)time(NULL))  /* Seed rand() */

#define MAX_DISTANCE  	  24	/* Max spacing between aminos of motif */
#define MIN_DISTANCE      1     /* Min distance specification */
#define MAXSEQS	  	  1000   /* Max number of sequences to be analyzed */
#define MINSEQS           2     /* Min number of sequences to be analyzed */
#define MAXFREQ           1000   /* Max occurences of motif in all seqs */
#define MAX_LENGTH	  5500  /* Max length of each sequence */
#define MIN_DOMAIN_WIDTH  10	/* Minimum width */
#define MAX_DOMAIN_WIDTH  55	/* Maximum width */
#define MAX_MERGE_WIDTH   55	/* Max. width of merged blocks */
#define RELEVANT_MOTIFS   50	/* Only top scoring motifs are retained */
#define MAX_MOTIFS	  100	/* Buffer motifs before discarding */
#define MINSCORE          1     /* Min block trimming column score (0-2500)*/
#define CLTHRES            80   /* Clustering identity percentage (0-100)*/
#define DROPSCORE         -10   /* Default std devs *10 for dropping block */
#define MOTAUTO4            3   /* max. # motifs for run type 4  */
#define MOTAUTO3	    6   /* min. # motifs for run type 3 */
#define MAXBLK             15   /* max # blocks for shotgun assembly */
#define MAXTITLE	   75   /* max sequence title length */

#define PROTEIN_SUBDIRECTORY "pros/"  /* Subdirectory containing proteins */
#define PROTEIN_EXTENSION    ".pro"    /* Extension for all protein files */
#define READ                 "r"       /* Code to read disk files */
#define SNAMELEN              20       /* Max length of sequence name */
#define IDLEN                 12       /* Max length of db id */
#define MINAC                  7	/* Min AC length */
#define MAXAC                 10	/* Max AC length */
#define FNAMELEN              80       /* Max length of file name */
#define MAXLINE               480      /* Max line length for ASCII file */
#define MATSIZE               21       /* Scoring matrix dimension */
#define HIGHPASS              4	       /* Default high pass filter value */

#define MAXDB 6				/* Max. # database formats */
#define GB 0				/* GenBank type */
#define PIR 1				/* PIR type */
#define EMBL 2				/* EMBL type */
#define UNI 3				/* UNIVERSAL type */
#define VMS 4				/* PIR/VMS type */
#define PROC 5				/* Proclass PCFam file */

#define round(x) ((x >= 0.0) ? (int) (x+0.5) : (int) (x-0.5))

/* Declare new data types */
typedef unsigned char *aa_type[20][20][MAX_DISTANCE];

/* Structure to store information about each motif: */
/*  NOTE: integer fields defined as unsigned char to save space;
	  they must not exceed 255 in value */
struct motif_struct {
  unsigned char aa1, aa2, aa3, distance1, distance2;
  /*  freq is the number of sequences with this motif */
  int freq, dups;
  /*   seq_no[freq] lists the sequence numbers that have the motif,
       pos[freq] lists the offset of the motif in the corresponding
       sequences; so pos[x] is the offset into sequence # seq_no[x], 
       NOT into sequence # x */
  int seq_no[MAXFREQ], pos[MAXFREQ];
  int score, scores[MAX_DOMAIN_WIDTH], domain, mots;
  char group, sub_group;
  };

/* Structure to store information about groups for motif map routine: */
struct group_struct {
  int group_no, sub_no, position;
  };

/*-------------------------------------------------------------------*/
/*  merged_motif is an array of motifs.  Each entry is one or more   */
/*    motifs.  Each can be thought of as a block of sequences aligned*/
/*    around all the motifs.                                         */
/*-------------------------------------------------------------------*/
struct merged_motif {
	int dropped;			/* YES if dropped */
	char aa[3];			/* Amino acid motif */
	int nmotif;			/* number of motifs, >= 0  */
					/* 0 => merged (inactive) */
	int nident;			/* number of identities */
					/* ..occurs >=SIGNIF in a col. */
	int max_score;			/* max. score of merged motifs */
	int domain;			/* displacement of merged motif blocks */
					/* block width = domain+1 */
	int distance;			/* width of motifs within block */
	int dups;			/* total # dups in all seqs */
	int loffset;			/* 1st position of motif within block*/
	int leftpos[MAXSEQS];		/* leftmost position of motif   */
					/*... for each sequence*/
	int cluster[MAXSEQS];		/* cluster number for each seq */
	int scores[MAX_MERGE_WIDTH];	/* column scores */
	int t_loffset;			/* 1st position of motif within */
					/*  trimmed block */
	int t_domain;			/* trimmed block width=t_domain+1*/
	int t_score;			/* score over trimmed block */
	int position[MAXSEQS];		/* position of block within each seq*/
	int maxpos;			/* max position in any seq */
	int minpos;			/* min position in any seq */
	int in_degree;			/* in-degree of block in DAG */
	int out_degree;			/* out-degree of block in DAG */
};

/*------------------------------------------------------------------------*/
/*   sequences contains all information about the sequences.              */
/*------------------------------------------------------------------------*/
struct sequences {
	int num;		/* number of sequences */
	int totlen;		/* total length of all sequences */
	int *len;		/* lengths of each sequence */
	int *offlen;		/* offset to start of each sequence */
	char *name;		/* 10 char name of each sequence */
	char *seq;		/* sequence bases */
};

/*------------------------------------------------------------------------*/
/*   aux_seq is a list of blocks ordered left to right within a sequence  */
/*  Each sequence has the same number of blocks, but the blocks may be
     arranged in different orders in each sequence.                       */
/*------------------------------------------------------------------------*/
struct aux_seq {
	int block[RELEVANT_MOTIFS];	/* index of block in each position*/
};

struct temp {			/* temporary structure for sorting */
	int value;
	int index;
	int flag;
};

/*-----------------------------------------------------------------------*/
/*    Structure for pairs of sequences.                                  */
/*     pair should be allocated as an array, & the number of the         */
/*     sequences forming the pair inferred from the array index.         */
/*-----------------------------------------------------------------------*/
struct pair {
	int score;		/* # of identities within trimmed block */
	int cluster;		/* cluster # for this pair */
};

/*-----------------------------------------------------------------------*/
/*  block_list is a list of blocks in an order that is consistent among
    all sequences;  it implies a partial multiple alignment.
    The next_block list is a list of all blocks, some of which may
    overlap.  The doubly linked next_best/prev_best list is a subset
    consisting of the best non-overlapping blocks in the list.           */
/*-----------------------------------------------------------------------*/
struct block_list {
	int b;			/* index of block (merged_motif) */
	int minprev;		/* min. distance from previous block */
	int maxprev;		/* max. distance from previous block */
	struct block_list *next_block;  /* all blocks in the list  */
	struct block_list *next_best;   /* best blocks in the list */
	struct block_list *prev_best;
};

/*------------------------------------------------------------------------*/
/*  path is a list of all possible paths through the blocks in all seqs.
     The first_block list includes all blocks, including those that
     possible overlap.  The first_best list includes the best sub-path
     of non-overlapping blocks.                                           */
/*------------------------------------------------------------------------*/
struct path {
	int nblocks;		/* # of blocks in path */
	int nbest;		/* # of blocks in best sub-path */
	int naas;		/* # of AAs in best sub-path */
	unsigned long totscore;	/* sum of scores of blocks in best sub-path*/
	int totmotif;		/* # motifs in best sub-path*/
	int totident;		/* # conserved residues in best sub_path */
	int nseqs;		/* # seqs in best sub-path */
	int seqs[MAXSEQS];	/* YES if path holds for sequence */
	struct block_list *first_block;  /* first block in path */
	struct block_list *first_best;	 /* first block in best sub-path*/

	struct path *next_path;
};

/*----------------------------------------------------------------------*/
/*  Ajacency matrix representation of distances between blocks in
    all sequences.                                                      */
/*----------------------------------------------------------------------*/
struct matrix {
	int npos;		/* # of seqs with positive diff in cell */
	int maxdiff;		/* maximum positive difference in cell  */
/*	int dist[MAXSEQS];	 distance from row to col for seq s */
	int mark;		/* all-purpose flag */
};

struct follow_data {
	struct path *path;
	int mark[RELEVANT_MOTIFS][RELEVANT_MOTIFS];
};

/* -------- Scoring matrix structure ----------------------------------*/
struct score {
	char scores[MATSIZE][MATSIZE];	/* valid range -127 to +128 */
	int highpass;			/* high pass filter value */
};

/*--------Sequence database format structure -------------------------*/
struct db_info {                             /*  Database format info */
   char *type, *start, *desc, *acc, *seq, *end;
   int title_offset, seq_offset;
};
/*-Structure to split up a file name of the form \.ext -*/
struct split_name {
	int dir_len, file_len, name_len;
};
/*------ Structure to hold the contents of a .lis or .lst file ------*/
struct db_id {
   char entry[SNAMELEN+1];	/* sequence name */
   char full_entry[2*SNAMELEN];	/* enhanced sequence name */
   char pir[IDLEN+1];		/* PIR entry name */
   char ps[2];			/* PS type=T, F or P */
   int len;			/* sequence length */
   int frag;			/* YES if seq is a fragment */
   int lst;			/* seq in .lst file */
   int found;			/* seq found in database */
   int block;			/* seq found in block */
   int search;			/* used by excluded.c => use seq for search*/
   int rank;			/* used by matodat.c, fastodat.c */
   int score;			/* used by matodat.c, fastodat.c */
   double pvalue;		/* P-value */
   struct db_id *next;
   struct db_id *prior;
};
/*  For pb_weights(), from BLIMPS  */
struct pb_counts {		/* for pb_weights() */
  double diffaas;		/* # of different aas in position */
  double naas[MATSIZE]; 	/* # of each aa in position */
};

ne EMBL 2				/* EMBL type */
#define UNI 3				/* UNIVERSAL type */
#define VMS 4				/* PIR/VMS type */
#define PROC 5				/* Proclass PCFam file */

#define round(x) ((x >= 0.0) ? (int) (x+0.5) : (int) (x-0.5))

/* Declare new data types */
typedef unsigned char *aa_type[20][20][MAX_DISTANCE];

/* Structure to store information about each motif: */
/*  NOTE: integer fields defined as unsignedblimps-3.9/protomat/blastdat.c000064400001460000012000000364621062461261200167700ustar00jorjastaff00000400000027/*========================================================================
BLASTDAT: (C) Copyright 1992-2001, Fred Hutchinson Cancer Research Center
        blastdat.c  reads BLASTP output file
	    eg:  blastdat PS00011.hom PS00011.lis
			  or
		 blastdat PS00011.hom none

      If .lis file is provided, looks for those sequences in the .hom file.
      Always appends statistics to file named blastdat.dat.

-------------------------------------------------------------------------*/
/*   4/6/92  From fastodat.c
     9/16/93 Added ".tns" file which is list of true negative seqs found
>>>>>>>>>>>>>  End of matrix test project - blastp 1.2.9 <<<<<<<<<<<<<
   12/8/95   Modified for blastp version 1.4.7; has a space preceding
	     sequence name now.
    1/7/96   Added Pearson's E and ROC.
    1/9/96   Ignore sequences in block.
    1/10/96  Fix problem with blastdat not getting written.
    1/12/96  Increased NSCORE from 400 to 1000.
    1/13/96  Added split_names(), modified blastdat.dat
    1/27/96  Fix problem with E values, etc.
    2/ 4/96  Changed 99.5 to 99.9th percentile
---------------------------------------------------------------------------
    6/26/00  Modifications for blastall version 2.0.11
===========================================================================*/
#include "motifj.h"

#define NSCORE 1000		/* Maximum # of scores in .hom file */
#define MAXBUCKET 50		/* Maximum # of frequency buckets */
#define SWISS 307271		/* Number of sequences in database */
#define BIGINT 32000		/* Scores > than BIGINT are set = to it */

int read_hom();
int write_mis();
int write_fnd();
/*---------Routines from motmisc.o ----------*/
struct db_id *makedbid();
int get_ids();
struct split_name *split_names();

unsigned long LisSeq, FragSeq, BlkSeq;
char HomName[FNAMELEN];

/*======================================================================*/
int main(argc, argv)
int argc;
char *argv[];
{
   FILE *fhom, *flis, *fout;
   char homfile[FNAMELEN], lisfile[FNAMELEN];
   int nscores;
   struct db_id *ids;
   struct split_name *homsplit;

   printf("\nBLASTDAT: (C) Copyright 1992-2000, Fred Hutchinson Cancer Research Center");
   if (argc > 1) { strcpy(homfile, argv[1]);  }
   else
   {
      printf("\nEnter name of BLASTP results file: ");
      gets(homfile);
   }
   if ( (fhom=fopen(homfile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", homfile);
      exit(-1);
   }
   else printf("\nReading %s...", homfile);
   homsplit = split_names(homfile);
   strncpy(HomName, homfile + homsplit->dir_len, homsplit->name_len);
   HomName[homsplit->name_len] = '\0';

/*------------- arg 2:  .lis file -------------------------------*/
   if (argc > 2)
      strcpy(lisfile, argv[2]);
   else
   {
      printf("\nEnter name of file containing list of sequences: ");
      gets(lisfile);
   }
   if (!strlen(lisfile)) flis = NULL;
   else if ( (flis=fopen(lisfile, "r")) == NULL)
   {
      printf("\nCannot open file %s", lisfile);
      printf("\nNo list of sequences will be checked.");
   }
/*---------------  Get the sequences in the .lis file -----------------*/
   LisSeq = FragSeq = BlkSeq = 0;
   ids = makedbid();
   if (flis != NULL)
      printf("\n%ld IDs in %s\n", (LisSeq=get_ids(flis, ids)), lisfile);
   fclose(flis);

/*----------- Read the BLAST output file, write out list of true negs--*/
   strcpy(homfile, HomName); strcat(homfile, ".tns");
   if ( (fout=fopen(homfile, "wt")) == NULL)
   {
      printf("\nCannot open file %s\n", homfile);
      exit(-1);
   }
   fprintf(fout, "# True negative sequences for %s\n", HomName);
   nscores = read_hom(fhom, fout, ids);
   printf("\n%d total scores\n", nscores);
   fclose(fhom); fclose(fout);

/*--------------------Write out the missing sequences -----------------*/
   strcpy(homfile, HomName); strcat(homfile, ".mis");
   if ( (fout=fopen(homfile, "wt")) == NULL)
   {
      printf("\nCannot open file %s\n", homfile);
      exit(-1);
   }
   fprintf(fout, "# Sequences missed for %s\n", HomName);
   nscores = write_mis(fout, ids);
   printf("\n%d missed sequences written to %s", nscores, homfile);
   fclose(fout);
   /*-------------  Write sequences found to .fnd file -------------*/
   strcpy(homfile, HomName); strcat(homfile, ".fnd");
   if ( (fout=fopen(homfile, "wt")) == NULL)
   {
      printf("\nCannot open file %s\n", homfile);
      exit(-1);
   }
   fprintf(fout, "# Sequences found for %s\n", HomName);
   nscores = write_fnd(fout, ids);
   printf("\n%d found sequences written to %s", nscores, homfile);
   fclose(fout);

   printf("\n");
   exit(0);
}  /*  end of main */
/*======================================================================*/
int read_hom(fhom, ftns, ids)
FILE *fhom, *ftns;
struct db_id *ids;
{
   FILE *fout;			/* statistics */
   int tns, i, rank, tscore, lenid, len;
   int lfreq[MAXBUCKET], lminrank, lmaxrank;
   int iminrank, imaxrank, ntp999, done, nhits, tphits, tnhits;
   unsigned long swiss999;
   int found, freq[MAXBUCKET], minseq, maxseq, tps, lower, upper;
   int pearson, frag, inblocks;
   double dpvalue, roc, tn[NSCORE], tp[NSCORE], minscore, maxscore;
   char line[MAXLINE], id[22], *ptr, *ptr1;
   struct db_id *did;

   /*   Count the fragments & sequences in the .lis file  */
   LisSeq = FragSeq = BlkSeq = 0;
   did = ids->next;
   while (did != NULL)
   {
      if (!did->block) LisSeq ++;
      if (did->frag) FragSeq ++;
      if (did->block) BlkSeq ++;
      did = did->next;
   }

   /*---------Get the 99.9% score ------------------------------------*/
/*>>>>>>>>>>>Read SWISS from the output file <<<<<<<<<<<<<<<<<<<*/
   /* NOTE:  since tn[] & tp[] contain the probs, smaller is better   */
   swiss999 = (unsigned long) (SWISS-LisSeq-FragSeq-BlkSeq)*.001;
   printf("%ld true positives (%ld of them fragments), %ld in block\n",
          LisSeq, FragSeq, BlkSeq);
   printf(" Default 99.9th rank = %ld\n", swiss999);

   /* Initialize*/
   for (i=0; i>>>>BLASTP specific:  get id, tscore, dpvalue, nhits */
   /*---- Copy first few lines -----*/
   done = YES;
   while (!feof(fhom) && fgets(line,MAXLINE,fhom) != NULL &&
          strstr(line, "Sequences producing") == NULL)
   {
      if (strstr(line, "Query") != NULL) done = NO;
      else if (strstr(line, "Searching") != NULL) done = YES;
      if (!done || strstr(line, "BLASTP") != NULL)  printf("%s", line);
   }
   fgets(line, MAXLINE, fhom);    /* next line is blank */
   /*---- Now process the results----------------------*/
   /* Results start after "Sequences producing" line & there is one
      result per line until the first blank line. Each line has a
      title for 66 chars, space, score, space, E-Value.  */
   done = NO;
   while (!done && !feof(fhom) && fgets(line,MAXLINE,fhom) != NULL)
   {
      if ((int) strlen(line) > 66)
      {
         /*------- Get the id -----------------*/
	 strncpy(id, line, SNAMELEN); id[SNAMELEN] = '\0';
         for (i=0; ientry may be different lengths, compare
                 only the basis of the shorter which should be a subset
                 of the longer  */
	 found = NO;
         lenid = strlen(id);
	 did = ids->next;
	 while (did != NULL)
	 {
            len = lenid;
            if (strlen(did->entry) < len) len = strlen(did->entry);
            if (!did->found &&
	        (strncmp(did->entry, id, len) == 0) )
	    {
               did->found = found = YES;
	       did->rank = rank;
	       did->score = tscore;
               did->pvalue = dpvalue;
               if (!did->block)
               {
	          i = (int) tscore/100;
	          if (i >= 0 && i < MAXBUCKET) ++lfreq[i];
	          tp[tps] = dpvalue;
	          tps++;  tphits += nhits;
	          if (rank < lminrank) lminrank = rank;
	          if (rank > lmaxrank) lmaxrank = rank;
	          if (tscore < minseq) minseq = tscore;
	          if (tscore > maxseq) maxseq = tscore;
	          printf("\nTP:Rank %.3d=%.20s, score=%d, P=%g",
			  rank, id, tscore, dpvalue);
	       }
               else if (did->block)
               {
                  inblocks++;
	          printf("\n BLOCK:Rank %.3d=%.20s, score=%d, P=%g",
			  rank, id, tscore, dpvalue);
               }
               if (did->frag)
               {
                  frag++;
/*	          printf("\n FRAGMENT:Rank %.3d=%.20s, score=%d, P=%g",
			  rank, id, tscore, dpvalue);
*/
               }
           }   /*  end of found  */
	    did = did->next;
	 } /* end of list entry */

         /*------  Write out true negatives --------------------*/
         if (!found)
         {
            fprintf(ftns, "%-20s", id);
            fprintf(ftns, "       P=%g", dpvalue);
            fprintf(ftns, "\n");
         }

         /*  Seqs not in list */
	 if (!found && tns < NSCORE)
	 {
	    i = (int) tscore/100;
	    if (i >= 0 && i < MAXBUCKET) ++freq[i];
	    tn[tns] = dpvalue;
	    if (tn[tns] < minscore) minscore = tn[tns];
	    if (tn[tns] > maxscore) maxscore = tn[tns];
	    if (rank < iminrank) iminrank = rank;
	    if (rank > imaxrank) imaxrank = rank;
	    if (tns==0)   printf("\n  1st TN score=%g", tn[0]);
	    else if ( ((tns+1)%100)==0 )
	        printf("\n  TN:%dth other score=%g",
                   tns+1, tn[tns]);
	    else if (tns == swiss999)
	        printf("\n  TN:%dth score(99.9)=%g", tns, tn[tns]);
	    /*  Print names of other top seqs */
	    if (rank <= LisSeq)
	    {
	        printf("\n  TN:Rank %.3d=%.20s, score=%d, P=%g",
			 rank, id, tscore, dpvalue);
	    }
	    tns++; tnhits += nhits;
            if (LisSeq > 0) roc += (double) tps / (double) LisSeq;
	 }  /* end of if !found */
      } /* end of if strlen(line) > 60 */
      else done=YES;
   }  /* end of while  for blastp output file */
   if (tns > 0) roc /= (double) tns;
   else roc = 1.0;

   printf("\n%d/%ld TP scores found, %d TN scores", tps, LisSeq, tns);
   printf("\n%d/%ld fragments found, %d/%ld of sequences in block found",
          frag, FragSeq, inblocks, BlkSeq);
/*
   printf("\nSummary of TP scores:  Maximum=%d, Median=%d, Minimum=%d",
             tp[0], tp[(int) tps/2], tp[tps-1]);
printf("\nSummary of TN scores:  Maximum=%d, Median=%d, Minimum=%d, 99th=%d",
      tn[0], tn[(int) tns/2], tn[tns-1],
      tn[(int) tns/100]);
*/
/*   printf("\nFrequency distribution of all scores:");
   printf("(*+=list, x/=other)");
   if (minseq < minscore) minscore = minseq;
   if (maxseq > maxscore) maxscore = maxseq;
   for (i=(int) minscore/100; i<= (int) maxscore/100; i++)
   {
      printf("\n %.4d-%.4d  %.4d  ", i*100, i*100+99, lfreq[i]+freq[i]);
      for (x=0; x< (int) lfreq[i]/5; x++)  printf("*");
      if ((freq[i]-5*x) > 0) printf("+");
      for (x=0; x< (int) freq[i]/5; x++)  printf("x");
      if ((freq[i]-5*x) > 0) printf("/");
   }
*/

/*=========================================================================*/
   /* NOTE:  since tn[] & tp[] contain the probs, smaller is better   */
/*---------Get the 99.9% score -------------------------------------------*/
   lower = swiss999;
   if (lower > tns-1) lower = tns-1;
   if (lower < 0) lower = 0;
   ntp999 = 0;		/* #tp seqs >= 99.9% of tn seqs */
   for (i=0; i < tps; i++)
      if (tp[i] <= tn[lower]) ntp999++;
   printf("\n%d/%ld true positive scores above ", ntp999, LisSeq);
   printf("99.9 percentile true negative score=%g", tn[lower]);

/*----- Pearson's E and ROC values -----------------------------*/
   pearson = LisSeq - tps;
   i = tps - 1;
   while (pearson >= 0 && pearson < tns &&
             i >= 0 && i < tps &&
             tn[pearson] < tp[i])
   { pearson++; i--; }
   printf("\n%d = Pearson equivalence number (%ld/%ld)",
              pearson, LisSeq - pearson, LisSeq);
   printf("\n%f = ROC area", roc);

/*----------Append statistics to blastdat.dat ----------------------------*/
   fout = NULL;
   if ((tns + tps + inblocks) > 0)	/* no stats if no results in file */
      if ( (fout=fopen("blastdat.dat", "a")) == NULL)
      {
	 printf("\nCannot open file blastdat.dat\n");
	 printf("\nNo statistics will be saved.");
      }
   if (fout != NULL)
   {
      fprintf(fout, "%s %d %ld %ld %ld %ld %d %d %d %d",
              HomName, tps+tns+inblocks, LisSeq+BlkSeq, BlkSeq, FragSeq, LisSeq,
              inblocks, frag, tps, tphits);
      /*  Median CI for z=2: order stat = (n+1)/2 - z*sqrt(n)/2.  */
      if (tps > 5)
      {
	 upper = (float) tps; upper=sqrt(upper);
	 upper += (float) (tps+1)/2;
      }
      else upper = (float) tps-1;
      if (upper < 0) upper= 0; if (upper > tps-1) upper=tps-1;
      /*  Info for seqs in the lis file (true positives)*/
/*
      fprintf(fout, " %d %d %d %d %d %d",
	lminrank, lmaxrank, tp[(int) upper],
	tp[tps-1], tp[(int) tps/2], tp[0]);
*/
      /*  Now add decile scores for seqs in the lis file */
/*
      tenth = (float) tps/10;
      for (i=9; i>=0; i--)
      {
	 x = (int) tenth/2 + i*tenth;
	 if (x<0) x = 0; if (x>tps-1) x=tps-1;
	 fprintf(fout, " %d", tp[x]); 
      }
*/
      /*  Info for seqs not in the lis file (true negatives) */
/*
      fprintf(fout, " %d %d %d %d %d %d",
	iminrank, imaxrank, tn[lower],
	tn[tns-1], tn[(int) tns/2], tn[0]);
*/
      fprintf(fout, " %d %d %d %d %f", tns, tnhits, ntp999,
        pearson, roc);
      fprintf(fout, "\n"); fclose(fout);
   }

   return(tns+tps+inblocks);
}  /* end of read_hom */
/*======================================================================*/
int write_mis(fmis, ids)
FILE *fmis;
struct db_id *ids;
{
   struct db_id *did;
   int nmiss;
 
   nmiss=0;
   did = ids->next;
   while (did != NULL)
   {
      if (did->rank <= 0 && !did->block)
      {
         fprintf(fmis, "%-20s", did->entry);
         if (strlen(did->ps)) fprintf(fmis, "  PS=%s", did->ps);
         if (did->len > 0) fprintf(fmis, "  LENGTH=%-6d", did->len);
         if (did->frag) fprintf(fmis, "  FRAGMENT");
         if (did->block) fprintf(fmis, "  BLOCK");
         if (did->lst) fprintf(fmis, "  LST");
         fprintf(fmis, "\n");
         nmiss++;
      }
      did = did->next;
   }

   return(nmiss);
}  /*  end of write_mis */
/*======================================================================*/
int write_fnd(ffnd, ids)
FILE *ffnd;
struct db_id *ids;
{
   struct db_id *did;
   int nfnd;
 
   nfnd=0;
   did = ids->next;
   while (did != NULL)
   {
      if (did->rank > 0 && !did->block)
      {
         fprintf(ffnd, "%-20s", did->entry);
         if (strlen(did->ps)) fprintf(ffnd, "  PS=%s", did->ps);
         if (did->len > 0) fprintf(ffnd, "  LENGTH=%-6d", did->len);
         if (did->frag) fprintf(ffnd, "  FRAGMENT");
         if (did->block) fprintf(ffnd, "  BLOCK");
         if (did->lst) fprintf(ffnd, "  LST");
         fprintf(ffnd, "       P=%g", did->pvalue);
         fprintf(ffnd, "\n");
         nfnd++;
      }
      did = did->next;
   }

   return(nfnd);
}  /*  end of write_fnd */
>block) BlkSeq ++;
      did = did->next;
   }

   /*---------Get the 99.9% score ------------------------------------*/
/*>>>>>>>>>>>Read SWISS from the output file <<<<<<<<<<<<<<<<<<<*/
   /* NOTE:  sinceblimps-3.9/protomat/blksort.c000064400001460000012000002217711054326072700166570ustar00jorjastaff00000400000027/* >>> struct best_block has fixed MAXSEQS sequences, but this is now 5433!!!
 <<<  */
/*=======================================================================
  (C) Copyright 1992-1998, Fred Hutchinson Cancer Research Center
	blksort.c  USE:  blksort #hits search_output blocks_db [-stats]
		   OR:   blksort blimps.cs
	    eg:  blksort #hits sample.hom none -stats
       There are three arguments:
          1. Number of hits to report
	  2. Name of output file from a PATMAT blocks search.
	  3. Name of blocks database searched (optional, use a nonsense
	     name to omit, eg "none").
	  4. Optionally -stats => statistics written to files blksort.dat &
	     blksort.rep (repeats)
       Tries to read files in the current directory, or in first DB directory
	if input file is a blimps.cs file:
	  1. blksort.stp:  documentation to print out; or prints.stp
	  2. blksort.stn:  percentiles for true negative blimps scores
	  3. repeats.dat:  number of repeats according to Prosite
	  4. blksort.bias: list of blocks with biased composition

     Assumed format of input file (output of a blimps search):
       [nl]Probe Sequence:...
       [nl][n]]Target Block File:...
       [nl][nl]
       [nl][block name][sp][block #][sp][ID & DE for 60][score for 5]...etc.
       Results start on 7th line.
       Block name is in columns 1-7.
       Description is in columns 15-73.
       Score is in columns 75-79.
       Frame is in columns 80-83.
       Offset in sequence is in columns 84-89.
       Alignment to block is in columns 90-.

--------------------------------------------------------------------------
  7/8/92   J. Henikoff

 12/ 4/98 1. Removed PRINTS_FLAG; look for blksort.stp in current directory
	     first, then in 1st DB directory
 12/15/98 1. Fixed bug when additional hits with same last score
          2. Fixed biased block bug for single blocks (eg PD02218)
  5/14/99 1. Revised blimps 3.2.6 output format
  6/12/99 1. Sequence names up to 18 characters long.
  7/ 4/99 1. Recognize Blimps 3.3
 12/17/99 1. Longer AC
  6/10/00 1. Fixed problems with longer AC
  3/11/01 1. Check for MAXSEQS in read_block()
  8/21/02 1. Use sprintf() instead of kr_itoa()
 12/23/06.1. Increased seq name len
==========================================================================*/

#include "motifj.h"

#define NSCORE 5000		/* Maximum # of scores in .hom file */
#define MAXHIT 10		/* Default # hits to report */
#define SEEK_SET 0		/* needed for UNIX fseek routine */
#define MINPAT 1000		/* Minimum patmat score for a hit */
#define MAXMAP 60		/* Maximum map width in columns */
#define MAXTILES 620		/* Max. # of lines in blksort.stn */
#define MAXGROUP 1000		/* Max. # lines in repeats.dat file */
#define MAXBIAS 1000		/* Max. # lines in blksort.bias file */
#define MAX_WIDTH 60		/* Max. width of block */
#define MAX_REPEAT 400		/* Max. #aas between repeats */
#define PROTEIN 1
#define DNA 3

struct hom {			/* search results structure */
   char ac[MAXAC+1];		/* block name, eg. PS00094A */
   char fam[MAXAC];		/* family part of ac */
   int min_rank;		/* minimum rank for this group of blocks */
   int rank;			/* rank of this result in search */
   int frame;			/* frame of alignment */
   int strength;		/* block strengh */
   int score;			/* patmat score */
   long offset;			/* offset of alignment */
   int width;			/* width of block */
   char title[25];		/* block description */
   char aa[MAX_WIDTH];	   	/* alignment to block */
   int map_flag;		/* used by map_blocks() */
				/* 0=>not hit, 1=>hit, 2=>repeat*/
				/* 3=>repeat/mapped, 4=>not hit/mapped */
};

struct best_block {			/* block structure */
   char ac[MAXAC+1];         		/* accession number */
   char fam[MAXAC];			/* family part of ac */
   int nseq, width, strength;		/* #seqs, width, strength */
   int minprev, maxprev;		/* distances from prev block */
   char name[MAXSEQS][SNAMELEN+1];	/* name of seq */
   long offset[MAXSEQS];		/* offset of seq */
   char aa[MAXSEQS][MAX_WIDTH];		/* aas for seq */
   int cluster[MAXSEQS];		/* cluster # for seq */
   int ncluster[MAXSEQS];		/* #seqs in same cluster */
   long dat_pos;			/* position of block in blocks.dat*/
   int query;				/* score if last seq is a query */
   int rank;				/* patmat rank if last seq is query*/
   struct best_block *next_block;	/* next block in path */
};

struct sorttemp {			/* sorting structure */
   char ac[MAXAC+1];
   int rank, index, map_flag, path, tpath;
};

struct minmax {				/* to check repeat overlaps */
   long min;
};

struct file_list {
   FILE *fdat;
   char datname[FNAMELEN];
   long prevAC;
   struct file_list *next_flist;
};

/*---- Functions in blksort.c -----*/
int read_config();
void print_blurb();
FILE *get_info();
void open_dbs();
void close_dbs();
int read_hom();
int print_results();
int check_dat();
struct best_block *read_block();
void fill_block();
void add_query();
int check_repeats();
double hypergeo();
int distance_okay();
long prev_dist();
int distance();
void map_blocks();
void align_blocks();
int closest_seq();
void consensus();
int strandcmp();			/* sorting routine */
int framecmp();				/* sorting routine */
int mincmp();				/* sorting routine */
int tempcmp();
int stempcmp();
int stempcmp2();
int read_tiles();			/* read percentiles file */
int read_repeats();			/* read repeats.dat */
int read_bias();			/* read blksort.bias */
int compute_loc();
struct file_list *make_flist();
void insert_flist();

/*-------Functions in motmisc.c --------*/
/*  void kr_itoa();  */
struct split_name *split_names();

/*------------Global variables -------------*/
char Version[12] = "12/23/06.1";/* Version number */
int BlimpsVer;			/* Blimps version */
char Query[SNAMELEN+1];		/* Query sequence name */
unsigned long QLen;		/* Query length */
int NBlock;			/* # blocks searched */
int SeqType;			/* =1 if amino acid, =3 if nucleotide */
int MaxHit;			/* # hits to report */
int Ntiles;			/* # of percentiles read in */
float Tiles[MAXTILES];		/* %-tiles values for scores 1000-1620 */
int Stats;			/* statistics flag */
char HomName[FNAMELEN];		/* Search file name for stats file */
char Qfilename[FNAMELEN];	/* Query file */
struct working {
  char ac[MAXAC+1];
  int num;
} Repeats[MAXGROUP], Bias[MAXBIAS];	/* Working area */
int NRepeat;			/* # of repeat values read in */
int MaxRepeat;			/* max # of repeats in any group */
int NBias;			/* # of bias values read in */
int Config_Flag;		/* 1st arg is blimps config file */
char DatDir[FNAMELEN];		/* Directory of database files */

/*======================================================================*/
int main(argc, argv)
int argc;
char *argv[];
{
   FILE *fhom, *fcf;
   char homfile[FNAMELEN], datfile[FNAMELEN], ctemp[FNAMELEN];
   char db[FNAMELEN];
   int i, nscores, ndb;
   struct split_name *datsplit;
   struct file_list *flist, *newdat;

   printf("\nBLKSORT Version %s\n", Version);
   if (argc < 2)
   {
      printf("COPYRIGHT 1992-8 Fred Hutchinson Cancer Research Center\n");
      printf("USAGE: blksort    [-stats]\n");
      printf("           = number of hits to report, use 0 for default\n");
      printf("     = blimps search output file\n");
      printf("     = blocks database searched by blimps\n");
      printf("    -stats          produces blksort.dat statistics file\n");
      printf("OR:    blksort \n");
      printf("     = name of blimps configuration file\n");
   }
   Stats = Config_Flag = NO;
   fcf = NULL;
   MaxHit = 0;

   /*-----------arg 1: # hits to report or config file---------------------*/
   ctemp[0] = '\0';
   flist = make_flist();
   ndb = 0;
   if (argc > 1) strcpy(ctemp, argv[1]);
   else
   {
      printf("\nEnter number of hits to report or ");
      printf("blimps configuration file name [%d]: ", MaxHit);
      gets(ctemp);
   }
   if (!strlen(ctemp)) strcpy(ctemp, "0");
   for (i=0; i 0) strcpy(datfile, flist->next_flist->datname);
         }
    }   /* end of read parameters from blimps config file */
    else
    {   /* parameters are on the command line */
          MaxHit = atoi(ctemp);

         /*------------- arg 2:  .hom file -------------------------------*/
         if (argc > 2)
            strcpy(homfile, argv[2]);
         else
         {
            printf("\nEnter name of file containing blocks search results: ");
            gets(homfile);
         }
         /*------------- arg 3:  blocks database file -----------------------*/
         db[0] = '\0';
         if (argc > 3)
            strcpy(datfile, argv[3]);
         else
         {
            printf("\nEnter name of blocks database searched: ");
            gets(datfile);
         }
         if (strlen(datfile))
         {
            newdat = make_flist();
            strcpy(newdat->datname, datfile);
            insert_flist(flist, newdat);
            ndb++;
         }

         /*------------- Option arg 4: collect stats ---------------------*/
         if (argc > 4 && strcmp(argv[4], "-stats") == 0) Stats = YES;
    }  /* end of non-config file input */

   /*  Get the directory of the first datbase file */
   datsplit = split_names(datfile);
   strncpy(DatDir, datfile, datsplit->dir_len);
   DatDir[datsplit->dir_len] = '\0';
   
   /*-------------------------------------------------------------------*/
   /*-----------------Open the search results --------------------------*/
   fhom = get_info(homfile);

   /*--- Set MaxHit based on sequence length & type to report at least
	  1 hit per 1000kb of DNA sequence ---*/
   if (MaxHit <= 0)
   {
      if (SeqType == DNA)
      {
         MaxHit = (int) QLen/1000 + 1;
         if (MaxHit < MAXHIT) MaxHit = MAXHIT;
      }
      else  MaxHit = MAXHIT;
   }

   /*---------------Open the blocks database files---------------------*/
   open_dbs(flist);

/*---------------------------------------------------------------------*/
   print_blurb();
   printf("\nQuery=%s, \n Size=%ld ", Qfilename, QLen);
   if (SeqType == PROTEIN) printf("Amino Acids");
   else if (SeqType == DNA) printf("Base Pairs");
   printf("\nBlocks Searched=%d\n", NBlock); 

/*---------------------------------------------------------------------*/
   Ntiles = read_tiles();
   NRepeat = read_repeats();
   NBias = read_bias();
   nscores = read_hom(fhom, flist);
   printf("\n%d possible hits reported\n", nscores);
   fclose(fhom);
   close_dbs(flist);
   exit(0);
}  /*  end of main */
/*============================================================================
  Read a blimps config file:  OU=blimps output file, DB=blocks db(s) searched
  How to override default MaxHit from here - NU ?
=============================================================================*/
int read_config(fcf, homfile, flist)
FILE *fcf;
char homfile[FNAMELEN];
struct file_list *flist;
{
   char line[MAXLINE], keyword[20], *ptr;
   int ndb;
   struct file_list *newdat;

   ndb = 0;
   homfile[0] = '\0';
   /*   Read until end of file or until "//" line is reached   */
   while ( !feof(fcf) && fgets(line, MAXLINE, fcf) != NULL &&
           (strncmp(line, "//", 2)) )
   {
      ptr = strtok(line, " \t\r\n");
      if (ptr != NULL && ptr[0] != ';')
      {
         strcpy(keyword,ptr);
         ptr = strtok(NULL, " \t\r\n;");
         if (ptr != NULL)
         {
            if (strncasecmp(keyword, "OU", 2) == 0)
            {
               strcpy(homfile, ptr);
            }
            else if (strncasecmp(keyword, "DB", 2) == 0)
            {
               newdat = make_flist();
               strcpy(newdat->datname, ptr);
               insert_flist(flist, newdat);
               ndb++;
            }
         }   /* end of if ptr */
      }  /* end of if ptr */
   }  /* end of fcf */

   return (ndb);
}  /* end of read_config */
/*======================================================================*/
void print_blurb()
{
   FILE *fstp;
   char fname[FNAMELEN], line[MAXLINE];

   /*   Look for blksort.stp first in current directory  */
   strcpy(fname, "blksort.stp");
   if ((fstp=fopen(fname, "r")) == NULL)
   {
      sprintf(fname, "%sblksort.stp", DatDir);
      fstp=fopen(fname, "r");
   }

   if (fstp == NULL)
   {
      printf("\n========================================");
      printf("=======================================");
      printf("\nHere are your search results from the BLOCKS searcher.");
      printf("\nPlease report problems to webmaster@blocks.fhcrc.org");
      printf(", include your query\nand this output.");
      printf(" To obtain help, send the word HELP on a single line to");
      printf("\nblocks@blocks.fhcrc.org");
      printf("\n========================================");
      printf("=======================================");
      printf("\nCopyright (c) 1992-6 by the Fred Hutchinson Cancer");
      printf(" Research Center");
      printf("\nIf you use BLOCKS in your research, please cite:");
      printf("\nSteven Henikoff and Jorja G. Henikoff,");
      printf(" Protein Family Classification Based");
      printf("\non Searching a Database of Blocks, Genomics 19:97-107 (1994).");
      printf("\n========================================");
      printf("=======================================");
      printf("\nEach numbered result consists of one");
      printf(" or more blocks from a PROSITE or PRINTS");
      printf("\ngroup found in the query sequence. One set");
      printf(" of the highest-scoring blocks that");
      printf("\nare in the correct order and separated");
      printf(" by distances comparable to the BLOCKS");
      printf("\ndatabase is selected for analysis.");
      printf(" If this set includes multiple blocks");
      printf("\nthe probability that the lower scoring");
      printf(" blocks support the highest scoring");
      printf("\nblock is reported. Maps of the database");
      printf(" blocks and query sequence are shown:");
      printf("\n  < indicates the sequence has been");
      printf(" truncated to fit the page");
      printf("\n  : indicates the minimum distance");
      printf(" between blocks in the database");
      printf("\n  . indicates the maximum distance");
      printf(" between blocks in the database");
      printf("\nThe maps are aligned on the highest");
      printf(" scoring block. The alignment of the");
      printf("\nquery sequence with the sequence");
      printf(" closest to it in the BLOCKS database");
      printf("\nis shown. Upper case in the query");
      printf(" sequence indicates at least one");
      printf("\noccurrence of the residue in that");
      printf(" column of the block.");
      printf("\n========================================");
      printf("=======================================");
      printf("\n");
   }
   else
   {
      while (!feof(fstp) && fgets(line, MAXLINE, fstp) != NULL)
         printf("%s", line);
      fclose(fstp);
   }

}  /* end of print_blurb */
/*=====================================================================
     Set global variables from the preface of the blimps results file
=========================================================================*/
FILE *get_info(homfile)
char homfile[FNAMELEN];
{
   FILE *fhom;
   char line[MAXLINE], db[FNAMELEN];
   char *ptr, *ptr1;
   int i, j, done;
   struct split_name *homsplit;

   if ( (fhom=fopen(homfile, "r")) == NULL)
   {
      printf("\nBLKSORT: Cannot open file blimps file %s\n", homfile);
      exit(-1);
   }
   homsplit = split_names(homfile);
   strncpy(HomName, homfile + homsplit->dir_len, homsplit->name_len);
   HomName[homsplit->name_len] = '\0';
   db[0] = Qfilename[0] = Query[0] = '\0';
   BlimpsVer = 326;				/* Blimps version */
   NBlock = 0; QLen = (unsigned long) 0;
   SeqType = PROTEIN;		/* amino acid is default type */
   done = NO;
   while (!done &&
	  !feof(fhom) && fgets(line,MAXLINE,fhom) != NULL)
   {
      if (strstr(line, "Version 3.2.5")) BlimpsVer = 325;
      if (strstr(line, "Version 3.2.4")) BlimpsVer = 324;
      if (strstr(line, "Version 3.2.3")) BlimpsVer = 323;
      if (strlen(line) > 10 && strstr(line, "Probe Sequence:") != NULL)
      {   /*  "Probe Sequence: query  Probe Size: length" */
         ptr = strstr(line, "Probe Sequence:");
         /* Copy up to SNAMELEN characters to Query name */
         j = strlen(ptr); if (j > FNAMELEN) j = FNAMELEN;
	 strncpy(Qfilename, ptr+16, j); Qfilename[j] = '\0';
         if (Qfilename[0] == '>') i = 1; else i = 0;
         j=0;
         while(i 10 && strstr(line, "Size") != NULL)
      {   /* Probe Size: length Amino Acids */
         ptr = strstr(line, ":"); 
         if (ptr != NULL)
         {
            if (strstr(ptr, "Base Pair") != NULL) SeqType = DNA;
            ptr1 = strtok(ptr, " ");
            if (ptr1 != NULL)
            {
               ptr1 = strtok(NULL, " \n\r");
               if (ptr1 != NULL) QLen = atol(ptr1);
            }
         }
      } 
      else if (strlen(line) > 10 && strstr(line, "Target") != NULL)
      {   /* Target File (s): database */
/*	 strcpy(db, &line[20]); db[strlen(db)-1] = '\0'; */
         ptr = strstr(line, ":"); 
         if (ptr != NULL)
         {
            ptr1 = strtok(ptr, " ");
            if (ptr1 != NULL)
            {
               ptr1 = strtok(NULL, " \n\r");
               if (ptr1 != NULL) strcpy(db, ptr1);
            }
         }
      }
      else if (strlen(line) > 10 && strstr(line, "Records") != NULL)
      {  /* Records Searched: nblock */
         ptr = strstr(line, ":");
         if (ptr != NULL)
         {
            ptr1 = strtok(ptr, " ");
            if (ptr1 != NULL)
            {
               ptr1 = strtok(NULL, " \n\r");
               if (ptr1 != NULL) NBlock = atoi(ptr1);
            }
         }
         done=YES;
      }
      else if (strncmp(line, "AC#", 3) == 0) done=YES;
   }

   return(fhom);

}   /*  end of get_info */
/*========================================================================
     Open all the files in the list of blocks databases searched
==========================================================================*/
void open_dbs(flist)
struct file_list *flist;
{
   struct file_list *fcur;

   fcur = flist->next_flist;
   while (fcur != NULL)
   {
      if ( (fcur->fdat=fopen(fcur->datname, "r")) == NULL)
      {
         printf("\nBLKSORT: Cannot open blocks file %s", fcur->datname);
      }
      else
      {
         fcur->prevAC = ftell(fcur->fdat);
         printf("Database=%s\n", fcur->datname); 
      }
      fcur = fcur->next_flist;
   }
}   /*  end of open_dbs */
/*========================================================================
     Close all the files in the list of blocks databases searched
==========================================================================*/
void close_dbs(flist)
struct file_list *flist;
{
   struct file_list *fcur;

   fcur = flist->next_flist;
   while (fcur != NULL)
   {
      if (fcur->fdat != NULL) fclose(fcur->fdat);
      fcur = fcur->next_flist;
   }
}   /* end of close_dbs */
/*======================================================================*/
int read_tiles()
{
   int ntiles, score, i;
   float tile;
   FILE *fstn;
   char fname[FNAMELEN], line[MAXLINE];

   ntiles = 0;

   /*   Look in current directory first */
   fstn=fopen("blksort.stn", "r");
   if (fstn == NULL)
   {
      sprintf(fname, "%sblksort.stn", DatDir);
      fstn=fopen(fname, "r");
   }

   if (fstn != NULL)
   {
      while (ntiles < MAXTILES && 
             !feof(fstn) && fgets(line, MAXLINE, fstn) != NULL)
      {
         if (line[0] != '>' && line[0] != '#')
         {
            sscanf(line, "%d %f", &score, &tile);
            for (i=ntiles; i<=(score-1000) ;i++)
               Tiles[i] = tile;
            ntiles = i;
         }
      }
      fclose(fstn);
   }

   return(ntiles);
}  /*  end of read_tiles */
/*======================================================================*/
int read_repeats()
{
   int nrep;
   FILE *frep;
   char line[MAXLINE], fname[FNAMELEN];

   nrep = 0;
   MaxRepeat = 0;

   /*   Look in current directory first */
   frep=fopen("repeats.dat", "r");
   if (frep == NULL)
   {
      sprintf(fname, "%srepeats.dat", DatDir);
      frep=fopen(fname, "r");
   }

   if (frep != NULL)
   {
      while (nrep < MAXGROUP && 
             !feof(frep) && fgets(line, MAXLINE, frep) != NULL)
      {
         if (line[0] != '>' && line[0] != '#')
         {
            sscanf(line, "%s %d", Repeats[nrep].ac, &Repeats[nrep].num);
            if (Repeats[nrep].num < 1) Repeats[nrep].num = 1;
            if (Repeats[nrep].num > MaxRepeat) MaxRepeat = Repeats[nrep].num;
            nrep++;
         }
      }
   }
   return(nrep);
}  /* end of read_repeats */
/*======================================================================*/
int read_bias()
{
   int nbias;
   FILE *fbias;
   char line[MAXLINE], fname[FNAMELEN];

   nbias = 0;

   /*   Look in current directory first */
   fbias = fopen("blksort.bias", "r");
   if (fbias == NULL)
   {
      sprintf(fname, "%sblksort.bias", DatDir);
      fbias = fopen(fname, "r");
   }

   if (fbias != NULL)
   {
      while (nbias < MAXBIAS && 
             !feof(fbias) && fgets(line, MAXLINE, fbias) != NULL)
      {
         if (line[0] != '>' && line[0] != '#')
         {
            sscanf(line, "%s %d", Bias[nbias].ac, &Bias[nbias].num);
            if (Bias[nbias].num < 1) Bias[nbias].num = 1;
            nbias++;
         }
      }
   }
   return(nbias);
}  /* end of read_bias */
/*=======================================================================*/
int read_hom(fhom, flist)
FILE *fhom;
struct file_list *flist;
{
   int i, j, rank, save_rank, min_rank, nhit, save_strand, strand;
   int ac_pos, title_pos, str_pos, score_pos, frame_pos, off_pos, aa_pos;
   int title_len, done;
   char line[MAXLINE], ctemp[8], save_ac[MAXAC+1], save_fam[MAXAC+1];
   struct hom *results;

/*------------- Load the search results into memory --------------------*/
   results = (struct hom *) malloc(NSCORE * sizeof(struct hom));
   if (results == NULL)
   {  printf("\nOUT OF MEMORY\n\n"); exit(-1); }
   if (BlimpsVer >= 326)
   {
      ac_pos=0; title_pos=12; str_pos=66; score_pos=73; frame_pos=80; 
      off_pos=82; aa_pos=90; title_len=25;
   }
   else		/* Blimps version 3.2.5 and earlier */
   {
      ac_pos=0; title_pos=14; str_pos=63; score_pos=70; frame_pos=77; 
      off_pos=79; aa_pos=87; title_len=25;
   }
   rank = 0;
   while (!feof(fhom) && fgets(line,MAXLINE,fhom) != NULL)
   {
      if (strlen(line) > aa_pos && rank < NSCORE)
      {
	 save_ac[0]= '\0';
	 strncpy(save_ac, &line[ac_pos], MAXAC); save_ac[MAXAC] = '\0';
         for (i=0; i= MINAC)
         {
            if (isalpha(save_ac[i])) { save_ac[i] = '\0'; done = YES; }
            else { i--; }
         }
         strcpy(results[rank].fam, save_ac);
	 results[rank].rank = results[rank].min_rank = rank + 1;
	 results[rank].title[0] = '\0';
	 strncpy(results[rank].title, &line[title_pos], title_len);
	 results[rank].title[title_len - 1] = '\0';
         strncpy(ctemp, &line[str_pos], 6); ctemp[6] = '\0';
         results[rank].strength = atoi(ctemp);
	 strncpy(ctemp, &line[score_pos], 6); ctemp[6] = '\0';
	 results[rank].score = atoi(ctemp);
	 strncpy(ctemp, &line[frame_pos], 2); ctemp[2] = '\0';
	 results[rank].frame = atoi(ctemp);
	 strncpy(ctemp, &line[off_pos], 7); ctemp[7] = '\0';
	 results[rank].offset = atol(ctemp);
	 results[rank].width = 0; i=aa_pos;
	 while (line[i++] != '\n') results[rank].width += 1;
	 if (results[rank].width > MAX_WIDTH)
		results[rank].width=MAX_WIDTH;
	 strncpy(results[rank].aa, &line[aa_pos], results[rank].width);
	 results[rank].aa[results[rank].width] = '\0';
         results[rank].map_flag = NO;
	 rank++;
      }
   }
/*   printf("\n%d results read", rank);
*/
   if (rank < 1) return(0);

/*----------Sort by strand and block name-----------*/
   qsort(results, rank, sizeof(struct hom), strandcmp);

/*--------Group the results & determine minimum rank -----------*/
   strcpy(save_fam, results[0].fam); save_rank = 0;
   if (results[0].frame < 0) save_strand = -1;
   else                   save_strand = 1;
   min_rank = results[0].rank;
   for (i=1; i save_rank)
	   for (j=save_rank; j save_rank)
       for (j=save_rank; j MINPAT)
         {
            good_score=YES; max_score = results[j].score;
         }
         /*    Print previous group; can print more than MaxHit results
               if there are more than MaxHit hits with the same max_score
               as the MaxHit-th one */
         if (i > save_nresult &&  good_score &&
             (nprint < MaxHit || max_score == last_score) )
	 {
	   /*---- Report all possible hits -----*/
              nhit++;
   printf("\n%d.-----------------------------------------------------------",
             nhit); printf("-------------");
   if (SeqType == DNA)
 printf("\nBlock     Rank Frame Score Strength   Location (bp) Description\n");
   else
 printf("\nBlock     Rank Frame Score Strength   Location (aa) Description\n");
	      for (j=save_nresult; jnext_flist != NULL)
	      {
		 ctemp[0] = '\0';
                 found = NO;
                 fcur = flist->next_flist;
                 while (!found && fcur != NULL)
		 {
		   if (save_nresult > 0 &&
		    strcmp(results[save_nresult].ac, results[last_hit].ac) <= 0)
			 rewind(fcur->fdat);
		   else fseek(fcur->fdat, fcur->prevAC, SEEK_SET);
		   found=check_dat(fstat, frep, fcur, save_nresult, i, results);
		   last_hit = save_nresult;
                   fcur = fcur->next_flist;
		 }
	      }   /*  end of if flist */
	      nprint++;
              last_score = max_score;
	 }  /* end of print previous group */
         save_strand = strand; 
	 if (i < nresult) strcpy(save_fam, results[i].fam);
         save_nresult = i;
	 good_score=NO;
      }   /*  end of a group of blocks */
   }  /* end of a hit */

   if (fstat != NULL) fclose(fstat);
   if (frep != NULL) fclose(frep);
   return(nhit);
}  /* end of print_results */
/*======================================================================*/
/*   Look up this group in blocks.dat                                   */
/*======================================================================*/
int check_dat(fstat, frep, fcur, min_t, max_t, results)
FILE *fstat, *frep;
struct file_list *fcur;
int min_t, max_t;
struct hom *results;
{
   struct best_block *block, *lblock, *fblock;
   int i, nblk, nrep;

   nblk = 0;
   block = fblock = lblock = NULL;

   /*----- Make a list of blocks in the database -----*/
   while ( (block = read_block(fcur->fdat, results[min_t].fam)) != NULL)
   {
      if (nblk > 0) lblock->next_block = block;
      else fblock = block;
      nblk++;
      lblock=block;
   }
   if (fblock == NULL) return(0);


   /*=======================Found blocks for this AC =====================*/
   fcur->prevAC = fblock->dat_pos;

   /*---- Add the query as the last sequence in each block in the list ---*/
   /*     P-value is computed in add_query()                              */
   /*     Blocks in hit are listed here                                   */
   add_query(fstat, min_t, max_t, results, fblock);

   /*------------------ Now check for repeats --------------------*/
   i = nrep = 0;
   while (i < NRepeat && 
          strcasecmp(Repeats[i].ac, results[min_t].fam) <= 0)
      i++;
   if (i > 0 && strcasecmp(Repeats[i-1].ac, results[min_t].fam) == 0 &&
       Repeats[i-1].num > 1)
            nrep = check_repeats(frep, min_t, max_t, results, Repeats[i-1].num - 1);

   /*--- Map the blocks if > 1 in database ----*/
   if (nblk > 1)
            map_blocks(min_t, max_t, results, fblock);
   else printf("\n");

   /*---Determine the closest block seq to the query seq & display them --*/
   align_blocks(min_t, max_t, results, fblock);

   /*---Free up some memory ----------*/
   block = fblock;
   while (block != NULL)
   {
      lblock = block;
      block = block->next_block;
      free(lblock);
   }

   return(nblk);
}  /*  End of check_dat */
/*=====================================================================
      Read the blocks database
      Assumes database entries are sorted by AC
=======================================================================*/
struct best_block *read_block(fdat, fam)
FILE *fdat;
char *fam;
{
   char line[MAXLINE], ctemp[MAXLINE], *ptr, *ptr1;
   struct best_block *block;
   int done, i, idone;

   done = NO;
   block = NULL;
   while (!done && !feof(fdat) && fgets(line, MAXLINE, fdat) != NULL)
   {
      if (strncmp(line, "AC   ", 5) == 0 && 
          strncasecmp(line+5, fam, strlen(fam)) > 0)
	        done = YES;
      else if (strncmp(line, "AC   ", 5) == 0 &&
          strncasecmp(line+5, fam, strlen(fam)) == 0)
      {
	 block = (struct best_block *) malloc(sizeof(struct best_block));
	 if (block == NULL)
	 {  printf("\nOUT OF MEMORY\n\n");  exit(-1);  }
	 block->next_block = NULL;
	 block->dat_pos = ftell(fdat);
         block->ac[0] = '\0';
         strcpy(ctemp, line);
         ptr = strtok(ctemp+5, "; \n\r\t");
         if (ptr != NULL) strcpy(block->ac, ptr);
         strcpy(block->fam, block->ac);
         i = strlen(block->fam); idone = NO;
         while (!idone && i >= MINAC)
         {
            if (isalpha(block->fam[i])) { block->fam[i] = '\0'; idone = YES; }
            else  { i--; }
         }
	 block->minprev = block->maxprev = -1;
	 block->query = NO;
         block->rank = NO;
/*
	 ptr = strtok(line+12, "(");
*/
         ptr = strtok(NULL, "(");
	 if (ptr != NULL)
	 {
	    ptr = strtok(NULL, ",");
	    if (ptr != NULL)
	    {
	       block->minprev = atoi(ptr);
	       ptr = strtok(NULL, ")");
	       if (ptr != NULL) block->maxprev = atoi(ptr);
	    }
	 }
      }
      else if (block != NULL && strncmp(line, "BL   ", 5) == 0)
      {
	 block->strength = 0;
	 ptr=strstr(line,"strength=");
	 if (ptr != NULL)
	 {
	    ptr1 = strtok(ptr, "="); ptr1=strtok(NULL, "\n\r");
	    block->strength = atoi(ptr1);
	 }
	 fill_block(fdat, block);
	 return(block);
      }
   }
   return(NULL);		/* no block found! */
}  /* end of read_block */
/*====================================================================
     Fill up the block structure
=======================================================================*/
void fill_block(fdat, block)
FILE *fdat;
struct best_block *block;
{
   int done, i, itemp, n, cluster, ncluster;
   char line[MAXLINE], *ptr, *ptr1;

   block->nseq = block->width = 0;
   cluster = ncluster = 0;
   done=NO;
   while (!done && !feof(fdat) && fgets(line,MAXLINE,fdat) != NULL)
   {
      if (strlen(line) == 1)		/* blank line => new cluster */
      {
	 /*  Set #seqs in cluster to seqs in previous cluster */
	 if (ncluster > 0)
	   for (n=0; nnseq; n++)
	      if (block->cluster[n] == cluster) block->ncluster[n] = ncluster;
	 cluster++; ncluster = 0;
      }
      else if (strlen(line) > 1)
      {
         /*>>> avoid MAXSEQS abort, but this needs to be fixed <<<*/
	 if (strncmp(line, "//", 2) == 0 || block->nseq == MAXSEQS) 
         {  done=YES; }
	 else
         {  if (strlen(line) > SNAMELEN && block->nseq < MAXSEQS)
	    {
	       ptr=strtok(line, "(");
               itemp = strlen(ptr);
               if (strlen(ptr) > SNAMELEN) itemp = SNAMELEN;
	       strncpy(block->name[block->nseq], ptr, itemp);
               block->name[block->nseq][itemp] = '\0';
               /*    Get rid of trailing spaces  */
               i=0;
               while(i < itemp && block->name[block->nseq][i] != ' ') i++;
               block->name[block->nseq][i] = '\0';

	       ptr=strtok(NULL, ")");
	       block->offset[block->nseq] = atol(ptr);
	       ptr1=strtok(NULL, "\n\r");
	       i=0;
	       while (ptr1[i] == ' ') i++;
	       ptr = ptr1+i;
               ptr = strtok(ptr1+i, " \n\r\t");
	       strcpy(block->aa[block->nseq], ptr);
	       block->cluster[block->nseq] = cluster;
	       ncluster++;		/* # seqs in current cluster */
	       block->width = strlen(block->aa[block->nseq]);
	       block->nseq++;
           }
	 }
      }
   }  /* end of fdat */
   /*  Compute weights for the last cluster */
   if (ncluster > 0)
	   for (n=0; nnseq; n++)
	      if (block->cluster[n] == cluster) block->ncluster[n] = ncluster;
}  /* end of fill_block */
/*=======================================================================
     Add the query sequence as the last sequence in each block for
     which it has a hit.
==========================================================================*/
void add_query(fstat, min_t, max_t, results, fblock)
FILE *fstat;
int min_t, max_t;
struct hom *results;
struct best_block *fblock;
{
   struct best_block *block, *maxblock;
   int i, j, t, imin, nblock, mblock, lastrank, maxbias;
   char ac[MAXAC+1], pline[2*MAXLINE], tline[40];
   struct temp *temp;
   double n, r, p, prob;
   float ptile;

   /*------- Need to know how many possible blocks there are ---*/
   nblock=0;
   block = fblock;
   while (block != NULL)
   {
      nblock++;
      block = block->next_block;
   }
   /*-------Assuming patmat is run with repeats -------------*/
/*   nblock *= SeqType*QLen;  */
   nblock *= QLen;

   /*------ Sort this group of hits by rank now --------------*/
   temp = (struct temp *) malloc((max_t - min_t) * sizeof(struct temp));
   if (temp == NULL)
   {
      printf("\nOUT OF MEMORY\n\n"); exit(-1);
   }
   /*   temp[i].flag == 1 for biased blocks   */
   for (i=0; iac) == 0 && !block->query &&
             (i==0 ||
	     distance_okay(results[t].offset, fblock, block)) )
	 {
	    /*--- Adds the query to the block  ------*/
	    strcpy(block->name[block->nseq], Query);
	    block->offset[block->nseq] = results[t].offset;
	    block->cluster[block->nseq] = -1;
	    block->ncluster[block->nseq] = 1;
	    strcpy(block->aa[block->nseq], results[t].aa);
	    block->query = results[t].score;
            block->rank = results[t].rank;
	    block->nseq++;
            results[t].map_flag = YES;

            /*--- Compute probability -----*/
            if (i==0)
            {
                maxblock = block;
                lastrank = temp[i].value;
		maxbias = temp[i].flag;
            }
            else if (i>0 && NBlock > 0 && QLen > 0)
            {
               mblock++;     /* number of supporting blocks so far */
               /* compute prob a block of this family could rank this high*/
               /* Call the blocks in the group "red". Compute prob. that
                  this red block had this rank using sampling without
                  replacement. At this point are assuming:
                    Total #blocks = #db blocks-rank of last red block drawn
                    Total #reds = #blocks in family - #reds drawn so far
                    Total blocks drawn = rank of this red - rank of last red
                    Want Prob. one of blocks drawn is red.   */
/*               n = (double) SeqType*QLen*NBlock-lastrank; */
               n = (double) QLen*NBlock-lastrank;
	       r = (double) temp[i].value-lastrank;
	       p = (double) nblock-mblock;
              /*      Avoid going beyond max. hypergeo value  */
               if (p * r >= n - p + 1) r = (double) ((int) (n - p + 1) / p);
	       prob *= hypergeo(n, r, p, 1.0);
               /* compute prob this block is this far from the anchor block */
               /* QLen may be in protein or dna units, distance is always
                  in protein units so multiply by SeqType to convert it to
                  correct units. Min dist = -1; Max dist = distance() */
               prob *= (double) SeqType*(distance(maxblock,block)+1) / QLen;
               strcat(pline, block->ac);
               if (temp[i].flag) strcat(pline, " (biased) ");
               else              strcat(pline, " ");
               lastrank = temp[i].value;
            }
	 }
         else if (strcmp(ac, block->ac) == 0)
            nblock--;                         /*  block doesn't fit */
	 block = block->next_block;
      }
   }  /*  end of for i = min to max for hit */
 
   /*-------------Print hit--------------------------------------------*/
   if (prob > 1.0) prob = 1.0;
   if (prob < 0.0) prob = 0.0;
   ptile = 0.0;
   if (Ntiles > 0)
   {
      i = maxblock->query - 1000;
      if (i < 0) i = 0;
      else if (i > Ntiles-1) i = Ntiles-1;
           { 
              ptile = Tiles[i];
 printf("\n%d=%.2fth percentile of anchor block scores for shuffled queries",
              maxblock->query, ptile);
           }
   }
   if (strlen(pline))
   {
      printf("\nP<%6.2g for ", prob);
      i=0;
      while (i < strlen(pline))
      {
         imin=36;
         if (i+imin > strlen(pline)) imin = strlen(pline) - i;
         strncpy(tline, pline+i, imin); tline[imin] = '\0';
         if (i==0) printf("%s", tline);
         else printf("\n              %s", tline);
         i += 36;
      }
      printf("in support of %s", maxblock->ac);
   }
   else printf("\nP not calculated for single block %s", maxblock->ac);
   if (maxbias) printf(" (biased)");
   free(temp);

   /*---------------Write hit statistics--------------------------*/
   if (fstat != NULL)
   {
      block = fblock;
      while (block != NULL)
      {
         if (block->query)
         fprintf(fstat, "%s %s %s 1 %d %d %6.2g %.16f %d %d %d %d %d %ld %.2f\n",
              HomName, Query, block->ac, maxblock->rank, mblock+1, prob, prob,
              block->rank, block->query, block->strength, block->width,
	      block->cluster[block->nseq-1], QLen, ptile);
         block = block->next_block;
      }
   }
}  /*  end of add_query */
/*=======================================================================*/
int check_repeats(fstat, min_t, max_t, results, maxrep)
FILE *fstat;
int min_t, max_t, maxrep;
struct hom *results;
{
   int i, ii, t, tt, lastrank, lastpath, mrep, report, width;
   int inew, ifirst, tpath, irep, ib;
   long min, over, diff;
   char lastac[MAXAC+1];
   struct sorttemp *stemp;
   struct minmax *overlap;
   double n, r, p, prob;

   printf("\nMaximum number of repeats (from Prosite MAX-REPEAT) = %d", maxrep);
   overlap = (struct minmax *) malloc(MaxRepeat * sizeof(struct minmax));
   if (overlap == NULL)
   {
      printf("\nOUT OF MEMORY\n\n"); exit(-1);
   }
   /*------ Sort this group of hits by block name ----------------*/
 stemp = (struct sorttemp *) malloc((max_t - min_t) * sizeof(struct sorttemp));
   if (stemp == NULL)
   {
      printf("\nOUT OF MEMORY\n\n"); exit(-1);
   }
   for (i=0; i 0 && report)
         {
            /*  compute probability */
            prob = 1.0;
            irep = ifirst - inew + 1;	/* # blocks of type ranked so far */
            ib = 0;			/* # blocks of type since last */
            lastrank = stemp[ifirst].rank;
            for (ii=ifirst+1; ii < i; ii++)
            {
               ib++;
               tt = stemp[ii].index;
               if (results[tt].map_flag)
               {
                  n = (double) QLen*NBlock-lastrank;
	          r = (double) stemp[ii].rank-lastrank;
                  p = QLen - irep;
                  /*      Avoid going beyond max. hypergeo value  */
                  if (p * r >= n - p + 1) r = (double) ((int) (n - p + 1) / p);
	          prob *= hypergeo(n, r, p, 1.0);
                  lastrank = stemp[ii].rank;
                  irep += ib; ib = 0;
               }
            }
            if (prob > 1.0) prob = 1.0;
            if (prob < 0.0) prob = 0.0;
/*          printf("\nR<%6.2g for ", prob);
*/
        printf("\n%d non-overlapping repeats in support of %s", mrep, lastac);
            if (fstat != NULL)
               fprintf(fstat, "%s %s %s 2 %d %d %6.2g %.16f\n",
                    HomName, Query, lastac, maxrep, mrep, prob, prob);
         }
         /*---------  new block ------------------*/
         inew = i;		/* first index for this block type */
         strcpy(lastac, stemp[i].ac);
         width = results[t].width;
         mrep = 0; report = NO; prob = 1.0;
         if (results[t].map_flag) ifirst = i;
         else ifirst = -1;
         if (stemp[i].path) report = YES;
         /*   set ii to the block that's in the path here */
         ii = stemp[i].tpath;
         overlap[0].min = results[ii].offset;
      }
      /*    Check for repeats now if block isn't in the path */
      if (!results[t].map_flag && mrep < maxrep)
      {
         over = NO;
         for (ii = 0; ii <= mrep; ii++)
         {
            min = results[t].offset;
            diff = min - overlap[ii].min;
            if (diff < 0) diff = 0 - diff;
            if (diff <= width ||
                (SeqType == DNA && diff > MAX_REPEAT))
                           over = YES;
         }
         if (!over)     /*  flag the repeats */
         {
            mrep++;
            if (report) results[t].map_flag = 2;
            overlap[mrep].min = results[t].offset;
            if (ifirst < 0) ifirst = i;
         }
         strcpy(lastac, stemp[i].ac);
      }
   }
   /*   final block */
   if (strlen(lastac) && mrep > 0 && report)
   {
       /*  compute probability */
       prob = 1.0;
       irep = ifirst - inew + 1;
       ib = 0;
       lastrank = stemp[ifirst].rank;
       for (ii=ifirst+1; ii < i; ii++)
       {
          ib++;
          tt = stemp[ii].index;
          if (results[tt].map_flag)
          {
             n = (double) QLen*NBlock-lastrank;
             r = (double) stemp[ii].rank-lastrank;
             p = QLen - irep;
             /*      Avoid going beyond max. hypergeo value  */
             if (p * r >= n - p + 1) r = (double) ((int) (n - p + 1) / p);
             prob *= hypergeo(n, r, p, 1.0);
             lastrank = stemp[ii].rank;
             irep += ib; ib = 0;
          }
       }
       if (prob > 1.0) prob = 1.0;
       if (prob < 0.0) prob = 0.0;
/*     printf("\nR<%6.2g for ", prob);
*/
       printf("\n%d non-overlapping repeats in support of %s", mrep, lastac);
       if (fstat != NULL)
            fprintf(fstat, "%s %s %s 2 %d %d %6.2g %.16f\n",
                    HomName, Query, lastac, maxrep, mrep, prob, prob);
   }
 
   free(stemp);
   return(mrep);

}  /* end of check_repeats */
/*===================================================================
    Compute probability from hypergeometric distribution:
    Assume there are n objects, p of one kind and n-p of another.
    Then when r objects are selected at random from among the n
    objects, the prob. that k of the r are of type p is:
  
      ( p )  ( n-p )        p!               (n-p)!
      ( k )  ( r-k )       ----- * -----------------------
                          k!(p-k)!  (r-k)!( (n-p)-(r-k) )!
    -----------------  =  ---------------------------------
         ( n )                       n!
         ( r )                   ----------
                                  r!(n-r)!

       p!         r!          (n-p)!         (n-r)!
  =  -------- * --------  * ----------  * -----------------
     k!(p-k)!    (r-k)!         n!         ( (n-r)-(p-k) )!

  Which can be simplified to a product of these expressions:
   1.  k terms:
       p*(p-1)*(p-2)*...(p-k+1) / k!
   2.  k terms:
       r*(r-1)*(r-2)*...(r-k+1)
   3.  p terms:
       1/(n*(n-1)*(n-2)*...(n-p+1))
   4.  p-k terms:
       (n-r)*(n-r-1)*....(n-r-(p-k)+1)
      
=====================================================================*/
double hypergeo(n, r, p, k)
double n, r, p, k;
{
   double prob, i;

   prob = 1.0;
   for (i=0.0; iquery)		/* query added to this block already */
      {
	 if (strcmp(block->ac, nblock->ac) < 0)
	    lblock = block;	/* closest block on the left */
	 else if (strcmp(block->ac, nblock->ac) > 0 && rblock == NULL)
	    rblock = block;	/* closest block on the right */
      }
      block = block->next_block;
   }
   /*---------  Check the distance to the left --------------------*/
   if (lblock != NULL)
   {
      mindist = maxdist = lblock->offset[lblock->nseq-1] + (long) lblock->width;
      block = lblock->next_block;
      while (block != NULL && block != nblock)
      {
	 if (strcmp(block->ac, nblock->ac) < 0)
         {
            mindist += block->width;
	    maxdist += prev_dist(block) + block->width;
         }
	 block = block->next_block;
      }
      if (mindist-1 > offset) return(NO); /* allow overlap of 1 */
      if (maxdist + prev_dist(nblock) < offset) return(NO);
   }
   /*----------Check the distance to the right ---------------------*/
   if (rblock != NULL)
   {
      mindist = maxdist = offset + (long) nblock->width;
      block = nblock->next_block;
      while (block != NULL && block != rblock)
      {
	 if (strcmp(block->ac, rblock->ac) < 0)
         {
            mindist += block->width;
	    maxdist += prev_dist(block) + block->width;
         }
	 block = block->next_block;
      }
      if (mindist-1 > rblock->offset[rblock->nseq-1]) return(NO);
      if (maxdist + prev_dist(rblock) < rblock->offset[rblock->nseq-1])
	 return(NO);
   }
   return(YES);
}  /*  end of distance_okay */
/*===================================================================
    Compute maximum distance preceding a block
=====================================================================*/
long prev_dist(block)
struct best_block *block;
{
   long dist;

/*
   dist = (long) block->minprev + block->maxprev;
*/
   dist = (long) 2 * block->maxprev;
   if (dist < 1) dist = 1;
   return(dist);
}  /* end of prev_dist */
/*===================================================================
     Compute maximum allowable distance between two blocks
====================================================================*/
int distance(fromblock, toblock)
struct best_block *fromblock, *toblock;
{
    long dist, maxdist;
    struct best_block *block, *lblock, *rblock;
  
    if (fromblock == NULL || toblock == NULL) return(-1);

    if (strcmp(fromblock->ac, toblock->ac) < 0)
    { lblock=fromblock; rblock=toblock;
      maxdist = QLen-(fromblock->offset[fromblock->nseq-1]+fromblock->width);
    }
    else
    { lblock=toblock; rblock=fromblock;
      maxdist = fromblock->offset[fromblock->nseq-1];
    }
    if (SeqType*maxdist > QLen) maxdist = (int) QLen/SeqType;

    dist = 0;
    block=lblock->next_block;
    while (block != NULL && block != rblock)
    {
       dist += prev_dist(block) + block->width;
       block = block->next_block;
    }
    dist += prev_dist(rblock);
    /*  Don't want possible distance to be larger than possible
        sequence positions! */
    if (dist > maxdist) dist = maxdist;
    return(dist);
}  /* end of distance */
/*====================================================================
    Map a path of blocks
    The mapping is done in three phases:
    1. The blocks in the database are mapped from the 1st position of
       the first block to the last position of the last block. This
       range divided by MAXMAP (number of columns for the map to occupy
       when printed) determines the scale of the map.
    2. The blocks in the query sequence that are consistent with the
       database are mapped to the same scale as the database blocks.
       The two maps are aligned on the highest scoring block (maxblock).
       The query map may occupy more than MAXMAP columns and may have
       to be truncated or compressed. A maximum of MAXLINE characters
       are mapped before compression.
    3. The blocks in the query sequence that are not consistent with the
       database are mapped to the same scale. Since these blocks may
       overlap one another, they may take more than one line. Each line
       is aligned with the left end of the map in 2.
=======================================================================*/
void map_blocks(min_t, max_t, results, fblock)
int min_t, max_t;
struct hom *results;
struct best_block *fblock;
{
   int totblks, maxdist, i, imin, imax, pos, maxspot, maxscore;
   int ilen, maxseq, spot, qspot, t, done, qleft, qright;
   double scale;
   struct best_block *block, *maxblock;
   char fam[MAXAC+1], dbline[MAXLINE], qline[MAXLINE], pline[MAXLINE];

   totblks = maxdist = maxscore = 0;
   /*--- Determine the scale for the database blocks (# aas per space) ---*/
   block = fblock;
   strcpy(fam, block->fam);
   while (block != NULL)
   {
      totblks++;
      /*------ Don't map distance before the first block --------------*/
      if (block != fblock)
         maxdist += block->maxprev;  /* distance from previous block */
      maxdist += block->width;    /* width of this block */
      if (block->query > maxscore)
      {  maxscore = block->query; maxblock = block; }
      block = block->next_block;
   }
   scale = (double) maxdist/MAXMAP;       /* max of 60 spaces per line */
   printf("\n                         |---%5d amino acids---|",
          (int) ((double) 0.5+(scale*25.0)) );

   /*---  1. Now map the database blocks ------------------------------*/
   for (spot=0; spotminprev/scale);
         imax = (int) ((double) 0.5+(block->maxprev-block->minprev)/scale);
         for (i=spot; i < spot+imin; i++) dbline[i] = ':';
         spot += imin;
         for (i=spot; i < spot+imax; i++) dbline[i] = '.';
         spot += imax;
      }
      imin = (int) ((double) 0.5+block->width/scale);
      if (imin < 1) imin = 1;
      ilen = strlen(block->ac); ilen--;
      for (i=spot; i < spot+imin; i++) strncpy(dbline+i, block->ac+ilen, 1);
      spot += imin;
      if (block==maxblock) maxspot=spot;
      block = block->next_block;
   }
   dbline[spot] = '\0';
   printf("\n%20s ", fam);
   printf("%s", dbline);

   /*---- 2. Now map the query sequence if there is one ----------------*/
   /*---Line up the highest scoring query block with the database ----*/
   /*---   Determine qspot = print position for beginning of anchor
           block in query . Line it up with maxspot = print position
           for beginning of anchor block in database line.--- */
   spot=qspot=0;
   pos=0;
   block = fblock;
   while (block != NULL)
   {
      if (block->query)
      {
	 imin = (int) ((double) 0.5+(block->offset[block->nseq-1]-pos)/scale);
         if (imin >= 0)   /* skip over blocks in wrong order */
         {
	    if (spot+imin > MAXLINE && spot+1 < MAXLINE)
               qline[spot++] = '<';
            else
            {
	       for (i=spot; iwidth/scale);
	    if (imin < 1) imin = 1;
            if (spot+imin < MAXLINE)
            {
               ilen = strlen(block->ac); ilen--;
	       for (i=spot; iac+ilen, 1);
	       spot += imin;
            }
	    pos = block->offset[block->nseq-1] + block->width;
	    if (block == maxblock) qspot = spot;
         }
      }
      block = block->next_block;
   }
   qline[spot] = '\0';

   /*------ If the query starts in the after the map, have to
            print some spaces first --------*/
   printf("\n%20s ", Query);
   if (qspot <= maxspot)
   {
       qleft = 0;
       for (i=qspot; i 0 && (pline[0] == '.' || pline[0] == ':')) pline[0] = '<';
   if (qright != strlen(qline)) pline[strlen(pline)-1] = '>';

   printf("%s", pline);

   /*---------3. Now map the repeats wrt consistent hits ---------------*/
   done = NO; 
   while (!done)
   {
      done=YES; spot = 0;
      pos = (int) qleft * scale;   /* offset of first qline with maxblock */
      for (i=0; i=0)
            {
               if (spot+imin < MAXLINE) 
               {
                  spot += imin;
                  imin = (int) ((double) 0.5+results[t].width/scale);
                  if (imin < 1) imin = 1;
                  if (spot+imin < MAXLINE)
                  {
                     ilen = strlen(results[t].ac); ilen--;
                     for (i=spot; i maxseq) 
         {
            if (qline[maxseq-1] == ' ') qline[maxseq-1] = '>'; 
            qline[maxseq] = '\0';
         }
         printf("%s", qline);
      }
   }

   /*--------4. Now map the inconsistent hom hits wrt consistent ones--*/
   done = NO; 
   while (!done)
   {
      done=YES; spot = 0;
      pos = (int) qleft * scale;   /* offset of first qline with maxblock */
      for (i=0; i=0)
            {
               if (spot+imin < MAXLINE) 
               {
                  spot += imin;
                  imin = (int) ((double) 0.5+results[t].width/scale);
                  if (imin < 1) imin = 1;
                  if (spot+imin < MAXLINE)
                  {
                     ilen = strlen(results[t].ac); ilen--;
                     for (i=spot; i maxseq) 
         {
            if (qline[maxseq-1] == ' ') qline[maxseq-1] = '>'; 
            qline[maxseq] = '\0';
         }
         printf("%s", qline);
      }
   }

   printf("\n");

}  /* end of map_blocks */
/*========================================================================
	Align the query sequence with the sequence closest to it in
	each block for which it has a hit.
	blkline[] = distances, datline[] = database segment, barline[] = marks,
	homline[] = query segment, repline[] = repeats.
=========================================================================*/
void align_blocks(min_t, max_t, results, fblock)
int min_t, max_t;
struct hom *results;
struct best_block *fblock;
{
   int s, i, t, savspot, repspot, spot, bspot, datmin, datmax, homdist;
   int first, itemp;
   char datline[MAXLINE], homline[MAXLINE], blkline[MAXLINE];
   char barline[MAXLINE], repline[MAXLINE], saveac[12], ctemp[10];
   struct best_block *block;

   for (i=0; iquery)
      {
	 datmin += block->minprev;
	 datmax += block->maxprev;
	 homdist = block->offset[block->nseq-1] - homdist;

         consensus(block);
	 s = closest_seq(block);

	 /*--- 28 spaces for name & offset on datline & homline;
	       30 spaces for distance info on blkline ----*/
	 bspot = block->width;
	 if (bspot < 30) bspot = 30;

         /*    Check to see whether this block will fit on the current line */
         /*  bspot could be 55; 55+28 = 83 */
	 if ((spot + bspot + 28) > 83)
         {
	    homline[spot]= datline[spot]= blkline[spot]= barline[spot]= '\0';
            repline[spot] = '\0';
	    printf("\n%s", blkline);
            printf("\n%s", datline); printf("\n%s", barline);
	    printf("\n%s\n", homline);
            for (i=0; i 0) spot += 3; }

itemp = (int) strlen(block->name[s]);
         strncpy(blkline+spot, block->ac, strlen(block->ac));
         strncpy(datline+spot, block->name[s], strlen(block->name[s]));
         strncpy(homline+spot, block->name[block->nseq-1],
              strlen(block->name[block->nseq-1]));
	 spot+=19;		/* seq name + 1 */

	 blkline[spot] = saveac[7];
	 strncpy(blkline+spot+1, "<->", 3);
	 blkline[spot+4] = block->ac[7];
/*	 kr_itoa(block->offset[s], ctemp, 10);   */
	 /* offset starts at 1 in */
	 sprintf(ctemp, "%d", block->offset[s]);
	 strncpy(datline+spot, ctemp, strlen(ctemp));
/*	 kr_itoa(block->offset[block->nseq-1]+1, ctemp,10); */
         sprintf(ctemp, "%d", block->offset[block->nseq-1]+1);
	 strncpy(homline+spot, ctemp, strlen(ctemp));
         /* save location in case there are repeats */
         savspot = spot;
	 spot+=8;		/* offset + 1 */

	 bspot = spot;
	 strncpy(blkline+bspot, "(", 1); bspot++;
/*	 kr_itoa(datmin, ctemp, 10); */
	 sprintf(ctemp, "%d", datmin);
	 strncpy(blkline+bspot, ctemp, strlen(ctemp));
	 bspot += strlen(ctemp);
	 strncpy(blkline+bspot, ",", 1); bspot++;
/*	 kr_itoa(datmax, ctemp, 10); */
	 sprintf(ctemp, "%d", datmax);
	 strncpy(blkline+bspot, ctemp, strlen(ctemp));
	 bspot += strlen(ctemp);
	 strncpy(blkline+bspot, ")", 1); bspot++;
	 strncpy(blkline+bspot, ":", 1); bspot++;
/*	 kr_itoa(homdist, ctemp, 10); */
         sprintf(ctemp, "%d", homdist);
	 strncpy(blkline+bspot, ctemp, strlen(ctemp));
	 bspot += strlen(ctemp);

	 for (i=0; iwidth; i++)
         {
	    strncpy(datline+spot, block->aa[s]+i, 1);
	    strncpy(homline+spot, block->aa[block->nseq-1]+i, 1);
            if (strncmp(datline+spot, homline+spot, 1) == 0)
                barline[spot] = '|';
	    spot++;
         }
         /*-------  Block may be narrower than offset heading.. */
         if (spot < bspot) spot = bspot;

         /*   Now look for repeats & print them */
         first = YES;
         for (t=min_t; t< max_t; t++)
         {
            if ((results[t].map_flag == 3 || results[t].map_flag == 2) &&
                   strcmp(block->ac, results[t].ac) == 0)
            {
               if (first)  /* have to print out everything else first */
               {
	    homline[spot]= datline[spot]= blkline[spot]= barline[spot]= '\0';
	          printf("\n%s", blkline);
                  printf("\n%s", datline); printf("\n%s", barline);
	          printf("\n%s\n", homline);
                  for (i=0; iwidth;
               repline[repspot] = '\0';
               printf("%s\n", repline);
            }
         }     /*  end of for t */
	 datmin = datmax = 0;
	 homdist = block->offset[block->nseq-1] + block->width;
	 strcpy(saveac, block->ac);
      }
      else
      {		/*  block not in query sequence */
	 datmin += block->minprev + block->width;
	 datmax += block->maxprev + block->width;
      }
      block = block->next_block;
   }
   if (spot > 0)
   {
   homline[spot] = datline[spot] = blkline[spot] = barline[spot] = '\0';
   printf("\n%s", blkline);
   printf("\n%s", datline); printf("\n%s", barline);
   printf("\n%s\n", homline);
   }
}  /* end of align_blocks */
/*======================================================================*/
/*--- Just find the sequence closest to the last sequence in the block
      based on the number of identities */
/*======================================================================*/
int closest_seq(block)
struct best_block *block;
{
   int npair, s1, s2, l1, l2, i, i1, i2;
   int maxscore, maxs1;
   struct pair *pairs;
/*SGI   delete above declaration of pairs and use fixed below */
/*SGI   struct pair pairs[MAXSEQS*(MAXSEQS-1)/2];  */

   npair = block->nseq;
/*SGI  delete malloc() and free(pairs) and used fixed allocation */
   pairs = (struct pair *) malloc(npair * sizeof(struct pair));
   if (pairs == NULL)
   {
      printf("\ncluster_seqs: Unable to allocate pair structure!\n");
      exit(-1);
   }

/*    Compute scores for all possible pairs of sequences            */
   for (s1=0; s1nseq-1; s1++)   		/* col = 0, n-2     */
   {
      l1 = 0;
      s2 = block->nseq-1;   /* last seq in block == the query sequence */
      l2 = 0;
      pairs[s1].score = 0;
      pairs[s1].cluster = -1;
      for (i=0; i<=block->width; i++)
      {
	 i1 = l1+i;  i2 = l2+i;
	 /* s1 is the block seq & is all caps, but s2 is the query
	    seq & it may have lower case chars in it */
	 if (i1 >= 0 && i1 < block->width &&
	     i2 >= 0 && i2 < block->width &&
		strncasecmp(block->aa[s1]+i1, block->aa[s2]+i2, 1) == 0)
		   pairs[s1].score += 1;
      }
   }  /* end of s1 */
   maxs1 = -1; maxscore = -1;
   for (s1=0; s1 < block->nseq-1; s1++)
      if (pairs[s1].score > maxscore)
      {
	 maxscore = pairs[s1].score;
	 maxs1 = s1;
      }

/*SGI   delete free(pairs) and used fixed allocation  */
      free(pairs);
      return(maxs1);
}  /*  end of closest_seq */
/*======================================================================
    If the search was of a matrix database, the sequence segment will be
    all lower case. Change any residue that matches any sequence in the
    block to upper case. The block segments are all upper case.
========================================================================*/
void consensus(block)
struct best_block *block;
{
   int s, s1, i;
   char seqaa[2];

   s = block->nseq - 1;		/* This is the query sequence */
   for (s1=0; s1 < s; s1++)
      for (i=0; i < block->width; i++)
      {
         if (strncasecmp(block->aa[s]+i, block->aa[s1]+i, 1) == 0)
         {
            strncpy(seqaa, block->aa[s]+i, 1);
            if (seqaa[0] >= 97 && seqaa[0] <= 122)
            {
               seqaa[0] -= 32;
               strncpy(block->aa[s]+i, seqaa, 1);
            }
         }
      }

}  /* end of consensus */
/*======================================================================*/
/*  Sort by strand (sign of frame) and block name */
int strandcmp(t1, t2)
struct hom *t1, *t2;
{
   int strand1, strand2;

   strand1=strand2=1;
   if (t1->frame < 0) strand1=-1; if (t2->frame < 0) strand2=-1;
   if (strand1 != strand2)  return(strand1 - strand2);
   else return (strcmp(t1->ac, t2->ac));
}  /* end of strandcmp */
/*======================================================================*/
/*  Sort by frame and block name */
int framecmp(t1, t2)
struct hom *t1, *t2;
{
   if (t1->frame != t2->frame)  return(t1->frame - t2->frame);
   else return (strcmp(t1->ac, t2->ac));
}  /* end of framecmp */
/*======================================================================*/
/*   Sort by min_rank, strand (sign of frame), block name & rank */
int mincmp(t1, t2)
struct hom *t1, *t2;
{
   int strand1, strand2;

   strand1=strand2=1;
   if (t1->frame < 0) strand1=-1; if (t2->frame < 0) strand2=-1;
   if (t1->min_rank != t2->min_rank) return(t1->min_rank - t2->min_rank);
   else if (strand1 != strand2) return(strand1 - strand2);
   else if (strcmp(t1->ac, t2->ac) != 0) return(strcmp(t1->ac, t2->ac));
   else return(t1->rank - t2->rank);
}  /* end of mincmp */
/*========================================================================*/
/*  Sort temp structure by value field */
int tempcmp(t1, t2)
struct temp *t1, *t2;
{
   return(t1->value - t2->value);
}
/*========================================================================*/
/*  Sort sorttemp structure by ac, map_flag (D) and rank field */
int stempcmp(t1, t2)
struct sorttemp *t1, *t2;
{
   int diff;

   diff = strcmp(t1->ac, t2->ac);
   if (diff != 0 ) return(diff);
   else
   {
      diff = t2->map_flag - t1->map_flag;
      if (diff != 0) return(diff);
      else return(t1->rank - t2->rank);
   }
} /*  end of stempcmp */
/*========================================================================*/
/*  Sort sorttemp structure by ac and rank field */
int stempcmp2(t1, t2)
struct sorttemp *t1, *t2;
{
   int diff;

   diff = strcmp(t1->ac, t2->ac);
   if (diff != 0 ) return(diff);
   else return(t1->rank - t2->rank);
} /*  end of stempcmp2 */
/*=========================================================================*/
   /*  frame  1:1 => bp 1,     2:1 => 2,         3:1 => 3
           bp = frame + 3 * offset
       frame -1:1 => bp QLen, -2:1 => QLen - 1, -3:l => QLen - 2 
           bp = frame + (QLen + 1) - 3 * offset
   */
int compute_loc(frame, offset)
int frame;
int offset;
{
   int loc;

   loc = (offset - 1) * SeqType;
   if (frame < 0) loc = (QLen + 1) - loc;
   loc += frame;
   if (frame == 0) loc++;	/* Blimps frame = 0 for protein */
   return(loc);
}   /* end of compute_loc */
/*==========================================================================
      First entry in the list is not used
============================================================================*/
struct file_list *make_flist()
{
   struct file_list *new;

   new = (struct file_list *) malloc(sizeof(struct file_list));
   return(new);
}  /*   end of make_flist()   */
/*==========================================================================*/
void insert_flist(flist, new)
struct file_list *flist, *new;
{
   struct file_list *fcur;

   fcur = flist;
   while (fcur->next_flist != NULL)
      fcur = fcur->next_flist;
   fcur->next_flist = new;
}   /* end of insert_flist  */
pot]= bblimps-3.9/protomat/blosum.c000064400001460000012000001077451062461260300164760ustar00jorjastaff00000400000027/*=======================================================================
     BLOSUM: (C) Copyright 1992, Fred Hutchinson Cancer Research Center
    Program to compute "blosum" scoring matrix from blocks database.

	 blosum blocks.dat minstr maxstr cluster scale

	    blocks.dat = a blocks database
	    minstr = minimum strength of blocks to count (0-9999)
	    maxstr = maximum strength of blocks to count (0-9999)
	    cluster = re-clustering threshold (n or e or 0-100)
	      If "n", does not cluster sequences.
	      If "w", uses weights as found in blocks.
              If "pn", computes position-based weights and uses
                       1/n as the parameter.
	      If "e", uses clusters as found in blocks (clusters of
	      sequences are separated by a blank line). If 0-100,
	      clusters sequences based on that percentage of pair-
	      wise identities.
            scale = scale for matrix;
	 	0: Let program decide based on entropy
		n: 1/n bits

	 Count all pairwise substitutions in all blocks in blocks.dat
	 with strength between minstr and maxstr. Pairs are only counted
	 for sequences in different clusters.

      Output includes:
          Standard output - various reports, including raw frequencies.
          blosumx.qij file - target frequencies (odds ratios), x=clustering %
          blosumx.sij file - scoring matrix in bits
          blosumx.iij file - scoring matrix rounded to integers and scaled
                             according to relative entropy
--------------------------------------------------------------------------
 9/23/91  J. Henikoff
>>>>>>>>>>>>>>>>>>>> Blocks 5.0 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 9/18/92  Changed scaling to variable bit fractions as in NCBI pam.c.
	  Changed sij[][] from int to double.
	  Changed positive matrix to +minsij instead of +8.
 9/24/92  Added printout of floating point sij in bit units.
 9/26/92  Write .qij, .sij and .iij output files.
          Compute B, Z and X entries as weighted averages.
10/17/92  Added comments. Removed Risler routine.
12/1/92   Added B,Z,X columns to positive matrix.
1/14/93   Replaced MAXNSEQ with MAXSEQS from motifj.h.
1/18/93   Fixed problem with BZ value.
6/7/93    Added scale option. 
9/22/93   Added B, Z and X to .sij file
9/29/93   Fixed problem reading blocks db with sequence weights
>>>>>>>>>>>>>>>>>>>>>  Blocks 7.x <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
1/27/94   Added option to make a single matrix using sequence weights
4/18/94   Normalize existing sequence weights (divide by total).
4/20/94	  Changed count to be product of sequence weights.
4/23/94   Added option for position-based weight series.
4/27/94   Separated total pairs from total weight (FTotPairs, FTotWeight).
4/28/94   Modified position-based weight option.
5/ 2/94   For position-based weight, assume total column weight is 4.0
          instead of 1.0 to get a wider range of matrices.
7/26/94   Skip over tabs in blocks (fill_block)
>>>>>>>>>>>>>>>>>>>>> Blocks 8 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
8/29/94   Report average number of clusters per block, Block.nclus
8/31/94   Report weighted average of clusters per block, TotClump
==========================================================================*/

#include "motifj.h"

#define AAS 20
#define MINSTR 0		/* Min. strength to count */
#define MAXSTR 9999		/* Max. strength to count */
#define PBTOTAL 4.0		/* Total column weight for position-based*/

/*---------------------Functions----------------------------------*/
int read_dat();
void fill_block();
void count_block();
void count_weight();
void count_cluster();
void count_position();
void cluster_seqs();
/*---------------------Functions in motmisc.o ----------------------*/
int aachar_to_num();
char *num_to_aachar();

struct block {				/* Block structure */
   char ac[10];
   int nseq, width, strength, nclus;
   int aa[MAXSEQS][MAX_MERGE_WIDTH];	/* aas for seq */
   double weight[MAXSEQS];		/* seq weights found in block */
   int cluster[MAXSEQS];		/* cluster # for seq */
   int ncluster[MAXSEQS];		/* #seqs in same cluster */
   double totdiag, totoffd, wtot;
} Block;

double Counts[AAS][AAS];
unsigned long TotPairs, TotSeqs, TotAas, TotWidth;
double FTotPairs, FTotWeight;
unsigned long TotBlk;			/* # blocks contributing to matrix */
double TotClump;			/* # clumps contributing to matrix */
unsigned long TotSeg;			/* # seqs contributing to matrix */
unsigned long AaPairs[AAS];			/*  Pairs for an AA */
double FAaPairs[AAS], PBParameter;
unsigned long AaFreq[AAS];			/* AA frequency */
int MinStr, MaxStr, Cluster;

/*=====================================================================*/
int main(argc, argv)
int argc;
char *argv[];
{
   FILE *fdat, *fout;
   char datfile[FNAMELEN], outfile[FNAMELEN], ctemp[6];
   unsigned long totaas;
   int totblk, row, col, tij[AAS][AAS], maxsij, minsij, sumsij;
   int iscale, is, itemp;
   double sij[AAS+3][AAS+3], totpairs, totdiag, totoffd;
   double dtemp, dtemp1, dtemp2, x, xx;
   double ftotpairs, ftotdiag, ftotoffd;
   double s, fij, fifj, oij, entropy, expected;
   double sumpi, sumqij;

   printf("BLOSUM: (C) Copyright 1992, Fred Hutchinson Cancer");
   printf(" Research Center\n");
 
   /*------------Arg 1, blocks database name ----------------*/
   if (argc > 1) strcpy(datfile, argv[1]);
   else
   {
      printf("Enter name of blocks database:\n");
      gets(datfile);
   }
   if ( (fdat=fopen(datfile, "r")) == NULL)
   {
      printf("Cannot open %s\n", datfile);
      exit(-1);
   }
   else printf("Reading %s\n", datfile);
   /*----------Arg 2, minimum block strength----------------------*/
   if (argc > 2)      MinStr = atoi(argv[2]);
   else
   {
      MinStr = MINSTR;
      printf("Enter minimum block strength [%d]: ", MinStr);
      gets(ctemp);
      if (strlen(ctemp)) MinStr = atoi(ctemp);
   }
   /*-----------Arg 3, Maximum block strength----------------------*/
   if (argc > 3)      MaxStr = atoi(argv[3]);
   else
   {
      MaxStr = MAXSTR;
      printf("Enter maximum block strength [%d]: ", MaxStr);
      gets(ctemp);
      if (strlen(ctemp)) MaxStr = atoi(ctemp);
   }
   printf("Minimum block strength=%d, Maximum block strength=%d\n",
       MinStr, MaxStr);

   /*----------Arg 4, Clustering ------------------------------------*/
   Cluster = -1;		/*  No clustering */
   if (argc > 4)      strcpy(ctemp, argv[4]);
   else
   {
      printf("Enter n for no clustering\n");
  printf("   or a number between 0 and 100 for percent identity clustering\n");
      printf("   or e for existing (implied) clusters\n");
      printf("   or w for existing sequence weights\n");
      printf("   or pn for position-based weights, PB weight = 1/n\n");
      printf("Enter clustering identity percentage or n/e/w/pn [e]: ");
      gets(ctemp);
   }
   /*  e => -1, n=> -2, w=> -3 p=> -4 */
   Cluster = -1;
   if (strlen(ctemp))
   {
      if (ctemp[0] == 'n' || ctemp[0] == 'N') {   Cluster=-2;  }
      else
      {
           if (ctemp[0] == 'w' || ctemp[0] == 'W') { Cluster=-3;  }
           else
           {
                if (ctemp[0] == 'p' || ctemp[0] == 'P')
                {
                    Cluster = -4;
                    itemp = atoi(ctemp+1);
                    if (itemp > 0) { PBParameter = sqrt((double) 1.0 / itemp);}
                    else           { PBParameter = 1.0;}
                }
                else
                {
                   if (ctemp[0] != 'e' && ctemp[0] != 'E')
	           { Cluster = atoi(ctemp);   }
                }
           }
      }
   }
   if (Cluster > 100) Cluster = -1;
   if (Cluster == -1) printf("Existing clustering will be used\n");
   else if (Cluster == -2) printf("No clustering will be used\n");
   else if (Cluster == -3) printf("Sequence weights will be used\n");
   else if (Cluster == -4)
        { printf("Position-based weights will be used");
          printf(" with parameter = %.2f\n", PBParameter);
        }
   else printf("Re-clustering percentage = %d\n", Cluster);

   /*-----------Arg 5, Scale --------------------------------------*/
   if (argc > 5)      iscale = atoi(argv[5]);
   else
   {
      iscale = 0;     
      printf("Enter scale n for 1/n bits [%d]: ", iscale);
      gets(ctemp);
      if (strlen(ctemp)) iscale = atoi(ctemp);
   }
   if (iscale < 0) iscale = 0;
   if (iscale > 100) iscale = 100;
   if (iscale == 0) printf ("Scale based on relative entropy\n");
   else printf("Requested scale = 1/%d bits\n", iscale);

   /*----------------Initialize--------------------------------------*/
   TotPairs = TotSeqs = TotWidth = TotAas = (unsigned long) 0;
   TotBlk = TotSeg = (unsigned long) 0;
   TotClump = FTotPairs = FTotWeight = 0.0;
   sumsij = 0; minsij = 999; maxsij = -999;
   for (row=0; row= 0)
   {
      printf(" %f clumps contributed pairs to matrix (%f)\n",
           TotClump, TotClump/FTotWeight);
      printf(" %ld segments contributed pairs to matrix (%f)\n",
           TotSeg, (float) TotSeg/TotBlk);
   }
   printf("%f total pairs, %f total weight\n", FTotPairs, FTotWeight);
   printf(" %ld total sequences, ", TotSeqs);
   printf("%ld total columns, ", TotWidth);
   printf("%ld total AAs\n\n", TotAas);

/*-------------------The frequency matrix ------------------------------*/
   printf("Frequencies = fij pairs (off-diagonals = 2*fij):\n");
   for (col=0; col= 0)
      sprintf(outfile, "blosum%d.qij", Cluster);
   else if (Cluster == -4)
      sprintf(outfile, "blosump%d.qij", (int) (1. / PBParameter));
   else if (Cluster == -3)
      sprintf(outfile, "blosumw.qij");
   else if (Cluster == -2)
      sprintf(outfile, "blosumn.qij");
   else if (Cluster == -1)
      sprintf(outfile, "blosume.qij");
   if ((fout=fopen(outfile, "wt"))==NULL) fout = stdout;
   printf("\nTarget Probabilities=qij in %s\n", outfile);
   fprintf(fout, "#  BLOSUM Clustered Target Frequencies=qij\n");
   fprintf(fout, "#  Blocks Database = %s\n", datfile);
   if (Cluster >= 0)
      fprintf(fout, "#  Cluster Percentage: >= %d\n", Cluster);
   else if (Cluster == -4)
      fprintf(fout, "#  Position-based Clustering Parameter: <= %.4f\n",
              PBParameter);
   else if (Cluster == -3)
      fprintf(fout, "#  Explicit Sequence Weights Used\n");
   else if (Cluster == -2)
      fprintf(fout, "#  No Sequence Clustering Used\n");
   else if (Cluster == -1)
      fprintf(fout, "#  Existing Clusters Used\n");
   for (col=0; col 0.000000001) oij = ftotpairs * fij / fifj;
	 else oij = 0.0;
	 /*--- Log odds ratio ----*/
	 if (oij > 0.000000001) s = log( (double) oij);
	 else s = -20.0;    		/* minus infinity */
	 /*--- Round off for the log base 10 matrix ----*/
	 dtemp = 10.0 * s / log (10.0);	/*-- log base 10 */
         tij[row][col] = round(dtemp);
	 /*--- Log base 2 (bit) matrix ---*/
	 s /= log (2.0);		/* log base 2 = bits */
	 /*--- compute entropy & expected value in bits */
	 if (row==col)
         {
	     entropy += (double) s * fij / ftotpairs;
	     expected += (double) s * fifj / (ftotpairs*ftotpairs);
         }
         else
         {
	     entropy += (double) 2.0 * s * fij  / ftotpairs;
	     expected += (double) 2.0 * s * fifj / (ftotpairs*ftotpairs);
         }
	 sij[row][col] = s;
      }
   }
   printf("\nEntropy=%.4f bits, expected=%.4f bits\n", entropy, expected);

/*----------------Fill in symmetric part of matrix----------------*/
   for (row=0; row= 0)
      sprintf(outfile, "blosum%d.sij", Cluster);
   else if (Cluster == -4)
      sprintf(outfile, "blosump%d.sij", (int) (1. / PBParameter));
   else if (Cluster == -3)
      sprintf(outfile, "blosumw.sij");
   else if (Cluster == -2)
      sprintf(outfile, "blosumn.sij");
   else if (Cluster == -1)
      sprintf(outfile, "blosume.sij");
   if ((fout=fopen(outfile, "wt"))==NULL) fout = stdout;
   printf("\nScoring matrix in bit units=sij in %s\n", outfile);
   fprintf(fout, "#  BLOSUM Clustered Scoring Matrix in Bit Units=sij\n");
   fprintf(fout, "#  Blocks Database = %s\n", datfile);
   if (Cluster >= 0)
      fprintf(fout, "#  Cluster Percentage: >= %d\n", Cluster);
   else if (Cluster == -4)
      fprintf(fout, "#  Position-based Clustering Parameter: <= %.4f\n",
              PBParameter);
   else if (Cluster == -3)
      fprintf(fout, "#  Explicit Sequence Weights Used\n");
   else if (Cluster == -2)
      fprintf(fout, "#  No Sequence Clustering Used\n");
   else if (Cluster == -1)
      fprintf(fout, "#  Existing Clusters Used\n");
   fprintf(fout, "#  Entropy = % 8.4f, Expected = % 8.4f\n",
        entropy, expected);
   for (col=0; col= 0)
      sprintf(outfile, "blosum%d.iij", Cluster);
   else if (Cluster == -4)
      sprintf(outfile, "blosump%d.iij", (int) (1. / PBParameter));
   else if (Cluster == -3)
      sprintf(outfile, "blosumw.iij");
   else if (Cluster == -2)
      sprintf(outfile, "blosumn.iij");
   else if (Cluster == -1)
      sprintf(outfile, "blosume.iij");
   if ((fout=fopen(outfile, "wt"))==NULL) fout = stdout;
   printf("\nInteger scoring matrix in 1/%d bit units in %s\n",
           iscale, outfile);
   fprintf(fout, "#  BLOSUM Clustered Scoring Matrix in 1/%d Bit Units\n",
           iscale);
   fprintf(fout, "#  Blocks Database = %s\n", datfile);
   if (Cluster >= 0)
      fprintf(fout, "#  Cluster Percentage: >= %d\n", Cluster);
   else if (Cluster == -4)
      fprintf(fout, "#  Position-based Clustering Parameter: <= %.4f\n",
              PBParameter);
   else if (Cluster == -3)
      fprintf(fout, "#  Explicit Sequence Weights Used\n");
   else if (Cluster == -2)
      fprintf(fout, "#  No Sequence Clustering Used\n");
   else if (Cluster == -1)
      fprintf(fout, "#  Existing Clusters Used\n");
   fprintf(fout, "#  Entropy = % 8.4f, Expected = % 8.4f\n",
         entropy, expected);
   for (col=0; col maxsij) maxsij = is;
      }
      fprintf(fout, "\n");
   }
   fclose(fout);
/*   for (col=0; col= MinStr && Block.strength <= MaxStr)
	 {
	     fill_block(fdat);
	     if (Cluster >= 0) cluster_seqs();    /*  re-cluster sequences */
	     if (Cluster == -2) count_block();     /* no clustering */
             else if (Cluster == -3) count_weight(); 
                  else if (Cluster == -4) count_position();
	               else count_cluster();		  /* clustering */
	     totblk++;
	 }
      }
   }

   return(totblk);
}  /* end of read_dat */
/*====================================================================
     Fill up the block structure
=======================================================================*/
void fill_block(fdat)
FILE *fdat;
{
   int done, i, li, n, cluster, ncluster;
   char line[MAXLINE], *ptr;

   Block.nseq = Block.width = 0;
   Block.totdiag = Block.totoffd = Block.wtot = (double) 0;
   cluster = ncluster = 0;
   done=NO;
   while (!done && !feof(fdat) && fgets(line,MAXLINE,fdat) != NULL)
   {
      if (strlen(line) == 1)		/* blank line => new cluster */
      {
	 /*  Set #seqs in cluster to seqs in previous cluster */
	 if (ncluster > 0)
	   for (n=0; n 1)
      {
	 if (strncmp(line, "//", 2) == 0) done=YES;
	 else if (strlen(line) > 20)
	 {
	    li=0;		/* skip over sequence name & offset */
            while (line[li] != ')') li++;
            li++;
	    while (line[li] == ' ') li++;  /* skip over spaces */
		/* assuming no spaces within block ! */
	    ptr=strtok(line+li, " \r\n\t");
	    for (i=0; i= 0 &&
		   Block.aa[Block.nseq][i] < AAS)
	       {
		  AaFreq[Block.aa[Block.nseq][i]]++;
		  TotAas++;
	       }
/*	       else
	       {
		  printf("\nBad char: %s %c", Block.ac, ptr[i]);
	       }
*/
	    }
            li += strlen(ptr);
            ptr = strtok(NULL, " \r\n\t");
            if (ptr != NULL)
            {
               Block.weight[Block.nseq] = atof(ptr);
               Block.wtot += Block.weight[Block.nseq];
            }
            else
               Block.weight[Block.nseq] = 0;
	    Block.cluster[Block.nseq] = cluster;
	    ncluster++;		/* # seqs in current cluster */
	    Block.width = i;
	    Block.nseq++;
	 }
      }
   }
   /*  Compute weights for the last cluster */
   if (ncluster > 0)
	   for (n=0; n=0 && Block.aa[seq1][col] < AAS &&
		Block.aa[seq2][col] >=0 && Block.aa[seq2][col] < AAS)
	    {
		  Counts[Block.aa[seq1][col]][Block.aa[seq2][col]] += 1.0;
		  FTotPairs += 1.0;
		  FTotWeight += 1.0;
		  if (Block.aa[seq1][col] ==
		      Block.aa[seq2][col])
			 Block.totdiag += 1.0;
		  else   Block.totoffd += 1.0;
	    }
/*   Output for SPSS job to count pairs by strength  */
     TotBlk++;
/*   printf("%s %9.2f %9.2f %9.2f %d\n",
	Block.ac, Block.totdiag, Block.totoffd, 
        Block.totoffd+Block.totdiag, Block.strength);
*/

}  /* end of count_block */
/*===================================================================*/
void count_position()
{
   int seq1, seq2, col, aa;
   double weight, pb[AAS], diffaas, naas[AAS];

/*printf("\n%s nseq=%d width=%d\n", Block.ac, Block.nseq, Block.width);*/
   for (col=0; col < Block.width; col++)
   {
      /*   compute the position-based weight & clump for each aa in col */
      diffaas = 0;
      for (aa=0; aa < AAS; aa++)
      {  naas[aa] = pb[aa] = 0.0; }

      /*  count how many of each AA in the column */
      for (seq1=0; seq1 < Block.nseq; seq1++)
         if (Block.aa[seq1][col] >=0 && Block.aa[seq1][col] < AAS)
         {
              naas[ Block.aa[seq1][col] ] += 1;
              Block.cluster[seq1] = seq1;	/* initial values */
              Block.ncluster[seq1] = 1;
         }

      /*   number of different types of AAs in col */
      for (aa = 0; aa < AAS; aa++)
         if (naas[aa] > 0.0) diffaas++;

      /*   now compute the position-based weight for each AA */
      for (aa = 0; aa < AAS; aa++)
         if (diffaas > 0.0 && naas[aa] > 0.0)
         {
            pb[aa] = sqrt(1.0 /(diffaas * naas[aa]));
/*printf("%.4f ", pb[aa]);*/
            /*   clump rows now by assigning same cluster */
            /*   now the cluster number is the sequence number, so
                 assign a cluster number always larger than that */
            if (pb[aa] < PBParameter )
               for (seq1=0; seq1 < Block.nseq; seq1++)
	          if (Block.aa[seq1][col] == aa)
                  {
                     Block.cluster[seq1] = MAXSEQS + aa;
                     Block.ncluster[seq1] = naas[aa];
                  }
         }
/*printf("\n");*/

      /*-------------------count between column clumps now ----------*/
      for (seq1=0; seq1 < Block.nseq; seq1++)
	 for (seq2=seq1+1; seq2 < Block.nseq; seq2++)
	    if (Block.aa[seq1][col] >=0 && Block.aa[seq1][col] < AAS &&
		Block.aa[seq2][col] >=0 && Block.aa[seq2][col] < AAS &&
                Block.cluster[seq1] != Block.cluster[seq2]) 
	    {
		  weight = (double) 1.0 / Block.ncluster[seq2];
		  weight *= (double) 1.0 / Block.ncluster[seq1];
		  Counts[Block.aa[seq1][col]][Block.aa[seq2][col]] +=
		       weight;
		  FTotPairs += 1.0;
		  FTotWeight += weight;
		  if (Block.aa[seq1][col] ==  Block.aa[seq2][col])
			 Block.totdiag += weight;
		  else   Block.totoffd += weight;
	    }
   }   /*  end of col */

/*  SPSS */
   if (Block.totoffd > 0.0 || Block.totdiag > 0.0)
   {
      TotBlk++;
/*    printf("%s %9.2f %9.2f %9.2f %d\n", Block.ac,
	   Block.totdiag,  Block.totoffd,
           Block.totdiag+Block.totoffd, Block.strength);
*/
   }
}  /* end of count_position */
/*===================================================================*/
void count_weight()
{
   int seq1, seq2, col;
   double weight;

   for (col=0; col < Block.width; col++)
      for (seq1=0; seq1 < Block.nseq; seq1++)
	 for (seq2=seq1+1; seq2 < Block.nseq; seq2++)
	    if (Block.aa[seq1][col] >=0 && Block.aa[seq1][col] < AAS &&
		Block.aa[seq2][col] >=0 && Block.aa[seq2][col] < AAS)
	    {
		  weight = Block.nseq * Block.weight[seq2] / Block.wtot;
		  weight *= Block.nseq * Block.weight[seq1] / Block.wtot;
		  Counts[Block.aa[seq1][col]][Block.aa[seq2][col]] +=
		       weight;
		  FTotPairs += 1.0;
		  FTotWeight += weight;
		  if (Block.aa[seq1][col] ==  Block.aa[seq2][col])
			 Block.totdiag += weight;
		  else   Block.totoffd += weight;
	    }
/*  SPSS */
   if (Block.totoffd > 0.0 || Block.totdiag > 0.0)
   {
      TotBlk++;
/*      printf("%s %9.2f %9.2f %9.2f %d\n", Block.ac,
	   Block.totdiag,  Block.totoffd,
           Block.totdiag+Block.totoffd, Block.strength);
*/
   }
}  /* end of count_weight */
/*===================================================================*/
void count_cluster()
{
   int seq1, seq2, col;
   double weight;

   for (col=0; col < Block.width; col++)
      for (seq1=0; seq1 < Block.nseq; seq1++)
	 for (seq2=seq1+1; seq2 < Block.nseq; seq2++)
	    if (Block.aa[seq1][col] >=0 && Block.aa[seq1][col] < AAS &&
		Block.aa[seq2][col] >=0 && Block.aa[seq2][col] < AAS &&
		Block.cluster[seq1] != Block.cluster[seq2])
	    {
		  weight = (double) 1.0 / Block.ncluster[seq2];
		  weight *= (double) 1.0 / Block.ncluster[seq1];

		  Counts[Block.aa[seq1][col]][Block.aa[seq2][col]] +=
		       weight;
		  FTotPairs += 1.0;
		  FTotWeight += weight;
		  if (Block.aa[seq1][col] ==  Block.aa[seq2][col])
			 Block.totdiag += weight;
		  else   Block.totoffd += weight;
	    }
/*  SPSS */
   if (Block.totoffd > 0.0 || Block.totdiag > 0.0)
   {
      TotBlk++;
      TotClump += (Block.totdiag + Block.totoffd) * Block.nclus;
      TotSeg += Block.nseq;
/*      printf("%s %9.2f %9.2f %9.2f %d\n", Block.ac,
	   Block.totdiag,  Block.totoffd,
           Block.totdiag+Block.totoffd, Block.strength);
*/
   }
}  /* end of count_cluster */
/*======================================================================*/
/*    Cluster sequences in a block based on the number of               */
/*    identities within the block. Sets Block.cluster & Block.ncluster  */
/*    Sets Block.nclus = total number of clusters                       */
/*      1. Compute number of identities for each possible pair of seqs. */
/*         Results stored in lower half of matrix (pairs).              */
/*      2. Use clustering threshold % of # of AAs in trimmed block.     */
/*      3. Cluster recursively by traversing cols, rows of matrix.      */
/*UNIX NOTE:  Program aborts when running under UNIX at free(pairs),
   so use the fixed size declaration pairs & remove the malloc() &
   free() calls when compiling for UNIX                                 */
/*======================================================================*/
void cluster_seqs()
{
   int clus, npair, threshold, s1, s2, l1, l2, px, i, i1, i2;
   int nclus[MAXSEQS], minclus, oldclus;
   struct pair *pairs;
/*UNIX   struct pair pairs[MAXSEQS*(MAXSEQS-1)/2];  */

   npair = Block.nseq*(Block.nseq-1)/2;
   pairs = (struct pair *) malloc (npair * sizeof(struct pair));
   if (pairs == NULL)
   {
      printf("\ncluster_seqs: Unable to allocate pair structure!\n");
      exit(-1);
   }
   threshold = (int) (Cluster*(Block.width))/100;

/*    Compute scores for all possible pairs of sequences            */
   for (s1=0; s1= 0 && i1 < Block.width &&
		i2 >= 0 && i2 < Block.width &&
		Block.aa[s1][i1] == Block.aa[s2][i2])
		   pairs[px].score += 1;
	 }
      }  /* end of s2 */
   }  /* end of s1 */

/*  Print scores */
/*   printf("\nThreshold=%d", threshold);
   for (s2=1; s2= threshold)	/*  cluster this pair */
	 {
	    if (Block.cluster[s1] < 0)          /* s1 not yet clustered */
	    {
	       if (Block.cluster[s2] < 0)       /* new cluster */
	       {
		  Block.cluster[s1] = clus++;
		  Block.cluster[s2] = Block.cluster[s1];
	       }
	       else  				/* use s2's cluster  */
		  Block.cluster[s1] =  Block.cluster[s2];
	    }
	    /*  use s1's cluster if it has one and s2 doesn't */
	    else if (Block.cluster[s1] >= 0 && Block.cluster[s2] < 0)
	       Block.cluster[s2] = Block.cluster[s1];
	    /* merge the two clusters into the lower number */
	    else if (Block.cluster[s1] >= 0 && Block.cluster[s2] >= 0)
	    {
	       minclus = Block.cluster[s1]; oldclus = Block.cluster[s2];
	       if (Block.cluster[s2] < Block.cluster[s1])
	       {
		  minclus = Block.cluster[s2]; oldclus = Block.cluster[s1];
	       }
	       for (i1=0; i1= 0)  nclus[Block.cluster[s1]]++;
   for (s1=0; s1start = ID   name; BLOCK.
		  AC   Block accession #
	->desc  = DE   description.
		  BL   block info.
		  sequences
	->end   = //                                                   */
/*---------------------------------------------------------------------*/
/*    8/5/92   J. Henikoff                                             */
/*    2/26/96  Looks for cobbler.pros sequence in blocks dir           */
/*    5/29/96  Looks for proweb.dat in blocks dir                      */
/*    5/30/96  Fix problem in get_cob() with lower case                */
/*    7/12/96  Fixed problem recognizing PDOC lines (PDOC00199)
      7/15/96  Modified proweb.dat format
      9/ 4/96  Added Version, read trees.dat
     11/ 6/96  Fixed bug in get_doc()
      3/ 6/97  Changes for Prints, separate args for each file
      7/31/97  Added map structures file
      5/ 8/98  Added blk2pdb.dat
      7/ 8/98  Added blinks.dat; links from individual blocks to ProDom
      9/ 7/98  Fixed problem finding prosite files
      7/ 1/99  Maps can start with ">" or "#MAP# "
     12/17/99  Longer AC; replaced get_cob() & get_tree() with get_fasta()
      5/20/00  Change IPR prefix to IPB and PS to BL (BlockFam)
      2/21/01  Added cyrca.dat  <<<<>>>
     10/ 4/02  Special fixes for Chrom entries
=======================================================================*/
#include "motifj.h"

/*		Routines from motmisc.c           */
void init_dbs();
int type_dbs();
struct split_name *split_names();

int get_blk();
void get_map();
void get_fasta();
void get_proweb();
void get_blinks();
void get_pdb();
void get_cyrca();
void get_prosite();
void get_doc();

char Version[12] = "  5/20/00.1";
char BlockFam[15];
/*======================================================================*/
int main(argc, argv)
int argc;
char *argv[];
{
   FILE *fblk, *fcob, *fweb, *flnk, *fmap, *ftre, *fdat, *fpdb, *fcyr, *fdoc;
   char blkfile[FNAMELEN], defname[FNAMELEN], cobfile[FNAMELEN];
   char prosite[FNAMELEN], webfile[FNAMELEN], mapfile[FNAMELEN];
   char treefile[FNAMELEN], pdbfile[FNAMELEN], lnkfile[FNAMELEN];
   char cyrfile[FNAMELEN];
   struct db_info *dbs[MAXDB];
   struct split_name *blksplit;
   int plen, done;

   if (argc < 3)
   {
      printf("GETBLOCK: (C) Copyright 1992-1999, ");
      printf("Fred Hutchinson Cancer Research Center\n");
      printf("Version %s\n", Version);
      printf("USAGE:  getblock AC blocks cobb maps trees proweb blinks blk2pdb cyrca ");
      printf("[prosite_dir]\n");
      printf("		AC = block accession (eg BL00094 or IPB001525)\n");
      printf("		blocks = name of blocks database file\n");
      printf("		cobb = name of cobbler database file\n");
      printf("		maps = name of map structure database file\n");
      printf("		trees = name of tree structure database file\n");
      printf("		proweb = name of Proweb database file\n");
      printf("		blinks = name of file of links to ProDom\n");
      printf("		blk2pdb = name of PDB cross-reference file\n");
      printf("		cyrca = name of CYRCA cross-reference file\n");
      printf("		prosite_dir = name of directory containing ");
      printf("prosite.dat and prosite.doc files\n");
   }
  
/*--------------------- Load DB format information ---------------------*/
   init_dbs(dbs);

/*------------------- arg 1:  Accession # ------------------------------*/
   if (argc > 1)
      strcpy(BlockFam, argv[1]);
   else
   {
      while(strlen(BlockFam) < MINAC)
      {
	 printf("\nEnter Block accession number: ");
	 gets(BlockFam);
      }
   }
   /*   Chop off any A-Z block designator at the end */
   /*   Can't do this for ChromDMT, etc  have to just truncate it  */
   plen = strlen(BlockFam);
   if (strncmp(BlockFam, "Chrom", 5) != 0)
   {
      done = NO;
      while (!done && plen >= MINAC)
      {
         if (isalpha(BlockFam[plen])) { BlockFam[plen] = '\0'; done = YES; }
         else { plen--; }
      }
   }
   else if (plen > 8)
   {  BlockFam[8] = '\0'; }
   /*  Change PS to BL and IPR to IPB  */
   if (toupper(BlockFam[0]) == 'P' && toupper(BlockFam[1]) == 'S')
   {   BlockFam[0] = 'B'; BlockFam[1] = 'L';     }
   else
   {
      if (toupper(BlockFam[0]) == 'I' && toupper(BlockFam[1]) == 'P' &&
          toupper( BlockFam[2]) == 'R')
      {   BlockFam[2] = 'B';  }
   }


/*------------------arg 2: blocks database name ----------------------*/
   if (argc > 2)
      strcpy(blkfile, argv[2]);
   else
   {
      strcpy(defname, "/howard/btest/bin/blocks.dat");
      printf("\nEnter name of Blocks database file [%s]:\n", defname);
      gets(blkfile);
      if (!strlen(blkfile))
	 strcpy(blkfile, defname);
   }
   if ( (fblk=fopen(blkfile, "r")) == NULL)
      printf("\nCannot open blocks database %s\n", blkfile);
   else
   {
      printf("\n%d blocks processed\n", get_blk(dbs, fblk) );
      fclose(fblk);
   }
   blksplit = split_names(blkfile);

   /*------------------arg 3: Cobbler file name ----------------------*/
   fcob = NULL;
   if (argc > 3)
      strcpy(cobfile, argv[3]);
   else
   {
      /*  Look for file "cobbler.pros" in the blocks db directory  */
      cobfile[0] = '\0';
      strncat(cobfile, blkfile, blksplit->dir_len);
      cobfile[blksplit->dir_len] = '\0';
      strcat(cobfile, "cobbler.pros");
   }
   if ( (fcob = fopen(cobfile, "r")) != NULL)
   {
      printf("\nCOBBLER sequence:\n");
      get_fasta(fcob);
      fclose(fcob);
   }
   printf("end cobbler\n");

   /*------------------arg 4: map file name ----------------------*/
   fmap = NULL;
   if (argc > 4)
      strcpy(mapfile, argv[4]);
   else
   {
      /*  Look for file "maps.dat" in the blocks db directory  */
      mapfile[0] = '\0';
      strncat(mapfile, blkfile, blksplit->dir_len);
      mapfile[blksplit->dir_len] = '\0';
      strcat(mapfile, "maps.dat");
   }
   if( (fmap = fopen(mapfile, "r")) != NULL)
   {
      get_map(fmap);
      fclose(fmap);
   }
   printf("end map\n");

   /*------------------arg 5: tree file name ----------------------*/
   ftre = NULL;
   if (argc > 5)
      strcpy(treefile, argv[5]);
   else
   {
      /*  Look for file "trees.dat" in the blocks db directory  */
      treefile[0] = '\0';
      strncat(treefile, blkfile, blksplit->dir_len);
      treefile[blksplit->dir_len] = '\0';
      strcat(treefile, "trees.dat");
   }
   if( (ftre = fopen(treefile, "r")) != NULL)
   {
      get_fasta(ftre);
      fclose(ftre);
   }
   printf("end tree\n");

   /*------------------arg 6: proweb file name ----------------------*/
   fweb = NULL;
   if (argc > 6)
      strcpy(webfile, argv[6]);
   else
   {
      /*  Look for file "proweb.dat" in the blocks db directory  */
      webfile[0] = '\0';
      strncat(webfile, blkfile, blksplit->dir_len);
      webfile[blksplit->dir_len] = '\0';
      strcat(webfile, "proweb.dat");
   }
   if ( (fweb = fopen(webfile, "r")) != NULL)
   {
      get_proweb(fweb);
      fclose(fweb);
   }
   printf("end proweb\n");

   /*------------------arg 7: blinks file name ----------------------*/
   flnk = NULL;
   if (argc > 7)
      strcpy(lnkfile, argv[7]);
   else
   {
      /*  Look for file "blinks.dat" in the blocks db directory  */
      lnkfile[0] = '\0';
      strncat(lnkfile, blkfile, blksplit->dir_len);
      lnkfile[blksplit->dir_len] = '\0';
      strcat(lnkfile, "blinks.dat");
   }
   if ( (flnk = fopen(lnkfile, "r")) != NULL)
   {
      get_blinks(flnk);
      fclose(flnk);
   }
   printf("end blinks\n");

   /*------------------arg 8: blk2pdb file name ----------------------*/
   fpdb = NULL;
   if (argc > 8)
      strcpy(pdbfile, argv[8]);
   else
   {
      /*  Look for file "trees.dat" in the blocks db directory  */
      pdbfile[0] = '\0';
      strncat(pdbfile, blkfile, blksplit->dir_len);
      pdbfile[blksplit->dir_len] = '\0';
      strcat(pdbfile, "blk2pdb.dat");
   }
   if( (fpdb = fopen(pdbfile, "r")) != NULL)
   {
      get_pdb(fpdb);
      fclose(fpdb);
   }
   printf("end pdb\n");

   /*------------------arg 9: cyrca file name ----------------------*/
   fcyr = NULL;
   if (argc > 9)
      strcpy(cyrfile, argv[9]);
   else
   {
      /*  Look for file "trees.dat" in the blocks db directory  */
      cyrfile[0] = '\0';
      strncat(cyrfile, blkfile, blksplit->dir_len);
      cyrfile[blksplit->dir_len] = '\0';
      strcat(cyrfile, "cyrca.dat");
   }
   if( (fcyr = fopen(cyrfile, "r")) != NULL)
   {
      get_cyrca(fcyr);
      fclose(fcyr);
   }
   printf("end cyrca\n");

   /*------------------arg 10: Prosite directory name --------------------*/
   fdat = fdoc = NULL;
   prosite[0] = '\0';
   if (argc > 10)
      strcpy(prosite, argv[10]);
/*
   else
   {
      strcpy(defname, "/howard/btest/bin/");
      printf("\nEnter Prosite directory [%s]:\n", defname);
      gets(prosite);
      if (!strlen(prosite))
	 strcpy(prosite, defname);
   }
*/
   if (strlen(prosite))
   {
      if (prosite[strlen(prosite)-1] != '/') strcat(prosite, "/");
      strcat(prosite, "prosite"); plen = strlen(prosite);
      strcat(prosite,".dat");
      if ( (fdat=fopen(prosite, "r")) == NULL)
         printf("\nCannot open prosite.dat file %s\n", prosite);
      else
      {
         prosite[plen] = '\0';
         strcat(prosite, ".doc");
         if ( (fdoc=fopen(prosite, "r")) == NULL)
            printf("\nCannot open prosite.doc file %s\n", prosite);
         printf("\n");
         get_prosite(dbs, fdat, fdoc);
         fclose(fdat);
         if (fdoc != NULL) fclose(fdoc);
      }
   }

/*--------------------------------------------------------------------*/
   printf("\n");
   exit(0);
}  /*  end of main */

/*======================================================================*/
int get_blk(dbs, fblk)
struct db_info *dbs[];
FILE *fblk;
{
   int i, nblk, db, goodpat, done, acdone, found;
   char line[MAXLINE], id[MAXLINE], fam[MAXLINE], ctemp[MAXLINE], *ptr;

   nblk = 0;
   acdone = done = found = NO;
   line[0] = '\0';
   db = type_dbs(fblk, dbs);

   if (db >= 0 && db < MAXDB)
   {
      do
      {
	 if (strncmp(line, dbs[db]->start, strlen(dbs[db]->start)) == 0)
	 {
	    fam[0] = '\0';  goodpat = NO;
	    strcpy(id, line);   /*  save this line */
	    if (fgets(line, MAXLINE, fblk) != NULL &&
		   strncmp(line, "AC   ", 5) == 0)
	    {
		strcpy(ctemp, &line[dbs[db]->title_offset]);
                ptr = strtok(ctemp, "; \n\r\t");
                if (ptr != NULL) strcpy(fam, ptr);
                i = strlen(fam); acdone = NO;
		/*   Strip off the block number to get family name */
                if (strncmp(BlockFam, "Chrom", 5) != 0)
                {
                   while(!acdone && i >= MINAC)
                   {
                      if (isalpha(fam[i])) {fam[i] = '\0'; acdone = YES; }
                      else {i--;}
                   }
                }
                else  /* just truncate Chrom entries */
                {  fam[8] = '\0';  }
/*printf("BlockFam=%s, fam=%s\n", BlockFam, fam); */
		if ( (strcasecmp(BlockFam, fam)) == 0 )
		{
		     goodpat = found = YES; nblk++;
		     printf("%s", id);      /* ID */
		     printf("%s", line);    /* AC */
		}
                else if (found == YES) done=YES;
		while(fgets(line, MAXLINE, fblk) != NULL &&
		     strncmp(line, dbs[db]->end, strlen(dbs[db]->end)) != 0 )
			if (goodpat) printf("%s", line);
		if (goodpat)
                {
		     printf("%s", line);   /*  //  */
                }
	     }   /*  now at end of AC */
	 }  /*  end of start of entry */
         else if (strlen(line) > 1 && strstr(line, "sparky") == NULL &&
                  strstr(line, "Steven") == NULL)
            printf("%s", line);
      }  while (!feof(fblk) && fgets(line, MAXLINE, fblk) != NULL && !done);
   }   /*  end of if db valid */
   printf("\n");

   return(nblk);
}  /* end of get_blk */

/*========================================================================
   proweb.dat entry:   PS00031 ! http: ... ! title
	One line per entry, don't assume it's sorted by AC
==========================================================================*/
void get_proweb(fweb)
FILE *fweb;
{
   char line[MAXLINE], *ptr;
   int nweb;

   nweb = 0;
   while(!feof(fweb) && fgets(line, MAXLINE, fweb) != NULL)
   {
      nweb++;
      if ( (strncasecmp(BlockFam, line, strlen(BlockFam) )) == 0 )
      {
/*         printf("%s", line); */
         ptr = strtok(line, "!"); 
         if (ptr != NULL) ptr = strtok(NULL, "\n\r");
         printf("%s\n", ptr);
      }
   }
}    /*  end of get_proweb */
/*========================================================================
  blinks.dat format:
	One line per entry, don't assume it's sorted by AC
==========================================================================*/
void get_blinks(flnk)
FILE *flnk;
{
   char line[MAXLINE];
   int nlnk;

   nlnk = 0;
   while(!feof(flnk) && fgets(line, MAXLINE, flnk) != NULL)
   {
      nlnk++;
      if ( (strncasecmp(BlockFam, line, strlen(BlockFam)) == 0 ) )
      {
         printf("%s", line); 
/*
         ptr = strtok(line, "!"); 
         if (ptr != NULL) ptr = strtok(NULL, "\n\r");
         printf("%s\n", ptr);
*/
      }
   }
}    /*  end of get_blinks */
/*========================================================================
	maps.dat format:

	#MAP# BL00011		or	>BL00011
	...
	//

==========================================================================*/
void get_map(fmap)
FILE *fmap;
{
   char line[MAXLINE];
   int nmap, done;

   nmap = 0;
   done = NO;
   while(!done && !feof(fmap) && fgets(line, MAXLINE, fmap) != NULL)
   {
      nmap++;
      /*   Just checking the number part of the name!    */
      if ( ( line[0] == '#' && 
             strncasecmp(BlockFam, line+6, strlen(BlockFam)) == 0 ) ||
           ( line[0] == '>' && 
             strncasecmp(BlockFam, line+1, strlen(BlockFam)) == 0 )    )
      {
         done = YES;
         do {
           printf("%s", line); 
           fgets(line, MAXLINE, fmap);
         } while (!feof(fmap) && line[0] != '#' && line[0] != '>');
      }
   }
}  /* end of get_map */

/*=====================================================================
    Use to get any fasta-style entry
=======================================================================*/
void get_fasta(fdat)
FILE *fdat;
{
   char line[MAXLINE];
   int  done;

   done = NO;
   while(!done && !feof(fdat) && fgets(line, MAXLINE, fdat) != NULL)
   {
      if ( line[0] == '>' && 
           strncasecmp(BlockFam, line+1, strlen(BlockFam)) == 0 )
      {
         done = YES;
         do {
           printf("%s", line); 
           fgets(line, MAXLINE, fdat);
         } while (!feof(fdat) && line[0] != '>');
      }
   }
}   /*  end of get_fasta  */

/*========================================================================
   blk2pdb.dat entry:  >BL00094 
			seqname	pdbs
==========================================================================*/
void get_pdb(fpdb)
FILE *fpdb;
{
   char line[MAXLINE];
   int npdb, done;

   npdb = 0;
   done = NO;
   while(!done && !feof(fpdb) && fgets(line, MAXLINE, fpdb) != NULL)
   {
      npdb++;
      if ( line[0] == '>' && 
           strncasecmp(BlockFam, line+1, strlen(BlockFam)) == 0 )
      {
         done = YES;
         do {
           printf("%s", line); 
           fgets(line, MAXLINE, fpdb);
         } while (!feof(fpdb) && line[0] != '>');
      }
   }
}  /* end of get_pdb */

/*========================================================================
   cyrca.dat entry:  BL00094 
==========================================================================*/
void get_cyrca(fcyr)
FILE *fcyr;
{
   char line[MAXLINE];
   int ncyr, done;

   ncyr = 0;
   done = NO;
   while(!done && !feof(fcyr) && fgets(line, MAXLINE, fcyr) != NULL)
   {
      ncyr++;
      if ( strncasecmp(BlockFam, line, strlen(BlockFam)) == 0 )
      {
         done = YES;
         printf("%s", line); 
      }
   }
}  /* end of get_cyrca */

/*======================================================================*/
void get_prosite(dbs, fdat, fdoc)
struct db_info *dbs[];
FILE *fdat, *fdoc;
{
   int  db, goodpat, done;
   char line[MAXLINE], id[MAXLINE], ac[MAXLINE];

   done = NO;
   line[0] = '\0';
   db = type_dbs(fdat, dbs);

   if (db >= 0 && db < MAXDB)
   {
      do
      {
	 if (strncmp(line, dbs[db]->start, strlen(dbs[db]->start)) == 0)
	 {
	    ac[0] = '\0';  goodpat = NO;
	    strcpy(id, line);   /*  save this line */
	    if (fgets(line, MAXLINE, fdat) != NULL &&
		   strncmp(line, "AC   ", 5) == 0)
	    {
		strcpy(ac, &line[dbs[db]->title_offset]); 
		ac[7] = '\0';
		if ( (strncmp(BlockFam+2, ac+2, 5)) == 0 )
		{
		     goodpat = YES;
		     printf("%s", id);      /* ID */
		     printf("%s", line);    /* AC */
		}
		while(fgets(line, MAXLINE, fdat) != NULL &&
		     strncmp(line, dbs[db]->end, strlen(dbs[db]->end)) != 0 )
			if (goodpat)
                        {
                            printf("%s", line);
                            if (fdoc != NULL && strncmp(line, "DO   ", 5)==0)
                               get_doc(fdoc, &line[dbs[db]->title_offset]);
                        }
		if (goodpat)
                {
		     printf("%s", line);   /*  //  */
                     done=YES;
                }
	     }   /*  now at end of AC */
	 }  /*  end of start of entry */
         else if (strlen(line) > 1) printf("%s", line);
      }  while (!feof(fdat) && fgets(line, MAXLINE, fdat) != NULL && !done);
   }   /*  end of if db valid */
   printf("\n");
}  /* end of get_prosite */
/*=======================================================================
     Documentation line starts with {PDOC00199} , ends with {END}
=========================================================================*/
void get_doc(fdoc, pdoc)
FILE *fdoc;
char *pdoc;
{
   int done;
   char line[MAXLINE];
   char ctemp[15];

   done=NO;
   if (strlen(pdoc) > 8) pdoc[9] = '\0';   /* PDOC????? */
   sprintf(ctemp, "{%s}", pdoc);
   while (!done && !feof(fdoc) && fgets(line, MAXLINE, fdoc) != NULL)
   {
      if (strncmp(ctemp, line, 11) == 0)
      {
         do
         {
            printf("%s", line);
         } while (!feof(fdoc) && fgets(line, MAXLINE, fdoc) != NULL &&
                  strncmp("{END}", line, 5) != 0);
         done=YES;
      }
   }
}   /*  end of get_doc */
blimps-3.9/protomat/getseq.c000064400001460000012000000076400774502755700165000ustar00jorjastaff00000400000027/*=====================================================================*/
/*(C) Copyright 1996 by Fred Hutchinson Cancer Research Center         */
/*        getseq.c   Un-indexed extract of one sequence from dbs       */
/*     USE: getseq seqname dbname                                      */
/*        seqname = name of sequence
	      GENBANK:  LOCUS name (FASTA type 1)
	      EMBL:     ID name (FASTA type 3)
	      PIR:	ENTRY name (NBRF/CODATA format, FASTA type 2))
	      VMS:	name immediately following the ; on the first line.
			(NBRF/VMS format, FASTA type 5)
	      UNI:      name immediately following the > on the first line.
			(FASTA type 0)
          dbname = name of database file, program will determine its type

     * One output file is created for each entry in "universal" format
	(>title $, then sequence, then *). The name of the file
	is the 1st 8 characters of the entry name followed by .dna for
	GENBANK and by .pro for EMBL and UNI. EG: "MTB1$BAC.pro".
  KNOWN PROBLEMS:  *If input database is not sorted by ID, may miss some
		    requested entries.
		   *If input list file has extension .lst, overwrites it.
		   *VMS format does not have fragment information.
--------------------------------------------------------------------------
 2/25/96 J.Henikoff
 1/23/99 exit(-2) if requested sequence not found.
=========================================================================*/

#include "motifj.h"

int get_ids();
int lst_list();
int lis_list();
/*--------------  Routines from motmisc.obj --------------------------*/
void init_dbs();
int type_dbs();
struct db_id *makedbid();
int extract_seqs();
char *dir_unix();
struct split_name *split_names();

char Pros[FNAMELEN];

/*======================================================================*/
int main(argc, argv)
int argc;
char *argv[];
{
   char infile[FNAMELEN], seqname[FNAMELEN];
   char foutname[FNAMELEN];
   struct db_info *dbs[MAXDB];
   int totseqs, nids, frag;
   FILE *fin, *fout;
   struct db_id *ids, *id;

   if (argc < 3)
   {
      printf("\nGETSEQ: (C) Copyright 1996 by Fred Hutchinson");
      printf(" Cancer Research Center\n");
      printf("USAGE: getseq  \n");
      printf("        = name of sequence to extract\n");
      printf("         = sequence database\n");
      printf("        = output file name\n");
   }
/*-------------  arg 1.  Name of sequence to extract ---------------------*/
   if (argc > 1)
      strcpy(seqname, argv[1]);
   else
   {
      printf("\nEnter name of sequence to extract: ");
      gets(seqname);
   }
   ids = makedbid();
   id = makedbid(); ids->next = id;
   strcpy(id->entry, seqname);
   nids = 1;

/*----------------- arg 2 database name --------------------------------*/
   if (argc > 2)
      strcpy(infile, argv[2]);
   else
   {
      printf("\nEnter name of database file to extract sequence from: ");
      gets(infile);
   }
   if ( (fin=fopen(infile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", infile);
      exit(-1);
   }
 
/*-------------  arg 3.  Output file name---------------------------------*/
   foutname[0] = '\0';
   if (argc > 3)
      strcpy(foutname, argv[3]);
   else
   {
      printf("\nEnter name of output file: ");
      gets(foutname);
   }
   if (strlen(foutname))
   {
      if ( (fout=fopen(foutname, "w+t")) == NULL)
      {
         printf("\nCannot open file %s\n", foutname);
         exit(-1);
      }
      else
         printf("\nExtracting sequence to %s", foutname);
   }
   else fout = stdout;

/*------------------- Extract the sequence ---------------------------*/
   Pros[0] = '\0';
   frag = YES;
   if (nids > 0)
   {
      init_dbs(dbs);		       /* load database infor. */
      totseqs = extract_seqs(nids, dbs, fin, ids, Pros, fout, frag);
   }
   else  totseqs = 0;
/*
   printf("\n%d sequences extracted\n",  totseqs);
*/
   fclose(fin);

   if (totseqs > 0) exit(0);
   else             exit(-2);
}  /*  end of main */

blimps-3.9/protomat/lislis.c000064400001460000012000000123401056464137700164730ustar00jorjastaff00000400000027/*========================================================================
   (C) Copyright 1995-2007 by Fred Hutchinson Cancer Research Center
	  lislis.c  Compares two .lis files
--------------------------------------------------------------------------
8/1/95  Modified to write a .lis file of sequences in 
        2nd but not in 1st file
1/3/06  Compare new Trembl names : Q9WUM8_MOUSE|Q9WUM8
2/14/07 Compare new Trembl names: P15143|P02F2_HUMAN == P02F2_HUMAN|P15143
=========================================================================*/
#include "motifj.h"
#include 
/*
#include 
*/
#include 


struct db_id *make_list();
void compare_lists();
int compare_names();

/*--------------  Routines from motmisc.obj --------------------------*/
int get_ids();
struct db_id *makedbid();

char Pros[FNAMELEN];

/*======================================================================*/
void main(argc, argv)
int argc;
char *argv[];
{
   char lisfile[FNAMELEN], lis2file[FNAMELEN];
   struct db_id *ids, *ids2;
   FILE *flis, *flis2;

   printf("\nLISLIS: (C) Copyright 1995-2007 by Fred Hutchinson Cancer");
   printf(" Research Center\n");
/*-------------  arg 1.  First .lis file ---------------------*/
   if (argc > 1)
      strcpy(lisfile, argv[1]);
   else
   {
      printf("\nEnter name of file containing first list of sequences: ");
      gets(lisfile);
   }
   if ( (flis=fopen(lisfile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", lisfile);
      exit(-1);
   }
   printf("Reading %s ... ", lisfile);
   ids = make_list(flis);

/*-------------  arg  2.  Second .lis file ---------------------*/
   if (argc > 2)
      strcpy(lis2file, argv[2]);
   else
   {
      printf("\nEnter name of file containing second list of sequences: ");
      gets(lis2file);
   }
   if ( (flis2=fopen(lis2file, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", lis2file);
      exit(-1);
   }
   printf("Reading %s ... ", lis2file);
   ids2 = make_list(flis2);

   compare_lists(ids, ids2);

   exit(0);
}  /*  end of main */
/*====================================================================*/
struct db_id *make_list(flis)
FILE *flis;
{
   char title[MAXLINE], stemp[MAXLINE], *ptr;
   int nids;
   struct db_id *ids;

   ids = makedbid();
   nids = get_ids(flis, ids);
   fclose(flis);
   printf("%d sequences read\n", nids);
   return(ids);

}  /*  end of make_list */

/*======================================================================*/
void compare_lists(ids1, ids2)
struct db_id *ids1, *ids2;
{
   struct db_id *id1, *id2;
   int tot1, tot2, n1, n2;
   double per1, per2;

   id2 = ids2->next;
   while (id2 != NULL)
   {
      id1 = ids1->next;
      while (id1 != NULL && !id2->found)
      {
/*        if (strcmp(id1->entry, id2->entry) == 0)
*/
         if (compare_names(id1->entry, id2->entry) == 1)
         {   id2->found = 1; id1->found = 2;    }
         id1 = id1->next;
      }
      id2 = id2->next;
   }

   printf("Sequences in first list but not in second list:\n");
   n1 = tot1 = 0;
   id1 = ids1->next;
   while (id1 != NULL)
   {
      tot1++;
      if (!id1->found)
      { printf("%s\n", id1->entry); n1++; }
      id1 = id1->next;
   }
   per1 = 100.0 * (double) n1 / (double) tot1;
   printf("%d/%d sequences (%.2f) in first list but not in second list:\n", 
           n1, tot1, per1);

   printf("Sequences in second list but not in first list:\n");
   n2 = tot2 = 0;
   id2 = ids2->next;
   while (id2 != NULL)
   {
      tot2++;
      if (!id2->found)
      { printf("%s\n", id2->entry); n2++;  }
      id2 = id2->next;
   }
   per2 = 100.0 * (double) n2 / (double) tot2;
   printf("%d/%d sequences (%.2f) in second list but not in first list:\n", 
          n2, tot2, per2);

   printf("\n");
}  /* end of compare_lists */
/*======================================================================
	Compare two multi-part sequence names and return flag if
	any one of them matches
=======================================================================*/
int compare_names(name1, name2)
char *name1, *name2;
{
   int match, n2, i;
   char *ptr1, *ptr2, parts[10][12], ctemp1[120], ctemp2[120];

   match = 0;
  
   /* strtok modified the strings */
   strcpy(ctemp1, name1);
   strcpy(ctemp2, name2);

   /*  strtok only tracks one string at a time, so pre-process name2 */
   /*  max of 10 name parts, 12 chars in length each */
   n2 = 0;
   ptr2 = strtok(ctemp2, "|");
   while (ptr2 != NULL)
   {
      strcpy(parts[n2], ptr2);
      n2++;
      ptr2 = strtok(NULL, "|");
   }

   ptr1 = strtok(ctemp1, "|");
   while (ptr1 != NULL)
   { 
      for (i=0; i strlen(name2))
   {   strcpy(name2, name1);  }
   
   return(match);

}  /* end of compare_names */
blimps-3.9/protomat/motifj.c000064400001460000012000001755561054326123000164660ustar00jorjastaff00000400000027/*------------------------------------------------------------------------*/
/*                      Motif identifier, Version 1.12.1                  */
/*									  */
/*                       Thomas Annau, Hamilton Smith                     */
/*                             August 19, 1989                            */
/*  Reference:  Hamilton O. Smith, Thomas M. Annau, Srinivasan
	Chandrasegaran, "Finding sequence motifs in groups of
	functionally related proteins", PNAS, Vol 87 (January 1990),
	pp. 826-830.                                                      */
/*             Modified 2/9/90 by Ken Fasman, BME Systems Inc. for        */
/*                     Microsoft & draft ANSI standard C                  */
/*-----------------------------------------------------------------------
    NOTES for Silicon Graphics compilers:  Change EOF to '\377'           */
/*------------------------------------------------------------------------
       motifj RunType Batch_Filename Signif Dups Distance Drop           
	Defaults: Signif = (int) ((NumSeqs+1)/2) + 1
		  Dups = 0
		  Distance = 17
		  Drop = 0
*/
/*------------------------------------------------------------------------*/
/* 3/21/90 Modified for PROTOMAT by J. Henikoff, Fred Hutchinson Cancer
           Research Center (JGH)
   USE: Interactive:  motifj (prompts for responses)
        Command line: motifj RunType lisname [Signif Dups Distance Drop]
         RunType=0,1,2,3 or 4. Recommended types are:
           0 interactive, non-iterative (similar to original motif program)
           1 non-interactive, non-iterative,
             all parameters specified on command line
	   2 interactive, iterative (will decrease Signif until >= MOTAUTO3
             motifs are found)
           3 non-interactive, iterative (non-interactive version of 2)
           4 shuffled, non-interactive, iterative (will increase Signif
             until <= MOTAUTO4 motifs are found, then executes RunType 3),
             all parameters determined by motifj
           5 shuffled, non-interactive, iterative (like RunType 2/3, not 4)
           See PROTOMAT documentation for more information.
         lisname=name of file containing list of proteins to analyze.
           First line can be a title starting with ">"
           Second line can be a directory, EG /home/proteins/PS00094/,
	    if missing the protein files are assumed to be in pros/.
           Assumes each subsequent line lists the name of a file which
            has extension ".pro". So if lisname contains "MTB1_BREEP",
            the file name must be "MTB1_BREEP.pro".
           All protein files must be in fasta format with a title line
	    beginning ">".
           Proteins must be in upper or lower case letters, the usual 20 amino
            acid abbreviations are recognized, plus B (changed to D) and Z
            (changed to E). X, O and J are changed to X and treated as
            place holders. All other characters are ignored.
           If lisname filename is preceded by "-", it is assumed that
	    the file contains all of the proteins to be analyzed in
            fasta format.
	   PLEASE VERIFY THAT YOUR PROTEINS ARE BEING READ CORRECTLY!!!
         Signif=Motif significance level, required number of proteins
           containing a motif.
         Dups=Maximum number of duplications of a motif among all sequences.
         Distance=Maximum motif distance. 
         Drop=drop score, motif score below which motifs will be dropped.

 >>>>>>>>>>>>>>>>>>>>>>>>Blocks 9.0 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 10/21/95 Write out sequences used in .motifj.pros file, write_pros()
 10/23/95 Flag min/max sequence lengths in .motifj.pros file
 11/14/95 Leave Title intact (don't remove MOTIFJ=[]) for mot2blk
  7/11/96 Changed to re-execute program in argv[0] instead of "motifj"
  6/29/97 Execute write_pros() right away.
 10/21/97 Added pb_weights()
 10/28/97 Modified cut_motifs() to take actual overlap into account;
          lowered min #mots for runtype 3 (MOTAUTO3) from 12 to 6 because
          now expect fewer motifs. Raised max #mots for runtype 4 (MOTAUTO4)
          from 2 to 3 to reduce running time.
 11/ 4/97 Modified cut_motifs() to group two motifs only if they match
	  in at least half of their common sequences 
 11/ 7/97 Modified cut_motifs() to drop excess motifs in the same group.
          Expect to now produce fewer motifs, but spread across more
          of the sequence length (groups are roughly equivalent to a
	  geographical region of the sequences).
  1/21/98 Removed pb_weights() error message.
  6/20/99 Longer sequence names (SNAMELEN = 18)
  3/31/00 MAX_LENGTH overrun problem
 12/23/06 Longer sequence names (SNAMELEN = 20)
*/
/*--------------------------------------------------------------------JGH*/

#include 
#include 
#include 	/* for execlp */
#include "motifj.h"

struct realign_struct {
	int sequence[MAXSEQS];
	int motif_pos[MAXSEQS];
	long int max_score[MAXSEQS], max2_score[MAXSEQS];
	int max_pos[MAXSEQS], max2_pos[MAXSEQS];
};
/*
Function Prototypes
*/
int main();
void print_motif();
int pamidx();
int wpamidx();
int cut_motifs();
void map_seqs();
int compare_scores();
int compare_groups();
int compare_motgrps(); 
int compare_subgrps(); 
FILE *getfile();
int getseqs();
int shuffle();
void print_stats();
int get_count();
int check_dup();
void score_mot();
void pb_weights();
void realign();
void write_motifs();
void write_pros();

/*----------These routines are in motmisc.c ----------------------------*/
int aachar_to_num();
char *num_to_aachar();
void pr_num_to_aa();
void pr_num_to_aa_space();
void getscore();
void kr_itoa();
struct split_name *split_names();

/* --------   Global variables ---------------------------------------------*/
char Version[12] = " 4/ 2/00.1";
int Short_Form, First;	
int NumSeqs, RunType, Signif, Dups, Distance;
unsigned int Drop;
int Len[MAXSEQS] = {0};
char Seqname[MAXSEQS][SNAMELEN];
int *Seq[MAXSEQS];
struct score *SMatrix;
char Batch_Filename[FNAMELEN], Mot_Filename[FNAMELEN];
char Title[MAXLINE];
struct split_name *Batsplit;

/*---------------------------------------------------------------------------*/
/*                             MAIN PROCEDURE                                */
/*---------------------------------------------------------------------------*/

int main(argc, argv)
int argc;
char *argv[];
{
/*   NOTE: Be careful of integers defined as char to save space:
	    char is        8bits, valid range is -128 to +127
	    unsigned char  8                        0 to +255
	    int            16                  -32768 to +32767
	    unsigned int   16                       0 to +65535
	    long           32
*/
int i, j, k, n;
int batch, shuffled, prevsig, prevdup, save_motifs, save_dups;
int total_motifs, real_total_motifs, found, duplicate;
int count, minseqs, d1, d2, group, max_group, domain_width;
unsigned long total_score = 0;
long int CPU_time;
char *ptr, intemp[MAXLINE], filepath[FNAMELEN]; 
char aa1, aa2, aa3;
char chsig[5], chdup[5], chdis[5], chdrop[6]; 
FILE *fp, *bf;
struct motif_struct *motif;
aa_type *aa3_obs;

   printf("\nMOTIFJ Version %s", Version);
   printf("\nPlease cite Hamilton O. Smith, et al,");
   printf(" PNAS 87 (1990), pp. 826-830.\n");

   /*---------Get the scoring matrix and high pass filter values ------------*/
   SMatrix = (struct score *) malloc (sizeof(struct score));
   if (SMatrix != NULL)    getscore(SMatrix);
   else {printf("\nCANNOT ALLOCATE SMatrix\n"); exit(-1);}

   /*--------Determine the run type -----------------------*/
   RunType = 0;	
   if (argc > 1) RunType = atoi(argv[1]);
   if (RunType < 0 || RunType > 5)  RunType = 0;	
   printf("\nUsing RunType=%d", RunType);

   /*------------------------------------------------------------------------*/
   /*              Get amino acid sequences from files.                      */
   /*------------------------------------------------------------------------*/
   Batch_Filename[0] = intemp[0] = '\0';
   if (argc > 2) strcpy(intemp, argv[2]);
   else 
   {
     printf("\n\nEnter input file name: ");
     gets(intemp);
   }
   if (strlen(intemp) && intemp[0] == '-')
   {
      batch = NO;
      strcpy(Batch_Filename, intemp+1);
   }
   else
   {
      batch = YES;
      strcpy(Batch_Filename, intemp);
   }

   /* Open input file */
   Batsplit = split_names(Batch_Filename);
   if ((bf = fopen(Batch_Filename, READ)) == NULL)
   {
      printf("Cannot open file %s not found\n", Batch_Filename);
      exit(-1);
   }
   if (batch)
     printf("\nReading batch file %s", Batch_Filename); 
   else
     printf("\nReading sequence file %s", Batch_Filename);

   NumSeqs = 0;
   Title[0] = '\0';
   if (batch)
   {
     /*    Process the batch file title, if there is one */
     fgets(Title, MAXLINE, bf);
     if (strlen(Title) && Title[0] != '>')
     {
	Title[0] = '\0';
	rewind(bf);
     }
     else
     {
	printf("\n%s", Title);
     }
     /* Read in all sequences (go through batch file)  */
     strcpy(filepath, PROTEIN_SUBDIRECTORY);      /* Initialize path */
     while (!feof(bf) && fgets(intemp, MAXLINE, bf) != NULL)
     {
        fp = getfile(intemp, filepath, Seqname[NumSeqs]);
        if (fp != NULL)
        {
	   n = getseqs(fp);		/* updates NumSeqs, etc.*/
    	   fclose(fp);
        }  /* end of if fp is not NULL */
     }  /* end of bf file */
   }  /* end of if batch */
   else
   {
     /*   Try to find a Title */
     intemp[0] = '\0';
     strncat(intemp, Batch_Filename,
             Batsplit->dir_len + Batsplit->name_len);
     intemp[Batsplit->dir_len + Batsplit->name_len] = '\0';
     strcpy(filepath, intemp); strcat(filepath, ".lst");
printf ("\nfilepath=%s\n", filepath);
     if ((fp = fopen(filepath, READ)) == NULL)
     {
        strcpy(filepath, intemp); strcat(filepath, ".lis");
        fp = fopen(filepath, READ);
     }
printf ("\nfilepath=%s\n", filepath);
     if (fp != NULL)
     {
        fgets(Title, MAXLINE, fp);
        fclose(fp);
     }
     n = getseqs(bf);				/* updates NumSeqs */
   }
printf ("\nNumSeqs=%d batch=%d Title=%s\n", NumSeqs, batch, Title);
   
   fclose(bf);
   if (NumSeqs < MINSEQS)
   {
      printf("\nToo few sequences to process(need at least 2).\n");
      exit(0);
   }
   else
   {
      printf("\n");
      for (n=0; n< NumSeqs; n++)
      {
	 printf("Sequence #%d:\t%s\t\t", n + 1, Seqname[n]);
    	 printf("Length of sequence #%d =  %d\n", n + 1, Len[n]);
      }
      printf("\n");
   }
   /*    Write out the sequences for Gibbs */
   write_pros();

   /*------------------------------------------------------------------------*/
   /*  If shuffling was selected, shuffle the sequences before analysis.     */
   /*------------------------------------------------------------------------*/
   shuffled = shuffle();

   /*------------------------------------------------------------------------*/
   /*        Perform brief statistical analysis on amino acid data.          */
   /*------------------------------------------------------------------------*/
   print_stats();

   /*---------------------------------------------------------------------*/
   /*     Get the parameters                                              */
   /*---------------------------------------------------------------------*/
   /*      Initialize the parameters        */
   Signif = Dups = Distance = Drop = 0;
   if (strlen(Title))
   {
	ptr = strstr(Title, "MOTIFJ=[");
	if (ptr != NULL)
        {
            strcpy(intemp, ptr);
/*          Title[strlen(Title)-strlen(ptr)] = '\0';
*/
            /*  Also look at title line for RunType 3 & 5 ? */
            if (RunType == 1 || RunType == 4)
            {
            /*  Read parameters off the title line */
	    /*  Assumes rigid format from uextract is:
                  MOTIFJ=[RunType,Signif,Dups,Distance]*/
            ptr = strtok(intemp, "["); ptr = strtok(NULL, ","); /* RunType */
	    ptr = strtok(NULL, ","); Signif = atoi(ptr);
	    ptr = strtok(NULL, ","); Dups = atoi(ptr);
	    ptr = strtok(NULL, "]"); 	/* don't use Distance */
	    Distance = 17;
            }
        }
   }
   minseqs = (int) ((NumSeqs+1)/2) + 1;    /* want more than half of seqs */
   if (argc > 3) Signif = atoi(argv[3]);
   else if (RunType == 0 || RunType == 2)
   {
     printf("\nEnter significance level [2-%d; %d]: ", NumSeqs, NumSeqs); 
     gets(intemp);   Signif = atoi(intemp); 
   }
   else if (RunType == 4 || Signif == 0)
     Signif = minseqs;	
   if ((RunType == 3 || RunType == 4 || RunType == 5)
       && Signif < minseqs) Signif = minseqs;
   if (Signif == 0 || Signif > NumSeqs) Signif = NumSeqs;
   if (Signif < MINSEQS)                Signif = MINSEQS;

   if (argc > 4) Dups = atoi(argv[4]);	
   else if (RunType == 0 || RunType == 2) 
   {
     Dups = MAXFREQ - NumSeqs;
     printf("Enter number of allowable internal duplicates [0-%d; 0]: ",
	     Dups);
     gets(intemp);  Dups = atoi(intemp); 
   }
   if (Dups + NumSeqs > MAXFREQ) Dups = MAXFREQ-NumSeqs;
   if (Dups < 0) Dups = 0;
   save_dups = Dups;
   if (shuffled) Dups = 0;

   if (argc > 5) Distance = atoi(argv[5]);
   else if (RunType == 0 || RunType == 2)
   {
     Distance = -1;
     printf("Enter search width [1-24; 17]: "); /* Distance=0 causes abort*/
     gets(intemp);
     if (strlen(intemp)) Distance = atoi(intemp);
     else                Distance = 17;
   }
   else Distance = 17;
   if (Distance <= 0 || Distance > MAX_DISTANCE) Distance = MAX_DISTANCE;

   if (argc > 6) Drop = atoi(argv[6]);
   else if (RunType == 0 || RunType == 2)
   {
     Drop = 0;			/* 18540 = 2500*55/sqrt(55)  */
     printf("Enter drop score [0-18540; %d]: ", Drop);
     gets(intemp);
     if (strlen(intemp)) Drop = atoi(intemp);
   }
   else Drop = 0;
   if (Drop <=0 || Drop > 18540) Drop = 0;

/*-------------------------------------------------------------------------*/
/*		 Allocate memory to dynamic structures.                    */
/*-------------------------------------------------------------------------*/
  printf("Allocating and initializing arrays...\n");

  aa3_obs = (aa_type *) malloc(sizeof(aa_type));
  if (aa3_obs == NULL) {
	printf("Couldn't allocate AA3_OBS pointer.\n");
	exit(-1);
	}
  for (i = 0; i < 20; i++) {
    for (j = 0; j < 20; j++) {
      for (n = 0; n < Distance; n++) {          /* was MAX_DISTANCE   JGH*/
	(*aa3_obs)[i][j][n] = (unsigned char *) malloc(Distance);   /*JGH*/
	  if ((*aa3_obs)[i][j][n] == NULL) {
		printf("Couldn't allocate AA3_OBS array.\n");
		exit(-1);
		}
	for (k = 0; k < Distance; k++)		/* was MAX_DISTANCE   JGH*/
	  (*aa3_obs)[i][j][n][k] = 0;
	}
      }
    }

  motif = (struct motif_struct *)
	      malloc(sizeof(struct motif_struct) * MAX_MOTIFS);
  if (motif == NULL) {
	printf("Couldn't allocate MOTIF.\n");
	exit(-1);
	}

/*---------------------------------------------------------------------------*/
/*   Find motifs by looking for three amino acids separated by identical     */
/*               distances in Signif number of proteins.                     */
/*---------------------------------------------------------------------------*/

REDO: CPU_time = time(0);			/* Record starting time */
    printf("\nRunType = %d, Normalized drop score = %d", RunType, Drop);
    printf("\nMotif parameters = [%d, %d, %d]", Signif, Dups, Distance);
    if (shuffled) printf(" with shuffled sequences.\n");
    else          printf("\n");
    total_motifs = real_total_motifs = 0;

  /* Step through the 20 amino acids as the first amino acid in a motif.
     Use a matrix to tabulate frequencies of all possible motifs built on
     that first amino acid.  The maximum spacing between amino acids of
     the motif is limited by the user's entry of the Distance parameter.

     aa1	First amino acid in motif.
     d1		Distance separating first aa from second.
     aa2	Second amino acid in motif.
     d2		Distance separating second aa from third.
     aa3	Third amino acid.

     (*aa3_obs)[aa2][aa3][d1][d2]  is the frequency of the motif
				   (matrix is redone for each aa1).
     */

  /* Start loop for first amino acid. */
  for (aa1 = 0; aa1 < 20; aa1++)               /* First amino acid */
  {
    printf(".");                                /* Look busy */

    /*>>>> RunType=4:  Only continue if haven't found too many yet */
    if (RunType != 4 ||
       (RunType == 4 && total_motifs <= MOTAUTO4))
    {
/*----------------------------------------------------------------------------*/
    /* Tabulate frequency matrix for all possible motifs within limits
       defined by user (d1 and d2 range from 0 to Distance): */
      for (n = 0; n < NumSeqs; n++)               /* Look through all seqs */
        for (i = 0; i < Len[n]; i++)              /* Step through each seq */
	  if (Seq[n][i] == aa1)                /* Search for aa1 */
          {
	  /* Found aa1, now assimilate Distance*Distance number of motifs
	     into array: */
	    for (j = i + 1; j < Len[n] && j < i + Distance + 1; j++)
	      for (k = j + 1; k < Len[n] && k < j + Distance + 1; k++)
                if (Seq[n][j] < 20 && Seq[n][k] < 20)  /* count only AAs */
	        /* (*aa3_obs) [  aa2    ] [  aa3    ] [ d1  ] [ d2  ]++ */
	           (*aa3_obs) [Seq[n][j]] [Seq[n][k]] [j-i-1] [k-j-1]++;
	  }
/*----------------------------------------------------------------------------*/

      /* Scan array for motifs that occurred at least Signif number of times */
      for (aa2 = 0; aa2 < 20; aa2++)
        for (aa3 = 0; aa3 < 20; aa3++)
	  for (d1 = Distance - 1; d1 >= 0; d1--)
	    for (d2 = Distance - 1; d2 >= 0; d2--)   
            {
/*----------------------------------------------------------------------------*/
              if ( (RunType != 4 ||
                    (RunType == 4 && total_motifs <= MOTAUTO4) ) &&
	          (*aa3_obs)[aa2][aa3][d1][d2] >= (unsigned char) Signif )
              {
                /* Record all information about motif in motif array: */
	        motif[total_motifs].aa1 = aa1;
	        motif[total_motifs].aa2 = aa2;
	        motif[total_motifs].aa3 = aa3;
	        motif[total_motifs].distance1 = d1 + 1;
	        motif[total_motifs].distance2 = d2 + 1;
		motif[total_motifs].freq = motif[total_motifs].dups = 0;
	        motif[total_motifs].group = motif[total_motifs].sub_group = 0;
                motif[total_motifs].mots = 1;
		count = get_count(&motif[total_motifs]);

      /* Now freq is the total frequency of the motif and count is the number
	 of different sequences the motif occurred in.  Therefore the number
	 of duplicates is (freq - count).  The next step is to make sure
	 motif occurs Dups or less in each sequence and that freq is over the
	 significance level.  If so, store the motif in the motif array: */

              if (motif[total_motifs].dups <= Dups && count >= Signif)   
              {
	        duplicate = NO;
		if (total_motifs)
		   duplicate = check_dup(&motif[total_motifs],
                                         &motif[total_motifs-1]);

              /* If it's not an obvious duplicate, add it to the motif list */
	      if (!duplicate)   
              {
	        domain_width = d1 + d2 + 3;		/* width of motif */
	        if (domain_width < MIN_DOMAIN_WIDTH)
	          domain_width = MIN_DOMAIN_WIDTH;
	        if (domain_width > MAX_DOMAIN_WIDTH)
	          domain_width = MAX_DOMAIN_WIDTH;
	        motif[total_motifs].domain = domain_width;

		score_mot(&motif[total_motifs]);

	        /*  Display motif */
	        pr_num_to_aa(aa1); pr_num_to_aa(aa2);
	        pr_num_to_aa(aa3); printf(",");
	        total_motifs++;

	        /* Flooded with too many motifs, sort and cut back to 
	                 RELEVANT_MOTIFS */
	        if (total_motifs == MAX_MOTIFS)
                {
	             save_motifs = total_motifs;
	             total_motifs = cut_motifs(motif, save_motifs);
                }
/*-------------------------------------------------------------------------*/

	  }  /* end of if !duplicate */
	}  /* end of if freq - count <= Dups  */
      }  /* end of if >= Signif */
      (*aa3_obs)[aa2][aa3][d1][d2] = 0;       /* Reset scoring matrix to 0 */

    } /* end of scan array */
   } /* >>>>  end of RunType check */
  }  /* End of aa1 loop */
/*------------------------------------------------------------------------*/
/*               Sort data and weed out redundant information.            */
/*------------------------------------------------------------------------*/
  printf("\n\n");

  /* Cut back to RELEVANT_MOTIFS, sorted by frequency and score */
  save_motifs = total_motifs;                                 /*JGH*/
  if (total_motifs > 0)
  {
      if (RunType != 4) total_motifs = cut_motifs(motif, save_motifs);
      else if (total_motifs > RELEVANT_MOTIFS)
		total_motifs = RELEVANT_MOTIFS;
  }
  real_total_motifs = total_motifs;

  printf("\nCPU time to find and sort motifs: %ld seconds.",
						time(0) - CPU_time);
/*------------------------------------------------------------------------*/
/*                      Consider results & decide what to do next         */
/*------------------------------------------------------------------------*/
  found = 0;
  if (real_total_motifs > 0)
	found = Signif;               /* signif level with motifs found JGH*/

  /* User has option of saving only top N scores:  */
  printf("\nFound %d motifs.", real_total_motifs);  
  total_motifs = real_total_motifs;
  if (RunType==0 || (RunType==2 && real_total_motifs >= MOTAUTO3))     /*4JGH*/
  {
     printf(" Enter number to save or -1 to redo [1-%d; %d]: ",
	      real_total_motifs, real_total_motifs);
     gets(chsig); total_motifs = atoi(chsig);
     if (total_motifs == 0 || total_motifs > real_total_motifs)
	 total_motifs = real_total_motifs;
     else if (total_motifs < 0) 
     {
       printf("\nPrevious significance level was %d.", Signif);
       printf(" Enter new level [2-%d; %d]: ", NumSeqs, Signif); 
       prevsig = Signif; gets(intemp);  Signif = atoi(intemp);  
       if (Signif < 2 || Signif > NumSeqs) Signif = prevsig;  
       printf("Previous number of internal duplications was %d.", Dups); 
       printf(" Enter new number [0-;%d]: ", Dups);  
       prevdup = Dups; gets(intemp);  Dups = atoi(intemp);  
       if (Dups < 0 || !strlen(intemp) ) Dups = prevdup;  
       printf(" Using previous distance  %d\n", Distance);
       goto REDO;
     }
  }

/*------ If nothing was found, try again automatically if specified     JGH*/
    if ( (RunType == 2 || RunType == 3 || RunType == 5) &&
	  real_total_motifs < MOTAUTO3 && Signif > MINSEQS)          /*6JGH*/
    {
       Signif--;
       if (Signif >= MINSEQS)  goto REDO;
    }
    if (RunType == 4)
    {
       prevsig = Signif;
       if (real_total_motifs > MOTAUTO4)      /* found too many */
       {
	  Signif++;
	  if (Signif < NumSeqs) goto REDO;
	  else                  goto EXIT;  /*too many motifs at all signif*/
       }
       else if (real_total_motifs <= MOTAUTO4 && found <= 0)
       {                              /* haven't found enough motifs yet  */
	  Signif = (int) ( (prevsig+1)/2 );
	  if (Signif == prevsig) Signif--;
	  if (Signif >= minseqs) goto REDO;
	  else                        /* no motifs at any signif */
          {  Signif = prevsig;
             goto EXIT;
          }
       }
       else if (real_total_motifs <= MOTAUTO4 && found > 0)
       {                   /*  some found, but not too many at this level */
	  goto EXIT;
       }
    }
    if (total_motifs < 1) goto EXIT;
/*NOTE:  Should be able to free aa3_obs now, but causes problems!   */

/*------------------------------------------------------------------------*/
/*                          Print out motifs.                             */
/*   NOTE:  print_motif() modifies the motif[] structures!             JGH*/
/*------------------------------------------------------------------------*/
/*   Default output is always short form.                              JGH*/
   Short_Form = YES; First = NO;
   if (RunType==0 || RunType==2)
   {
     printf("Enter 'g' to print first motif in each group: ");
     gets(chsig);
     if (chsig[0] == 'g' || chsig[0] == 'G') First = YES;
     printf("Enter 'l' for long form:  "); 
     gets(chsig);
     if (chsig[0] == 'l' || chsig[0] == 'L') Short_Form = NO;
  }
/*-------------------------------------------------------------------------*/
  /* Separate groups of related proteins with horizontal line: */
  /* Print out all motifs: */
  /*  Sort motifs by group first for printing.   JGH*/
  qsort(motif, total_motifs, sizeof(struct motif_struct), compare_motgrps);
  max_group = 0;
  for (j = 0; j < total_motifs; j++)
  {
    if (motif[j].freq > 0 && motif[j].group > max_group) {
      group = motif[j].group;
      max_group = group;
      printf("\n_________________________________Group #%d_________________________________\n\n", group);
      print_motif(&motif[j]);

      total_score += (unsigned long) motif[j].score;

      for (k = j + 1; k < total_motifs && motif[j].freq > 0; k++)
	if (motif[k].freq > 0 && motif[k].group == group)
	  {
	      if (!Short_Form && !First) printf("\n");
	      if (!First) print_motif(&motif[k]);
	      total_score += (unsigned long) motif[k].score;
	    }
    }
  }  /* end of for j */

  printf("\n___________________________________________________________________________\n\n");
  printf("Printed %d motifs out of %d total.\nMean score: %ld \n",
	total_motifs, real_total_motifs,
	(unsigned long) total_score/total_motifs);

/*-----------------------------------------------------------------------*/
/*                   Write the motifs out to a file                   JGH*/
/*-----------------------------------------------------------------------*/
  write_motifs(total_motifs, motif);

/*------------------------------------------------------------------------*/
/*                       Print out motif maps.                            */
/*------------------------------------------------------------------------*/
  if (max_group > 9) max_group = 9;
  n = 0;
  if (RunType == 0 || RunType == 2)
  {
     printf("Enter number of motif groups to map (maximum %d)", max_group);
     printf(" or 0 to assemble blocks: ");
     gets(chsig); n = atoi(chsig);
  }
  else  n = 0; 
  if (n <= 0) goto EXIT;
  if (n > max_group) n = max_group;
  max_group = n;
  map_seqs(max_group, total_motifs, motif);

/*------------------------------------------------------------------------*/
/*     Finish up                                                          */
/*------------------------------------------------------------------------*/
EXIT:
   /* Free up all memory and quit. */
/*  still used if run type 4
   free(motif);
*/
   for(i = 0; i < NumSeqs; free(Seq[i++]));                     /*JGH*/
/*   for (i = 0; i < 20; i++)       **causes program to hang**
    for (j = 0; j < 20; j++)
      for (n = 0; n < Distance; n++)
	free ( (*aa3_obs)[i][j][n] );
*/
   free(aa3_obs);

/*---- Get maximum normalized block score for blocks with the motif
       in Signif sequences -------*/
   if (RunType == 4)
   {
      n = 0;      /* Get maximum normalized block score */
      for (j=0; j n)  n = k;
	 }
      }
      printf("\nStarting motifj...\n");
      kr_itoa(Signif, chsig, 10);
      kr_itoa(save_dups, chdup, 10);
      kr_itoa(Distance, chdis, 10);
      kr_itoa(n, chdrop, 10);
      fflush(stdout);
      if (batch == NO)
      {  strcpy(intemp, "-"); strcat(intemp, Batch_Filename); }
      else strcpy(intemp, Batch_Filename);
      execlp(argv[0], argv[0], "3", intemp,
	     chsig, chdup, chdis, chdrop, NULL);
   }
   else if (total_motifs > 0)
   {
      printf("\nStarting motomat...\n");
      fflush(stdout);
      execlp("motomat", "motomat", Mot_Filename, "1", NULL);
   }
   else  printf("\n");
   exit(0);
}  /*  end of main */
/*------------------------------------------------------------------------*/
/*                       END OF MAIN PROCEDURE                            */
/*------------------------------------------------------------------------*/

/*------------------------------------------------------------------------*/
/*                   Function to print out motifs.                        */
/*   Also calls re-alignment routine, this is because some of the         */
/*   information from the re-alignment is printed, but not saved          */
/*------------------------------------------------------------------------*/
void print_motif(pat)
struct motif_struct *pat;
{
int i, x, aa_freq[20], aa, firstaa;
int offset, p_index, conserved;
int motseq, seq, pos, count;
char prototype[MAX_DOMAIN_WIDTH];
struct realign_struct realign_data;

  /* Print out the three aa sequence and the score: */
  printf("\nMotif: ");
  pr_num_to_aa(pat->aa1);
  pr_num_to_aa(pat->aa2);
  pr_num_to_aa(pat->aa3);
  printf(" in %d proteins (%d duplicates), Merged %d, Score %d\n", 
         pat->freq - pat->dups, pat->dups, pat->mots, pat->score);
  if (!Short_Form) printf("\n");

  count = pat->freq - pat->dups;
  offset = (int) (pat->domain - pat->distance1 - pat->distance2 - 1) / 2;

  /* Calculate frequency of each aa in each column of the block
     and print the conservation line heading */
  for (i = 0; i < 20; i++) aa_freq[i] = 0;
  for (i = 0; i < pat->domain; i++)
  {
    /* See if column is composed of a single amino acid (if so, c = 1) or
       is composed of more than 50% of a single amino acid (if so, record
       in prototype array for 50% degenerate pattern): */
    conserved = YES;
    firstaa = -1;
    for (x = 0; x < pat->freq; x++)
    {
      pos = pat->pos[x] + i - offset;
      if (pos >= 0 && pos < Len[ pat->seq_no[x] ])
      {
         aa = Seq[ pat->seq_no[x] ][pos];
         aa_freq[aa]++;
         if (x == 0) firstaa = aa;
         else if (aa != firstaa) conserved = NO;
      }
      else conserved = NO;	/* Any null in column => not conserved */
    }
    prototype[i] = -1;
    for (x = 0; x < 20; x++)
    {
      if (aa_freq[x] > count / 2) prototype[i] = x;
      aa_freq[x] = 0;
    }

    /* Print out conservation evaluation line (line over block composed
       of +, * and amino acid symbols): */
    p_index = pat->scores[i];
    if (conserved)
       pr_num_to_aa_space(Seq[pat->seq_no[0]][pat->pos[0] + i - offset]);
      else if(p_index < SMatrix->highpass) printf("  ");
      else if(p_index < 1000) printf("+ ");
      else printf("* ");
  }


  /* Realign every sequence against block and print it out: */
  realign(pat, &realign_data);

  if (!Short_Form) printf("  Score (Position) for best two fits.\n");
  for (x = 0; x < NumSeqs; x++) 
  {
      seq = realign_data.sequence[x];
      if (!Short_Form && x == count) 
      {
	for (i = 0; i < pat->domain - 1; i++) printf("--");
	printf("\n");
      }

      /* Print out sequence, using '.' when off one end: */
      for (i = 0; i < pat->domain; i++)
      {
        pos = realign_data.max_pos[x] + i - offset;
	if (!Short_Form && pos >= 0 && pos < Len[seq] )
	  pr_num_to_aa_space(Seq[seq][pos]);
	else if (!Short_Form) printf(". ");
      }

      /* Report scores and positions */
      if (!Short_Form)
      {
	 printf("  %3ld (%3d)  %3ld (%3d)  %s",
		realign_data.max_score[x]/10000,
                realign_data.max_pos[x] + 1,
		realign_data.max2_score[x]/10000,
                realign_data.max2_pos[x] + 1, 
                Seqname[seq]);
         /*----  Indicate seqs with motif that were realigned ------*/
         /*  Find first corresponding pat-> sequences, could be > 1 if
             mot->dups is > 0 */
         i = 0;
         motseq = -1;
         while (motseq < 0 && i < pat->freq)
         {
            if (pat->seq_no[i] == seq)
            {
                motseq = seq;
                if (pat->pos[i] != realign_data.motif_pos[x])
	           printf(" (Motif at %d)", realign_data.motif_pos[x] + 1); 
            }
            i++;
         }
         printf("\n");
      }
  }  /*  end of sequence  x */

  /* Print prototype (50% degenerate pattern): */
  if (!Short_Form)
  {
       printf("\n");
       for (i = 0; i < pat->domain; i++)
	 pr_num_to_aa_space(prototype[i]);
       printf("  Most common amino acids\n\n");
  }
}     /*  end of print_motif */

/*------------------------------------------------------------------------*/
/*                 Function to calculate un-weighted pam index            */
/*------------------------------------------------------------------------*/

/* Performs pairwise comparison of all amino acids in a column (col) of
   length len.  Reports average score multiplied by 100 to retain two
   place accuracy while keeping scores to integers for speed: */
int pamidx(len, col)
int len, col[MAXFREQ];
{
int *col_i, *col_j;
int val = 0, real_len = len, *end_of_col;

  end_of_col = col + len;

  /* Go through all two letter combinations.
     Note: -1 marks an empty column (which is ignored in calculation). */
  for (col_i = col; col_i < end_of_col - 1; col_i++)
    if (*col_i != -1) {
      for (col_j = col_i + 1; col_j < end_of_col; col_j++)
	if (*col_j != -1) val += SMatrix->scores[*col_i][*col_j];
      }
     else real_len--;

  if (*(end_of_col - 1) == -1) real_len--;
  if (real_len > 1)
		return((int) ((long int) val * 100 / (real_len * (real_len - 1) / 2)));
  else return(0);
} /* end of pamidx */
/*------------------------------------------------------------------------*/
/*                 Function to calculate weighted pam index               */
/*------------------------------------------------------------------------*/

/* Performs pairwise comparison of all amino acids in a column (col) of
   length len.  Reports average score multiplied by 100 to retain two
   place accuracy while keeping scores to integers for speed: */
int wpamidx(len, col, wts)
int len, col[MAXFREQ];
double wts[MAXFREQ];
{
  int seq_i, seq_j, nval;
  double val;

  nval = 0;
  val = 0.0;
  /* Go through all two letter combinations.
     Note: -1 marks an empty column (which is ignored in calculation). */
  for (seq_i = 0; seq_i < len; seq_i++)
    if (col[seq_i] != -1)
    {
      for (seq_j = seq_i + 1; seq_j < len; seq_j++)
	if (col[seq_j] != -1)
        {
           val += (wts[seq_i]*wts[seq_j]*
                (double)SMatrix->scores[col[seq_i]][col[seq_j]]);
           nval++;
        }
     }

   if (nval > 0)
   {
      val *= 100.0;
      val /= (double) nval;
      return( round(val) );
   }
   else return(0);

}  /* end of wpamidx */
/*======================================================================
   Remove motifs that are slightly offset from a more significant
     motif or a higher scoring motif, in that order of priority.
     (More significant means more sequences have the motif).
   Lower motif is compared with higher & dropped if the starting positions
     of the two motifs in all sequences in the lower are the same 
     distance apart & that distance is <= 10.
     If this is true for at least 4 sequences, then the lower is put in
     the higher's group.
   Modified alg to eliminate more low-scoring motifs:
     Lower motif is discarded if it the same distance apart as indicated
     above indicates any overlap between the two motifs.
=======================================================================*/
int cut_motifs(motif, total_motifs)
struct motif_struct *motif;
int total_motifs;
{
  int i, j, k, x, real_total_motifs, dist, matches, group, sub_group;
  int seq_list[MAXSEQS], countk, widthk, widthj, mincount, maxcount;
  int firstk, lastk, maxkeep;

/*---- First, descending sort of motifs by freq-dups & score -------------*/
  printf(":\ncutting %d", total_motifs);
  qsort(motif, total_motifs, sizeof(struct motif_struct), compare_scores);

/*-----Clear out groups & get ready to re-group ---------*/
  for (j=0; j 0 && (int) motif[j].score  < Drop)
    {  motif[j].freq = 0; real_total_motifs--; }

/*-----Third, if two motifs overlap, drop the
    lower scoring one by setting its freq to 0 ---------------------------*/
    if (motif[j].freq > 0)
    {
       /*   Set the group number  */
       if (motif[j].group < 1)
       {
          motif[j].group = group++;
          motif[j].sub_group = 1;
          sub_group = 2;
       }

       /*  Compare motif[j] with all motifs below it   */
       /* motif[k] is dropped if all of its sequences are in [j],
          and all overlap. The motifs don't have to be the
          SAME distance apart in all sequences ... */
       widthj = (int) motif[j].distance1 + (int) motif[j].distance2 + 3;
       for (k = j + 1; k < total_motifs && motif[j].freq > 0; k++)
         if (motif[k].freq > 0)   /*  may have already been dropped */
	 {
	     matches = 0;
             /*  seq_list[i] == # of times sequence i is in motif[k] */
             for (x = 0; x < NumSeqs; x++) seq_list[x] = 0;
             widthk = (int) motif[k].distance1 + (int) motif[k].distance2 + 3;
             countk = motif[k].freq - motif[k].dups;
	     for (x = 0; x < motif[k].freq; x++)
	     {
	        /* Make sure sequence numbers match before comparing
		   positions, if a sequence is represented by dups
                   will only use the first position */
                seq_list[ motif[k].seq_no[x] ]++;
                if (seq_list[ motif[k].seq_no[x] ] == 1)
                {
                   i = 0;
                   while (i < motif[j].freq &&
		          motif[k].seq_no[x] != motif[j].seq_no[i]) 
                              i++;
                   if (i < motif[j].freq )
                   {
	              /* Do we overlap?  */
                      dist = motif[j].pos[i] - motif[k].pos[x];
                      /*  dist >= 0:  kkkkkkkkkkkk
                                                 jjjjjjjjjjjjjjjj
                          dist <= 0:  jjjjjjjjjjjj
                                                 kkkkkkkkkkkkkk         */
                      if ((dist >= 0 && dist <= widthk)  ||
                          (dist <= 0 && (0-dist) <= widthj) )
	                        matches++;
                   }
                 }
	      }
	      /* Mark redundant motifs with a zero freq so that during
	       the next sort, those motifs will drop to bottom. */
	      if (matches == countk )
              {
	         motif[k].freq = 0;
	         motif[j].mots = motif[j].mots + 1;
	         /* Dropping motif out, so keep track of how many are left: */
	         real_total_motifs--;
	      }
              /*  Same group if at least half the common sequences match */
	      else if (matches >= round( (float) countk / 2.0) &&
                       motif[k].group < 1)
              {
	         motif[k].group = motif[j].group;
	         motif[k].sub_group = sub_group++;
	      }
	  }  /* end of if motif[k].freq > 0 */
    }  /* end of if motif[j].freq > 0 */
  }  /*  end of for j */
  printf(" %d", real_total_motifs);

/*-------- Fourth, if there are more than RELEVANT_MOTIFS left, then
           save no more than #mots/#groups in each group  ------------*/
  /*   sort by group, sub_group and freq-dups , but group 0 are first */
  if (real_total_motifs > RELEVANT_MOTIFS)
  {
/*NOTE>>>  Might be better to use compare_motgrps() instead ...  */
  qsort(motif, total_motifs, sizeof(struct motif_struct), compare_subgrps);
  maxkeep = round( (double) real_total_motifs / group );
  if (maxkeep < 1 ) maxkeep = 1;
  firstk = 0;
  while (firstk < total_motifs && motif[firstk].group == 0) firstk++;
  for (j=1; j < group; j++)
  {
      maxcount = 0;
      mincount = NumSeqs;
      k = firstk;
      while (k < total_motifs && motif[k].group == j)
      {
         if (motif[k].freq > 0)
         {
            if (motif[k].sub_group > maxkeep)
            {
                motif[k].freq = 0;
	        real_total_motifs--;
            }
/*
            countk = motif[k].freq - motif[k].dups;
            if (countk < mincount) mincount = countk;
            if (countk > maxcount) maxcount = countk;
*/
         }
         k++;
      }
      lastk = k - 1;
/*
      if (mincount < maxcount)
      {
         for (k = lastk; k > firstk; k--)
         {
            if ((motif[k].freq - motif[k].dups) == mincount)
            {
                motif[k].freq = 0;
	        real_total_motifs--;
            }
         }
      }
*/
      firstk = lastk + 1;
  } /* end of group j */
  }   /* end of RELEVANT_MOTIF check */
  printf(" %d", real_total_motifs);

/*-------- Fifth, sort again by freq-dups and score so 
           zero frequency motifs drop out ----------------------------*/
  /*---NOTE: This sort can scramble group order! ------*/
  qsort(motif, total_motifs, sizeof(struct motif_struct), compare_scores);

  if (real_total_motifs > RELEVANT_MOTIFS)
      real_total_motifs = RELEVANT_MOTIFS;
  if (real_total_motifs < 0) real_total_motifs = 0;
  printf(" %d:", real_total_motifs);
  printf(" last score = %d, groups = %d\n",
          motif[real_total_motifs - 1].score, group);

   return(real_total_motifs);
}  /* end of cut_motifs */
/*=======================================================================*/
/*    Map motifs in all sequences                                        */
/*=======================================================================*/
void map_seqs(max_group, total_motifs, motif)
int max_group, total_motifs;
struct motif_struct *motif;
{
  struct group_struct *groups;
  int i, j, x, group_no;

  groups = (struct group_struct *)
	      malloc(sizeof(struct group_struct) * total_motifs);
  if (groups == NULL) {
	printf("Couldn't allocate GROUPS.\n");
	exit(-1);
	}

  for (x = 0; x < NumSeqs; x++)  {
    group_no = 0;
    for (i = 0; i < total_motifs; i++)
      for (j = 0; j < motif[i].freq; j++)
	if (motif[i].seq_no[j] == x) {
	  groups[group_no].position = motif[i].pos[j];
	  groups[group_no].group_no = motif[i].group;
	  groups[group_no++].sub_no = motif[i].sub_group;
	  }
    if (group_no > 0) {
      qsort(groups, group_no, sizeof(struct group_struct), compare_groups);
      i = group_no;
      for (group_no = 0, j = 1; j < i; j++)
	if (groups[group_no].group_no == groups[j].group_no &&
	    groups[j].position - groups[group_no].position < 12)
	  groups[group_no].sub_no = 0;
	else { groups[++group_no].position = groups[j].position;
	       groups[group_no].group_no = groups[j].group_no;
	       groups[group_no].sub_no = groups[j].sub_no;}
      group_no++;
      }

    printf("                    Protein %s:\n", Seqname[x]);

    j = -1;
    for (i = 0; i < group_no; i++)  {
      for (j++; j < groups[i].position / 6; j++) printf(".");
      if (groups[i].group_no <= max_group) printf("%d",groups[i].group_no);
	else printf(".");
      if (groups[i].sub_no > 0) printf("%c",(char) groups[i].sub_no + 64);
      }
    for (j++; j < Len[x] / 6; j++) printf(".");
    printf(" %d\n\n",Len[x]);
    }
   free(groups);
}  /*  end of map_seqs */

/*------------------------------------------------------------------------*/
/*  Routines to convert amino acid symbols to numbers and vice versa.     */
/*    These routines can be found in "motmisc.c"                          */
/*------------------------------------------------------------------------*/
/*-----------------------------------------------------------------------*/
/*              Routines used by the sorting procedure                   */
/*-----------------------------------------------------------------------*/

/* Function to compare two motifs by frequency and score, in that
   order of priority.  Used to sort motif array in descending order
   by frequency, number of "merged" motifs and score: */
int compare_scores(motif_1, motif_2)
struct motif_struct *motif_1, *motif_2;
{
int sequences;

  /* Frequencies without the internal duplicates */
  sequences = (motif_2->freq - motif_2->dups) -
	      (motif_1->freq - motif_1->dups);

  /* If frequencies are identical, sort by #of motifs: */
  if (!sequences) sequences = (motif_2->mots - motif_1->mots);
   else return(sequences);
  /* If frequencies and motifs identical, sort by score */
  if (!sequences) return(motif_2->score - motif_1->score);
   else return(sequences);
}
/*====================================================================*/
/* Compare two motifs by group, count = freq-dups, #merged motifs,
    and score */
int compare_motgrps(motif_1, motif_2)
struct motif_struct *motif_1, *motif_2;
{
   int diff;

   diff = (motif_1->group - motif_2->group);
   if (diff) return(diff);
   else
   {
      diff = (motif_2->freq - motif_2->dups) -
             (motif_1->freq - motif_1->dups);
      if (diff) return(diff);
      else
      {
         diff = (motif_2->mots - motif_1->mots);
         if (diff) return(diff);
         else return(motif_2->score - motif_1->score);
      }
   }
}  /*  end of compare_motgrps()  */
/*====================================================================*/
/* Compare two motifs by group and sub_group   */
int compare_subgrps(motif_1, motif_2)
struct motif_struct *motif_1, *motif_2;
{
   int diff;

   diff = (motif_1->group - motif_2->group);
   if (diff) return(diff);
   else
   {
      diff = (motif_1->sub_group - motif_2->sub_group);
      if (diff) return(diff);
      else
      {
         diff = (motif_2->freq - motif_2->dups) -
                (motif_1->freq - motif_1->dups);
         return(diff);
      }
   }
}  /*  end of compare_subgrps()  */
 
/*======================================================================*/
/* Function to compare two groups by position.  Used to rank groups
   in ascending order by position for map_seqs()                        */
int compare_groups(group_1, group_2)
struct group_struct *group_1, *group_2;
{
  return(group_1->position - group_2->position);
}  /* end of compare_groups */

/*=======================================================================
     Opens a sequence file, reads line[], updates filepath[] and
     seqname[]
=======================================================================*/
FILE *getfile(line, filepath, seqname)
char *line, *filepath, *seqname;
{
   FILE *fp;
   char *ptr, ctemp[FNAMELEN];
   
   fp = NULL;
   seqname[0] = '\0';
   /*     Check for new path  */
   if (strstr(line, "/") != NULL || strstr(line, ":") != NULL)
   {
	ptr = strtok(line, " \n\t\r");
	strcpy(filepath, ptr);
   }
   /*    If not a title, assume it's a file name */
   else if (line[0] != '>')
   {
	ptr = strtok(line, " \n\t\r");
	if (ptr != NULL)
	{
		if ((int) strlen(ptr) > SNAMELEN - 1) ptr[SNAMELEN - 1] = '\0';
		strcpy(seqname, ptr);
		strcpy(ctemp, filepath);
		strcat(ctemp, seqname);
		strcat(ctemp, PROTEIN_EXTENSION);
		if ( (fp = fopen(ctemp, READ) ) == NULL)
			printf("***%s not found\n", ctemp);
	}
   }

   return(fp);
}  /*  end of getfile  */

/*======================================================================
       Read all sequences in file, fasta format assumed
	Updates global variables NumSeqs, Seqname[], Seq[], Len[]
========================================================================*/
int getseqs(fp)
FILE *fp;
{
   int n, ns, itemp, i, j, toolong;
   char line[MAXLINE], *ptr;

   n = 0;
   ns = NumSeqs - 1;
   
   while (!feof(fp) && fgets(line, MAXLINE, fp) != NULL)
   {
	if (line[0] == '>')
	{
	   n++; ns++;
	   ptr = strtok(line+1, " \t\r\n");
	   if ((int) strlen(ptr) > SNAMELEN - 1) ptr[SNAMELEN - 1] = '\0';
	   strcpy(Seqname[ns], ptr);
	   Seq[ns] = (int *) malloc(MAX_LENGTH * sizeof(int));
	   if (Seq[ns] == NULL)
	   {
		printf("Couldn't allocate Seq[%d]\n", ns);
		exit(-1);
	   }
	   Len[ns] = j = toolong = 0;
        }
        else if (Seq[ns] != NULL && Len[ns] < MAX_LENGTH + (int) strlen(line) )
        {
	   for (i=0; i < (int) strlen(line); i++)
           {
                if (toolong) i = strlen(line);
                itemp = aachar_to_num(line[i]);
		if (itemp >= 0 && itemp <= 20)
                {
                   if (j+1 < MAX_LENGTH)
                   {
  	  	      Seq[ns][j++] = itemp;
		      Len[ns] += 1;
                   }
                   else
                   {
                printf("ERROR reading %s, sequence longer than %d, truncated\n",
                        Seqname[ns], Len[ns]+1);
                       toolong = 1;
                   }
                }
           }
	}
   }

   NumSeqs = ns + 1;
   return(n);
}  /*  end of getseqs */
/*=====================================================================
	See if sequences should be shuffled, and do it
========================================================================*/
int shuffle()
{
   int shuff, i, j, k, n;
   char temp, shuffle[3];

   shuff = NO;
   if (RunType == 0 || RunType == 2)
   {
     printf("\n");
     printf("Use shuffled sequences [y/n; n]? ");
     gets(shuffle);
   }
   else if (RunType == 4 || RunType == 5)
     strcpy(shuffle, "y");
   else  
     strcpy(shuffle,"n");

   /*---- For RunTypes 4 or 5, sequences are always shuffled the same way.
       This is assured by reseting the generator with the same seed ---- */
   if (shuffle[0] == 'y' || shuffle[0] == 'Y')
   {
      shuff = YES;
      randomize();
      for (n = 0; n < NumSeqs; n++)
      {
          j = Len[n];
          for(i = 0; i < j; i++)
          {
             if (RunType == 4 || RunType == 5)
                 srand(i);                      /* i is the amino acid index */
             k = rand() % j;
             temp = Seq[n][i];
             Seq[n][i] = Seq[n][k];
             Seq[n][k] = temp;
          }
      }
   }

   return(shuff);
}  /* end of shuffle */
/*=====================================================================
	Print some basic statistics
	Expects global variables NumSeqs & Seq[][]
========================================================================*/
void print_stats()
{
   unsigned int aa_obs[20], total_aa;
   int n, i;

   for (i=0; i < 20; i++) aa_obs[i] = 0;
   total_aa = 0;

  for (n = 0; n < NumSeqs; n++)  {
    total_aa += Len[n];			/* Compute total number of aa's in */
    for (i = 0; i < Len[n]; i++)	/* all sequences and individual    */
      aa_obs[Seq[n][i]]++;		/* frequencies of the aa's.	   */
    }

  for (i = 0; i < 20; i++) {
    printf("  ");
    pr_num_to_aa(i);			/* Print amino acid's letter code */
    printf("   ");
    }
  printf("\n");

  /* Print aa frequency table: */
  for (i = 0; i < 20; i++) printf("%5d ", aa_obs[i]);
  printf("\n");

  /* Print frequencies as fraction of total number of aa's: */
  for (i = 0; i < 20; i++)  printf("%5.3f ", (float) aa_obs[i]/total_aa);
  printf("\n");

  printf("Total amino acids in %d proteins: %d\n\n", NumSeqs, total_aa);
}  /* end of print_stats */
/*======================================================================*/
   /* Found a three amino acid motif that occurs at least Signif
      number of times.  Scan seqs for the motif 
      and see how many sequences motif occurred in (variable count): */
int get_count(motif)
struct motif_struct *motif;
{
   int d1, d2, count, n, i, flag;

   count = 0;
   motif->freq = 0;
   for (i=0; i < MAXFREQ; i++)
   {  motif->seq_no[i] = motif->pos[i] = 0; }
   d1 = motif->distance1 - 1;
   d2 = motif->distance2 - 1;
   for (n = 0; n < NumSeqs; n++)   
   {
      flag = 0;
      for (i = 0; i < Len[n]; i++)
            if (Seq[n][i]==motif->aa1 &&
                i+1+d1 < Len[n] &&
                Seq[n][i+1+d1]==motif->aa2 &&
                i+2+d1+d2 < Len[n] &&
                Seq[n][i+2+d1+d2]==motif->aa3 &&
                              motif->freq < MAXFREQ)
            {
                motif->seq_no[motif->freq] = n;
                motif->pos[motif->freq++] = i;
                flag++;
            }

            if (flag) count++;
    }
    motif->dups = motif->freq - count;
    return(count);
}  /*  end of get_count */
/*==========================================================================*/
	/* Weed out sequential duplicates that start with the same first
	   amino acid in the same position (eliminates alternative
	   combinations of three aa's from motif of four aa's or higher): */
int check_dup(motif1, motif2)
struct motif_struct *motif1, *motif2;
{
   int duplicate, x;

   duplicate = YES;
   for (x = 0; x < motif1->freq && duplicate; x++)
      duplicate = (motif1->pos[x] == motif2->pos[x] &&
	           motif1->seq_no[x] == motif2->seq_no[x]);
   return(duplicate);
}  /* end of check_dup */
/*=======================================================================
	Makes an aa column vector for pamidx
========================================================================*/
void score_mot(motif)
struct motif_struct *motif;
{
   int offset, col, pos, seq, iseq, p_index, aa[MAXFREQ];
   double weights[MAXFREQ];

   /*   compute sequence weights and nident */
   pb_weights(motif, weights);

   offset = (int) (motif->domain - motif->distance1 - motif->distance2 - 1) / 2;
   motif->score = 0;
   for (col = 0; col < motif->domain; col++) 
   {
      for (iseq = 0; iseq < motif->freq; iseq++)
      {
         pos = motif->pos[iseq] + col - offset;
         seq = motif->seq_no[iseq];
         if (pos >= 0 && pos < Len[seq]) aa[iseq] = Seq[seq][pos]; 
         else                            aa[iseq] = -1;
      }
      motif->scores[col] = (p_index=wpamidx(motif->freq, aa, weights));
/*
      motif->scores[col] = (p_index=pamidx(motif->freq, aa));
*/

      /* Only add in high pam scores and convert back to
	            standard pam scores (by subtracting HighPass): */
      if (p_index >= SMatrix->highpass)
         motif->score += (p_index - SMatrix->highpass);
   }  /*  end of col */

   motif->score = motif->score / sqrt((float) motif->domain);

}  /*  end of score_mot */
/*======================================================================
	Put position-based sequence weights in the weights array
	col = block column, pos = sequence position
	Version for motifj:
======================================================================*/
void pb_weights(block, weights)
struct motif_struct *block;
double weights[MAXFREQ];
{
   struct pb_counts *pb;
   double factor, dtemp;
   int iseq, seq, pos, col, aa, width, offset, nident;

   offset = (int) (block->domain - block->distance1 - block->distance2 - 1) / 2;
   width = block->domain;
   nident = 0;

   pb = (struct pb_counts *) malloc(width*sizeof(struct pb_counts));

   for (col = 0; col < width; col++)
   { 
      pb[col].diffaas = 0.0;
      for (aa = 0; aa < MATSIZE; aa++)
         pb[col].naas[aa] = (double) 0.0;
   }
  
   for (col = 0; col < width; col++)
   {
      for (iseq = 0; iseq < block->freq; iseq++)
      {
         seq = block->seq_no[iseq];
	 pos = block->pos[iseq] + col - offset;
	 if (pos >= 0 && pos < Len[seq] )
	 {
	     aa = Seq[seq][pos];
             if (aa >= 0 && aa <= 19)
             {
                pb[col].naas[aa] += 1;
             }
/*
             else
             {
                printf("pb_weights:%d ignored\n", aa);
             }
*/
         }
      }
   }

   for (col = 0; col < width; col++)
   { 
      for (aa = 0; aa < 20; aa++)
      {
         if (pb[col].naas[aa] > 0.0)
         {
            pb[col].diffaas += 1;	/* # of different types of aas in col */
         }
	 if (pb[col].naas[aa] >= (double) Signif)
	 {
	     nident += 1; 	/* # of conserved cols in block */
	 }
      }
   }

   for (iseq = 0; iseq < block->freq; iseq++)
   {
      seq = block->seq_no[iseq];
      weights[iseq] = 0.0;
      for (col = 0; col < width; col++)
      {
	 pos = block->pos[iseq] + col - offset;
	 if (pos >= 0 && pos < Len[seq] )
	 {
	     aa = Seq[seq][pos];
             dtemp = pb[col].diffaas * pb[col].naas[aa];
             if (dtemp > 0.0) weights[iseq] += 1.0 / dtemp;
         }
      } 
   }
 
   /*  Normalize weights to add to #seqs == block->freq  */
   dtemp = 0.0;
   for (iseq = 0; iseq < block->freq; iseq++) dtemp += weights[iseq];
   factor = 1.0;
   if (dtemp > 0.0) factor = (double) block->freq/dtemp;
   for (iseq = 0; iseq < block->freq; iseq++) weights[iseq] *= factor;

   free(pb);
}  /* end of pb_weights */
/*===================================================================
    Realign sequences in the motif & return some information.
    Assigns positions to sequences not having the motif,
    may assign new positions to sequences with motif.
    Probably should re-compute column and block scores, but doesn't
    (motomat does).
=====================================================================*/
void realign(mot, dat)
struct motif_struct *mot;
struct realign_struct *dat;
{
   int x, i, j, k, count, offset, pos, position, datseq, motseq;
   int iscore, aa1, aa2, aas[20][MAX_DOMAIN_WIDTH];
   long int score;

   offset = (int) (mot->domain - mot->distance1 - mot->distance2 - 1) / 2;
   count = mot->freq - mot->dups;

   /*  Initialize  */
   for (x=0; x < NumSeqs; x++)
   {  
     dat->sequence[x] = 0;
     dat->max_score[x] = dat->max2_score[x] = (long int) 0;
     dat->max_pos[x] = dat->max2_pos[x] = 0;
     dat->motif_pos[x] = 0;
   }

  /*-----------------------------------------------------------------------*/
  /*    Order sequences with motif before those without */
  /*   seq_no[] may appear more than once in mot->, but only once in dat->
     EG: suppose NumSeqs = 5, mot->dups = 1, mot->freq = 5, count = 4
          x	mot->seq_no[x]		dat->sequence[x]
	  0	0			0
	  1	1			1
	  2	1			2
	  3	2			4  count = 4 seqs with motif
          4	4 mot->freq = 5		3  NumSeqs = 5
	-------------
	  5     3	(sequences without the motif)
  -------------------------------------------------------------------------*/
  j = 0;         				/* j is sequence counter */
  k = 0;					/* k is duplication counter */
  for (x = 0; x < NumSeqs + mot->dups; x++)
  {
      if (mot->seq_no[j + k] == x - k)
	dat->sequence[j++] = x - k;
      else
      {
	 if (j > 0 && mot->seq_no[j + k] == x - k - 1) k++;
	 else dat->sequence[x-k-j + count] = x-k;
      }
  }
 
  /*-----------------------------------------------------------------------*/
  /*  Compute Smith's "sliding sequence column scores",  aas[aa][i] is
      the average pam score of aa in col i of all occurences of motif */
   for (i=0; i < mot->domain; i++)
   {
      for (aa1=0; aa1 < 20; aa1++)
      {
         score = 0;
         for (x=0; x < mot->freq; x++)
         {
            pos = mot->pos[x] + i - offset;
            if (pos >= 0 && pos < Len[ mot->seq_no[x] ]  )
            {
               aa2 = Seq[ mot->seq_no[x] ][pos];
               score += (long int) (SMatrix->scores[aa1][aa2] + 1) * 100 - SMatrix->highpass;
            }
         }
         if (score > 0) aas[aa1][i] = (int) (score / mot->freq);
         else               aas[aa1][i] = 0;
      }
   }


  /*-----------------------------------------------------------------------*/
  /*   Now realign each sequence in dat->sequence[] order  
       The scores used for the realignment are never modified  */
  for (x = 0; x < NumSeqs; x++) 
  {
      datseq = dat->sequence[x];
      dat->max_score[x] = 0;
      dat->max_pos[x] = -1;

      /* Move along entire length of protein, looking for maximum fit
	 (also records next best fit in max2_pos): */
      for (position = 0; position < Len[datseq]; position++)
      {
	score = 0;
	for (i = 0; i < mot->domain; i++)
        {
          iscore = mot->scores[i] - SMatrix->highpass;
          if (iscore <= 0) iscore = 0;
          pos = position + i - offset;
	  if (pos >= 0 && pos < Len[datseq])
	  {
	      aa1 = Seq[datseq][pos];
	      if ( (aa1 >= 0 && aa1 < 20) && iscore)
		score += (long int) aas[aa1][i] * iscore;
	  }
        }
	if (score > dat->max_score[x]) 
        {
	  dat->max2_score[x] = dat->max_score[x];
	  dat->max2_pos[x] = dat->max_pos[x];
	  dat->max_score[x] = score;
	  dat->max_pos[x] = position;
	}
      } /* end of for position */

      position = dat->max_pos[x];
      /*---  Add info about sequences without the motif            JGH*/
      /*  This assumes the first "count" sequence numbers in
          dat->sequence[] are the unique numbers among the first
          mot->freq entries of mot->seq_no[] (see example above) */
      if (x >= count) 
      { 
	 mot->seq_no[x + mot->dups] = datseq; 
	 mot->pos[x + mot->dups] = position;
      } 
      /*---- Update info about sequences with motif that were realigned */
      else 
      {
          /*  Find first corresponding mot->seq_no[] sequences 
              (can occur more than once if mot->dups > 0  */
          motseq = -1;
          i = 0;
          while (motseq < 0 && i < mot->freq)
          {
             if (mot->seq_no[i] == datseq)
             {
                motseq = datseq;
                dat->motif_pos[x] = mot->pos[i];
                mot->pos[i] = position;
             }
             i++;
         }
      }
 }   /*  end of sequence x */

}  /* end of realign */
/*========================================================================
       Write an output file for motomat
==========================================================================*/
void write_motifs(total_motifs, motif)
int total_motifs;
struct motif_struct *motif;
{
  FILE *mot;
  char temp;
  int i, j;

  /* Open an output file for the motifs:  Batch_Filename.mot               */
  if (strlen(Batch_Filename) != 0)
  {
     Mot_Filename[0] = '\0';
     strncat(Mot_Filename, Batch_Filename+Batsplit->dir_len,
             Batsplit->name_len);
     Mot_Filename[Batsplit->name_len] = '\0';
     strcat(Mot_Filename, ".mot");
  }
  else
     strcpy(Mot_Filename, "motifj.mot");
  if ( (mot=fopen(Mot_Filename, "w+b")) == NULL)
  {
     printf("\nUnable to open file %s", Mot_Filename);               /*JGH*/
     exit(-1);
  }
  i = VERSION;
  fwrite(&i, sizeof(int), 1, mot);
  fwrite(&RunType, sizeof(int), 1, mot);
  fwrite(&Signif, sizeof(int), 1, mot);
  fwrite(&Dups, sizeof(int), 1, mot);
  fwrite(&Distance, sizeof(int), 1, mot);
  fwrite(&NumSeqs, sizeof(int), 1, mot);
  fwrite(&total_motifs, sizeof(int), 1, mot);
  fwrite(Len, sizeof(int), NumSeqs, mot);
  fwrite(Seqname, SNAMELEN*sizeof(char), NumSeqs, mot);
  for (i=0; i max) {max = Len[i]; imax = i;}
  }
  /* Open an output file for the pros:  Batch_Filename.pros               */
  if (strlen(Batch_Filename) != 0)
  {
     filename[0] = '\0';
     strncat(filename, Batch_Filename+Batsplit->dir_len,
             Batsplit->name_len);
     filename[Batsplit->name_len] = '\0';
     strcat(filename, ".motifj.pros");
  }
  else
     strcpy(filename, "motifj.pros");
  if ( (out=fopen(filename, "w+b")) == NULL)
  {
     printf("\nUnable to open file %s", filename);               /*JGH*/
  }
  else
  {
     for (i=0; i%s %d", Seqname[i], Len[i]);
        if (i == imin)      fprintf(out, " MINIMUM\n");
        else if (i == imax) fprintf(out, " MAXIMUM\n");
             else           fprintf(out, "\n");
        for (j=0; j>>  some routines are duplicated in ../blimps/protomat.c <<<
-------------------------------------------------------------------------
   6/20/91  J. Henikoff
   2/26/98 Changed get_ids() to mark sequences as fragments if PS=P in .lis
   4/18/98 Backed out 7/7/97; caused "ACH3_CAEEL" to be extracted for
		"H3_CAEEL", etc.
   6/ 6/98 Changed extract_seqs() to match any |-delimited field following >.
   8/24/99 Changed check_entry() to match any part of |-delimited fields
		in either .lis or db name
  11/18/99 Changed check_entry() to return 1st sequence if id->entry = "-"
   2/20/00 Changed check_entry() to modify id->full_entry
   5/ 2/00 check_entry() bug fix
   >>>>>>>>>>>>>>>   Blimps 3.4 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
   6/25/00 Changed get_ids() & check_entry() to use only first 2 parts of seq_name
   8/11/00 init_dbs() Added dbs[]->acc
  10/10/05 check_entry(): New trembl format; O88996_RAT , etc.
  12/26/06 Problem with get_ids() for uextract when : on seq line
=========================================================================*/
#include 
#include 
#include "motifj.h"

struct db_id *check_entry();

/*=======================================================================*/
/*---- Global scoring matrix , order is :
		  A R N D C Q E G H I L K M F P S T W Y V X   -----------*/

/* BLOSUM60 matrix with each cell offset by 8 to make all scores
   non-negative */
int bl60_highpass = 8;
char bl60_matrix[21][21]={
12, 7, 7, 6, 7, 7, 7, 8, 7, 7, 7, 7, 7, 6, 8, 9, 8, 5, 6, 8, 8, /*A*/
 7,13, 8, 7, 5, 9, 8, 6, 8, 5, 6,10, 7, 6, 6, 7, 7, 6, 6, 6, 8, /*R*/
 7, 8,14, 9, 6, 8, 8, 8, 8, 5, 5, 8, 6, 5, 6, 9, 8, 6, 6, 5, 8, /*N*/
 6, 7, 9,14, 4, 8, 9, 7, 7, 5, 5, 7, 5, 5, 6, 8, 7, 4, 6, 5, 8, /*D*/
 7, 5, 6, 4,17, 6, 5, 6, 5, 7, 7, 5, 6, 6, 6, 7, 7, 5, 5, 7, 8, /*C*/
 7, 9, 8, 8, 6,13,10, 6, 9, 6, 6, 9, 8, 5, 7, 8, 7, 6, 6, 6, 8, /*Q*/
 7, 8, 8, 9, 5,10,13, 6, 8, 5, 6, 9, 6, 5, 7, 8, 7, 6, 6, 6, 8,
 8, 6, 8, 7, 6, 6, 6,14, 6, 5, 5, 7, 5, 5, 6, 8, 7, 6, 5, 5, 8,
 7, 8, 8, 7, 5, 9, 8, 6,15, 5, 5, 7, 6, 7, 6, 7, 6, 6, 9, 5, 8,
 7, 5, 5, 5, 7, 6, 5, 5, 5,12,10, 6, 9, 8, 5, 6, 7, 6, 7,11, 8,
 7, 6, 5, 5, 7, 6, 6, 5, 5,10,12, 6,10, 8, 6, 6, 7, 6, 7, 9, 8,
 7,10, 8, 7, 5, 9, 9, 7, 7, 6, 6,12, 7, 5, 7, 8, 7, 5, 6, 6, 8,
 7, 7, 6, 5, 6, 8, 6, 5, 6, 9,10, 7,14, 8, 6, 6, 7, 6, 7, 9, 8,
 6, 6, 5, 5, 6, 5, 5, 5, 7, 8, 8, 5, 8,14, 5, 6, 6, 9,11, 7, 8,
 8, 6, 6, 6, 6, 7, 7, 6, 6, 5, 6, 7, 6, 5,15, 7, 7, 5, 6, 6, 8,
 9, 7, 9, 8, 7, 8, 8, 8, 7, 6, 6, 8, 6, 6, 7,12, 9, 6, 6, 6, 8,
 8, 7, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 9,12, 6, 6, 8, 8,
 5, 6, 6, 4, 5, 6, 6, 6, 6, 6, 6, 5, 6, 9, 5, 6, 6,18,10, 6, 8,
 6, 6, 6, 6, 5, 6, 6, 5, 9, 7, 7, 6, 7,11, 6, 6, 6,10,15, 7, 8,
 8, 6, 5, 5, 7, 6, 6, 5, 5,11, 9, 6, 9, 7, 6, 6, 8, 6, 7,12, 8,
 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 0  /* X */
};

/* BLOSUM62 matrix with each cell offset by 4 to make all scores
   non-negative */
int bl62_highpass = 4;
/* A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  X  */
char bl62_matrix[21][21]={
   8, 3, 2, 2, 4, 3, 3, 4, 2, 3, 3, 3, 3, 2, 3, 5, 4, 1, 2, 4, 0, 
   3, 9, 4, 2, 1, 5, 4, 2, 4, 1, 2, 6, 3, 1, 2, 3, 3, 1, 2, 1, 0, 
   2, 4,10, 5, 1, 4, 4, 4, 5, 1, 1, 4, 2, 1, 2, 5, 4, 0, 2, 1, 0, 
   2, 2, 5,10, 1, 4, 6, 3, 3, 1, 0, 3, 1, 1, 3, 4, 3, 0, 1, 1, 0, 
   4, 1, 1, 1,13, 1, 0, 1, 1, 3, 3, 1, 3, 2, 1, 3, 3, 2, 2, 3, 0, 
   3, 5, 4, 4, 1, 9, 6, 2, 4, 1, 2, 5, 4, 1, 3, 4, 3, 2, 3, 2, 0, 
   3, 4, 4, 6, 0, 6, 9, 2, 4, 1, 1, 5, 2, 1, 3, 4, 3, 1, 2, 2, 0, 
   4, 2, 4, 3, 1, 2, 2,10, 2, 0, 0, 2, 1, 1, 2, 4, 2, 2, 1, 1, 0, 
   2, 4, 5, 3, 1, 4, 4, 2,12, 1, 1, 3, 2, 3, 2, 3, 2, 2, 6, 1, 0, 
   3, 1, 1, 1, 3, 1, 1, 0, 1, 8, 6, 1, 5, 4, 1, 2, 3, 1, 3, 7, 0, 
   3, 2, 1, 0, 3, 2, 1, 0, 1, 6, 8, 2, 6, 4, 1, 2, 3, 2, 3, 5, 0, 
   3, 6, 4, 3, 1, 5, 5, 2, 3, 1, 2, 9, 3, 1, 3, 4, 3, 1, 2, 2, 0, 
   3, 3, 2, 1, 3, 4, 2, 1, 2, 5, 6, 3, 9, 4, 2, 3, 3, 3, 3, 5, 0, 
   2, 1, 1, 1, 2, 1, 1, 1, 3, 4, 4, 1, 4,10, 0, 2, 2, 5, 7, 3, 0, 
   3, 2, 2, 3, 1, 3, 3, 2, 2, 1, 1, 3, 2, 0,11, 3, 3, 0, 1, 2, 0, 
   5, 3, 5, 4, 3, 4, 4, 4, 3, 2, 2, 4, 3, 2, 3, 8, 5, 1, 2, 2, 0, 
   4, 3, 4, 3, 3, 3, 3, 2, 2, 3, 3, 3, 3, 2, 3, 5, 9, 2, 2, 4, 0, 
   1, 1, 0, 0, 2, 2, 1, 2, 2, 1, 2, 1, 3, 5, 0, 1, 2,15, 6, 1, 0, 
   2, 2, 2, 1, 2, 3, 2, 1, 6, 3, 3, 2, 3, 7, 1, 2, 2, 6,11, 3, 0, 
   4, 1, 1, 1, 3, 2, 2, 1, 1, 7, 5, 2, 5, 3, 2, 2, 4, 1, 3, 8, 0, 
   0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0  
};
/*=======================================================================*/
/* Number to amino acid                  */
char *num_to_aachar(num)
int num;
{
  switch (num) {
    case 0: return("A");
    case 1: return("R");
    case 2: return("N");
    case 3: return("D");
    case 4: return("C");
    case 5: return("Q");
    case 6: return("E");
    case 7: return("G");
    case 8: return("H");
    case 9: return("I");
    case 10: return("L");
    case 11: return("K");
    case 12: return("M");
    case 13: return("F");
    case 14: return("P");
    case 15: return("S");
    case 16: return("T");
    case 17: return("W");
    case 18: return("Y");
    case 19: return("V");
    case 20: return("X");
    case -1: return(".");
    default: return("*");		/* Should never happen */
    }
}
/*======================================================================*/
/* Amino acid to number                  */
/*  B is changed to D, Z is changed to E, O and J are changed to X  */
int aachar_to_num(ch)
char ch;
{
  if (ch >= 97 && ch <= 122) ch = ch - 32;	/* Make letters upper case */
  switch (ch) {
    case 'A': return(0);
    case 'R': return(1);
    case 'N': return(2);
    case 'D': return(3);
    case 'B': return(3);
    case 'C': return(4);
    case 'Q': return(5);
    case 'E': return(6);
    case 'Z': return(6);
    case 'G': return(7);
    case 'H': return(8);
    case 'I': return(9);
    case 'L': return(10);
    case 'K': return(11);
    case 'M': return(12);
    case 'F': return(13);
    case 'P': return(14);
    case 'S': return(15);
    case 'T': return(16);
    case 'W': return(17);
    case 'Y': return(18);
    case 'V': return(19);
    case 'J': return(20);
    case 'O': return(20);
    case 'X': return(20);
    case '.': return(-1);
    default: return(-1);
    }
}
/*=====================================================================*/
/* Use internal numerical representation to print amino acid: */
void pr_num_to_aa(num)
char num;
{
  switch (num) {
    case 0: printf("A"); break;
    case 1: printf("R"); break;
    case 2: printf("N"); break;
    case 3: printf("D"); break;
    case 4: printf("C"); break;
    case 5: printf("Q"); break;
    case 6: printf("E"); break;
    case 7: printf("G"); break;
    case 8: printf("H"); break;
    case 9: printf("I"); break;
    case 10: printf("L"); break;
    case 11: printf("K"); break;
    case 12: printf("M"); break;
    case 13: printf("F"); break;
    case 14: printf("P"); break;
    case 15: printf("S"); break;
    case 16: printf("T"); break;
    case 17: printf("W"); break;
    case 18: printf("Y"); break;
    case 19: printf("V"); break;
    case 20: printf("."); break;
    case -1: printf("."); break;
    default: printf("*");		/* Should never happen */
    }
}
/*======================================================================*/
void pr_num_to_aa_space(c)
char c;
{
	pr_num_to_aa(c);
	printf(" ");
}
/*=======================================================================
      getscore reads a file containing a scoring matrix and
      loads it into Score[MATSIZE][MATSIZE].  Assumes alphabet for file is
      listed on first non-blank line.
=========================================================================*/
void getscore(matrix)
struct score *matrix;
{
   char filename[FNAMELEN], line[MAXLINE], chigh[6], *ptr;
   FILE *fin, *fstp;
   int alpha[MATSIZE+10], nrows, ncols, row, col, i;

   if ((fstp = fopen("protomat.stp", "rt")) == NULL)
   {
      fin = NULL;
      strcpy(filename, "def");
   }
   else
   {
      line[0] = filename[0] = '\0';
      while(fgets(line, sizeof(line), fstp) != NULL)
      {
	  if (strncmp(line, "SCORE", 5) == 0)
	  {
	     ptr = strtok(line, " ,\t\n");
	     if (ptr != NULL)
	     {
		ptr = strtok(NULL, " ,\t\n");
		if (ptr != NULL) strcpy(filename, ptr);
	     }
	     if ((fin = fopen(filename, "rt")) == NULL)
	     {
	printf("Could not open %s, using default BLOSUM scoring matrix\n",
			    filename);
		strcpy(filename, "def");
	     }
	  }
	  else if (strncmp(line, "HIGH", 4) == 0)
	  {
	     ptr = strtok(line, " ,\t\n");
	     if (ptr != NULL)
	     {
		ptr = strtok(NULL, " ,\t\n");
		if (ptr != NULL) strcpy(chigh, ptr);
		matrix->highpass = atoi(chigh);
	     }
	  }
      }
      fclose(fstp);
   }

/*----------Read file until first non-blank line --------------*/
   if (fin != NULL)
   {
      printf("\nUsing scoring matrix from %s\n", filename);
      line[0] = '\0';
      while (strlen(line) < 1 && fgets(line, sizeof(line), fin) != NULL)
	    ;
/*------See if the first line has characters on it ------------*/
      for (col=0; col < 30; col++) alpha[col] = -1;
      if (strstr(line, "A") != NULL)	/* This line has characters */
      {
	 row = 0;	/* # of alphabetic characters on the line */
	 for (i=0; i= 0)
	    {
	       alpha[row] = col;
	       row++;
	    }
	    else if (isalpha(line[i])) row++; /* skip over other alpha */
	 }
      }
/*-------Get the data values now ------------*/
      for (row=0; rowscores[row][col] = -99;		/* Null value */
      nrows = 0;
      line[0] = '\0';
      while (fgets(line, sizeof(line), fin) != NULL)
      {
	 if (strlen(line) > 1)
	 {
	    if (alpha[nrows] >= 0 && alpha[nrows] < MATSIZE)
	    {
	       row = alpha[nrows]; ncols = 0;
	       ptr = strtok(line, " ,\t\n");
	       while (ptr != NULL)
	       {
		  if (strspn(ptr, "+-0123456789") == strlen(ptr))
		  {
		     col = alpha[ncols];
		     if (col >= 0 && col < MATSIZE)
			matrix->scores[row][col] = atoi(ptr);
		     ncols++;
		  }
		  ptr = strtok(NULL, " ,\t\n");
	       }
	    }
	    nrows++;
	 }
      }

/*-------If some entries are still missing, assume symmetry ---------*/
      for (row=0; rowscores[row][col] == -99)
		  matrix->scores[row][col] = matrix->scores[col][row];
/*	   printf("%2d ", matrix->scores[row][col]); */
	}
/*	printf("\n"); */
      }
      fclose(fin);
   }
   else    /*   no input file  */
   {
      printf("\nUsing BLOSUM62 scoring matrix.\n");
      matrix->highpass = bl62_highpass;
      for (row=0; rowscores[row][col] = bl62_matrix[row][col];
/*	    printf("%2d ", matrix->scores[row][col]);*/
	 }
/*	 printf("\n");*/
      }
   }
   matrix->highpass *= 100;
/*   printf("HighPass = %d", matrix->highpass);*/
}   /* end of getscore() */
/*======================================================================*/
void init_dbs(dbs)
struct db_info *dbs[];
{
   int i;

   for (i=0; itype = (char *) malloc(10 * sizeof(char));
      dbs[i]->start = (char *) malloc(12 * sizeof(char));
      dbs[i]->desc = (char *) malloc(12 * sizeof(char));
      dbs[i]->seq = (char *)  malloc(12 * sizeof(char));
      dbs[i]->end = (char *)  malloc(6 * sizeof(char));
   }

   dbs[GB]->type = "GENBANK";
   dbs[GB]->start = "LOCUS";
   dbs[GB]->desc = "DEFINITION";
   dbs[GB]->acc = "ACCESSION";
   dbs[GB]->seq = "ORIGIN";
   dbs[GB]->end = "//";
   dbs[GB]->title_offset = 12;
   dbs[GB]->seq_offset = 10;

   dbs[PIR]->type = "PIR";
   dbs[PIR]->start = "ENTRY";
   dbs[PIR]->desc = "TITLE";
   dbs[PIR]->seq = "SEQUENCE";
   dbs[PIR]->end = "///";
   dbs[PIR]->title_offset = 16;
   dbs[PIR]->seq_offset = 8;

   dbs[EMBL]->type = "EMBL";
   dbs[EMBL]->start = "ID";
   dbs[EMBL]->desc = "DE";
   dbs[EMBL]->acc = "AC";
   dbs[EMBL]->seq = "SQ";
   dbs[EMBL]->end = "//";
   dbs[EMBL]->title_offset = 5;
   dbs[EMBL]->seq_offset = 5;

   dbs[UNI]->type = "UNI";
   dbs[UNI]->start = ">";
   dbs[UNI]->desc = ">";
   dbs[UNI]->seq = "";
   dbs[UNI]->end = "*";
   dbs[UNI]->title_offset = 1;
   dbs[UNI]->seq_offset = 0;

   dbs[VMS]->type = "VMS";
   dbs[VMS]->start = ">";		/* first line */
   dbs[VMS]->desc = "";			/* second line */
   dbs[VMS]->seq = "";			/* third line */
   dbs[VMS]->end = "*";
   dbs[VMS]->title_offset = 4;		/* first line only */
   dbs[VMS]->seq_offset = 0;

   dbs[PROC]->type = "PROCLASS";	/* PCFam, not PCSeq  */
   dbs[PROC]->start = "PCF_AC";
   dbs[PROC]->desc = "PCF_DE";
   dbs[PROC]->seq = "PCS_ID";
   dbs[PROC]->end = "//";
   dbs[PROC]->title_offset = 12;
   dbs[PROC]->seq_offset = 12;

}   /*  end of init_dbs */
/*======================================================================
      type_dbs() determines what type a database is from the allowable
      types
========================================================================*/
int type_dbs(fin, dbs)
FILE *fin;
struct db_info *dbs[];
{
   int db, i;
   char line[MAXLINE];

   db = -1;
/*---------  Figure out what type of input file it is ------------------*/
   while (db < 0 && fgets(line, sizeof(line), fin) != NULL)
      for (i=0; istart, strlen(dbs[i]->start)) == 0)
	    db = i;
   if (db == VMS && line[3] != ';')	/* start=='>' is ambiguous */
	db = UNI;
   if (db < 0 || db >= MAXDB) db = -1;	/* can't tell what it is */

   rewind (fin);
   return(db);
}  /* end of type_dbs */
/*====================================================================*/
/*  This is Kernighan & Ritchie's ASCII to integer conversion (p. 58) */
/*====================================================================*/
int kr_atoi(s)
char s[];
{
   int i, n, sign;

   for (i=0; s[i]==' ' || s[i]=='\n' || s[i]=='\t'; i++)
		;
   sign = 1;
   if (s[i] == '+' || s[i] == '-')
      sign = (s[i++]=='+') ? 1 : -1;
   for (n=0; s[i] >= '0' && s[i] <= '9'; i++)
      n = 10 * n + s[i] - '0';
   return(sign * n);
}  /* end of kr_atoi */
/*=====================================================================*/
/*  This is Kernighan & Ritchie's integer to ASCII conversion (p. 60) */
/*====================================================================*/
void kr_itoa(n, s)
int n;
char s[];
{
   int c, i, j, sign;

   sign = n;
   if (sign < 0) n = -n;
   i = 0;
   do {
      s[i++] = n % 10 + '0';
   }  while ( (n /= 10) > 0);
   if (sign < 0) s[i++] = '-';
   s[i] = '\0';
   for (i=0, j=strlen(s)-1; idir_len=new->file_len=new->name_len=0;
   i = strlen(filename);
   /*-------  Read the file name backwards ---------------*/
   while (i>=0 && (!ext_len || !new->dir_len))
   {
      /*---  Last period in string => file extension ----*/
      if (filename[i] == '.') ext_len = strlen(filename)-i;
      /*--- Last slash in string => directory -----------*/
      if (filename[i] == '/' && new->dir_len == 0) new->dir_len = i+1;
      /*--- Last colon and no slash after it => DOS directory -----*/
/*      if (filename[i] == ':' && new->dir_len == 0) new->dir_len = i+1; */
      i--;
   }
   new->file_len = strlen(filename)-new->dir_len;
   new->name_len = new->file_len - ext_len;

   return(new);
}
/*========================================================================
  dir_dos(): DOS code to get name of directory from line and
       create it if necessary
===========================================================================*/
/*char *dir_dos(line)
char *line;
{
   char tname[FNAMELEN], mem[MAXLINE], pros[FNAMELEN], *ptr;
   char filename[FNAMELEN];
   int test;
   FILE *ftmp;

   pros[0] = '\0';
   if (line[0] != '>' &&
	  (strstr(line, "\\") != NULL || strstr(line, ":") != NULL) )
   {
         ptr = strtok(line, "\n\r");
         strcpy(pros, ptr);
	 if (pros[strlen(pros)-1] != '\\') strcat(pros, "\\");
   }
*/
/*-------------------Create the directory ---------------------------------*/
/*
   if (strlen(pros))
   {
      tmpnam(tname);
      strcpy(filename, pros);
      strcat(filename, tname);
      if ( (ftmp=fopen(filename, "w"))== NULL)
      {
	 strcpy(tname, pros);     
	 tname[strlen(pros)-1] = '\0';
	 sprintf(mem, "md %s", tname);
	 test = system(mem);
	 if (test == 0) printf("\nCreated directory %s", tname);
	 else
	 {
	    printf("\nUnable to create directory %s", tname);
	    printf("\nProtein files will be placed in current directory");
	    pros[0] = '\0';
	 }
      }
      else
      {
	 fclose(ftmp);
	 unlink(filename);
      }
   }
   return(pros);
} 
*/
/*=======================================================================
  dir_unix(): UNIX code to get name of directory from line and
	      create it if necessary
==========================================================================*/
char *dir_unix(line)
char *line;
{
   char tname[FNAMELEN], mem[MAXLINE], pros[FNAMELEN], *ptr;
   int test;
   DIR *dp;

   pros[0] = '\0';
   if ( (line[0] != '>') && (strstr(line, "/") != NULL) )
   {
         ptr = strtok(line, "\n\r");
         strcpy(pros, ptr);
	 if (pros[strlen(pros)-1] != '/') strcat(pros, "/");
   }
/*-----------------Create the directory ---------------------------------*/
   if (strlen(pros))
   {
      strcpy(tname, pros);
      tname[strlen(pros)-1] = '\0';
      sprintf(mem, "mkdir %s", tname);
      if ((dp=opendir(tname))==NULL)
      {
         test=system(mem);
         if (test == 0) printf("\nCreated directory %s\n", tname);
         else
         {
            printf("\nUnable to create directory %s", tname);
            printf("\nProtein files will be placed in current directory\n");
            pros[0] = '\0';
         }
      }
   }
   return(pros);
}    /* end of dir_unix */
/*======================================================================
     Create & intialize a db_id structure
========================================================================*/
struct db_id *makedbid()
{
   struct db_id *new;

   new = (struct db_id *) malloc (sizeof(struct db_id));
   new->entry[0] = new->full_entry[0] = '\0';
   new->pir[0] = '\0';
   new->ps[0] = '\0';
   new->len = 0;
   new->rank = new->score = 0;
   new->lst = NO;
   new->found = NO;
   new->block = NO;
   new->frag = NO;
   new->search = NO;
   new->pvalue = (double) 0.0;
   new->next = NULL;
   new->prior = NULL;
   return(new);
}  /*  end of makedbid */

/*======================================================================
     get_ids() reads a .lis or .lst file & inserts the sequences
       found in it into a list sorted by sequence name.
========================================================================*/
int get_ids(flis, ids)
FILE *flis;
struct db_id *ids;
{
   char line[MAXLINE], ctemp[20], *ptr;
   struct db_id *id, *last, *new;
   int len, nids, i, bar;

   nids = 0;
   while(!feof(flis) && fgets(line, MAXLINE, flis) != NULL)
   {		/* skip over title or unix directory lines */
      if (strlen(line) && 
          line[0] != '>' && strstr(line, "/") == NULL)
      {
	 nids += 1;
	 new = makedbid();
/*-----  Copy up to the first space or carriage return ------------*/
	 len = strcspn(line, " \t\r\n");
	 if (len > 2*SNAMELEN) len = 2*SNAMELEN;
	 strncpy(new->full_entry, line, len);  new->full_entry[len] = '\0';
	 if (len > SNAMELEN) len = SNAMELEN;
	 strncpy(new->entry, line, len);  new->entry[len] = '\0';
	 /* Only want max of two parts in id->entry   */
         bar=NO; i=0;
	 for (i=0; ientry[i] == '|')
		{
		   if (!bar) { bar=YES;   }
		   else { new->entry[i] = '\0'; i = len;  }
		}
         }
	 last = ids;  id = ids->next;
/*-------- Get any other information on the .lis file line --------*/
	 if (strstr(line, "FRAGMENT") != NULL) new->frag = YES;
	 if (strstr(line, "BLOCK") != NULL) new->block = YES;
	 if (strstr(line, "LST") != NULL) new->lst = YES;
	 ptr = strstr(line, "PS=");
	 if (ptr != NULL)
         {
	    strncpy(new->ps, ptr+3, 1); new->ps[1] = '\0';
            if (strcmp(new->ps, "P") == 0) new->frag = YES;
         }
	 ptr = strstr(line, "LENGTH=");
	 if (ptr != NULL)
	 {
	    len = strcspn(ptr+7, " \t\r\n");
	    if (len > 0)
	    {
	       strncpy(ctemp, ptr+7, len); ctemp[len] = '\0';
	       new->len = atoi(ctemp);
	    }
	 }
/*------  Insert id into a sorted list ----------------------------*/
	 while (id != NULL && id->entry != NULL &&
	     strcmp(id->entry, new->entry) < 0)
	 {
	    last = id;
	    id = id->next;
	 }
	 new->prior = last;
	 new->next = id;
	 last->next = new;
	 if (id != NULL) id->prior = new;
	 new = NULL;
      }
   }
   return(nids);
}  /*  end of get_ids */

/*======================================================================
     Extracts the sequences from file fin if they appear in the
     sorted list ids.
=======================================================================*/
int extract_seqs(nids, dbs, fin, ids, pros, fout, frag)
int nids, frag;
struct db_info *dbs[MAXDB];
FILE *fin, *fout;
struct db_id *ids;
char *pros;
{
   struct db_id *id;
   int nseq, i, db, out, here, nout;
   char line[MAXLINE], title[MAXLINE], temp[MAXLINE], *ptr;
   char foutname[FNAMELEN];

   nseq = nout = 0;
   if (fout == NULL) here = YES;	/* create output files here */
   else here = NO;		
   db = type_dbs(fin, dbs);
   if (db < 0 || db >= MAXDB)
   {
      printf("\nCannot determine type of input file");
      return(-1);
   }
   printf("\nProcessing input file as %s", dbs[db]->type);
   if (db==VMS)
   {
      printf("\n WARNING: Titles are sometimes truncated in this format;");
      printf("\n          I may not be able to distinguish fragments.");
   }


   /*--------Get the first record  -------------------------------*/
   fgets(line, MAXLINE, fin);
   /*---------Read and process the rest of the file -----------*/
   while (!feof(fin) && nseq < nids)
   {
      if (strncmp(line, dbs[db]->start, strlen(dbs[db]->start)) == 0)
      {
	 /*----- Make VMS work like UNI by getting the 2nd title line --*/
	 if (db == VMS )	/* get the 2nd line, too */
	 {
	   ptr=strtok(line, "\n\r");		/* get rid of CRLF */
	   strcat(line, " ");
	   if (fgets(temp, MAXLINE, fin) != NULL) strcat(line, temp);
	 }

	 /*--------Check to see if this sequence is in the list --------*/
	 /* Don't assume the entry is of any particular length, just
	    copy from the offset until the first whitespace */
         strcpy(temp, line);
         ptr = strtok(temp+dbs[db]->title_offset, " \n\t\r");

	 /*  See if want this entry  */
	 id = check_entry(ids, ptr);
	 if (id != NULL)		/*  want this entry */
	 {
	    nseq++;  id->found = YES; id->len = 0;
	    /*----  Check to see if this sequence is a fragment ----- */
	    if (strstr(line, "FRAGMENT") != NULL ||
		   strstr(line, "fragment") != NULL) id->frag = 1;
           /*----- Don't create an output file if the sequence is a
                   fragment or a Prosite "possible" ----------------*/
            out = YES;
            if (!frag &&
                (id->frag || (strcmp(id->ps, "P") == 0))) out = NO;
	   /*------ Create the output file ---------*/
            if (out)
            {
               nout++;
	       printf("\n%d. Entry %s found...", nseq, id->entry);
               if (here)		/* separate file */
               {  
	          strcpy(foutname, pros);
	          strcpy(temp, id->entry);  temp[SNAMELEN-1] = '\0';
	          strcat(foutname, temp);
	          if (db == GB) strcat(foutname, ".dna");
	          else strcat(foutname, ".pro");
	          printf("Creating %s", foutname);
	          /*---Open file: should check whether it already exists... */
	          if ( (fout = fopen(foutname, "w+t")) == NULL)
	          {
		     printf("\nCannot open %s\n", foutname);
	   	     return(-1);
	          }
               }
            }
            else
            {
	       printf("\n%d. Entry %s found...but not extracted",
                       nseq, id->entry);
               printf(" because FRAGMENT or PROSITE=P");
            }

	    /*------- Set up the title, write it out if UNI/VMS ----*/
	    if (db == UNI || db == VMS)
	    {
		   strcpy(temp, &line[dbs[db]->title_offset]);
                   if (strlen(temp) > MAXTITLE)
                   { temp[MAXTITLE-1] = '\n'; temp[MAXTITLE] = '\0'; }
                   if (out) fprintf(fout, ">%s", temp);
	    }
	    else		/*  EMBL, GENBANK, PIR */
	    {
		  ptr = strtok(&line[dbs[db]->title_offset], " ");
		  strcpy(title, ptr);
	    }

	    /*------ Process other records for this entry -------*/
	    while (!feof(fin) && fgets(line, MAXLINE, fin) != NULL &&
		 strncmp(line, dbs[db]->end, strlen(dbs[db]->end)) != 0 &&
		 strncmp(line, dbs[db]->start, strlen(dbs[db]->start)) != 0)
	    {
	       /* ---For UNI & VMS, just write it back out & count length- */
	       if (db == UNI || db == VMS)
	       {
		     if (out) fputs(line, fout);
		     for (i=0; ilen = id->len + 1;
	       }
	       else    /* EMBL, GENBANK, PIR */
	       {
		   /*-----There might be more title to get ---------*/
		   if (strncmp(line,dbs[db]->desc,strlen(dbs[db]->desc))==0 &&
			 strlen(title) + strlen(line) < MAXLINE )
		   {
			strcpy(temp, title); strcat(temp, " ");
			strcat(temp, &line[dbs[db]->title_offset]);
			ptr = strtok(temp, "\n\r");   /* remove CRLF */
			strcpy(title, temp);
		   }
                   /*--- Kludge to get PIR entry name from EMBL files ---*/
                   else if (db == EMBL && strncmp(line, "DR   PIR", 8) == 0)
                   {
                       ptr = strtok(line+9, ";");
                       if (ptr != NULL)
                       {
                          ptr = strtok(NULL, ".\n\r");
                          if (ptr != NULL) 
                          {
                             if (ptr[0] == ' ') strcpy(id->pir, ptr+1);
                             else strcpy(id->pir, ptr);
                          }
                       }
                   }
		   /*------ Process the sequence ------------------------*/
		   if (strncmp(line,dbs[db]->seq,strlen(dbs[db]->seq))==0)
		   {
		   /*- Check again to see if this sequence is a fragment -*/
		      if (strstr(title, "FRAGMENT") != NULL ||
			    strstr(title, "fragment") != NULL) id->frag = 1;
		      /*-- Write out the title ---*/
                      strcpy(temp, title);
                      if (strlen(temp) > MAXTITLE) temp[MAXTITLE] = '\0';
		      if (out) fprintf(fout, ">%s\n", temp);  /*print title*/
		      /*---  Write out the sequence & count its length --*/
		      while(!feof(fin) &&
			   fgets(line, MAXLINE, fin) != NULL &&
			  strncmp(line,dbs[db]->end,strlen(dbs[db]->end))!=0)
		      {
                          if (strpbrk(&line[dbs[db]->seq_offset],
                              "ARNDCQEGHILKMFPSTWYVBZXactg") != NULL)
                          {
		             if (out) fprintf(fout, &line[dbs[db]->seq_offset]);
                             for (i=dbs[db]->seq_offset; ilen = id->len + 1;
                          }
		      }  /*  end of sequence lines*/
		  }  /* end of if ->seq */
	       }   /*  end of if not UNI and not VMS */
	    }  /*  end of records for entry */
	    if (out && here) fclose(fout);

	    /*---- Extra processing for VMS -------*/
	    if (db == VMS &&
		strncmp(line, dbs[db]->start, strlen(dbs[db]->start)) == 0)
	    {                           /* get the 2nd line, too */
		   ptr = strtok(line, "\n\r");        /* remove CRLF */
		   strcat(line, " ");
		   if (fgets(temp, MAXLINE, fin) != NULL) strcat(line, temp);
	    }
	 }  /*  end of found entry */
	 else fgets(line, MAXLINE, fin);
      }   /*  end of if ->start */
      else fgets(line, MAXLINE, fin);
   }  /*  end of db file */

   return(nout);
}  /* end of extract_seqs */
/*====================================================================
    See if a an entry name is in a list of entries
======================================================================*/
struct db_id *check_entry(ids, entry)
struct db_id *ids;
char *entry;
{
   struct db_id *id;
   int i, tot, bar, len, xlen;
   char *ptr, idtemp[SNAMELEN*6 + 6], dbtemp[SNAMELEN*6 + 6];
   char ctemp[SNAMELEN*6 + 6], xtemp[SNAMELEN];
   char idlist[10][SNAMELEN*6 + 6];

   id = ids->next;
   while (id != NULL)
   {
      if (id->found == NO)
      {
         if (strcmp(id->entry, "-") == 0)  /* just take the first sequence */
         {
             return(id);
         }
         else
         {
            /*	Store the id names because can't use strtok
		for two things simultaneously    */
            strcpy(idtemp, id->entry);
            tot = 0;
            ptr = strtok(idtemp, "| \0\r\n\t");
            while(ptr != NULL)
            {
	      if (tot < 10) { strcpy(idlist[tot++], ptr); }
              ptr = strtok(NULL, "| \0\r\n\t");
            }

	    len = strlen(entry);
            /*  Truncate database name here  */
	    if (len > SNAMELEN*6) len = SNAMELEN*6;
            strncpy(dbtemp, entry, len); dbtemp[len] = '\0';
            ptr = strtok(dbtemp, "| \0\r\n\t");
            while(ptr != NULL)
            {
               /*  entry==ptr could be O88996_RAT, want it to match O88996*/
               xtemp[0] = '\0';
               xlen = strcspn(ptr, "_");
               if (xlen > 0)
               {
                 strncpy(xtemp, ptr, xlen); xtemp[xlen] = '\0';
               }
               for (i=0; i< tot; i++)
               {
	         if ( (strcmp(ptr, idlist[i]) == 0) ||
                      ((strlen(xtemp) > 0) && strcmp(xtemp, idlist[i]) == 0) )
                 {
                   strncpy(ctemp, entry, len); ctemp[len] = '\0'; 
	           /* Only want max of two parts in id->entry   */
                   bar=NO; i=0;
	           for (i=0; ifull_entry, ctemp);
                    return(id);
                 }
               }
               ptr = strtok(NULL, "| \0\r\n\t");
            }
         }
      }
      id = id->next;
   }
   return(NULL);
}  /* end of check_entry */

/*==================================================================
	strnjcmp.c
	Case in-sensitive version of strncmp for alphabetic characters
    A-Z are decimal 065-090
    a-z are decimal 097-122  (A+32, etc.)
=====================================================================*/
int strnjcmp(st1, st2, nchar)
char *st1, *st2;
int nchar;
{
   int i;
   char up1[2], up2[2];

   up1[1] = up2[1] = '\0';
   /*--------Convert st1 and st2 to upper case for comparison ---------*/
   for (i=0; i= 97 && up1[0] <= 122) up1[0] = up1[0] - 32;
      if (up2[0] >= 97 && up2[0] <= 122) up2[0] = up2[0] - 32;
      if (up1[0] != up2[0]) return(up1[0] - up2[0]);
   }
   return(0);
}
ds, dbs, fin, ids, pros, fout, frag)
int nids, frag;
struct db_info *dbs[MAXDB];
FILE *fin, *fout;
struct db_id *ids;
char *pros;
{
   struct db_id *id;
   int nseq, i, db, out, here, nout;
   char line[MAXLINE], title[Mblimps-3.9/protomat/motomat.c000064400001460000012000001603171054326113000166420ustar00jorjastaff00000400000027/*======================================================================*/
/* (C) Copyright 1991-2000 by Fred Hutchinson Cancer Research Center    */
/*     motomat.c   Block extension and assembly program                 */
/*   USE: motomat      */
/*                 EG:  motomat PS00094.mot 1 80 -10                    */
/*        input file = .mot file from motifj.c (this is a binary file)  */
/*        cutoff score = average PAM score for all possible pairs of    */
/*         amino acids in a column of the block (0-2500).               */
/*         If the cutoff score = 1, motomat will determine the best     */
/*         block extension. This is the recommended choice. If the      */
/*         cutoff score =2, lots of intermediate output is produced.    */
/*        cluster % = Percent identical AAs to cluster seqs in .blk file*/
/*        drop sd = sd of blocks score * 10, blocks scoring lower will  */
/*         be dropped and not assembled. EG -25 => -2.5 sds             */
/*         If drop sd == asis, blocks will not be merged, dropped or    */
/*           extended; duplicate blocks will be dropped                 */
/*        outputs blocks with the extension ".blk" and file name made   */
/*         up of the 1st 7 chars of the input file title plus one       */
/*         character for each assembled block; EG PS00094A.blk          */
/*   Reference:  S. Henikoff & J. Henikoff, NAR 19:23, 6565-6572 (1991)
      See PROTOMAT documentation file for description of algorithms.    */
/*----------------------------------------------------------------------
 6/20/90  J. Henikoff
>>>>>>>>>>>>>>>>>>>>>  Blocks 9.0  <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 6/29/97 Changed execlp() to use argv[0]
10/21/97 Round proportion of sequences instead of truncate in best_path()
10/28/97 Added pb_weights() to score_block() & score_cols()
11/ 8/97 Make min drop score == highpass value
11/10/97 Weight blocks in best_path() by nident instead of nmotif
         Fixed bug in check_pos()
	 Added list of seqs not in best path to print_best()
11/11/97 Weight blocks in best_path() by nmotif from motifj
12/30/97 Added reduce_overlap()
 1/19/98 Weight blocks in best_path() by sqrt(nmotif) instead of nmotif.
 1/21/98 Fixed argv[0] error in restart(). Removed pb_weights() error message.
 1/25/98 Moved reduce_overlap() to after blocks are dropped for low score.
 1/28/98 Fixed reduce_overlap() bug, wrong block trimmed
         New option (-asis) => don't drop any blocks, don't extend,
		don't reduce overlap, etc.
 2/12/98.1 Added version date (VerDate[]). Drop blocks < 4 wide.
           Don't shorten block in reduce_overlap() if resulting block
	   will be < MIN_DOMAIN_WIDTH=10 wide.
           Fixed overcounting of block->nident in score_block()
	   Added Overlap = #times reduce_overlap() shortened a block to
		motomat.err
 2/16/98.1 Drop blocks < 5 wide.
 2/28/98.1 Modified trim_block() to never make block narrower.
 6/20/99.1 Longer sequence names (SNAMELEN=18)
 7/ 6/99.1 Longer AC names (MAXAC=10)
 3/ 3/00.1 Memory bug fix
 6/ 6/00.1 Fix blk_filename for BlockMaker; save all blocks in one file
	   save_block();
12/23/06.1 Longer sequence names (SNAMELEN=20)
==========================================================================*/
#include 
#include 
#include 
#include "motifj.h"

/*--------------------Function prototypes--------------------------------*/
void dump_data();
struct merged_motif *init_mm();
void merge_blocks();
int check_align();
int check_pos();
int check_overlap();
void dup_blocks();
void reduce_overlap();
void trim_block();
void extend_block();
void print_block();
void print_head();
void save_block();
void cluster_seqs();
void print_seq();
void write_seq();
void score_cols();
void score_block();
void pb_weights();
void restart();
/*    Shotgun assembly stuff;   code is in motomat2.c */
int prune_blocks();
void order_blocks();
int tempcmp();
void build_dag();
void find_paths();
void next_arc();
struct path *makepath();
struct block_list *makebllist();
void ins_path();
struct path *copypath();
void free_path();
struct matrix *makematrix();
void follow_arcs();
void ins_bllist();
struct path *best_paths();
void best_path();
void check_seqs();
void print_best();
void print_path();
void save_plot();
int left();
int right();
/*---------------Routines from motmisc.c -----------------------------*/
char *num_to_aachar();
int aachar_to_num();
void getscore();
void kr_itoa();
struct split_name *split_names();

/*------------------Global vars------------------------------------------*/
char VerDate[12] = " 6/ 6/00.1";
int Debug = NO;		/* Flag for debugging print-out */
int AsIs = NO;		/* if argv[5] exists  */
int MinScore;		/* Minimum column score for block extension */
int ClThres;		/* Clustering threshold (%) */
int DropScore;		/* # of sds from mean before block is dropped */
long TopScore;		/* Actual drop score */
char Mot_Filename[FNAMELEN];    /* Name of the .mot input file */
char Blk_Filename[FNAMELEN];	/* Name of the .blk output file */
int Version, RunType, Signif, Dups, Distance;	/*  motifj parameters */
int RSignif;					/* reduces significance */
int NumSeqs;					/* number of sequences */
int Total_Motifs;				/* # motifs from motifj */
int Overlap;					/* # reduce_overlap()  */
char AC[MAXAC+1], ACName[MAXLINE], ID[MAXLINE], DE[MAXLINE];
int MinDist, MaxDist;
int Gibbs = NO;		/* Gibbs input flag */
struct matrix *Dag[RELEVANT_MOTIFS][RELEVANT_MOTIFS];	/* Graph */
struct score *SMatrix;				/* Scoring matrix */
char Argv0[MAXLINE];		/* Save argv[0] for restart */
FILE *Fblk;			/* .blks output file */

/*=======================================================================*/
int main(argc, argv)
int argc;
char *argv[];
{
   FILE *mot, *err;
   char title[MAXLINE], ctemp[MAXLINE], *ptr;
   int done, i, j, b, c, totb, motauto, maxdups;
   int lastscore, lastthres, lastdrop;
   int pseqs[MAXSEQS];
   double ftemp, fmean, fsdev;
   struct sequences *seqs;
   struct motif_struct *motif;
   struct merged_motif *blocks;
   struct path *paths;
   struct split_name *motsplit;

   printf("\nMOTOMAT %s: ", VerDate);
   printf("(C) Copyright 1991 by Fred Hutchinson Cancer Research Center");
   printf("\nPlease cite: S.Henikoff & J.Henikoff, NAR 19:6565-6572 (1991).");
/*-------Get the scoring matrix and high pass filter values --------*/
   SMatrix = (struct score *) malloc(sizeof(struct score));
   if (SMatrix != NULL)     getscore(SMatrix);
   else {printf("\nCANNOT ALLOCATE SMatrix\n"); exit(-1);}

   strcpy(Argv0, argv[0]);

/*----------------Get the input file -------------------------------*/
   if (argc > 1)
      strcpy(Mot_Filename, argv[1]);
   else
   {
      printf("\n");
      system("ls -al *.mot");
      printf("\nEnter name of file containing motifs: ");
      gets(Mot_Filename);
   }
   ptr = strrchr(Mot_Filename, '.');   /* check for extension */
   if (ptr == NULL) strcat(Mot_Filename, ".mot");
   if ( (mot=fopen(Mot_Filename, "rb")) == NULL)
   {
      printf("\nCannot open file %s\n", Mot_Filename);
      exit(-1);
   }
   motsplit=split_names(Mot_Filename);   /* split up name */
   Blk_Filename[0] = '\0';
   strncat(Blk_Filename, Mot_Filename+motsplit->dir_len, motsplit->name_len);
   Blk_Filename[motsplit->name_len] = '\0';

/*----------------Read the data file ------------------------------------*/
   title[0] = '\0';
   NumSeqs = Total_Motifs = -1;
   fread(&Version, sizeof(int), 1, mot);
   if (Version != VERSION)
   {
      printf("\n\nInput file was created using wrong motifj version!\n");
      fclose(mot);
      exit(-1);
   }
   fread(&RunType, sizeof(int), 1, mot);
   fread(&Signif, sizeof(int), 1, mot);
   fread(&Dups, sizeof(int), 1, mot);
   fread(&Distance, sizeof(int), 1, mot);
   fread(&NumSeqs, sizeof(int), 1, mot);		/*  # sequences */
   fread(&Total_Motifs, sizeof(int), 1, mot);		/* # motifs */

   seqs = (struct sequences *) malloc(sizeof (struct sequences));
   seqs->num = NumSeqs;

   seqs->len = (int *) malloc(NumSeqs * sizeof (int));
   fread(seqs->len, sizeof(int), NumSeqs, mot);	/*  sequence lengths */

   seqs->totlen = 0;
   seqs->offlen = (int *) malloc(NumSeqs * sizeof (int));
   for (i=0; iofflen+i) = seqs->totlen;	/*  offset to ith sequence */
     seqs->totlen += *(seqs->len+i);
   }
					/* sequence names */
   seqs->name = (char *) malloc(SNAMELEN * NumSeqs * sizeof (char));
   fread(seqs->name, SNAMELEN*sizeof(char), NumSeqs, mot);

   seqs->seq = (char *) malloc(seqs->totlen * sizeof(char));
   fread(seqs->seq, sizeof(char), seqs->totlen, mot);	/* sequences */

   if (Total_Motifs > 0)
   {
      motif = (struct motif_struct *) 
          malloc(Total_Motifs * sizeof(struct motif_struct));
      /*---  For Gibbs, Total_Motifs is the maximum number, may be fewer */
      for (i=0; i 0) i++;
   if (i < Total_Motifs) Total_Motifs = i;

   printf("\n%s\n", title);
   printf("\n%d blocks read", Total_Motifs);
   printf(" using parameters [%d, %d, %d].", Signif, Dups, Distance);
   printf(" %d sequences.", NumSeqs);

   /*--------------------------------------------------------------------*/
   /*  Get AC, ID, DE from title line */
   /*--   General form is >ACxxxxx ;ID;Description;$ -------*/
   ACName[0] = '\0';
   strcpy(ID, "none"); strcpy(DE, "none");
   /*  title is missing or too short  */
   if (!(strlen(title)) || title[0] != '>')
   {
      strcat(ACName, Blk_Filename);	/* use the filename as AC */
   }
   else
   {
      ptr = strtok(title+1, ";");
      if (ptr != NULL)
      {
         strcpy(ACName, ptr);
         ptr = strtok(NULL, ";");
         if (ptr != NULL)
         {
            strcpy(ID, ptr);
            ptr = strtok(NULL, ";");
            if (ptr != NULL)
            {
               strcpy(DE, ptr);
            }
         }
      }
      else
      {
         strcpy(ACName, title+1);
      }
   }

   ACName[MAXAC-1] = '\0';
   for (i=0; i 2)
   {
      strcpy(ctemp, argv[2]);
      MinScore = atoi(ctemp);
   }
   if (MinScore == 2)
   {
      Debug = YES; MinScore = 1;
   }
   if (MinScore == 1)		/* Automatic determination of parameters */
   {
      motauto = YES;  RunType = 3;
   }
   else if (MinScore < 100 || MinScore > 2500) MinScore = MINSCORE;
   lastscore = MinScore;

   if (argc > 3)		/* Clustering threshold percentage */
   {
      strcpy(ctemp, argv[3]);
      ClThres = atoi(ctemp);
   }
   if (ClThres <= 0 || ClThres > 100) ClThres = CLTHRES;
   lastthres = ClThres;

   if (argc > 4)		/* Block drop score stand. dev. */
   {
      if (strcasecmp(argv[4], "asis") == 0) AsIs = YES;
      else DropScore = atoi(argv[4]);
   }
   else if (motauto)
   {
      DropScore = -10;		/* default = -1sd */
   }
   if (DropScore < -30 || DropScore > 30) DropScore = DROPSCORE;
   lastdrop = DropScore;

   printf("\nProcessing blocks in %s using a cut-off score of %d ",
		      Mot_Filename, MinScore);
   printf("\n   and a clustering threshold of %d percent.", ClThres);


/*----------------------Quit if nothing to do -------------------------*/
   if (Debug)
      dump_data(motif, seqs);
   if (Total_Motifs < 1)
   {
      printf("\nQuitting becasuse no motifs to work on.\n");
      exit(0);
   }

/*-------------------Redirect standard error output --------------------*/
   err = freopen("motomat.err", "a", stderr);

/*------------------Initialize sequences to save to all-----------------*/
   for (i=0; i 0)
      {
	 if (!AsIs && blocks[b].domain+1 < MAX_MERGE_WIDTH)
	 {
	    blocks[b].loffset = blocks[b].t_loffset =
	     (int) (blocks[b].loffset +
		    (MAX_MERGE_WIDTH-blocks[b].domain-1)/2);
	    blocks[b].domain = blocks[b].t_domain = MAX_MERGE_WIDTH-1;
	 }
	 printf(".");
	 score_cols(&blocks[b], seqs);
      }


/*--------- Extend, cluster & print out the top merged blocks -----------*/
    printf("\nExtending blocks...");
    totb=0;				/* total surviving blocks */
    RSignif=Signif;			/* reduced significance */
    sprintf(ctemp, "%s.blks", Blk_Filename);
    if ((Fblk=fopen(ctemp, "w+t")) == NULL)
    {
	printf("\nCannot open %s\n", ctemp);
	exit(-1);
    }
    printf("Saving blocks to %s\n", ctemp);
    for (b=0; b 1 && MinScore < 100) ||
		       MinScore <= 0 || MinScore > 2500)
			      MinScore = lastscore;
		  lastscore = MinScore;
		  printf("Enter clustering identity threshold [1-100; %d]: ",
		    lastthres);
		  gets(ctemp);
		  ClThres = atoi(ctemp);
		  if (ClThres <= 0 || ClThres > 100) ClThres = lastthres;
		  lastthres = ClThres;
		  printf("\nProcessing block %d in %s using a cut-off score of %d ",
		     b, Mot_Filename, MinScore);
		  printf("\n   and a clustering threshold of %d percent.", ClThres);
	       } /* end of runtype = 0 or 2 */
	       totb++;
	       if (MinScore == 1)
	       {
		  extend_block(&blocks[b]);
		  if (blocks[b].t_domain+1 < MIN_DOMAIN_WIDTH)
		  {
		     MinScore = SMatrix->highpass;
		     while (blocks[b].t_domain+1 < MIN_DOMAIN_WIDTH &&
			    MinScore >= (SMatrix->highpass - 50))
		     {
			printf("\nExtended width was %d",
			     blocks[b].t_domain+1);
			printf(", re-extending with cutoff score of %d.",
			     MinScore);
			trim_block(&blocks[b]);
			MinScore -= 50;
		     }
		     MinScore = 1;
		  }
		  if (blocks[b].t_domain+1 < 5)
                  { 
	             blocks[b].dropped = YES;
	             printf("\nBlock %d has been dropped for low width:", b);
	             print_head(&blocks[b]);
                  }
	       }  /* end of if MinScore==1 */
	       else
	       {
		   trim_block(&blocks[b]);
	       }

	       if (RunType==0 || RunType==2)
	       {
		   score_block(&blocks[b], seqs);
		   cluster_seqs(&blocks[b], seqs);
		   print_block(&blocks[b], seqs);
		   printf("\n\nType S[ENTER] to save this block,");
		   printf(" or N[ENTER] to skip to next block,");
		   printf("\nor anything else[ENTER] to re-extend this block...");
		   c=getchar(); getchar();    /*  2nd get is for ENTER */
		   if (c == 's' || c == 'S')
		   {
		      save_block(&blocks[b], seqs, pseqs);
		      c = 'N';
		   }
	       }
	    }  while ((RunType==0 || RunType==2) && c != 'N' && c != 'n');

	  }  /*  end of if !AsIs  */
        }  /* end of else not merged */
   }  /*  end of for b */

/*-----------Merge extended blocks if not from Gibbs -----------*/
   if (!Gibbs && !AsIs)
   {
      printf("\n\nMerging extended blocks....");
      merge_blocks(blocks, 1);
   }
   else
   {
      printf("\n\nRemoving duplicate blocks....");
      dup_blocks(blocks);
   }

/*---------------------------------------------------------------------*/
/*  Shotgun assembly of all unmerged, high-scoring blocks.             */
/*---------------------------------------------------------------------*/
   if (RunType == 0 || RunType == 2)
   {
      printf("\nEnter drop standard deviations [-30 to 30; %d]: ", lastdrop);
      gets(ctemp);
      DropScore = atoi(ctemp);
      if (DropScore < -30 || DropScore > 30) DropScore = lastdrop;
      lastdrop = DropScore;
   }
   printf("\nUsing a drop score of %d standard deviations or %d.",
	  (int) DropScore/10, SMatrix->highpass);
/*--------- Re-score blocks and compute mean and sd -----------*/
   totb = maxdups = 0;
   fmean = fsdev = 0.0;
   for (b=0; b 1)
   {
      fsdev = fsdev - (double) fmean*fmean/totb;
      fsdev = (double) fsdev/(totb-1);
      if (fsdev > 0.0)
         fsdev = sqrt(fsdev);			/* standard deviation */
      else fsdev = 0.0;
      fmean = (double) fmean/totb;			/* mean */
   }
   else
      fsdev = 0.0;
   printf("\nMean score=%.2f, standard deviation=%.2f", fmean, fsdev);
/*-----If sdev==0.0, then either all blocks have same score, or there
       is only one block; don't want to drop them all ------------------*/
   if (fsdev > 0.01) ftemp = fmean + fsdev * DropScore / 10;
   else ftemp = 1.0;
   TopScore = (long) ftemp - 1.0;	            /*  Round down */
   /*    Possibly raise the drop score, but be careful not to drop
	 all the blocks!  */
   if (fmean >= SMatrix->highpass &&
       TopScore < SMatrix->highpass) TopScore = SMatrix->highpass;
   if (!AsIs)
   {
      printf("\nDropping blocks with score below %ld...", TopScore);
      printf("\n unless they have more than one merged motif");
   }
   totb = 0;
   for (b=0; bmaxdups) maxdups = blocks[b].dups;
	  cluster_seqs(&blocks[b], seqs);
	  printf("\nBlock %d:", b);
	  print_block(&blocks[b], seqs);
      }

/*   if (totb > MAXBLK)
      totb = prune_blocks(blocks);
*/
   printf("\nSurviving blocks=%d, max dups=%d", totb, maxdups);
/*------------------------------------------------------------------*/
/*         Check each pair of surviving
           blocks and look at those that overlap. By this point,
           they don't overlap consistently in all the sequences or
           they would have been merged. However, if they overlap
           consistently in most of the sequences and if that overlap is
           small, then trim one or both blocks so they don't overlap
	   any more. (Addresses the PS00031 problem without adding
	   gaps). See motomat2.c lines 140-157.
*/
   Overlap = 0;
   if (!AsIs)
   {
      printf("\nReducing block overlaps ...\n");
      reduce_overlap(blocks, seqs);
   }

/*---- Reduce significance level if there are dups. However, be
  sure that RSignif > (NumSeqs-RSignif) to prevent cycles in the DAG ---*/
   RSignif = Signif - ((int) maxdups/4);
   if (RSignif <= (NumSeqs-RSignif) )
      RSignif = ((int) NumSeqs/2) + 1;  /* R must be more than half N */
   if (RSignif < 2) RSignif = Signif;	/* not sure what to do here */
   if (RSignif < Signif)
      printf(", reduced significance=%d", RSignif);

   if (totb > 0)			/* Don't try if no blocks left */
   {
      printf("\n\nLooking for best path...");
      order_blocks(blocks);
      build_dag(blocks);
      paths = makepath();
      find_paths(paths, blocks);
      printf(", npath=%d", paths->nblocks);
      if (paths->next_path != NULL)
      {
	  printf(", nseqs=%d\n", paths->next_path->nseqs);
	  if (maxdups > 0) check_seqs(paths->next_path, blocks);
	  print_path(paths->next_path);
	  print_best(paths->next_path, blocks, seqs);
      }
   }
   else
      printf("\nNo surviving blocks");

   fclose(Fblk);
   printf("\n");
/*----------Print a summary of results in stderr--------------------*/
   fprintf(stderr, "%s %d %d %d %d %d %d %d %d %d %d %d %d %ld %d %d %d\n",
      ACName, NumSeqs, Signif, Dups, Distance, Total_Motifs, MinScore,
      ClThres, DropScore, totb, paths->nblocks, paths->next_path->nbest,
      paths->next_path->totmotif, paths->next_path->totscore,
      paths->next_path->naas, paths->next_path->nseqs, Overlap);
   fclose(err);
   exit(0);
}    /*  end of main */

/*======================================================================
     Print the motifs and sequences
========================================================================*/
void dump_data(motif, seqs)
struct motif_struct *motif;
struct sequences *seqs;
{
   int i, j, k, offset, jj, kk;

   printf("\nNumSeqs=%d, Total_Motifs=%d", NumSeqs, Total_Motifs);
   k=0;
   for (i=0; iname+SNAMELEN*i, *(seqs->len+i) );
      if (i>0) k += *(seqs->len+i-1);
      printf(" %.5s", seqs->seq+k);
   }

/*------NOTE:  motif[].domain is the ACTUAL domain width, while in
      blocks[].domain it is the displacement, or ACTUAL-1 -----*/
   for (i=0; i>>>>> Confused about this!
      offset++;
>>>>>>>>*/
      for (j=0; jname+SNAMELEN*jj, kk);
	 for (k=0; k= 0 && kk < *(seqs->len+jj) )
	       printf("%.1s", seqs->seq+seqs->offlen[jj]+kk);
	    else  printf(".");
	 }
	 printf("\n                   ");
	 for (k=0; k 1) new[m].nmotif = 2; 
*/
      new[m].nmotif = 1;
      new[m].nmotif = motif[m].mots;
      new[m].nident = 0;
      ftemp = (double) motif[m].domain;
      new[m].max_score = (int) (motif[m].score/sqrt(ftemp));
      /*--NOTE: block domain is displacement, not actual with  ---*/
      new[m].domain = new[m].t_domain = motif[m].domain - 1;
      new[m].distance = motif[m].distance1 + motif[m].distance2;
      new[m].dups = motif[m].dups;
      /*--- loffset is not really offset, but 1st position ???--*/
      /* NOTE: If the block width is the motif width, loffset is zero */
      new[m].loffset = new[m].t_loffset =
       (int) (motif[m].domain-motif[m].distance1-motif[m].distance2-1)/2;
      new[m].t_score = -1;       /* -1 => block has not been trimmed */
      for (s=0; s 0)
	 for (b2=b1+1; b2  0 &&
		check_align(&blocks[b1], &blocks[b2]) &&
		check_overlap(&blocks[b1], &blocks[b2], flag) )
	    {
/*--- lb1,2 and rb1,2 are the end positions of blocks b1 and b2
      respectively for sequence 0.  They are used to compute the relative
      positions of the two blocks.  This technique only works if 1) All
      sequences are aligned the same way in both blocks, and 2) sequence
      0 extends all the way across both blocks (?) ----*/
	       lb1 = blocks[b1].leftpos[0]-blocks[b1].t_loffset;
	       lb2 = blocks[b2].leftpos[0]-blocks[b2].t_loffset;
	       rb1 = lb1 + blocks[b1].t_domain;
	       rb2 = lb2 + blocks[b2].t_domain;
	       ldiff = lb1 - lb2;	      /*-- difference at left end*/
	       rdiff = rb1 - rb2;  	     /*-- difference at right end*/
	       left = UMIN(lb1, lb2);
	       right = UMAX(rb1, rb2);
/*--------  Merge only if the total width is not too big ----------*/
	       if ( (right-left) < MAX_MERGE_WIDTH )
	       {

/*---- Update the block information ---*/
		  printf("\nMerging motif %d into motif %d", b2, b1);
		  blocks[b1].nmotif = blocks[b1].nmotif + 1;
		  blocks[b2].nmotif = 0;
		  if (blocks[b2].dups > blocks[b1].dups)
		     blocks[b1].dups = blocks[b2].dups;
		  if (!flag) blocks[b1].domain = right - left;
		  blocks[b1].t_domain = right - left;

		  left = UMIN(blocks[b1].leftpos[0], blocks[b2].leftpos[0]);
		  right = UMAX(blocks[b1].leftpos[0]+blocks[b1].distance,
			   blocks[b2].leftpos[0]+blocks[b2].distance);
		  blocks[b1].distance = right - left;
		  blocks[b1].t_loffset = left - UMIN(lb1, lb2);
		  if (!flag) blocks[b1].loffset = left - UMIN(lb1, lb2);
		  for (s=0; s 0 && rdiff > 0) /* b2 is leftmost */
		  {
		     overlap = 1 + rb2 - lb1;
		     bleft = b2; bright = b1;
		  }
		  if (overlap > 0 && bleft >= 0 && bright >= 0)
		  {
		     ov1 = (int) (overlap/2); ov2 = overlap - ov1;
		     blocks[bleft].domain = blocks[bleft].domain - ov1;
		     if ( (blocks[bleft].loffset + blocks[bleft].distance) >
			  blocks[bleft].domain)
			 blocks[bleft].distance =
			    blocks[bleft].domain - blocks[bleft].loffset;
		     blocks[bleft].t_domain = blocks[bleft].t_domain - ov1;

		     blocks[bright].domain = blocks[bright].domain - ov2;
		     blocks[bright].t_domain = blocks[bright].t_domain - ov2;
		     blocks[bright].loffset = blocks[bright].loffset - ov2;
		     if (blocks[bright].loffset < 0)
		     {
			 temp = blocks[bright].loffset;
			 blocks[bright].distance = blocks[bright].distance
			      + temp;
			 blocks[bright].loffset = 0;
		     }
		     blocks[bright].t_loffset = blocks[bright].t_loffset - ov2;
		     if (blocks[bright].t_loffset < 0)
			blocks[bright].t_loffset = 0;
		     for (s=0; sleftpos[s]-b2->leftpos[s];
   do  {
      s++;
   }  while (sleftpos[s]-b2->leftpos[s] == diff);
   if (s == NumSeqs) return(YES);
   else return(NO);
}  /*  end of check_align */

/*=====================================================================
   check_pos returns YES if all the sequences in two blocks have the
     same left position.
========================================================================*/
int check_pos(b1, b2)
struct merged_motif *b1, *b2;
{
   int s;

   s=0;
/*	Used to be
	     b1->leftpos[s] == b2->leftpos[s])
*/
   while (sleftpos[s] - b1->t_loffset == b2->leftpos[s] - b2->t_loffset)
        s++;
   if (s == NumSeqs) return(YES);
   else return(NO);
}  /*  end of check_pos */

/*=====================================================================
   check_overlap returns YES if the first sequence in each of two
     blocks overlap anywhere within the blocks' motif area.
   Flag=0 means check for overlap in motif region; flag=1 means check
   anywhere in the extended region.
   May not catch a block that overlaps in only some of the sequences,
	but flag=2 forces it to check all sequences.
========================================================================*/
int check_overlap(b1, b2, flag)
struct merged_motif *b1, *b2;
int flag;
{
   int left1, left2, s, over;

   if (flag == 0)      /* check motif regions */
   {
/*   Find start of 1st sequence in both blocks  */
      left1 = b1->leftpos[0];
      left2 = b2->leftpos[0];
      if ( (left2 >= left1 && left2 <= left1 + b1->distance) ||
	   (left1 >= left2 && left1 <= left2 + b2->distance) )
	      return(YES);
      else    return(NO);
   }
   else if (flag == 1)        /*  check full regions  */
   {
      left1 = b1->leftpos[0] - b1->t_loffset;
      left2 = b2->leftpos[0] - b2->t_loffset;
      if ( (left2 >= left1 && left2 <= left1 + b1->t_domain) ||
	   (left1 >= left2 && left1 <= left2 + b2->t_domain) )
	      return(YES);
      else    return(NO);
   }
   else 	/* check ALL seqs in full regions */
   {
      s = 0; over = NO;
      while (sleftpos[s] - b1->t_loffset;
         left2 = b2->leftpos[s] - b2->t_loffset;
         if ( (left2 >= left1 && left2 <= left1 + b1->t_domain) ||
	      (left1 >= left2 && left1 <= left2 + b2->t_domain) )
	      over = YES;
         s++;
      }
      return(over);
   }
}  /*  end of check_overlap  */

/*========================================================================
      dup_blocks eliminates blocks that are exact duplicates by setting
       the merged flag. Blocks are duplicates if they have the same
       width & same offsets for all sequences
=========================================================================*/
void dup_blocks(blocks)
struct merged_motif *blocks;
{
   int b1, b2;

   for (b1=0; b1 0)
	 for (b2=b1+1; b2  0 &&
                blocks[b1].domain == blocks[b2].domain &&
                   check_pos(&blocks[b1], &blocks[b2]))
                      blocks[b2].nmotif = 0;
          }
}  /* end of dup_blocks */

/*========================================================================
   reduce_overlap trims blocks that overlap only slightly but consistently
     in most sequences
=========================================================================*/
void reduce_overlap(blocks, seqs)
struct merged_motif *blocks;
struct sequences *seqs;
{
   int b1, b2, s, diff[MAXSEQS], bleft, bright, left, right, over[MAXSEQS];
   int samediff, minover;

   for (b1=0; b1 0)
      {
	 for (b2=b1+1; b2  0 &&
                 check_overlap(&blocks[b1], &blocks[b2], 2) &&
		 !check_align(&blocks[b1], &blocks[b2])        )
            {
            /*>>>  Find out how many overlap & by how much
                if it's most & they all overlap by the
                same amount, then trim the left one by reducing
                ->t_domain & re-score it  */
               samediff = YES;
               minover = 0;
               for (s=0; s 0)
                  {
                     if ( (diff[0] <= 0 && diff[s] > 0) ||
                          (diff[0] >= 0 && diff[s] < 0)   )  samediff = NO;
                  }
                  if (diff[s] < 0) {  bleft = b2; bright = b1; }
                  else             {  bleft = b1; bright = b2; }
                  left =  blocks[bleft].leftpos[s] - blocks[bleft].t_loffset +
			  blocks[bleft].t_domain;
                  right = blocks[bright].leftpos[s] - blocks[bright].t_loffset;
                  over[s] = right - left - 1;
                  if (over[s] < minover) minover = over[s];
               }  /* end of sequence s */
               /* Now check:  1) diff[s] same sign for all s
                  2) over[s] has a limited number of values, will be < 0
                  if there is an overlap: EG, if over = 0 for 2/10 seqs
                  and = -2 for 8/10, then trim 2 off the right end of bleft.
                  Count #different negative values in over[], if the
                  largest negative value is not too small, trim left block
                  by that amount. EG -10 is probably too much overlap,
                  but -5 may not be if left block is wide enough */
               if (samediff && minover < 0 && minover >= -5)
               {
                  /* Don't shorten if resulting block < 4 wide  */
                  if ( (blocks[bleft].t_domain + minover) > MIN_DOMAIN_WIDTH )
                  {
                     blocks[bleft].t_domain += minover;
		     score_block(&blocks[bleft], seqs);
		     Overlap++;
                     printf("Block %d has been trimmed by %d to eliminate overlap with Block %d.\n", 
                             bleft, minover, bright);
                  }
               }
            } /* end of if b1 and b2 overlap inconsistently */
          }  /* end of b2 */
      } /* end of if b1 is still active */
   }   /* end of b1 */
}  /*  end of reduce_overlap */

/*=======================================================================
    trim_block  trims a block around the motifs.                      
    It is mis-named, since what it actually does is EXTEND the block out
    from the outer edges of the merged motifs up to the full width of
    the block received from motifj. So it is the motifj block that is
    trimmed.							
=======================================================================*/
void trim_block(block)
struct merged_motif *block;
{
   int left, right;

   left = block->loffset;
	 do
	 {
	    left -= 1;
	 }  while (left >= 0 && block->scores[left] >= MinScore);

   right = block->loffset + block->distance;
	 do
	 {
	    right += 1;
	 } while (right <= block->domain &&
		  block->scores[right] >= MinScore);

   /* update block only if it is wider than before  */
   if ( (right - left - 2) > block->t_domain)
   {
      block->t_loffset = block->loffset - left - 1;
      block->t_domain = right - left - 2;
   }
}  /*  end of trim_block */
/*=======================================================================*/
/*    extend_block  extends a block out from the motifs.                 */
/*  Computes all possible blocks using all possible left and right
    extensions. Takes block with maximum block score = Smith's score
    divided by sqrt(width).                                              */
/*=======================================================================*/
void extend_block(block)
struct merged_motif *block;
{
   int left, middle, right, i, rn, ln, r, l, max_l, max_r;
   double ftemp, motif_sum, max_score, l_score, r_score, l_sum, r_sum;

   left = block->loffset;		   /* left edge of motif */
   middle = block->distance + 1;          /* width of motif */
   right = left + block->distance;         /* right edge  */
   motif_sum = 0;
   for (i=left; i<=right; i++)
      if (block->scores[i] >= SMatrix->highpass)
	 motif_sum += (block->scores[i]-SMatrix->highpass);
   ftemp = (double) middle;
   max_score = (double) ( (motif_sum/sqrt(ftemp)) );
   max_l = left;  max_r = right;

/*-----------  Extend right only -----------------------------*/
   r_sum = motif_sum; rn = middle;
   for (r=right+1; r<=block->domain; r++)
   {
     rn++;
     if (block->scores[r] >= SMatrix->highpass)
	   r_sum += (block->scores[r]-SMatrix->highpass);
     ftemp = (double) rn;
     r_score = (double) ( (r_sum/sqrt(ftemp)) );
     if (r_score > max_score)
     {
	max_score = r_score; max_r = r; max_l = left;
     }
   }

/*--Extend left & try all possible right extensions for each left -----*/
   l_sum = motif_sum; ln = middle;
   for (l=left-1; l>=0; l--)
   {
      ln++;
      if (block->scores[l] >= SMatrix->highpass)
		l_sum += block->scores[l]-SMatrix->highpass;
      ftemp = (double) ln;
      l_score = (double) ( (l_sum/sqrt(ftemp)) );
      if (l_score > max_score)
      {
	 max_score = l_score; max_l = l; max_r = right;
      }
      r_sum = l_sum; rn = ln;
      for (r=right+1; r<=block->domain; r++) /*--- all possible right ---*/
      {
	 rn++;
	 if (block->scores[r] >= SMatrix->highpass)
		 r_sum += (block->scores[r]-SMatrix->highpass);
	 ftemp = (double) rn;
	 r_score = (double) ( (r_sum/sqrt(ftemp)) );
	 if (r_score > max_score)
	 {
	    max_score = r_score; max_r = r; max_l = l;
	 }
      }
   }

/*------Now max_r and max_l are the best right & left extensions ------- */
   block->t_loffset = block->loffset - max_l;
   block->t_domain = max_r - max_l;
   block->t_score = max_score;
}  /*  end of extend_block */

/*=======================================================================
    Print out a trimmed block.
=========================================================================*/
void print_block(block, seqs)
struct merged_motif *block;
struct sequences *seqs;
{
   int s, i, j, x, sout;
   char tempname[30];

   print_head(block);
   if (RunType==0 || RunType == 2 || Debug)
   {
	 printf("\nScore              ");
	 for (i= block->loffset-block->t_loffset;
	      i<=block->loffset-block->t_loffset+block->t_domain;
	      i++)
	 {
	    x = (int) (block->scores[i]/100);
	    if (x >= 10) strcpy (tempname, "*");
	    else  kr_itoa(x, tempname, 10);
/*   Print sequence characters at the motif extremes
      Just takes 1st sequence value... */
	    if (i == block->loffset ||
		i == block->loffset+block->distance)
	    {
	       j = block->leftpos[0] - block->loffset + i;
	       strncpy(tempname, seqs->seq+seqs->offlen[0]+j, 1);
	    }
	    printf("%1s", tempname);
	 }

/*---- Print out in cluster order -------------*/
	 sout = 0;			/* # seqs printed for block */
	 for (s=0; scluster[s] < 0)    /* unclustered first */
	    {
	       print_seq(block, seqs, s);
	       sout++;
	    }
	 i = 0;				/* cluster # */
	 while (sout < NumSeqs)
	 {
	    for (s=0; scluster[s] == i)
	       {
		  print_seq(block, seqs, s);
		  sout++;
	       }
	    i++;
	 }
   }  /* end of RunType check */
}   /*  end of print_block */
/*======================================================================*/
void print_head(block)
struct merged_motif *block;
{
   printf("\n %.1s%.1s%.1s (extended width=%d, score=%d",
		num_to_aachar(block->aa[0]),
		num_to_aachar(block->aa[1]),
		num_to_aachar(block->aa[2]),
		block->t_domain+1, block->t_score );
   printf("  motifs=%d, motif width=%d, conserved=%d)",
		block->nmotif, block->distance+1, block->nident);
}  /* end of print_head */

/*=======================================================================
    Save a block.  Include the sequences flagged in pseqs.
    Requires global variable FILE *Fblk
=========================================================================*/
void save_block(block, seqs, pseqs)
struct merged_motif *block;
struct sequences *seqs;
int pseqs[MAXSEQS];			/* seqs to print */
{
    int s, i, sout, prevsout, pumseqs;

/*---------------  Build the output file name --------------------------*/
   /*   AC, MinDist and MaxDist are set in print_best()   */
    printf("\nSaving block %.1s%.1s%.1s",
		num_to_aachar(block->aa[0]),
		num_to_aachar(block->aa[1]),
		num_to_aachar(block->aa[2]) );
   /*-------------- Open and write the output file -----------------------*/
    fprintf(Fblk, "ID   %s; BLOCK\n", ID);
    fprintf(Fblk, "AC   %s;", AC);
    fprintf(Fblk, " distance from previous block=(%d,%d)\n", 
		MinDist, MaxDist);
    fprintf(Fblk, "DE   %s\n", DE);
    if (Gibbs)
    fprintf(Fblk, "BL   %.1s%.1s%.1s gibbs=[%d,%d,%d] motomat=[%d,%d,%d]",
		num_to_aachar(block->aa[0]),
		num_to_aachar(block->aa[1]),
		num_to_aachar(block->aa[2]),
	        Signif, Dups, Distance,
	        MinScore, ClThres, DropScore);
    else
    fprintf(Fblk, "BL   %.1s%.1s%.1s motif=[%d,%d,%d] motomat=[%d,%d,%d]",
		num_to_aachar(block->aa[0]),
		num_to_aachar(block->aa[1]),
		num_to_aachar(block->aa[2]),
	        Signif, Dups, Distance,
	        MinScore, ClThres, DropScore);
    fprintf(Fblk, " width=%d", block->t_domain+1);
/*-------------- Write sequences in cluster order --------------------*/
    pumseqs = 0;		/* # seqs to be printed for block */
    for (s=0; scluster[s] < 0)   /* unclustered first */
      {
	  write_seq(Fblk, block, seqs, s);
	  fprintf(Fblk, "\n\n");
	  sout++;
      }
    i = 0;				/* cluster # */
    while (sout < pumseqs)
    {
       prevsout = sout;
       for (s=0; scluster[s] == i)
	 {
	    write_seq(Fblk, block, seqs, s);
	    fprintf(Fblk, "\n");
	    sout++;
	  }
	 if (sout != pumseqs && sout > prevsout)
	    fprintf(Fblk, "\n"); /* Extra line bw clusters*/
	 i++;
     }
     fprintf(Fblk, "//\n");
}   /*  end of save_block */

/*======================================================================*/
/*    Cluster sequences in a trimmed block based on the number of       */
/*    identities within the block.                                      */
/*      1. Compute number of identities for each possible pair of seqs. */
/*         Results stored in lower half of matrix (pairs).              */
/*      2. Use clustering threshold % of # of AAs in trimmed block.     */
/*      3. Cluster recursively by traversing cols, rows of matrix.      */
/*======================================================================*/
void cluster_seqs(block, seqs)
struct merged_motif *block;
struct sequences *seqs;
{
   int nclus, npair, threshold, s1, s2, l1, l2, px, i, i1, i2;
   int oldclus, minclus;
   struct pair *pairs;

   npair = (NumSeqs*(NumSeqs-1))/2;
   pairs = (struct pair *) malloc (npair * sizeof(struct pair));
   if (pairs == NULL)
   {
      printf("\ncluster_seqs: Unable to allocate pair structure!\n");
      exit(-1);
   }
   threshold = (int) (ClThres*(block->t_domain+1))/100;

/*    Compute scores for all possible pairs of sequences            */
   for (s1=0; s1leftpos[s1] - block->t_loffset;
      for (s2=s1+1; s2leftpos[s2] - block->t_loffset;
	 px = INDEXCOLROW(NumSeqs, s1, s2);
	 pairs[px].score = 0;
	 pairs[px].cluster = -1;
	 for (i=0; i<=block->t_domain; i++)
	 {
	    i1 = l1+i;  i2 = l2+i;
	    if (i1 >= 0 && i1 < *(seqs->len+s1) &&
		i2 >= 0 && i2 < *(seqs->len+s2) &&
		strncmp(seqs->seq + seqs->offlen[s1] + i1,
			seqs->seq + seqs->offlen[s2] + i2, 1) == 0 )
		   pairs[px].score += 1;
	 }
      }  /* end of s2 */
   }  /* end of s1 */

/*  Print scores */
/*   printf("\nThreshold=%d", threshold);
   for (s2=1; s2cluster[s1] = -1;			/* clear out old values */
   nclus = 0;
   for (s1=0; s1= threshold)
	 {
	    if (block->cluster[s1] < 0)	     /*  s1 has no cluster yet */
	    {
	       if (block->cluster[s2] < 0)    /* new cluster */
	       {
		  block->cluster[s1] = nclus++;
		  block->cluster[s2] = block->cluster[s1];
	       }
	       else  			/* s2 has a cluster, use it */
		  block->cluster[s1] =  block->cluster[s2];
	    }
            /* use s1's cluster if it has one and s2 doesn't */
            else if (block->cluster[s1] >= 0 && block->cluster[s2] < 0)
	       block->cluster[s2] = block->cluster[s1];
            /* merge the two clusters into the lower number */
            else if (block->cluster[s1] >= 0 && block->cluster[s2] >= 0)
            {
               minclus = block->cluster[s1]; oldclus = block->cluster[s2];
               if (block->cluster[s2] < block->cluster[s1])
               { minclus = block->cluster[s2]; oldclus = block->cluster[s1]; }
               for (i1=0; i1cluster[i1] == oldclus)
                      block->cluster[i1] = minclus;
            }
	 }
      }   /* end of s2 */

   free(pairs);
}  /*  end of cluster_seqs */
/*======================================================================*/
/*  The blocks score is the sum of the column scores at or over HighPass
    divided by the square root of the block width.
    Scores only trimmed blocks. */
/*======================================================================*/
void score_block(block, seqs)
struct merged_motif *block;
struct sequences *seqs;
{
   int a, s, col, aa[20], pos, offset, flag;
   double ftemp, block_sum, ident_sum, weights[MAXSEQS];
   char c1, c[2];

   pb_weights(block, seqs, weights);		/* add sequence weights */

   block->nident = 0;				/* could be a re-count */
   block->t_score = 0;
   block_sum = ident_sum = 0.0;
   offset = block->loffset - block->t_loffset;
   for (col=0; col<=block->t_domain; col++)
   {
      flag = NO;			/* flag this col if an ident */
      for (a=0; a<20; a++)  aa[a] = 0;
      for (s=0; sleftpos[s] - block->t_loffset + col;
	  if (pos >= 0 && pos < *(seqs->len+s) )
	  {
	     strncpy(c, seqs->seq + seqs->offlen[s] + pos, 1);
	     c1 = c[0];
	     a = aachar_to_num(c1);
	     aa[a]++;
	  }
      }
      /*  Note: may be more than one aa in a col at least Signif times,
	  but are only counting such a column once */
      for (a=0; a<20; a++) if (aa[a] >= Signif) flag = YES;
      if (flag)
      {
          block->nident += 1;
	  ident_sum += (block->scores[col+offset] - SMatrix->highpass);
      }
      if (block->scores[col+offset] >= SMatrix->highpass)
	  block_sum += (block->scores[col+offset] - SMatrix->highpass);
   }  /*  end of col */
/*printf(" block_sum=%d, ident_sum=%d", (int) block_sum, (int) ident_sum); */
/*   ftemp = (double) block->t_domain + 1 + block->nident; */
   ftemp = (double) block->t_domain + 1;
   if (ftemp > 0)
      block->t_score = (int) ( block_sum/sqrt(ftemp) );
}  /* end of score_block */

/*======================================================================
	Put position-based sequence weights in the weights array
	col = block column, pos = sequence position
======================================================================*/
void pb_weights(block, seqs, weights)
struct merged_motif *block;
struct sequences *seqs;
double weights[MAXSEQS];
{
   struct pb_counts *pb;
   double factor, dtemp;
   int seq, pos, col, aa, width;
   char c1, c[2];

   width = block->t_domain;
   pb = (struct pb_counts *) malloc(width*sizeof(struct pb_counts));

   for (col = 0; col < width; col++)
   { 
      pb[col].diffaas = 0.0;
      for (aa = 0; aa < 20; aa++)
         pb[col].naas[aa] = (double) 0.0;
   }
  
   for (col = 0; col < width; col++)
      for (seq = 0; seq < NumSeqs; seq++)
      {
	 pos = block->leftpos[seq] - block->t_loffset + col;
	 if (pos >= 0 && pos < *(seqs->len+seq) )
	 {
	     strncpy(c, seqs->seq + seqs->offlen[seq] + pos, 1);
	     c1 = c[0];
	     aa = aachar_to_num(c1);
             if (aa >= 0 && aa <= 19)
             {
                pb[col].naas[aa] += 1;
             }
/*
             else
             {
                printf("pb_weights:%d ignored\n", aa);
             }
*/
         }
      }
   factor = 1.0;
   for (col = 0; col < width; col++)
   { 
      for (aa = 0; aa < 20; aa++)
      {
         if (pb[col].naas[aa] > 0.0)
         {
            pb[col].diffaas += 1;	/* # of different types of aas in col */
         }
      }
   }

   for (seq = 0; seq < NumSeqs; seq++)
   {
      weights[seq] = 0.0;
      for (col = 0; col < width; col++)
      {
	 pos = block->leftpos[seq] - block->t_loffset + col;
	 if (pos >= 0 && pos < *(seqs->len+seq) )
	 {
	     strncpy(c, seqs->seq + seqs->offlen[seq] + pos, 1);
	     c1 = c[0];
	     aa = aachar_to_num(c1);
             dtemp = pb[col].diffaas * pb[col].naas[aa];
             if (dtemp > 0.0) weights[seq] += 1.0 / dtemp;
         }
      } 
   }
 
   /*  Normalize weights to add to NumSeqs  */
   dtemp = 0.0;
   for (seq = 0; seq < NumSeqs; seq++) dtemp += weights[seq];
   for (seq = 0; seq < NumSeqs; seq++) 
	weights[seq] *= ((double) NumSeqs/dtemp);

   free(pb);
}  /* end of pb_weights */

/*======================================================================*/
/*    Print a sequence                                                  */
/*======================================================================*/
void print_seq(block, seqs, s)
struct merged_motif *block;
struct sequences *seqs;
int s;
{
   int left, right, i;

   left = block->leftpos[s] - block->t_loffset;
   right = left + block->t_domain;
   printf("\n%20s (% 5d) ", seqs->name+SNAMELEN*s, left+1);
   for (i=left; i<=right; i++)
   {
      if (i >= 0 && i < *(seqs->len+s) )
	  printf("%.1s", seqs->seq+seqs->offlen[s]+i );
      else
	  printf(".");
   }
   printf(" % 3d", block->cluster[s]);
}  /*  end of print_seq */

/*======================================================================*/
/*   Write  a sequence to an output file                                */
/*======================================================================*/
void write_seq(out, block, seqs, s)
FILE *out;
struct merged_motif *block;
struct sequences *seqs;
int s;
{
   int left, right, i;

   left = block->leftpos[s] - block->t_loffset;
   right = left + block->t_domain;
   /*  Print out the actual starting position of the sequence in
       the block, not the offset to it  */
   fprintf(out, "%20s (% 5d) ", seqs->name+SNAMELEN*s, left+1);
   for (i=left; i<=right; i++)
   {
     if (i >= 0 && i < *(seqs->len+s) )
	fprintf(out, "%.1s", seqs->seq+seqs->offlen[s]+i );
     else
	fprintf(out, "X");
   }
}  /*  end of write_seq */

/*======================================================================*/
/*   Calculate column scores for a block.
     Looks at all possible pairs of sequence AAs in a block column
     and takes average score. If one or both sequences has no AA in
     a column, because the block goes off one end or the other of the
     sequence, uses the score for 'J' */
/*======================================================================*/
void score_cols(block, seqs)
struct merged_motif *block;
struct sequences *seqs;
{
   int col, s1, s2, sum, npair, col1, col2;
   double weights[MAXSEQS];
   char c1, c2, c[2];

   pb_weights(block, seqs, weights);		/* add sequence weights */

   npair = (int) NumSeqs * (NumSeqs-1) / 2;  /* all possible pairs */
   for (col=0; col<=block->domain; col++)
   {
      sum = 0;				/* sum of all AA pairs */
      for (s1=0; s1leftpos[s1] - block->loffset + col;
	 if (col1 >= 0 && col1 < *(seqs->len+s1) )
	 {
	    strncpy(c, seqs->seq+seqs->offlen[s1]+col1, 1);
	    c1 = c[0];
	 }
	 else { c1 = 'X';}		/* off end of seq 1 */
	 for (s2=s1+1; s2leftpos[s2] - block->loffset + col;
	    if (col2 >= 0 && col2 < *(seqs->len+s2) )
	    {
	       strncpy(c, seqs->seq+seqs->offlen[s2]+col2, 1);
	       c2 = c[0];
	       sum += SMatrix->scores[aachar_to_num(c1)][aachar_to_num(c2)];
	    }
	    else { c2 = 'X';}		/* off end of seq 2 */
	 }  /* end of s2 */
      }  /* end of s1 */
      block->scores[col] = (int) ((long int) sum * 100 / npair);
   }  /* end of col */
}  /*  end of score_cols */
/*======================================================================*/
/*   Increase drop score and restart motomat.                           */
/*======================================================================*/
void restart()
{
   char arg2[5], arg3[5], arg4[5];
   int row, col;

   printf("\n>>>MOTOMAT out of memory!");
   if (DropScore <= 28)
   {
      DropScore += 2;
      printf("  Restarting with DropScore = %d\n", DropScore);
      kr_itoa(MinScore, arg2, 10);
      kr_itoa(ClThres, arg3, 10);
      kr_itoa(DropScore, arg4, 10);
/*---  Have to free enough memory to reload motomat ----------------------*/
      for (row=0; row= 0 && i1 < *(seqs->len+s1) &&
		i2 >= 0 && i2 < *(seqs->len+s2) &&
		strncmp(seqs->seq + seqs->offlen[s1] + i1,
			seqs->seq + seqs->offlen[s2] + i2, 1) == 0 )
		   pairs[px].score += 1;
	 }
      }  /* end of s2 */
   }  /* end of s1 */

/*  Print scores */
/*   printfblimps-3.9/protomat/motomat2.c000064400001460000012000001067611054326116300167350ustar00jorjastaff00000400000027/* (C) Copyright 1991 by Fred Hutchinson Cancer Research Center         */
/*    motomat2.c is second part of motomat.c; see comments there        */
/*======================================================================*/
/*   prune_blocks sets TopScore so there are <= MAXBLK surviving blocks.*/
/*   NOTE:  Not currently used. */
/*======================================================================*/
int prune_blocks(blocks)
struct merged_motif *blocks;
{
   struct temp *temp;
   int b, ntemp;

   temp = (struct temp *) malloc(Total_Motifs*sizeof(struct temp));
   if (temp == NULL)
   {
      fprintf(stderr,"%s\n", ACName);
      fprintf(stderr, " prune_blocks: Unable to allocate temp structure!\n");
      restart();
   }
/*---------  Sort blocks by trimmed score  */
   ntemp = 0;
   for (b=0; b 0)
      {
	 temp[ntemp].value = blocks[b].t_score;
	 temp[ntemp].index = b;
	 temp[ntemp++].flag = 0;
      }
   qsort(temp, ntemp, sizeof(struct temp), tempcmp);
/*    A descending sort would make it easier... */
   if (ntemp > MAXBLK)
   {
      b = ntemp - MAXBLK;  ntemp = MAXBLK;
   }
   else            b = 0;            /*  take min score if <= 25 blocks */
   TopScore = temp[b].value;
   printf("\nRevised TopScore=%ld", TopScore);
   free(temp);
   return(ntemp);
}  /*  end of prune_blocks */
/*=====================================================================*/
/*   order_blocks orders all blocks within each sequence in ascending
      order by the left-most amino acid in each block.  Blocks may
      overlap.  Orders only unmerged blocks that have not been dropped
      because of low score.                                            */
/*=====================================================================*/
void order_blocks(blocks)
struct merged_motif *blocks;
{
   struct temp *temp;
   int s, b, ntemp, i;

   temp = (struct temp *) malloc(Total_Motifs*sizeof(struct temp));
   if (temp == 0)
   {
      fprintf(stderr,"%s\n", ACName);
      fprintf(stderr," order_blocks: Unable to allocate temp structure!\n");
      restart();
   }
   for (s=0; s blocks[b].maxpos)
	       blocks[b].maxpos = blocks[b].position[s];
	    if (blocks[b].position[s] < blocks[b].minpos)
	       blocks[b].minpos = blocks[b].position[s];
	 }
      }

   free(temp);
}  /*  end of order_blocks */

/*=====================================================================*/
/*   tempcmp sorts a temp structure in ascending order by value, index
       and flag when it is used by qsort.                              */
/*=====================================================================*/
int tempcmp(t1, t2)
struct temp *t1, *t2;
{
   if (t1->value != t2->value)  return(t1->value - t2->value);
   if (t1->index != t2->index)  return(t1->index - t2->index);
   return(t1->flag - t2->flag);

}  /*  end of tempcmp */

/*=====================================================================*/
/*   build_dag creates a directed acyclic graph where the nodes are the
       motif blocks and the arcs represent all orderings of the blocks
       among all sequences.  The graph is represented by an adjacency
       matrix.  Only those cells of the matrix for which the arc from
       the row block to the column block is positive are allocated.  An
       arc is positive if the column block comes after the row block in
       at least RSignif sequences.
       NOTE: In order to insure the graph contains no cycles, RSignif
       must be no less than NumSeqs/2, since different sequences may be
       in different arcs. */
/*  3/18/91 Changed so that b1 must start before b2 in at least RSignif
    seqs AND b1 cannot overlap b2 in those seqs in order for there to
    be an arc from b1 to b2 */
/*=====================================================================*/
void build_dag(blocks)
struct merged_motif *blocks;
{
   int row, col, s, diff, nposrc, nposcr, maxdiffrc, maxdiffcr;
   int distrc, distcr;

   for (row=0; row= 0 && distrc >= 0)
		  {
		     nposrc += 1;
		     if (diff > maxdiffrc) maxdiffrc = diff;
		  }
		  else if (diff < 0 && distcr >= 0)
		  {
		     diff = 0-diff;
		     nposcr += 1;
		     if (diff > maxdiffcr) maxdiffcr = diff;
		  }
	       }  /*  end of sequence s */
	       if (nposrc >= RSignif)
	       {
		  Dag[row][col] = makematrix();
		  Dag[row][col]->npos = nposrc;
		  Dag[row][col]->maxdiff = maxdiffrc;
		  blocks[row].out_degree = blocks[row].out_degree + 1;
		  blocks[col].in_degree = blocks[col].in_degree + 1;
/*		  for (s=0; sdist[s] =
		      left(s, col, blocks) - right(s, row, blocks) - 1;
*/
	       }
	       if (nposcr >= RSignif)
	       {
		  Dag[col][row] = makematrix();
		  Dag[col][row]->npos = nposcr;
		  Dag[col][row]->maxdiff = maxdiffcr;
		  blocks[col].out_degree = blocks[col].out_degree + 1;
		  blocks[row].in_degree = blocks[row].in_degree + 1;
/*		  for (s=0; sdist[s] =
		      left(s, row, blocks) - right(s, col, blocks) - 1;
*/
	       }
	 }  /*  end of col */
      }  /*  end of row */
      if (Debug)
	 for (row=0; rownpos);
	       else
		  printf("   x");
	 }

}  /*  end of build_dag */
/*======================================================================*/
/*   Make and return a new matrix structure. */
/*======================================================================*/
struct matrix *makematrix()
{
   struct matrix *new;

   new = (struct matrix *) malloc(sizeof(struct matrix));
   if (new == NULL)
   {
      fprintf(stderr,"%s\n", ACName);
      fprintf(stderr," makematrix: Unable to allocate matrix structure!\n");
      restart();
   }
   new->npos = 0;
   new->maxdiff = 0;
   new->mark = -1;
   return(new);
}  /*  end of makematrix */
/*=======================================================================*/
/*   makepath allocates and intializes a new path.                       */
/*=======================================================================*/
struct path *makepath()
{
  struct path *new;
  int s, row, col;

  new  = (struct path *) malloc(sizeof(struct path));
  if (new == NULL)
  {
     fprintf(stderr,"%s\n", ACName);
     fprintf(stderr," makepath: Unable to allocate path structure!\n");
/*---  Have to free enough memory to reload motomat ----------------------*/
     for (row=0; rownblocks = new->nbest = new->naas = new->totmotif = new->totident = 0;
  new->totscore = (unsigned long) 0;
  new->nseqs = 0;
  for (s=0; sseqs[s] = YES;
  new->first_block = new->first_best = NULL;
  new->next_path = NULL;
  return(new);
}  /* end of makepath */
/*=======================================================================*/
/*   ins_path inserts a new path at the end of a list of paths.          */
/*=======================================================================*/
void ins_path(list, new)
struct path *list, *new;
{
   struct path *cur;

   cur = list;
   while (cur->next_path != NULL)
     cur = cur->next_path;

   cur->next_path = new;
   list->nblocks = list->nblocks + 1;  /* This is the # of paths */
   if (list->nblocks > 1500)
   {
      fprintf(stderr,"%s\n", ACName);
      fprintf(stderr," ***MOTOMAT STOPPING BECAUSE >1500 PATHS***");
      restart();
   }

}  /* end of ins_path */

/*=======================================================================*/
/*   copypath copies an existing path into a new path.                   */
/*=======================================================================*/
struct path *copypath(old)
struct path *old;
{
   struct path *new;
   struct block_list *bold, *bnew, *blas;
   int s;

   new = makepath();
   new->nblocks = old->nblocks; new->nbest = old->nbest;
   new->naas = old->naas; new->totscore = old->totscore;
   new->nseqs = old->nseqs;
   new->totmotif = old->totmotif;
   new->totident = old->totident;

   for (s=0; sseqs[s] = old->seqs[s];

   bold = old->first_block;
   if (bold != NULL)
   {                            /*  copy first block */
      bnew = makebllist();
      bnew->b = bold->b;
      new->first_block = bnew;
      bold = bold->next_block;
      while (bold != NULL)  /*  copy other blocks */
      {
	 blas = bnew;
	 bnew = makebllist();
	 bnew->b = bold->b;
	 blas->next_block = bnew;
	 bold = bold->next_block;
      }
   }
/*------Have to copy best path pointers: old->first_best, bold->next_best,
	bold->prev_best-----*/

   return(new);
}  /* end of copypath */
/*=======================================================================*/
/*   free_path frees all memory allocated to a path  .                   */
/*=======================================================================*/
void free_path(old)
struct path *old;
{
   struct block_list *bold, *bfree;

   if (old != NULL)
   {
      bold = old->first_block;
      while (bold != NULL)            /*  free blocks */
      {
	 bfree = bold;
	 bold = bold->next_block;
	 free(bfree);
      }
      free(old);	 	   /*  free path */
   }

}  /* end of free_path */
/*========================================================================*/
/*    find_paths finds all positive paths through the DAG.
       Does not consider whether or not blocks in the
       path overlap.  Stops building a path when fewer than RSignif
       sequences are represented.              */
/*=======================================================================*/
void find_paths(paths, blocks)
struct path *paths;
struct merged_motif *blocks;
{
   int row, col, more, ntemp, i;
   struct path *newpath;
   struct temp *temp;

/*---- First add all single blocks as possible paths of one block each --*/
   for (i=0; imark < 0 &&
	     Dag[row][col]->npos >= RSignif)     /*  was NumSeqs */
		more = YES;
      }
/* ---------  See if there are more starting paths in this row ----------*/
      if (more)
      {
	 newpath = makepath();
	 ins_bllist(row, newpath);
         if (Debug) printf("\n\nfind_paths: more-----------");
         /*  don't need to call best_path() here because would
             have already been checked with singles
	 best_path(newpath, paths, blocks);  */
	 follow_arcs(paths, newpath, row, blocks);
      }
      else if (ntemp == 1)          /*  Only one block */
      {
	 newpath = makepath();
	 ins_bllist(row, newpath);
	 best_path(newpath, paths, blocks);
      }
   }

   free(temp);
}  /*  end of find_paths */

/*======================================================================*/
/*   follow_arcs does a recursive depth first search of the DAG,
     finding all postive paths.                                         */
/*======================================================================*/
void follow_arcs(paths, curpath, row, blocks)
struct path *paths, *curpath;
int row;
struct merged_motif *blocks;
{
   int col1, ntemp, ntemp1, nbranch, i, savnpath, s, nseq;
   struct path *newpath, *savpath;
   struct block_list *tblock;
   struct temp *temp;

   savpath = newpath = NULL;
   savnpath = paths->nblocks;  /* This is really the # of paths */
/*------  See if there is an unmarked fully positive column, and take
	  the one with the closest next position if there is ------------*/
/*-------  Make a list of unmarked columns for this row, sorted in
	     increasing order of maxdiff -----------*/
   temp = (struct temp *) malloc(Total_Motifs*sizeof(struct temp));
   if (temp == NULL)
   {
      fprintf(stderr,"%s\n", ACName);
      fprintf(stderr," follow_arcs: Unable to allocate temp structure!\n");
      restart();
   }
/*--- Continue topological sort of graph nodes (lowest in-degree next)---*/
   ntemp = 0;
   for (col1=0; col1mark < savnpath &&
	  Dag[row][col1]->npos >= RSignif)
	  {
	     temp[ntemp].index = col1;
	     temp[ntemp].value = blocks[col1].in_degree;
	     temp[ntemp++].flag = Total_Motifs - blocks[col1].out_degree;
	  }
    qsort(temp, ntemp, sizeof(struct temp), tempcmp);
    if (Debug)
    {
	printf("\n\nfollow:  row=%d, ntemp=%d", row, ntemp);
	printf("\n curpath blocks=");
	tblock = curpath->first_block;
	while (tblock != NULL)
	{
	    printf("%d ", tblock->b);
	    tblock = tblock->next_block;
	}
	printf("\n curpath_seqs:");
	for (s=0; sseqs[s]);
    }

/*--- There are ntemp possible ways to continue this path, but not
   all of them may have enough sequences remaining.  ntemp1 is the
   number of ways to continue that still have enough sequences -----*/
    ntemp1 = ntemp;
    for (i=0; iseqs[s] == NO ||
	     blocks[temp[i].index].position[s] < blocks[row].position[s])
		   nseq--;
       if (Debug)
	  printf("\n row=%d temp[i].index=%d nseq=%d",
		     row, temp[i].index, nseq);
       if (nseq >= RSignif)
	  temp[i].flag = YES;   /* NOTE: re-using flag (was out_degree)*/
       else
       {
	  temp[i].flag = NO;
	  if (Dag[row][temp[i].index] != NULL)
	      Dag[row][temp[i].index]->mark = savnpath;
	  ntemp1--;
       }
    }

/*-- If there is no way to continue the path, insert it in list of paths --*/
    if (ntemp1 <= 0 && curpath->nblocks > 0)
    {
       /*   Remove this if Paths are evaluated each time a block is added*/
       best_path(curpath, paths, blocks); 		/*NOTENOTE*/
       free(temp);
       if (savpath != NULL) free(savpath);
       if (Debug) printf("\nEnd of follow_arcs for %d", row);
    }
    else   /* continue along */
    {
       nbranch = 0;           /* number of branches at this point */
       for (i=0; imark < savnpath &&
	      Dag[row][temp[i].index]->npos >= RSignif)
	  {
	      nbranch += 1;
	      if (nbranch > 1)             /* start a new path */
		 newpath = copypath(savpath);
	      else   /* continue along the current path, and... */
	      {      /*  save it for future branches*/
		 newpath = curpath;
		 if (ntemp > 1) savpath = copypath(curpath);
	      }
/*------------  Add new block to path & update sequences in path --- */
	      for (s=0; sseqs[s] = NO;
	      ins_bllist(temp[i].index, newpath);
/*---Add this if evaluate the path so far 
              best_path(newpath, paths, blocks);        NOTENOTE*/
/*-----------  Mark blocks already in this path and continue */
	      tblock = newpath->first_block;
	      while (tblock != NULL)
	      {
		 if (Dag[tblock->b][temp[i].index] != NULL)
		     Dag[tblock->b][temp[i].index]->mark = savnpath;
		 tblock = tblock->next_block;
	       }
	       follow_arcs(paths,newpath,temp[i].index,blocks);
	  }
       }   /*  end of else ntemp1 > 0 */

}  /*  end of follow_arcs */
/*======================================================================*/
/*  ins_bllist inserts a block at the end of the block list for a path. */
/*======================================================================*/
void ins_bllist(b, path)
int b;
struct path *path;
{
   struct block_list *bcur, *bnew;

   bnew = makebllist();
   bnew->b = b;

   bcur = path->first_block;
   if (bcur == NULL)
      path->first_block = bnew;
   else
   {
      while(bcur->next_block != NULL)
	 bcur = bcur->next_block;
      bcur->next_block = bnew;
   }
   path->nblocks += 1;

}  /*  end of ins_bllist */
/*======================================================================*/
/*   Allocate and return a new block_list structure */
/*======================================================================*/

struct block_list *makebllist()
{
   struct block_list *new;

   new = (struct block_list *) malloc(sizeof(struct block_list));
   if (new == NULL)
   {
      fprintf(stderr,"%s\n", ACName);
      fprintf(stderr," makebllist: Unable to allocate block_list structure!\n");
      restart();
   }
   new->b = -1;
   new->minprev = 9999;  new->maxprev = -9999;
   new->next_block = new->next_best = new->prev_best = NULL;
   return(new);
}  /*  end of makebllist */
/*======================================================================*/
/*  best_paths finds the best sub-path in each path.
     Paths are "best" if the blocks are in the same order in RSignif
     sequences, and if adjacent blocks don't overlap for any sequence.
     If there are multiple adjacent overlapping blocks, the "best"
     block is the one with the highest score and with the most motifs.
     When best_paths gets the paths, the blocks are already in the
     same order in RSignif sequences, however they may overlap in some or
     all of the sequences in different ways (if two blocks overlap the
     same way in all sequences within the motif region they would have
     been merged earlier).    */
/*======================================================================*/
struct path *best_paths(paths, blocks)
struct path *paths;
struct merged_motif *blocks;
{
   struct path *cpath, *allpaths;

/*-----  Looks at all paths in  "paths" & keeps best one in "allpaths" ---*/
   allpaths = makepath();
   cpath = paths->next_path;
   while (cpath != NULL)
   {
      best_path(cpath, allpaths, blocks);
      cpath = cpath->next_path;
   }
   return(allpaths->next_path);
}  /*  end of best_paths */
/*======================================================================*/
/*   Given a new path, compute the best non-overlapping sub-path and
     compare it with the current best path, possibly replacing the best
     path with it. "paths" points to one path here, the current best path */
/*========================================================================*/
void best_path(newpath, paths, blocks)
struct path *newpath, *paths;
struct merged_motif *blocks;
{
   struct path *bestpath, *temppath;
   struct block_list *cblock, *pblock, *lblock;
   int maxdist, mindist, s, b, lastb, pb;
   int allb[MAXSEQS], thisb[MAXSEQS], saveb[MAXSEQS];
   int tots, temp, thisseq, saveseq, prop;
   double dtemp;

/*---- Note on variables:  There are three sets
      1. Current block in path =   {cblock, b, thisb[s], thisseq}
      2. Last best block in path = {lblock, lastb, saveb[s], saveseq}
	 This block is next in line to be added, once all blocks that
	 overlap with it are checked.
      3. Last block in best path = {pblock, pb, allb[s], tots}
	 This is the current state of the path     --------*/
/*-----Note on path: path->seqs[s] flags all variables in the path.
    However, since some overlapping blocks will be dropped when the best
    path is selected, more sequences than those flagged may end up in
    the best path */

   bestpath = paths->next_path;
   temppath = copypath(newpath);
   paths->nblocks += 1;		/* number of paths tested so far */

   if (Debug)
   {
      printf("\nbest_path: paths->nblocks=%d", paths->nblocks);
      tots=0;
      for (s=0; sseqs[s] == YES) tots++;
	 printf("\n New path: nblocks=%d, tots=%d",
		 temppath->nblocks, tots);
   }

   cblock = temppath->first_block;             /*  Get first block */
   b = cblock->b;
   tots = saveseq = NumSeqs;
   for (s=0; snext_block;
   while (cblock != NULL)
   {
       b = cblock->b;
/*----- For all sequences still in the path in which b follows lastb,
   compute the distance from the end of lastb to the beginning of b
   to see if they overlap, and see if there are enough non-overlapping
   sequences left. allb[s] are seqs in current path, which includes
   neither lastb nor b. saveb[s] are seqs with current path plus lastb,
   which hasn't been added yet.-------*/
       maxdist = -9999; mindist = 9999; thisseq = 0;
       for (s=0; s= 0)
	    {
	       temp = left(s, b, blocks) - right(s, lastb, blocks) - 1;
	       if (temp < mindist) mindist = temp;
	       if (temp > maxdist) maxdist = temp;
	       if (temp >= 0) {thisb[s] = YES; thisseq++;} /*no overlap*/
	    }
	    else
	       thisb[s] = NO;
       }
       if (Debug)
       {   printf("\n (%d, %d) B%d %.1s%.1s%.1s", mindist, maxdist, b,
		num_to_aachar(blocks[b].aa[0]),
		num_to_aachar(blocks[b].aa[1]),
		num_to_aachar(blocks[b].aa[2]));
	   printf("\n   thisb: ");
	   for (s=0; s= RSignif)  /* Enough non-overlapping sequences */
	 {
	    temppath->nbest += 1;
	    temppath->naas += blocks[lastb].t_domain + 1;
            dtemp = sqrt(blocks[lastb].nmotif);
	    dtemp *= (double) blocks[lastb].t_score;
	    temppath->totscore += (unsigned long) dtemp;
	    temppath->totmotif += blocks[lastb].nmotif;
	    temppath->totident += blocks[lastb].nident;
	    lblock->prev_best = pblock;
	    if (pblock == NULL)
	       temppath->first_best = lblock;
	    else
	       pblock->next_best = lblock;

	    pblock = lblock; pb = lastb;
	    lblock = cblock; lastb = b;
	    tots = saveseq;  saveseq = thisseq;
	    for (s=0; s 0)
	 {
	    lblock = cblock; lastb = b;
/*  Now thisb[] is incorrect since lastb has been eliminated, so figure
    out saveb[] directly, unless this is still 1st block */
	    if (pb >= 0) 		/* Any blocks in path yet ? */
	    {
	       saveseq = 0;
	       for (s=0; s= 0 &&
			  temp >= 0)
		      { saveb[s] = YES; saveseq++;}
		   }
	       }  /* end of for s */
	    }  /* end of if pb */
	 }   /*  end of if overlap  and better score */
	 cblock = cblock->next_block;
      }
/*------------  Final block in the path ------------------------------- */
      temppath->nbest += 1;
      temppath->naas += blocks[lastb].t_domain + 1;
      dtemp = sqrt(blocks[lastb].nmotif);
      dtemp *= (double) blocks[lastb].t_score;
      temppath->totscore += (unsigned long) dtemp;
      temppath->totmotif += blocks[lastb].nmotif;
      temppath->totident += blocks[lastb].nident;
      lblock->prev_best = pblock;
      if (pblock == NULL)
	 temppath->first_best = lblock;
      else
	 pblock->next_best = lblock;
      tots = saveseq;
      for (s=0; stotscore;
    temppath->totscore = (unsigned long) dtemp;

/*---------------------------------------------------------------------*/
   if (Debug)
   {
      printf("\n ");
      printf("Best sub-path:%d blocks, %d AAs, total score=%ld",
	       temppath->nbest, temppath->naas, temppath->totscore);
      printf(",\n total motifs=%d, total idents=%d",
	       temppath->totmotif, temppath->totident);
      printf(", total sequences=%d, prop=%d", tots, prop);
   }

/*---------------------------Update best path ---------------------------*/
      if (bestpath == NULL ||
	  temppath->totscore > bestpath->totscore ||
	  (temppath->totscore == bestpath->totscore &&
	   temppath->totmotif > bestpath->totmotif) )
      {
	  paths->next_path = temppath;      /* New best path */
	  free_path(bestpath);  /*  Throw away old best path */
	  if (Debug) printf("\n >>>NEW BESTPATH");
	  /*---- update info for best path ----*/
	  temppath->nseqs = tots;
	  for (s=0; sseqs[s] = allb[s];
	  /*---- first block in best path, distance from start of seq ---*/
	  lblock=temppath->first_best;
	  mindist=9999; maxdist=-9999;
	  for (s=0; sseqs[s] == YES)
	     {
		   temp=left(s,lblock->b,blocks);
		   if (temp maxdist) maxdist=temp;
	     }
	  lblock->minprev=mindist; lblock->maxprev=maxdist;
	  /*---- rest of the blocks in best path ----*/
	  cblock=lblock->next_best;
	  while (cblock != NULL)
	  {
	     mindist=9999; maxdist=-9999;
	     for (s=0; sseqs[s] == YES)
		{
		   temp=left(s,cblock->b,blocks)-right(s,lblock->b,blocks)-1;
		   if (temp maxdist) maxdist=temp;
		}
	     cblock->minprev=mindist; cblock->maxprev=maxdist;
	     lblock = cblock;
	     cblock=cblock->next_best;
	  }
      }
      else
	  free_path(temppath);  /* Throw away new path */

}  /*  end of best_path */
/*=======================================================================
   If there are DUPS, take a look at the sequences left out of the best
   path and see if they can be added. They can be if they have all the
   blocks in some non-overlapping order, not necessarily the same order
   as in the best path sequences.
======================================================================*/
void check_seqs(path, blocks)
struct path *path;
struct merged_motif *blocks;
{
   int s, b, lastb, ntemp, i, overlap;
   struct block_list *cblock;
   struct temp *temp;

   temp = (struct temp *) malloc(Total_Motifs*sizeof(struct temp));
   if (temp == NULL)
   {
      fprintf(stderr,"%s\n", ACName);
      fprintf(stderr," check_seqs: Unable to allocate temp structure!\n");
      restart();
   }
   for (s=0; sseqs[s] == NO)
      {
	ntemp = 0;
	cblock = path->first_best;
	while (cblock != NULL)
	{
	   temp[ntemp].index = cblock->b;
	   temp[ntemp].value = blocks[cblock->b].position[s];
	   temp[ntemp++].flag = 0;
	   cblock = cblock->next_best;
	}
/*------- Sort blocks in best path by their order in the sequence, which
     is probably different than their order in the best path.
     Then check to see whether they overlap in the sequence. If they
     don't, then add the sequence to the best path ----*/
	qsort(temp, ntemp, sizeof(struct temp), tempcmp);
	lastb = temp[0].index; overlap = NO;
	for (i=1; iseqs[s] = YES; path->nseqs += 1; }
      }  /*  end of s == NO */
   }

   free(temp);
}  /* end of check_seqs */
/*====================================================================*/
/*    print_best prints the best path.                                */
/*====================================================================*/
void print_best(path, blocks, seqs)
struct path *path;
struct merged_motif *blocks;
struct sequences *seqs;
{
  struct block_list *cblock;
  int s, b, nseq, nb, allb[MAXSEQS], plt_cursor, aclen;
  FILE *plt;

/*------------Write out blocks------------------------------------------*/
/*--   Open the plotting file ---*/
   plt = NULL;
/*
  temp[0] = '\0';
  strcpy(temp, Blk_Filename); strcat(temp, ".plt");
  if ( (plt=fopen(temp, "w+t")) == NULL)
     printf("\nCannot open file %s, no plotting output.\n", temp);
  plt_cursor = 0;
*/
/*--   Problem with passing path->seqs to save_block.... */
  for (s=0; sseqs[s];

  printf("\nBest path has %d sequences out of %d:", path->nseqs, NumSeqs);
  nb = 0;
  cblock = path->first_best;
  while (cblock != NULL)
  {
     b = cblock->b;
     printf("\n (%d, %d) B%d %.1s%.1s%.1s", cblock->minprev, cblock->maxprev,
		cblock->b,
		num_to_aachar(blocks[cblock->b].aa[0]),
		num_to_aachar(blocks[cblock->b].aa[1]),
		num_to_aachar(blocks[cblock->b].aa[2]));
     nb += 1;
     strcpy(AC, ACName);
     aclen = strlen(AC);
     if ( (nb == 1 && path->nbest >1) || nb > 1)
     {  AC[aclen] = ' '; aclen++; AC[aclen] = '\0';   }

     if (nb == 1) 
     {  if (path->nbest > 1) AC[aclen-1] = 'A';   }
     else if (nb == 2)  AC[aclen-1] = 'B';
     else if (nb == 3)  AC[aclen-1] = 'C';
     else if (nb == 4)  AC[aclen-1] = 'D';
     else if (nb == 5)  AC[aclen-1] = 'E';
     else if (nb == 6)  AC[aclen-1] = 'F';
     else if (nb == 7)  AC[aclen-1] = 'G';
     else if (nb == 8)  AC[aclen-1] = 'H';
     else if (nb == 9)  AC[aclen-1] = 'I';
     else if (nb == 10) AC[aclen-1] = 'J';
     else if (nb == 11) AC[aclen-1] = 'K';
     else if (nb == 12) AC[aclen-1] = 'L';
     else if (nb == 13) AC[aclen-1] = 'M';
     else if (nb == 14) AC[aclen-1] = 'N';
     else if (nb == 15) AC[aclen-1] = 'O';
     else if (nb == 16) AC[aclen-1] = 'P';
     else if (nb == 17) AC[aclen-1] = 'Q';
     else if (nb == 18) AC[aclen-1] = 'R';
     else if (nb == 19) AC[aclen-1] = 'S';
     else if (nb == 20) AC[aclen-1] = 'T';
     else if (nb == 21) AC[aclen-1] = 'U';
     else if (nb == 22) AC[aclen-1] = 'V';
     else if (nb == 23) AC[aclen-1] = 'W';
     else if (nb == 24) AC[aclen-1] = 'X';
     else if (nb == 25) AC[aclen-1] = 'Y';
     else if (nb > 25)  AC[aclen-1] = 'Z';
     MinDist = cblock->minprev; MaxDist = cblock->maxprev;
     save_block(&blocks[b], seqs, allb);
     if (plt != NULL)
  save_plot(&plt_cursor, cblock->minprev, cblock->maxprev, plt, &blocks[b]);
     cblock = cblock->next_best;
  }
  if (plt != NULL) fclose(plt);

  /*----------Summary of the best path --------------------------------*/
  printf("\n%d blocks, %d AAs, total score=%ld, total motifs=%d",
	       path->nbest, path->naas, path->totscore, path->totmotif);
  printf(", total conserved=%d", path->totident);
  printf("\n total sequences=%d out of %d", path->nseqs, NumSeqs);

  /*------Print seqs in path----------------------------------------------*/
  printf("\nSequences in the best path:");
  nseq = 0;
  for (s=0; sseqs[s] == YES)
    {
	if (nseq%5 == 0) printf("\n");
	nseq++;
	printf("%.3d:%20s ", s, seqs->name+SNAMELEN*s);
    }
  }

  /*------Print seqs NOT in path----------------------------------------*/
  printf("\nSequences not in the best path:");
  nseq = 0;
  for (s=0; sseqs[s] == NO)
    {
	if (nseq%5 == 0) printf("\n");
	nseq++;
	printf("%.3d:%20s ", s, seqs->name+SNAMELEN*s);
    }
  }


}  /*  end of print_best */
/*==================================================================*/
/*      print a path  */
/*==================================================================*/
void print_path(path)
struct path *path;
{
  struct block_list *cblock;

  printf("\nPath:");
  cblock = path->first_block;
  while (cblock != NULL)
  {
     printf(" %d", cblock->b);
     cblock = cblock->next_block;
  }
}  /*  end of print_path */
/*=======================================================================
    save_plot adds plotting information for a block to the plot file
     and updates the plotting cursor, which is the x-axis value.
=========================================================================*/
void save_plot(cursor, minprev, maxprev, plt, block)
int *cursor, minprev, maxprev;
FILE *plt;
struct merged_motif *block;
{
   int c, temp;

   /*-----  Plot zeros or ones between blocks ---------*/
   for (c=0; cloffset - block->t_loffset;		/* offset */
   for (c=0; c <= block->t_domain; c++)
   {
      if (plt != NULL)
	 fprintf(plt, "%d  %d\n", *cursor, block->scores[c+temp]);
      *cursor = *cursor + 1;
   }
}  /* end of save_plot */
/*====================================================================*/
/*   Return the left-hand block position */
/*======================================================================*/

int left(s, b, blocks)
int s, b;
struct merged_motif *blocks;
{
   return(blocks[b].leftpos[s] - blocks[b].t_loffset);
}  /*  end of left */
/*====================================================================*/
/*  Return the right-hand block position */
/*======================================================================*/

int right(s, b, blocks)
int s, b;
struct merged_motif *blocks;
{
   return(left(s, b, blocks) + blocks[b].t_domain);
}  /*  end of right */
 dtemp;
      tblimps-3.9/protomat/multimat.c000064400001460000012000001644621054326101200170220ustar00jorjastaff00000400000027/*=====================================================================*/
/*(C) Copyright 1991-9 by Fred Hutchinson Cancer Research Center         */
/*        multimat.c  reads several BLIMPS MATRIX search output files
	   and merges the results.  Writes stats to multimat.dat.
	    eg:  multimat 10 blocks.dat PS00094.lis PS00094*.hom or
		 multimat 15 none none PS00094A.hom PS00094B.hom ... (up to 26)

	   1st arg = number of hits to report
	   2nd arg = name of blocks database (use non-existent file name
		     to skip it, if file is found, will open it & compare
		     search results with blocks of same name)
           3rd arg = name of list of true positive sequences (use
                     non-existent file name to omit it) If file is found
                     will only report hits NOT in file. 
	   4rd arg = name of matrix search output files, etc.
			EG PS00094A, PS00094B, PS00094C

	Name restrictions:
		AC name in the blocks in the blocks database (2nd arg)
			must be unique and <= 8 characters long.
			The blocks database must be sorted in AC order.
			It is assumed that all of the blocks from the
			same family have all the same AC except for the
			last character.
		Search result file names (4th arg) must match the AC names of
			the blocks that were the queries for the search.
		Sequence names in the blocks in the blocks db (2nd arg)
			and in the list of true positives (3rd arg)
			must be unique, and must match the sequence
			names in the database searched. It is assumed that
			searches are for blocks belonging to the same
			family.
--------------------------------------------------------------------------
     8/1/91  J. Henikoff

   5/15/99 1. Format changes for Blimps 3.2.6
   6/26/99 1. Sequence name length from 10 to 18
   6/11/00 1. AC length from 7 to 9
  12/23/06 1. Sequence name length from 18 to 20
====================================================================*/
#include "motifj.h"

#define SWISS 69113		/* Swiss35 */
#define NSCORE 5000		/* Maximum # of scores in .hom file */
#define MAXHOM 26		/* Maximum # of .hom files */
#define MAXHIT 10		/* Maximum # of hits to report */
#define MAXMEM 64000		/* Maximum bytes for DOS array */
#define SEEK_SET 0
#define PROTEIN 1
#define DNA 3
#define MAXMAP 60		/* Maximum map width in characters */
#define MAX_WIDTH 100		/* Maximum block width expected */

struct hom {			/* search results structure */
   char ac[MAXAC+1];		/* block name, eg. PS00094A */
   int norm;			/* normalized score */
   int max_norm;		/* max normalized score for this group */
   int min_rank;		/* minimum rank for this group of blocks */
   int rank;			/* rank of this result in search */
   int frame;			/* frame of alignment */
   int strength;		/* block strengh */
   int score;			/* patmat score */
   int offset;			/* offset of alignment */
   double seqlen;			/* db sequence length */
   int width;			/* width of block */
   char title[30];		/* block description */
   char seq_id[25];		/* patmat sequence id */
   char aa[MAX_WIDTH]; 	/* alignment to block */
   int map_flag;		/* used by map_blocks */
   int tp;			/* true positive flag, 1 if tp, 2 if in block*/
};

struct best_block {			/* block structure */
   char ac[MAXAC+1];         		/* accession number */
   int nseq, width, strength;		/* #seqs, width, strength */
   int s995;				/* 99.5 percentile score */
   int minprev, maxprev;		/* distances from prev block */
   char name[MAXSEQS][SNAMELEN+5];		/* name of seq */
   int offset[MAXSEQS];			/* offset of seq */
   char aa[MAXSEQS][MAX_WIDTH];	/* aas for seq */
   int cluster[MAXSEQS];		/* cluster # for seq */
   int ncluster[MAXSEQS];		/* #seqs in same cluster */
   long dat_pos;			/* position of block in blocks.dat*/
   int query;				/* score if last seq is a query */
   int rank;				/* rank if last seq is a query */
   int anchor;				/* anchor block flag */
   struct best_block *next_block;	/* next block in path */
};

/*---- Functions also in blksort.c -----*/
void print_blurb();
void check_dat();
struct best_block *read_block();
void fill_block();
int add_query();
double hypergeo();
int distance_okay();
int prev_dist();
int distance();
void map_blocks();
void align_blocks();
int closest_seq();
int tempcmp();
int read_hom();
int check_tp();
void show_hom();
int id_cmp();
int rank_cmp();
int idnorm_cmp();
int norm_cmp();
struct best_block *get_blocks();
void consensus();
int compute_loc();
void re_normalize();
/*--------------------Routines from motmisc.o------------------------*/
struct db_id *makedbid();
int get_ids();
struct split_name *split_names();
void kr_itoa();

/*------------Global variables -------------*/
char Version[12] = " 6/11/00.1";/* Version number */
int Ask;			/* Interactive flag */
char AC[30];				/* Global variables */
int ACLen;				/* Length of AC */
int NScore;				/* Max# scores for DOS */
int LisSeq;				/* #seqs in TP list file */
int FragSeq;
int BlkSeq;
int SeqType;			/* DNA or PROTEIN database searched */
char Query[SNAMELEN];		/* Query file name */
double DBLen;			/* DB sequence length */
int NBlock;			/* # blocks in family */
double NSeq;			/* # sequences searched */
double NRank;			/* # of ranks assigned in search */
int DBType;			/* =1 if amino acid, =3 if nucleotide */
int MaxHit;			/* # hits to report */
FILE *Fout;			/* multimat.lis statistics file (not TPs) */
FILE *Fdat;			/* multimat.dat statistics file (TPs) */
FILE *Fmis;			/* multimat.mis file (missed TPs)     */
FILE *Ffnd;			/* multimat.fnd file (missed TPs)     */
/*======================================================================*/
int main(argc, argv)
int argc;
char *argv[];
{
   FILE *fhom, *fblk, *flis;
   char homfile[MAXHOM][FNAMELEN], *ptr, *ptr1, ctemp[FNAMELEN];
   char datfile[FNAMELEN], lisfile[FNAMELEN];
   int totscores, i, nhom;
   struct hom *temp;
   struct db_id *ids, *did;
   struct best_block *blocks;

   printf("MULTIMAT: (C) Copyright 1991 by Fred Hutchinson Cancer ");
   printf("Research Center\n");
   printf("Version %s\n", Version);
   if (argc <= 4)
   {
      printf("USAGE:   multimat    \n");
      printf("              = Maximum # of hits to report\n");
      printf("             = File containing blocks for comparison\n");
      printf("               = File containing list of TP sequences\n");
      printf("             = Blimps search result files, ");
      printf(" blocks vs sequence db\n");
   }
/*   Fout = fopen("multimat.lis", "a");	 */
   Fdat = fopen("multimat.dat", "a");		/* statistics file */

/*--------------arg 1: Number of hits to report---------------------*/
   MaxHit = MAXHIT;
   ctemp[0] = '\0';
   if (argc > 1) strcpy(ctemp, argv[1]);
   else
   {
      printf("\nEnter maximum number of hits to report [%d]: ", MaxHit);
      gets(ctemp);
   }
   if (strlen(ctemp)) MaxHit = atoi(ctemp);
   if (MaxHit < 1 || MaxHit > NSCORE) MaxHit = MAXHIT;
/*------------- arg 2:  blocks database file -----------------------------*/
   if (argc > 2)
      strcpy(datfile, argv[2]);
   else
   {
      printf("\nEnter name of blocks database:\n");
      gets(datfile);
   }
   if ( (fblk=fopen(datfile, "r")) == NULL)
   {
      printf("\nCannot open file %s", datfile);
      printf(";\nsearch results will not be compared with blocks database.");
   }
   else
   {
      printf("\nSearch results will be compared with %s", datfile);
   }

/*------------- arg 3:  .lis file ----------------------------------------*/
   if (argc > 3)
      strcpy(lisfile, argv[3]);
   else
   {
      printf("\nEnter name of file containing list of true positives:\n");
      gets(lisfile);
   }
   if ( (flis=fopen(lisfile, "r")) == NULL)
   {
      printf("\nCannot open file %s;", lisfile);
    printf("\nsearch results will not be compared with true positive list.\n");
      LisSeq = FragSeq = BlkSeq = 0;  ids = NULL;
   }
   else
   {
      printf("\nSearch results will be compared with %s;", lisfile);
      printf("\nonly hits not in this list will be reported\n");
      ids = makedbid();
      printf("%d IDs in %s\n", (LisSeq=get_ids(flis, ids)), lisfile);
      fclose(flis); 
      /*----------- Count the true positive sequences -------------------*/
      LisSeq = FragSeq = BlkSeq = 0;
      did = ids->next;
      while (did != NULL) 
      {
         did->found = NO;
         if (!did->block && !did->frag)  	LisSeq++;
         if (did->block)           BlkSeq++;
         if (did->frag)            FragSeq++;
         did = did->next;
      }
      Fmis = fopen("multimat.mis", "w");		/* statistics file */
      Ffnd = fopen("multimat.fnd", "w");		/* statistics file */
   }

/*------------- args 4-:  .hom files -------------------------------*/
   nhom = 0;
   if (argc > MAXHOM+4) argc=MAXHOM+4;
   if (argc > 4)
   {
      for (i=4; i 1) AC[strlen(AC)-1] = '\0';
   if ((int) strlen(AC) > 9)
   {
      printf("\nWARNING: AC family name truncated to 9 characters. ");
      AC[9] = '\0';
   }
   printf("AC family name = %s\n", AC);
   ACLen = strlen(AC);

/*------------------Make a list of the blocks in the database----*/
   /*    For this AC => all but last character of AC must be the same for */
   /*    all block queries */
   if (fblk != NULL)
   {
      blocks = get_blocks(fblk, AC);
      re_normalize(temp, totscores, blocks);
      fclose(fblk);
   }
   else blocks = NULL;

/*-----------------Sort and present the results -----------------------*/
   show_hom(temp, totscores, blocks);

/*------------Write a file of the tps not found ------------------------*/
   if (ids != NULL)
   {
      did = ids->next;
      while (did != NULL) 
      {
         if (!did->found)
         {
            fprintf(Fmis, "%s", did->entry);
            if (did->block) fprintf(Fmis, "\tBLOCK");
            if (did->frag) fprintf(Fmis, "\tFRAGMENT");
            fprintf(Fmis, "\n");
         }
         else
         {
            fprintf(Ffnd, "%s", did->entry);
            if (did->block) fprintf(Ffnd, "\tBLOCK");
            if (did->frag) fprintf(Ffnd, "\tFRAGMENT");
            fprintf(Ffnd, "\n");
         }
         did = did->next;
      }
   }
/*---------------------------------------------------------------------*/
   if (Fout != NULL) fclose(Fout);
   if (Fdat != NULL) fclose(Fdat);
   if (Fmis != NULL) fclose(Fmis);
   if (Ffnd != NULL) fclose(Ffnd);
   printf("\n");
   exit(0);
}  /*  end of main */
/*============================================================================
BLIMPS (BLocks IMProved Searcher)   Version 3.2.5  1998/05
(C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center



Block File: /howard/jorja/seqs/PACA.blk

Target File (s) : stuff.dna

Records Searched:   18

Scores Done:        108

Alignments Done:    32866

AC#                      Description                                                Score RF  AA# Length
pa01l_141.s1         0   CHROMAT_FILE: pa01l_141.s1 PHD_FILE: pa01l_141.s1.phd.1 TI 2081 -1   116    260 rYArlvKemsEkvqfiyithnkiaMEMAdqlmgvTmhEpgcsrlVavDveeav

NOTE: Uses hard-coded positions on Blimps output line, mainly because there
      are spaces in the Description.
=============================================================================*/
int read_hom(fhom, temp, first, tps)
FILE *fhom;
struct hom *temp;
int first;
struct db_id *tps;
{
   int t, i, v324, v326, minlen, offscore, offframe, offoffset, offlen;
   int offtitle;
   char line[MAXLINE], ctemp[30], *ptr;

   SeqType = PROTEIN;		/* default database type */
   t = first;    /* first available position in temp array */
   v324 = NO;	/* format changed with Blimps 3.2.4  */
   v326 = YES;  /* format changed again with Blimps 3.2.6 */
   minlen = 105; offscore = 84; offframe = 89; offoffset = 92; offlen = 98;
   offtitle = 22;
   while (!feof(fhom) && fgets(line, MAXLINE, fhom) != NULL)
   {
      if (strstr(line, "Version 3.2.3") ||
          strstr(line, "Version 3.2.2") || strstr(line, "Version 3.2.1")   )
      {  
         v324 = v326 = NO;
         minlen = 96; offscore = 75; offframe = 80; offoffset = 83; offlen = 89;
         offtitle = 14;
      }
      else if ( strstr(line, "Version 3.2.4") || strstr(line, "Version 3.2.5") )
      {  
         v324 = YES; v326 = NO;
         minlen =105; offscore = 84; offframe = 89; offoffset = 92; offlen = 98;
         offtitle = 24;
      }
      else if (strstr(line, "Records Searched:"))
      {
         ptr = strtok(line, ":"); ptr = strtok(NULL, "\t\r\n");
	 NSeq = atof(ptr);
      }
      else if (strstr(line, "Scores Done:"))
      {
         ptr = strtok(line, ":"); ptr = strtok(NULL, "\t\r\n");
	 NRank = atof(ptr);
      }
      else if ((int) strlen(line) > minlen && (t-first) < NScore)
      {
	 strcpy(temp[t].ac, AC);
         if (v324 || v326)
         {
	    strncpy(temp[t].seq_id, &line[0], 20); temp[t].seq_id[20]='\0';
         }
         else
         {
	    strncpy(temp[t].seq_id, &line[0], 12); temp[t].seq_id[12]='\0';
         }
	 strncpy(temp[t].title, &line[offtitle], 19); 
         temp[t].title[19] = '\0';
	 strncpy(ctemp, &line[offscore], 4); ctemp[4]='\0';
	 temp[t].score = atoi(ctemp);
	 strncpy(ctemp, &line[offframe], 2); ctemp[2]='\0';
	 temp[t].frame = atoi(ctemp);
	 if (temp[t].frame != 0) SeqType = DNA;
	 /*   BLIMPS frames are only non-zero for DNA databases */
	 if (temp[t].frame != 0) DBType = DNA;
	 strncpy(ctemp, &line[offoffset], 5); ctemp[5]='\0';
	 temp[t].offset = atoi(ctemp);
	 strncpy(ctemp, &line[offlen], 6); ctemp[6]='\0';
	 temp[t].seqlen = atof(ctemp);
	 temp[t].width = 0; i=minlen;

	 /*  truncates wide blocks */
	 while (line[i] != '\n' && temp[t].width < MAX_WIDTH) 
         {
            temp[t].aa[temp[t].width] = line[i++];
            temp[t].width += 1;
         }
         temp[t].aa[temp[t].width] = '\0';
         strcpy(ctemp, temp[t].seq_id);
         if (tps != NULL)
            temp[t].tp = check_tp(ctemp, tps);
	 temp[t].min_rank = temp[t].rank = t-first;
	 temp[t].map_flag = NO;
	 t++;
      }
   }
   /*    Compute normalized score */
   for (i = first; i < t; i++)
   {
      temp[i].norm = round((float) 1000. * temp[i].score / temp[t-1].score);
      temp[i].max_norm = temp[i].norm;
   }
   return(t-first);
}  /* end of read_hom */
/*=====================================================================
    See if sequence id is in the list of true positives
	Write info to multimat.dat if it's a TP not in the blocks
========================================================================*/
int check_tp(id, tps)
char *id;
struct db_id *tps;
{
   struct db_id *did;
   
   did = tps->next;
   while (did != NULL)
   {
      if (strncmp(id, did->entry, strlen(did->entry)) == 0)
      {
	 did->found = YES;
         if (did->block) return(2);
         else return(YES);
      }
      did = did->next;
   }
   return(NO);
}  /* end of check_tp */
/*=====================================================================*/
void show_hom(temp, tot, blocks)
struct hom *temp;
int tot;
struct best_block *blocks;
{
   int i, t, nhit, ntp, itn, itp, nblock, save_t, pearson, tp999, tn999;
   int tn[NSCORE], tp[NSCORE], rank, nfrag;
   int save_norm, save_strand, strand;
   long locfirst, loclast;
   double roc;
   char save_id[25];

   /*   Sort by strand, seq id, normalized score (d)  */
   qsort(temp, tot, sizeof(struct hom), idnorm_cmp);
   /*   Propagate maximum normalized score to all blocks for a group */
   strcpy(save_id, temp[0].seq_id); save_norm = temp[0].max_norm;
   if (temp[0].frame < 0) save_strand = -1;
   else                   save_strand = 1;
   save_t = 0;
   for (t=1; t 0)
         roc += (double) ntp / (double) (LisSeq + FragSeq);
      if (SeqType == DNA)
      {
	locfirst = compute_loc(temp[t].frame, temp[t].offset+1, temp[t].seqlen);
	loclast = compute_loc(temp[t].frame, temp[t].offset + temp[t].width,
			      temp[t].seqlen);
      }
      else
      {
	locfirst = temp[t].offset+1; loclast = temp[t].offset+temp[t].width;
      }
      printf("\n%d.---------------------------------------", nhit);
      printf("-------------------------------------------");
      printf("\n%8s  %4d  %2d    %4d  %7ld-%7ld %s %s",
	 temp[t].ac, temp[t].rank+1, temp[t].frame, temp[t].norm,
	 locfirst, loclast,
         temp[t].seq_id, temp[t].title);
   } /* end of not in the true positive list */
   else
   {	/*  In the TP list */
      if (temp[t].tp == 2) { nblock++; }
      else { ntp++; tp[itp++] = rank; rank++; }
   }
   strcpy(save_id, temp[t].seq_id);
   save_norm = temp[t].max_norm;
   if (temp[t].frame < 0) save_strand = -1; else save_strand = 1;
   save_t = t;
   t++;
   /*-------------------Print the rest of the hits -----------------*/
   /*  New hit if different seq_id or if same seq_id but different strand */
   while(nhit <= MaxHit && t <= tot)
   {
      if (temp[t].frame < 0) strand = -1; else strand = 1;
      if ( strcmp(temp[t].seq_id, save_id) != 0 ||
          (strcmp(temp[t].seq_id, save_id) == 0 &&
           strand != save_strand) )    /*  new group */
      {
	 if (blocks != NULL && !temp[save_t].tp)     /* process previous group */
	 {
	     if (blocks != NULL) check_dat(save_t, t, temp, blocks);
             else printf("\nBlocks not found in database\n");
	 }
	 strcpy(save_id,temp[t].seq_id);
         if (temp[t].frame < 0) save_strand = -1; else save_strand = 1;
         save_t = t;
	 if (t < tot && !temp[t].tp)
         {
            nhit++; tn[itn++] = rank; rank++; 
            if ( (LisSeq+FragSeq) > 0)
                roc += (double) ntp / (double) (LisSeq + FragSeq);
            if (nhit <= MaxHit)
            {
               printf("\n%d.---------------------------------------", nhit);
               printf("-------------------------------------------");
            }
	 }   /* end of if not a TP */
         else
         {
            if (temp[t].tp == 2) { nblock++; }
            else { ntp++; tp[itp++] = rank; rank++; }
         }
      }
      if (nhit <= MaxHit && t < tot && !temp[t].tp)
      {
         if (SeqType == DNA)
         {
	   locfirst = compute_loc(temp[t].frame,
		 temp[t].offset+1, temp[t].seqlen);
	   loclast = compute_loc(temp[t].frame, temp[t].offset + temp[t].width,
			      temp[t].seqlen);
         }
         else
         {
	   locfirst = temp[t].offset+1; loclast = temp[t].offset+temp[t].width;
         }
	 printf("\n%8s  %4d  %2d    %4d  %7ld-%7ld %s %s",
	    temp[t].ac, temp[t].rank+1, temp[t].frame, temp[t].norm,
	    locfirst, loclast,
            temp[t].seq_id, temp[t].title);
      }  /*  end of if not in the true positive list */
      t++;
   }

/*-------------------------------------------------------------------*/
   /*-- For statistics calcs, notice that the "scores" in the tn[] and
       tp[] arrays are really ranks & so are sorted in reverse order
       compared with matodat/blastdat/fastodat results; lower value
       is "higher" score --*/
   if (nhit > 0) roc /= (double) nhit;
   else roc = 1.0;

   tn999 = (int) ( (double) (SWISS-LisSeq-FragSeq-BlkSeq) * 0.001);
   if (tn999 > nhit) tn999 = nhit - 1;
   if (tn999 < 0) tn999 = 0;
   tp999 = 0;
   for (i=0; i < ntp; i++)
      if (tp[i] <= tn[tn999]) tp999++;

   pearson = LisSeq + FragSeq - ntp;
   i = ntp - 1;
   while (pearson >= 0 && pearson < nhit &&
          i >= 0 && i < ntp &&
          tn[pearson] < tp[i])
   {  pearson++; i--; }
   /*  ntp=#tps found not in block, nblock=#tps found in block,
       nhit=#found not in .lis file => tns for testing purposes */
   if (Fdat != NULL)
     fprintf(Fdat, "%s %d %d %d %d %d %d %d %d %d %d %d %f\n",
        AC, NScore, MaxHit, LisSeq, BlkSeq, FragSeq, LisSeq+FragSeq,
        nblock, ntp, nhit, tp999, pearson, roc);

}   /* end of show_hom */
/*======================================================================*/
/*   Sort by strand, seq id, rank */
int id_cmp(t1,t2)
struct hom *t1, *t2;
{
   int strand1, strand2;

   strand1 = strand2 = 1;
   if (t1->frame < 0) strand1 = -1;
   if (t2->frame < 0) strand2 = -1;

   if (strand1 != strand2) return(strand1 - strand2);
   else if (strcmp(t1->seq_id, t2->seq_id) > 0)  return(1);
   else if (strcmp(t1->seq_id, t2->seq_id) < 0)  return(-1);
   else                       return(t1->rank -  t2->rank);
}  /* end of id_cmp */
/*======================================================================*/
/*   Sort by strand, seq id, normalized score (d)  */
int idnorm_cmp(t1,t2)
struct hom *t1, *t2;
{
   int strand1, strand2;

   strand1 = strand2 = 1;
   if (t1->frame < 0) strand1 = -1;
   if (t2->frame < 0) strand2 = -1;

   if (strand1 != strand2) return(strand1 - strand2);
   else if (strcmp(t1->seq_id, t2->seq_id) > 0)  return(1);
   else if (strcmp(t1->seq_id, t2->seq_id) < 0)  return(-1);
   else                       return(t2->norm -  t1->norm);
}  /* end of idnorm_cmp */
/*======================================================================*/
/*   Sort by min_rank, strand, seq id, hom name */
int rank_cmp(t1,t2)
struct hom *t1, *t2;
{
   int strand1, strand2;

   strand1 = strand2 = 1;
   if (t1->frame < 0) strand1 = -1;
   if (t2->frame < 0) strand2 = -1;

   if (t1->min_rank != t2->min_rank)  return(t1->min_rank - t2->min_rank);
   else if (strand1 != strand2)  return(strand1 - strand2);
   else if (strcmp(t1->seq_id, t2->seq_id) > 0)          return(1);
   else if (strcmp(t1->seq_id, t2->seq_id) < 0)          return(-1);
   else                               return(strcmp(t1->ac, t2->ac));
}  /* end of rank_cmp */
/*======================================================================*/
/*   Sort by max normalized score (d), strand, seq id, hom name */
int norm_cmp(t1,t2)
struct hom *t1, *t2;
{
   int strand1, strand2;

   strand1 = strand2 = 1;
   if (t1->frame < 0) strand1 = -1;
   if (t2->frame < 0) strand2 = -1;

   if (t1->max_norm != t2->max_norm)  return(t2->max_norm - t1->max_norm);
   else if (strand1 != strand2)  return(strand1 - strand2);
   else if (strcmp(t1->seq_id, t2->seq_id) > 0)          return(1);
   else if (strcmp(t1->seq_id, t2->seq_id) < 0)          return(-1);
   else                               return(strcmp(t1->ac, t2->ac));
}  /* end of norm_cmp */
/*======================================================================*/
void print_blurb()
{
   FILE *fstp;
   char line[MAXLINE];

   if ((fstp=fopen("blksrch.stp", "r")) == NULL)
   {
      printf("\n========================================");
      printf("=======================================");
      printf("\nSearch results from the BLOCKS e-mail searcher.");
      printf("\nPlease report problems to jorja@sparky.fhcrc.org");
      printf(", include your query\nand this output.");
      printf(" To obtain help, send the word HELP on a single");
      printf("\nline to blocks@howard.fhcrc.org");
      printf("\n========================================");
      printf("=======================================");
      printf("\nCopyright (c) 1992 by the Fred Hutchinson Cancer Research Center");
      printf("\nIf you use BLOCKS in your research, please cite:");
      printf("\nSteven Henikoff and Jorja G. Henikoff,");
      printf(" Automated assembly of protein");
      printf("\nblocks for database searching, NAR 19:23 (1991), 6565-6572.");
/*   printf("\n2. James C. Wallace and Steven Henikoff,");
      printf(" PATMAT: a searching and extraction");
      printf("\n   program for sequence, pattern and block queries");
      printf(" and databases,");
      printf("\n   CABIOS 8:3 (1992), 249-254.");
*/
      printf("\n========================================");
      printf("=======================================");
      printf("\nEach numbered result consists of one");
      printf(" or more blocks from a PROSITE group");
      printf("\nfound in the query sequence. One set");
      printf(" of the highest-scoring blocks that");
      printf("\nare in the correct order and separated");
      printf(" by distances comparable to the BLOCKS");
      printf("\ndatabase is selected for analysis.");
      printf(" If this set includes multiple blocks");
      printf("\nthe probability that the lower scoring");
      printf(" blocks support the highest scoring");
      printf("\nblock is reported. Maps of the database");
      printf(" blocks and query sequence are shown:");
      printf("\n  < indicates the sequence has been");
      printf(" truncated to fit the page");
      printf("\n  : indicates the minimum distance");
      printf(" between blocks in the database");
      printf("\n  . indicates the maximum distance");
      printf(" between blocks in the database");
      printf("\nThe maps are aligned on the highest");
      printf(" scoring block. The alignment of the");
      printf("\nquery sequence with the sequence");
      printf(" closest to it in the BLOCKS database");
      printf("\nis shown. Upper case in the query");
      printf(" sequence indicates at least one");
      printf("\noccurrence of the residue in that");
      printf(" column of the block.");
      printf("\n========================================");
      printf("=======================================");
      printf("\n");
   }
   else
   {
      while (!feof(fstp) && fgets(line, MAXLINE, fstp) != NULL)
         printf("%s", line);
      fclose(fstp);
   }

}  /* end of print_blurb */
/*======================================================================*/
/*   Look up this group in blocks.dat                                   */
/*======================================================================*/
void check_dat(min_t, max_t, results, fblock)
int min_t, max_t;
struct hom *results;
struct best_block *fblock;
{
   int nblock;

   /*---- Add the query as the last sequence in each block in the list ---*/
   nblock = add_query(min_t, max_t, results, fblock);

   /*--- Map the blocks if more than one in the hit ----*/
   if (nblock > 1) map_blocks(min_t, max_t, results, fblock);
   else            printf("\n");

   /*---Determine the closest block seq to the query seq & display them --*/
   align_blocks(fblock);

}  /*  End of check_dat */
/*=====================================================================
      Read the blocks database
      Truncates blocks wider than MAX_WIDTH
=======================================================================*/
struct best_block *read_block(fblk, ac)
FILE *fblk;
char *ac;
{
   char line[MAXLINE], *ptr, *ptr1;
   struct best_block *block;
   int done, aclen;

   done = NO;
   block = NULL;
   aclen = strlen(ac);
   while (!done && !feof(fblk) && fgets(line, MAXLINE, fblk) != NULL)
   {
      if (strncmp(line, "AC   ", 5) == 0 &&
          strncmp(line+5, ac, aclen) > 0)
	  done = YES;
      else if (strncmp(line, "AC   ", 5) == 0 &&
               strncmp(line+5, ac, aclen) == 0)
      {
	 block = (struct best_block *) malloc(sizeof(struct best_block));
	 if (block == NULL)
	 {  printf("\nOUT OF MEMORY\n\n");  exit(-1);  }
         block->query = block->anchor = NO;
	 block->next_block = NULL;
	 block->dat_pos = ftell(fblk);
	 strncpy(block->ac, line+5, aclen + 1); block->ac[aclen + 1] = '\0';
	 if (block->ac[aclen] == ';') block->ac[aclen] = '\0';
	 block->minprev = block->maxprev = -1;
	 block->query = NO; block->rank = 9999;
	 ptr = strtok(line+12, "(");
	 if (ptr != NULL)
	 {
	    ptr = strtok(NULL, ",");
	    if (ptr != NULL)
	    {
	       block->minprev = atoi(ptr);
	       ptr = strtok(NULL, ")");
	       if (ptr != NULL) block->maxprev = atoi(ptr);
	    }
	 }
      }
      else if (block != NULL && strncmp(line, "BL   ", 5) == 0)
      {
	 block->s995 = 0;
	 ptr=strstr(line,"99.5\%=");
	 if (ptr != NULL)
	 {
	    ptr1 = strtok(ptr, "="); ptr1=strtok(NULL, "\n\r");
	    block->s995 = atoi(ptr1);
	 }
	 block->strength = 0;
	 ptr=strstr(line,"strength=");
	 if (ptr != NULL)
	 {
	    ptr1 = strtok(ptr, "="); ptr1=strtok(NULL, "\n\r");
	    block->strength = atoi(ptr1);
	 }
	 fill_block(fblk, block);
	 return(block);
      }
   }
   return(NULL);		/* no block found! */
}  /* end of read_block */
/*====================================================================
     Fill up the block structure
=======================================================================*/
void fill_block(fblk, block)
FILE *fblk;
struct best_block *block;
{
   int done, i, n, cluster, ncluster;
   char line[MAXLINE], ctemp[MAXLINE], *ptr, *ptr1;

   block->nseq = block->width = 0;
   cluster = ncluster = 0;
   done=NO;
   while (!done && !feof(fblk) && fgets(line,MAXLINE,fblk) != NULL)
   {
      if (strlen(line) == 1)		/* blank line => new cluster */
      {
	 /*  Set #seqs in cluster to seqs in previous cluster */
	 if (ncluster > 0)
	   for (n=0; nnseq; n++)
	      if (block->cluster[n] == cluster) block->ncluster[n] = ncluster;
	 cluster++; ncluster = 0;
      }
      else if ((int) strlen(line) > (int) 1)
      {
	 if (strncmp(line, "//", 2) == 0) done=YES;
	 else if ((int) strlen(line) > 20)
	 {
	    ptr=strtok(line, "(");
	    /*  need to strip leading spaces off ptr here  */
	    strcpy(ctemp, ptr);
	    i=0;
	    while (ctemp[i] == ' ') i++;
	    strcpy(block->name[block->nseq], ctemp+i);
	    ptr=strtok(NULL, ")");
	    block->offset[block->nseq] = atoi(ptr);

	    ptr1=strtok(NULL, "\n\r");
	    i=0;
	    while (ptr1[i] == ' ') i++;
	    ptr = strtok(ptr1+i, " \t\r\n");

            /* Truncate wide blocks   */
            if (strlen(ptr) > MAX_WIDTH) ptr[MAX_WIDTH - 1] = '\0';
	    strcpy(block->aa[block->nseq], ptr);
	    block->cluster[block->nseq] = cluster;
	    ncluster++;		/* # seqs in current cluster */
	    block->width = (int) strlen(block->aa[block->nseq]);
	    block->nseq++;
	 }
      }
   }
   /*  Compute weights for the last cluster */
   if (ncluster > 0)
	   for (n=0; nnseq; n++)
	      if (block->cluster[n] == cluster) block->ncluster[n] = ncluster;
}  /* end of fill_block */
/*=======================================================================
     Add the query sequence as the last sequence in each block for
     which it has a hit.
==========================================================================*/
int add_query(min_t, max_t, results, fblock)
int min_t, max_t;
struct hom *results;
struct best_block *fblock;
{
   struct best_block *block, *maxblock;
   int i, t, j, imin, nblock, mblock, lastrank, one;
   char ac[10], pline[MAXLINE], tline[40];
   struct temp *temp;
   double prob;

   /*------- Need to know how many possible blocks there are ---*/
   /*--------Clear out any previous sequence information -------*/
   nblock=0;
   block = fblock;
   while (block != NULL)
   {
      nblock++;
      block->name[block->nseq][0] = '\0';
      block->offset[block->nseq] = 0;
      block->cluster[block->nseq] = -1;
      block->ncluster[block->nseq] = -1;
      block->aa[block->nseq][0] = '\0';
      if (block->query) block->nseq--;
      block->query = NO;
      block = block->next_block;
   }
   if (nblock == 1) one = YES;
   else             one = NO;

   /*------ Sort this group of hits by rank now --------------*/
   temp = (struct temp *) malloc((max_t-min_t)*sizeof(struct temp));
   if (temp == NULL)
   {
      printf("\nOUT OF MEMORY\n\n"); exit(-1);
   }
   for (i=0; iac) == 0 && !block->query &&
             (i==0 ||
	     distance_okay(results[t].offset, fblock, block)) )
	 {
	    /*--- Adds the query to the block  ------*/
	    strncpy(block->name[block->nseq], results[t].seq_id, SNAMELEN);
            block->name[block->nseq][SNAMELEN] = '\0';
	    block->offset[block->nseq] = results[t].offset;
	    block->cluster[block->nseq] = -1;
	    block->ncluster[block->nseq] = 1;
            /*   Search alignment may be shorter than block ... 
                 pad with spaces */
            if ((int) strlen(results[t].aa) < block->width )
            {
               for (j = strlen(results[t].aa); j < block->width; j++)
                      results[t].aa[j] = ' ';
               results[t].aa[block->width] = '\0';
            }
	    strcpy(block->aa[block->nseq], results[t].aa);
               
	    block->query = results[t].score;
	    block->rank = results[t].rank;
	    block->nseq++;
            results[t].map_flag = YES;
	    /*--- Compute probability -----*/
            if (i==0)
            {
                maxblock = block;
                maxblock->anchor = YES;
                lastrank = temp[i].value;
            }
            else if (i>0 && NRank > 0.0 && DBLen > 0.0)
            {
               mblock++;     /* number of supporting blocks so far */
               block->anchor = NO;

/* blksort calcs: compute prob a block of this family could rank this high
               n = (double) DBType*DBLen*NBlock-lastrank;
	       r = (double) temp[i].value-lastrank;
	       p = (double) nblock-mblock;
	       prob *= hypergeo(n, r, p, 1.0);
*/
               /*   Probability supporting block ranks this high */
               prob *= (double) (temp[i].value + 1) / NRank;
               /* Compute prob this block is this far from the anchor block */
               /* DBLen is always in protein units, distance is always
                  in protein units no need to multiply by DBType to convert to
                  correct units. Min dist = -1; Max dist = distance() */
               prob *= (double) (distance(maxblock,block)+1) / DBLen;
               strcat(pline, block->ac); strcat(pline, " ");
               lastrank = temp[i].value;
            }
	 }
/* blksort calcs         else if (strcmp(ac, block->ac) == 0)
            nblock--;                           block doesn't fit 
*/
	 block = block->next_block;
      }
   }
   if (prob > 1.0) prob = 1.0;
   if (prob < 0.0) prob = 0.0;
   if (maxblock != NULL && strlen(pline))
   {
      printf("\n\nP<%6.2g for ", prob);
      i=0;
      while (i < (int) strlen(pline))
      {
         imin=36;
         if (i+imin > (int) strlen(pline)) imin = (int) strlen(pline) - i;
         strncpy(tline, pline+i, imin); tline[imin] = '\0';
         if (i==0) printf("%s", tline);
         else printf("\n                %s", tline);
         i += 36;
      }
      printf("in support of %s", maxblock->ac);
   }
   else if (maxblock != NULL)
   {   printf("\n\nNo P-value computed for single block hits."); }
   else
   {   printf("\n\nERROR: Anchor block not found in blocks database."); }

   /*----- multimat.dat statistics ------------------------------*/
   for (i=0; iquery)		/* query added to this block already */
      {
	 if (strcmp(block->ac, nblock->ac) < 0)
	    lblock = block;	/* closest block on the left */
	 else if (strcmp(block->ac, nblock->ac) > 0 && rblock == NULL)
	    rblock = block;	/* closest block on the right */
      }
      block = block->next_block;
   }
   /*---------  Check the distance to the left --------------------*/
   if (lblock != NULL)
   {
      mindist = maxdist = lblock->offset[lblock->nseq-1] + lblock->width;
      block = lblock->next_block;
      while (block != NULL && block != nblock)
      {
	 if (strcmp(block->ac, nblock->ac) < 0)
         {
            mindist += block->width;
	    maxdist += prev_dist(block) + block->width;
         }
	 block = block->next_block;
      }
      if (mindist-2 > offset) return(NO); /* allow overlap of 2 */
      if (maxdist + prev_dist(nblock) < offset) return(NO);
   }
   /*----------Check the distance to the qright ---------------------*/
   if (rblock != NULL)
   {
      mindist = maxdist = offset + nblock->width;
      block = nblock->next_block;
      while (block != NULL && block != rblock)
      {
	 if (strcmp(block->ac, rblock->ac) < 0)
         {
            mindist += block->width;
	    maxdist += prev_dist(block) + block->width;
         }
	 block = block->next_block;
      }
      if (mindist-2 > rblock->offset[rblock->nseq-1]) return(NO);
      if (maxdist + prev_dist(rblock) < rblock->offset[rblock->nseq-1])
	 return(NO);
   }
   return(YES);
}  /*  end of distance_okay */
/*===================================================================
    Compute maximum distance preceding a block
=====================================================================*/
int prev_dist(block)
struct best_block *block;
{
   int dist;

/*
   dist = block->minprev + block->maxprev;
*/
   dist = 2 * block->maxprev;
   if (dist < 1) dist = 1;
   return(dist);
}  /* end of prev_dist */
/*===================================================================
     Compute maximum allowable distance between two blocks
====================================================================*/
int distance(fromblock, toblock)
struct best_block *fromblock, *toblock;
{
    int dist, maxdist;
    struct best_block *block, *lblock, *rblock;
  
    if (fromblock == NULL || toblock == NULL) return(-1);

    if (strcmp(fromblock->ac, toblock->ac) < 0)
    { lblock=fromblock; rblock=toblock;
      maxdist = DBLen-(fromblock->offset[fromblock->nseq-1]+fromblock->width);
    }
    else
    { lblock=toblock; rblock=fromblock;
      maxdist = fromblock->offset[fromblock->nseq-1];
    }
/*     For BLIMPS matrix search, DBLen is always in protein units
    if (DBType*maxdist > DBLen) maxdist = (int) DBLen/DBType;
*/
    if (maxdist > DBLen) maxdist = (int) DBLen;

    dist = 0;
    block=lblock->next_block;
    while (block != NULL && block != rblock)
    {
       dist += prev_dist(block) + block->width;
       block = block->next_block;
    }
    dist += prev_dist(rblock);
    /*  Don't want possible distance to be larger than possible
        sequence positions! */
    if (dist > maxdist) dist = maxdist;
    return(dist);
}  /* end of distance */
/*====================================================================
    Map a path of blocks
    The mapping is done in three phases:
    1. The blocks in the database are mapped from the 1st position of
       the first block to the last position of the last block. This
       range divided by MAXMAP (number of columns for the map to occupy
       when printed) determines the scale of the map.
    2. The blocks in the query sequence that are consistent with the
       database are mapped to the same scale as the database blocks.
       The two maps are aligned on the highest scoring block (maxblock).
       The query map may occupy more than MAXMAP columns and may have
       to be truncated or compressed. A maximum of MAXLINE characters
       are mapped before compression.
    3. The blocks in the query sequence that are not consistent with the
       database are mapped to the same scale. Since these blocks may
       overlap one another, they may take more than one line. Each line
       is aligned with the left end of the map in 2.
=======================================================================*/
void map_blocks(min_t, max_t, results, fblock)
int min_t, max_t;
struct hom *results;
struct best_block *fblock;
{
   int totblks, maxdist, i, imin, imax, pos, maxspot, firstpos, lastpos;
   int spot, qspot, firstspot, lastspot, t, done, qleft, qright;
   double scale;
   struct best_block *block, *maxblock;
   char ctemp[20], dbline[MAXLINE], qline[MAXLINE], pline[MAXLINE];

   totblks = maxdist = 0;
   maxblock = NULL;
   /*--- Determine the scale for the database blocks (# aas per space) ---*/
   block = fblock;
   while (block != NULL)
   {
      totblks++;
      if (block != fblock)
         maxdist += block->maxprev;  /* distance from last block */
      maxdist += block->width;    /* width of this block */
      if (block->query && block->anchor) maxblock = block;
      block = block->next_block;
   }
   scale = (double) maxdist/MAXMAP;       /* max of 60 spaces per line */

   for (spot=0; spotminprev/scale);
         imax = (int) ((double) 0.5+(block->maxprev-block->minprev)/scale);
         for (i=spot; i < spot+imin; i++) dbline[i] = ':';
         spot += imin;
         for (i=spot; i < spot+imax; i++) dbline[i] = '.';
         spot += imax;
      }
      imin = (int) ((double) 0.5+block->width/scale);
      if (imin < 1) imin = 1;
      for (i=spot; i < spot+imin; i++) strncpy(dbline+i, block->ac+ACLen, 1);
      spot += imin;
      if (block==maxblock) maxspot=spot;
      block = block->next_block;
   }
   dbline[spot] = '\0';
   
   printf("\n                         |-----%5d residues----|",
          (int) ((double) 0.5+(scale*25.0)) );
   printf("\n%-20s ", AC);		/* need SNAMELEN here to line up */
   printf("%s", dbline);

   /*---- 2. Now map the query sequence if there is one ----------------*/
   /*---Line up the highest scoring query block with the database 
        pos = sequence position,
        spot=scaled pos in qline , qspot=scaled pos of anchor block in query,
        maxspot=scaled pos of anchor block in block map */
   /* firstpos & lastpos are first & last sequence positions mapped into qline
      firstspot is position of firstpos in qline, etc. */
   spot=qspot=pos=0;
   firstpos = lastpos = firstspot = lastspot = -1;
   block = fblock;
   while (block != NULL)
   {
      if (block->query)
      {
         if (firstpos < 0) firstpos = block->offset[block->nseq-1];
         lastpos = block->offset[block->nseq-1] + block->width;
	 imin = (int) ((double) 0.5+(block->offset[block->nseq-1]-pos)/scale);
         if (imin >= 0)   /* skip over blocks in wrong order */
         {
	    if (spot+imin > MAXLINE && spot+1 < MAXLINE)
               qline[spot++] = '<';
            else
            {
	       for (i=spot; iwidth/scale);
	    if (imin < 1) imin = 1;
            if (spot+imin < MAXLINE)
            {
	       for (i=spot; iac+ACLen, 1);
	       spot += imin;
            }
	    pos = block->offset[block->nseq-1] + block->width;
	    if (block == maxblock) qspot = spot;
         }
      }
      block = block->next_block;
   }
   qline[spot] = '\0';

   /*  Line up qline/qspot with dbline/maxspot */
   strncpy(ctemp, results[min_t].seq_id, SNAMELEN); ctemp[SNAMELEN] = '\0';
   printf("\n%-20s ", ctemp);
   if (qspot <= maxspot)
   {
       qleft = 0; firstspot = maxspot - qspot;
       for (i=qspot; i 0 && (pline[0] == '.' || pline[0] == ':')) pline[0] = '<';
   if (qright != (int) strlen(qline)) pline[(int) strlen(pline)-1] = '>';
   printf("%s\n", pline);

   /*--------3. Now map the inconsistent hom hits wrt consistent ones--*/
   /* Take the hits as they come, as many as will fit on a line        */
   done = NO; 
   while (!done)
   {
      done=YES; spot=0;
      for (i=0; i= 0 && spot < MAXLINE && qline[spot] == ' ')
            {
               imin = (int) ((double) 0.5+results[t].width/scale);
               if (imin < 1) imin = 1;
               i = spot;
               while (i < spot+imin && i < MAXLINE)
               {
                  strncpy(qline+i, results[t].ac+ACLen, 1);
                  if (i > lastspot) lastspot = i;
	          i++;
               }
               done = NO;
               results[t].map_flag = YES;
            }
         }
      }  /* end of a line of output */
      qline[lastspot+1] = '\0';
      if (!done && strlen(qline))
      {
         printf("%-20s %s\n", ctemp, qline); /* ctemp is hit name */
      }
   } /* end of inconsistent hits */

   printf("\n");

}  /* end of map_blocks */
/*========================================================================
	Align the query sequence with the sequence closest to it in
	each block for which it has a hit.
	datline from blocks database
	homline from blimps search results
=========================================================================*/
void align_blocks(fblock)
struct best_block *fblock;
{
   struct best_block *block;
   int s, i, itemp, spot, bspot, datmin, datmax, homdist;
   char datline[MAXLINE], homline[MAXLINE], blkline[MAXLINE];
   char barline[MAXLINE], saveac[MAXAC+1];
   char ctemp[MAXLINE];

   for (i=0; iquery)
      {
	 datmin += block->minprev;
	 datmax += block->maxprev;
	 homdist = block->offset[block->nseq-1] - homdist;
         consensus(block);
/*>>> if aborts on call to closest_seq(), reduce MAXSEQS in motifj.h
	or set s = 0
<<<*/
	 s = closest_seq(block);
	 bspot = block->width;
	 /*--- 28 spaces for name & offset on datline & homline;
	       27 spaces for distance info on blkline ----*/
	 if (bspot < 27) bspot = 27;   /* min blkline width */
	 if ((spot + bspot + 28) > 80) 
         {
            itemp = spot;
            if (bspot > itemp) itemp = bspot;
	    homline[itemp]= datline[itemp]= blkline[itemp]= barline[itemp]= '\0';
	    printf("\n%s", blkline);
            printf("\n%s", datline); printf("\n%s", barline);
	    printf("\n%s\n", homline);
            for (i=0; iac);		/* SNAMELEN */
	 strncpy(blkline+spot, ctemp, strlen(ctemp));
         sprintf(ctemp, "%-20s", block->name[s]);	/* SNAMELEN */
	 strncpy(datline+spot, ctemp, strlen(ctemp));
	 sprintf(ctemp, "%-20s", block->name[block->nseq-1]);
	 strncpy(homline+spot, ctemp, strlen(ctemp));
	 spot+=SNAMELEN + 1;   /* name width + 1 */
/*
         strncpy(blkline+spot, block->ac, strlen(block->ac));
         strncpy(datline+spot, block->name[s], strlen(block->name[s]));
         strncpy(homline+spot, block->name[block->nseq-1],
              strlen(block->name[block->nseq-1]));
*/

	 sprintf(ctemp, "%c<->%c", saveac[ACLen], block->ac[ACLen]);
	 strncpy(blkline+spot, ctemp, strlen(ctemp));
	 sprintf(ctemp, "%6d", block->offset[s]);
	 strncpy(datline+spot, ctemp, strlen(ctemp));
	 sprintf(ctemp, "%6d", block->offset[block->nseq-1] + 1);
	 strncpy(homline+spot, ctemp, strlen(ctemp));
	 spot+=9;   /* offset width + 2 */
/*
	 blkline[spot] = saveac[ACLen];
	 strncpy(blkline+spot+1, "<->", 3);
	 blkline[spot+4] = block->ac[ACLen];
	 kr_itoa(block->offset[s], ctemp, 10);
	 strncpy(datline+spot, ctemp, strlen(ctemp));
	 kr_itoa(block->offset[block->nseq-1]+1, ctemp,10);
	 strncpy(homline+spot, ctemp, strlen(ctemp));
*/

	 bspot = spot;
         sprintf(ctemp, "(%d,%d):%d", datmin, datmax, homdist);
/*
	 strncpy(blkline+bspot, "(", 1); bspot++;
	 kr_itoa(datmin, ctemp, 10);
	 strncpy(blkline+bspot, ctemp, strlen(ctemp));
	 bspot += strlen(ctemp);
	 strncpy(blkline+bspot, ",", 1); bspot++;
	 kr_itoa(datmax, ctemp, 10);
	 strncpy(blkline+bspot, ctemp, strlen(ctemp));
	 bspot += strlen(ctemp);
	 strncpy(blkline+bspot, ")", 1); bspot++;
	 strncpy(blkline+bspot, ":", 1); bspot++;
	 kr_itoa(homdist, ctemp, 10);
*/
	 strncpy(blkline+bspot, ctemp, strlen(ctemp));
	 bspot += strlen(ctemp);

	 for (i=0; iwidth; i++)
         {
	    strncpy(datline+spot, block->aa[s]+i, 1);
	    strncpy(homline+spot, block->aa[block->nseq-1]+i, 1);
            if (strncmp(datline+spot, homline+spot, 1) == 0)
                barline[spot] = '|';
	    spot++;
         }
	 spot+=3;	/* space between blocks on same line */
	 datmin = datmax = 0;
	 homdist = block->offset[block->nseq-1] + block->width;
	 strcpy(saveac, block->ac);
      }
      else
      {		/*  block not in query sequence */
	 datmin += block->minprev + block->width;
	 datmax += block->maxprev + block->width;
      }
      block = block->next_block;
   }
   itemp = spot;
   if (bspot > itemp) itemp = bspot;
   homline[itemp] = datline[itemp] = blkline[itemp] = barline[itemp] = '\0';
   printf("\n%s", blkline);
   printf("\n%s", datline); printf("\n%s", barline);
   printf("\n%s\n", homline);
}  /* end of align_blocks */
/*======================================================================*/
/*--- Just find the sequence closest to the last sequence in the block
      based on the number of identities */
/*======================================================================*/
int closest_seq(block)
struct best_block *block;
{
   int npair, s1, s2, l1, l2, i, i1, i2;
   int maxscore, maxs1;
   struct pair pairs[MAXSEQS*(MAXSEQS-1)/2]; 

   npair = block->nseq;

/*    Compute scores for all possible pairs of sequences            */
   for (s1=0; s1nseq-1; s1++)   		/* col = 0, n-2     */
   {
      l1 = 0;
      s2 = block->nseq-1;   /* last seq in block == the query sequence */
      l2 = 0;
      pairs[s1].score = 0;
      pairs[s1].cluster = -1;
      for (i=0; i<=block->width; i++)
      {
	 i1 = l1+i;  i2 = l2+i;
	 /* s1 is the block seq & is all caps, but s2 is the query
	    seq & it may have lower case chars in it */
	 if (i1 >= 0 && i1 < block->width &&
	     i2 >= 0 && i2 < block->width &&
		strncasecmp(block->aa[s1]+i1, block->aa[s2]+i2, 1) == 0)
		   pairs[s1].score += 1;
      }
   }  /* end of s1 */
   maxs1 = -1; maxscore = -1;
   for (s1=0; s1 < block->nseq-1; s1++)
      if (pairs[s1].score > maxscore)
      {
	 maxscore = pairs[s1].score;
	 maxs1 = s1;
      }

      return(maxs1);
}  /*  end of cluster_seqs */
/*====================================================================*/
int tempcmp(t1, t2)
struct temp *t1, *t2;
{
   return(t1->value - t2->value);
}  /* end of tempcmp */
/*====================================================================*/
struct best_block *get_blocks(fblk, ac)
FILE *fblk;
char *ac;
{
   struct best_block *block, *fblock, *lblock;
   int nblk;

   nblk = 0;
   block = fblock = lblock = NULL;

   /*----- Make a list of blocks in the database -----*/
   while ( (block = read_block(fblk, ac)) != NULL)
   {
      if (nblk > 0) lblock->next_block = block;
      else fblock = block;
      nblk++;
      lblock=block;
   }
   if (fblock == NULL)
      printf("\nNo blocks for family %s found in database.", ac);
   return(fblock);
}  /* end of get_blocks */
/*======================================================================
    If the search was of a matrix database, the sequence segment will be
    all lower case. Change any residue that matches any sequence in the
    block to upper case. The block segments are all upper case.
========================================================================*/
void consensus(block)
struct best_block *block;
{
   int s, s1, i;
   char seqaa[2];

   s = block->nseq - 1;		/* This is the query sequence */
   for (s1=0; s1 < s; s1++)
      for (i=0; i < block->width; i++)
      {
         if (strncasecmp(block->aa[s]+i, block->aa[s1]+i, 1) == 0)
         {
            strncpy(seqaa, block->aa[s]+i, 1);
            if (seqaa[0] >= 97 && seqaa[0] <= 122)
            {
               seqaa[0] -= 32;
               strncpy(block->aa[s]+i, seqaa, 1);
            }
         }
      }

}  /* end of consensus */
/*=========================================================================
       Blimps reports seqlen in AAs for Block vs DNA search

  frame  1:1 => bp 1,     2:1 => 2,         3:1 => 3
           bp = frame + 3 * offset
       frame -1:1 => bp QLen, -2:1 => QLen - 1, -3:l => QLen - 2 
           bp = frame + (QLen + 1) - 3 * offset
=========================================================================*/
int compute_loc(frame, offset, seqlen)
int frame;
int offset;
double seqlen;
{
   int loc;

   loc = (offset - 1) * SeqType;
   if (frame < 0) loc = (seqlen * SeqType + 1) - loc;
   loc += frame;
   if (frame == 0) loc++;	/* Blimps frame = 0 for protein */
   return(loc);
}   /* end of compute_loc */
/*========================================================================
       If the blocks have 99.5 score in them, renormalize with it
=========================================================================*/
void re_normalize(temp, totscores, blocks)
struct hom *temp;
int totscores;
struct best_block *blocks;
{
   int i;
   struct best_block *block;

   for (i=0; i < totscores; i++)
   {
      block = blocks;
      while (block != NULL)
      {
         if (strcmp(temp[i].ac, block->ac) == 0 &&
             block->s995 > 0)
         {
      temp[i].norm = round((float) 1000. * temp[i].score / block->s995);
      temp[i].max_norm = temp[i].norm;
         }
         block = block->next_block;
      }
   }
}   /* end of re_normalize */
ake the hits as they come, as many as will fit on a line        */
   done = NO; 
   while (!done)
   {
      done=YES; spot=0;
      for (i=0; istart = ID   name; PATTERN.
		  AC   Prosite accession #.
	->desc  = DE   description.
		  PA   pattern.  (can be > 1 line)
		  MA   matrix. (can be > 1 line)
	->seq   = DR   P07507, MGP$BOVIN , T; (etc.)
	->end   = //                                                   */
/*   Outputs file "name.lis" containing a list of Swiss-Prot IDs
     for true positive and false negative sequences in the PROSITE
     entry. The title line of the ".lis" file contains parameter
     information for the MOTIFJ program. If the swiss name is provided,
     executes UEXTRACT.                                                */
/*---------------------------------------------------------------------*/
/*    8/9/90   J. Henikoff
>>>>>>>>>>>>>>>>>>>>>>>> Blocks 8.0 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
    3/10/94  Added check for MAX-REPEAT. 
    7/31/94  Look for MA entries in Prosite (new with release 12)
   12/ 5/95 Modified format of /FALSE_NEG on NR line (changed w/ release 13)
>>>>>>>>>>>>>>>>>>>>>>>> Blocks 9.0 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
   12/12/95 Changed dups from MAX-REPEAT - 1 to nhit - npos; print nhit/npos.
>>>>>>>>>>>>>>>>>>>>>>>> Blocks 10.0 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
    2/27/98 Create repeats.dat file: (MAX-REPEAT - 1)
    4/22/98 Create pdb.dat file: (first 3D line)
    7/26/98 AC="all" now means all PATTERN or MATRIX, "one" now means
	    what "all" used to mean: skip ID = _2, etc.
=========================================================================*/
#include 
/*#include */
#include  
#include "motifj.h"

void init_dbs();
int type_dbs();
int strnjcmp();

int get_pat();
int find_swiss();
int screen_pat();
int classify();

char PatName[15], Prefix[15], Pros[FNAMELEN];
int NoAC;

/*======================================================================*/
void main(argc, argv)
int argc;
char *argv[];
{
   FILE *fdat, *frep, *fpdb;
   char infile[FNAMELEN], defname[FNAMELEN], swiss[FNAMELEN];
   struct db_info *dbs[MAXDB];
   int totpats;

   if (argc < 4)
   {
      printf("PROTOMOT: (C) Copyright 1991 by Fred Hutchinson");
      printf(" Cancer Research Center\n");
      printf("For PROSITE, please cite:  A. Bairoch, PROSITE:");
      printf(" A Dictionary of Protein\n Sites and Patterns,");
      printf(" U. Geneva, 5th Release (1990).\n");
      printf("USAGE: protomot  all none none\n");
      printf("  or   protomot  PS00094 PS00094 none\n");
   }

/*------------- arg 1:  prosite.dat file -------------------------------*/
   if (argc > 1)
      strcpy(infile, argv[1]);
   else
   {
      strcpy(defname, "/cdrom/prosite/prosite.dat");
      printf("\nEnter name of ProSite data file [%s]:\n", defname);
      gets(infile);
      if ((int) strlen(infile) < 2)
	 strcpy(infile, defname);
   }
   if ( (fdat=fopen(infile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", infile);
      exit(-1);
   }
/*------------------- arg 2:  Accession # in prosite.dat ----------------*/
   if (argc > 2)
      strcpy(PatName, argv[2]);
   else
   {
      printf("\nEnter accession number of ProSite pattern [all]: ");
      gets(PatName);
   }
   if ((int) strlen(PatName) < 2)   strcpy(PatName, "all");
   else
   {
      if (PatName[0] == 'p') PatName[0] = 'P';
      if (PatName[1] == 's') PatName[1] = 'S';
   }
   NoAC = NO;
   if (strcmp(PatName, "all") == 0) NoAC = YES;
   if (strcmp(PatName, "one") == 0) NoAC = YES;
/*------------------- arg 3:  Name Prefix for output files --------------*/
   strcpy(defname, PatName);
   if (argc > 3)
      strcpy(Prefix, argv[3]);
   else if (!NoAC)
   {
      printf("\nEnter name (1-7 characters) for this group of proteins [%s]: ",
	      defname);
      gets(Prefix);
   }
   if ((int) strlen(Prefix) < 2)
      strcpy(Prefix, defname);
/*------------------- arg 4:  Location of Swiss-Prot database -----------*/
   if (argc > 4)
      strcpy(swiss, argv[4]);
   else
   {
      printf("\nEnter name SWISS-PROT database file [none]:\n");
      gets(swiss);
   }
   if ((int) strlen(swiss) < 2)   strcpy(swiss, "none");
/*------------------- arg 5:  Directory for extracted proteins ----------*/
   getcwd(defname, 40);  strcat(defname, "/");
   if (!NoAC)
   {
      strcat(defname, Prefix); strcat(defname, "/");
   }
   if (argc > 5)
      strcpy(Pros, argv[5]);
   else if (strcmp(swiss, "none") != 0)
   {
      printf("\nEnter directory into which proteins extracted from %s",
	      swiss);
      printf("\n should be deposited [%s]: ", defname);
      gets(Pros);
   }
   if ((int) strlen(Pros) < 2)   strcpy(Pros, defname);
/*           Make sure directory ends with a backslash; expected by
		 uextract and motifj */
   if (Pros[(int) strlen(Pros)-1] != '/') strcat(Pros, "/");

/*---------- Append to repeats.dat file---------------------------------*/
   if ( (frep=fopen("repeats.dat", "a+t")) == NULL)
      printf("Cannot open repeats.dat\n");

/*---------- Append to pdb.dat file---------------------------------*/
   if ( (fpdb=fopen("pdb.dat", "a+t")) == NULL)
      printf("Cannot open pdb.dat\n");

/*--------------------- Load DB format information ---------------------*/
   init_dbs(dbs);

/*---------------------------------------------------------------------*/
   totpats = get_pat(dbs, fdat, frep, fpdb);
   printf("\n%d patterns processed\n", totpats);
   fclose(fdat); fclose(frep); fclose(fpdb);
   if ((strcmp(swiss, "none") != 0) && !NoAC)
   {
      strcpy(defname, Prefix); strcat(defname,".lis");
      printf("\nStarting extract of sequences from %s...\n", swiss);
      execlp("uextract", "uextract", defname, swiss, NULL);
   }
   printf("\n");
   exit(0);
}  /*  end of main */
/*==========================================================================
   Order in a prosite.dat entry:
   ID, AC, DT, DE, PA, NR, CC (repeats), DR (seqs), 3D (pdbs), DO (doc), //
===========================================================================*/
int get_pat(dbs, fdat, frep, fpdb)
struct db_info *dbs[];
FILE *fdat, *frep, *fpdb;
{
   int nseq, npat, nswiss, i, db, goodpat, done;
   char line[MAXLINE], title[MAXLINE], id[25], *ptr;
   char pattern[3*MAXLINE], counts[3*MAXLINE], ac[10], filename[12];
   char repeats[3*MAXLINE], pdbs[3*MAXLINE];
   FILE *flis;
/* FILE *fpat;           Removed pattern file */

   nseq = npat = 0;
   pattern[0] = title[0] = id[0] = counts[0] = repeats[0] = pdbs[0] = '\0';
   done = NO;
   db = type_dbs(fdat, dbs);
   if (db >= 0 && db < MAXDB)
   {
      printf("\nLooking for pattern %s...", PatName);
      do
      {
	 if (strncmp(line, dbs[db]->start, (int) strlen(dbs[db]->start)) == 0)
	 {
	    nseq += 1;
	    id[0] = ac[0] = pattern[0] = counts[0] = repeats[0] = pdbs[0] ='\0';
	    ptr = strtok(&line[dbs[db]->title_offset], " ");
	    strcat(id, ptr);
	    ptr = strtok(NULL, ".");
	    if (strnjcmp(ptr, "PATTERN", 7) == 0 ||
                strnjcmp(ptr, "MATRIX", 6)  == 0)
	    {
	       while(fgets(line, MAXLINE, fdat) != NULL &&
		  strncmp(line, "DR", 2) != 0 &&
		  strncmp(line, dbs[db]->end, (int) strlen(dbs[db]->end)) != 0 )
	       {
		  if (strncmp(line, "AC", 2) == 0)
		  {
		     strcpy(ac, &line[dbs[db]->title_offset]);
		     ac[7] = '\0';
		     strcpy(title, ">");
		     strcat(title, ac);
		     strcat(title, " ;");	/* leave space for A,B...*/
		     strcat(title, id);
		  }
		  else if (strncmp(line, "DE", 2) == 0)
		  {
		     strcat(title, &line[dbs[db]->title_offset]);
		     ptr = strtok(title, "\r\n");
		     strcat(title, ";");
		  }
		  else if (strncmp(line, "DO", 2) == 0)
		  {
		     strcat(title, &line[dbs[db]->title_offset]);
		     ptr = strtok(title, "\r\n");
		     strcat(title, ";");
		  }
		  else if (strncmp(line, "PA", 2) == 0)
		  {
		     strcat(pattern, &line[dbs[db]->title_offset]);
		     ptr = strtok(pattern, "\r\n");
		  }
		  else if (strncmp(line, "NR", 2) == 0)
		  {
		     strcat(counts, &line[dbs[db]->title_offset]);
		     ptr = strtok(counts, "\r\n");
		  }
		  else if (strncmp(line, "CC", 2) == 0 &&
                           strstr(line, "/MAX-REPEAT") != NULL)
		  {
		     strcat(repeats, &line[dbs[db]->title_offset]);
		     ptr = strtok(repeats, "\r\n");
		  }
	       }   /*  now at DR or end */
/*               Fix up title;  change $ to %  */
	       for (i=0; i< (int) strlen(title); i++)
		  if (title[i] == '$') title[i] = '%';

/*    Check to see if we want this entry, & write it out if we do (we
      either look for one entry, or for all entries)  */
	       goodpat = NO;
	       if ( (NoAC || strcmp(PatName, ac) == 0) &&
		     (screen_pat(ac, pattern, title, counts, repeats, frep) == YES) )
	       {
		  goodpat = YES;
		  npat++;
		  strcat(title, "$");    /*  finish off title */

	       }
	       if (!NoAC && goodpat) done = YES;
	       if (goodpat)
	       {
/*------ Process the sequences, if there are any-------------------------*/
                  pdbs[0] = '\0';
		  nswiss = 0;
		  if (strncmp(line, "DR", 2) == 0)
		  {
		     if (NoAC) strcpy(filename, ac);
		     else  strcpy(filename, Prefix);
		     strcat(filename,".lis");
		     printf("\nCreating batch file %s for entry %s",
			     filename, ac);
		     if ( (flis=fopen(filename, "w+t")) == NULL)
		     {
			printf("\nCannot open file %s\n", filename);
			exit(-1);
		     }
		     fprintf(flis, "%s\n", title);    /* Title */
		     fprintf(flis, "%s", Pros);       /* Directory */
		     if (NoAC) fprintf(flis,"%s/",ac);
		     fprintf(flis, "\n");
		     printf("\nCollecting sequences for %s...", ac);
		     nswiss += find_swiss(&line[dbs[db]->seq_offset], flis);
		     while(!feof(fdat) && fgets(line, MAXLINE, fdat) != NULL &&
		       strncmp(line, dbs[db]->end, strlen(dbs[db]->end)) != 0 &&
		       strncmp(line, "DR", 2) == 0)
		     {
			nswiss += find_swiss(&line[dbs[db]->seq_offset], flis);
		     }  /*  end of sequence */
                     /*  Still haven't read 3D & DO lines for entry ... */
		  }
                  /*  Just get the first 3D line */
		  if (!strlen(pdbs) && strncmp(line, "3D", 2) == 0)
		  {
		     strcat(pdbs, &line[dbs[db]->title_offset]);
		  }
		  fclose(flis);
		  printf("Found %d sequences", nswiss);
                  if (strlen(pdbs)) fprintf(fpdb, "%s %s", ac, pdbs);
	       }  /*  end of if goodpat  */
	    }  /*  end of PATTERN */
	 }  /*  end of start of entry */
      }  while (!feof(fdat) && fgets(line, MAXLINE, fdat) != NULL && !done);
   }   /*  end of if db valid */
   printf("\n");

   return(npat);
}  /* end of get_pat */
/*===================================================================*/
/*  find_swiss                                                       */
/*     Finds XXXX..X$YYYY...Y in a string which can have up to 3     */
/*     sets of this form:  "P07507, MGP$BOVIN , T;"                  */
/*===================================================================*/
int find_swiss(line, flis)
char *line;
FILE *flis;
{
   int nswiss, len;
   char *ptr, swiss_key[20], temp[20];

   nswiss = 0;
   ptr = strtok(line, ",");			/* skip past "PO7507" */
   while (ptr != NULL)
   {
	 ptr = strtok(NULL, ",");	/*  now ptr = " MGP$BOVIN " */
	 if (ptr != NULL)
	 {
	       strcpy(temp, ptr);
	    /*  get rid of leading spaces   */
	       len = strspn(temp, " ");
	       strcpy(swiss_key, &temp[len]);
	    /*  get rid of trailing spaces  */
	       len = strcspn(swiss_key, " ");
	       swiss_key[len] = '\0';
	       ptr = strtok(NULL, ";");   /* now ptr = " T" */
	    /* get true positives (T), false negatives (N) and
		potential sequences (P)  */
	       if (ptr != NULL &&
		   (strcmp(ptr, " T") == 0 || strcmp(ptr, " N") == 0 ||
		    strcmp(ptr, " P") == 0) )
	       {
		  nswiss += 1;
		  fprintf(flis, "%-12s  PS=%s\n", swiss_key, ptr+1);
	       }
	       ptr = strtok(NULL, ",");     /*  now ptr = "P08493" */
	 }
   }
   return(nswiss);
}  /*  end of find_swiss */
/*=====================================================================*/
/*    Pattern must have at least one substitution, which means at
      least one [] or {}. It cannot have the words "signature 2" or
      "signature 3" anywhere in its description. It must have at least
      the value MINSEQS as true positives on the NR line; ie
      ... /POSITIVE=nn(mm) ...  mm >= MINSEQS                          */
/*=====================================================================*/
int screen_pat(ac, pattern, title, counts, repeats, frep)
char ac[10];
char *pattern;
char *title;
char *counts, *repeats;
FILE *frep;
{
   char *temp, *ptr, mem[40], tempc[MAXLINE];
   int npos, nhit, dups, runtype, distance, type, n, nl, d1, d2;
   int a1, a2, a3, nrep;

/*------ First see if we want this entry at all ---------------------*/
/*       Check for second or third signatures if one of each PDOC selected */
if (strcmp(PatName, "one") == 0) 
{
   if ( strstr(title, "_2;") != NULL)         return(NO);
   if ( strstr(title, "_3;") != NULL)         return(NO);
   if ( strstr(title, "signature 2") != NULL) return(NO);
   if ( strstr(title, "signature 3") != NULL) return(NO);
}

/*       How many true positive sequences are there?                  */
   strcpy(tempc, counts);
   temp = strstr(tempc, "/POSITIVE=");
   if (temp == NULL)                          return(NO);
   nhit = npos = 0;
   ptr = strtok(temp, "=");
   ptr = strtok(NULL, "(");
   if (ptr != NULL)
   {
      nhit = atoi(ptr);
      ptr = strtok(NULL, ")");
      npos = atoi(ptr);
   }
/*       How many false negative sequences are there?                  */
   strcpy(tempc, counts);
   temp = strstr(tempc, "/FALSE_NEG=");
   if (temp != NULL)
   {
      ptr = strtok(temp, "=");
      if (ptr != NULL)
      {
	 nhit = nhit + atoi(ptr);
	 npos = npos + atoi(ptr);
      }
   }
/*       How many repeats are there?                  */
   strcpy(tempc, repeats);
   temp = strstr(tempc, "/MAX-REPEAT=");
   if (temp != NULL)
   {
      ptr = strtok(temp, "=");
      ptr = strtok(NULL, "(");
      if (ptr != NULL) nrep = atoi(ptr);
      if (frep != NULL) fprintf(frep, "%s %6d\n", ac, (nrep - 1) );
   }
   if (npos < MINSEQS)                        return(NO);

/*---------- Determine MOTIFJ parameters & add them to the title line ----*/
   runtype = 4;
   dups = nhit - npos; 
   printf("\nnhit = %d, npos = %d, dups = %d, nhit/npos = %f\n",
          nhit, npos, dups, (float) nhit / npos);
/*   dups = nrep - 1;         Why did we do this???? */
   distance = MAX_DISTANCE;
   d1 = d2 = nl = n = 0;
   a1 = a2 = a3 = NO;
/*   NOTE:  strtok doesn't work with the intervening call to classify! */
   while ( (n=strcspn(&pattern[nl], "-.")) > 0)
   {
      strncpy(&tempc[0], &pattern[nl], n);
      tempc[n] = '\0';
      nl += (n+1);
      type = classify(tempc);
      if (type < 0)			/* ambiguous distance; restart */
      {
	 a1 = a2 = a3 = NO; d1 = d2 = 0;
      }
      else if (type == 0)		/* amino acid */
      {
	 if (a1 == NO)      a1 = YES;
	 else if (a2 == NO) a2 = YES;
	 else if (a3 == NO) a3 = YES;
      }
      else				/* distance */
      {
	 if (a2 == YES)      d2 += type;
	 else if (a1 == YES) d1 += type;
      }
      if (a1 == YES && a2 == YES && a3 == YES)
      {
/*	 distance = UMIN(distance, UMAX(d1, d2)+1); */
	 if (d2 > d1) d2 = d1; d1++;
	 if (d1 < distance) distance = d1;
	 a1 = a2 = a3 = NO; d1 = d2 = 0;
      }
   }
   sprintf(mem, " MOTIFJ=[%d,%d,%d,%d];",
	   runtype, npos, dups, distance);
   strcat(title, mem);

   return(YES);
}  /*  end of screen_pat */
/*=====================================================================*/
/*   Classify pattern token into one of three categories:
       -1   ambiguous distance if x(m,n), [..](m,n), {..}(m,n)
	1+  distance if x, x(n), [..], [..](n), {..}, {..}(n)
	0   amino acid
========================================================================*/
int classify(token)
char *token;
{
   char *ptr, tempc[30];

   if (strstr(token, "x") != NULL ||
       strstr(token, "[") != NULL ||
       strstr(token, "{") != NULL )
   {
      if (strstr(token, ",") != NULL)         return(-1);   /* x(m,n) */
      if (strstr(token, "(") == NULL)         return(1);    /* just x */
      strcpy(tempc, token);
      ptr = strtok(tempc, "(");
      ptr = strtok(NULL, ")");
      return(atoi(ptr));
   }
   else return (0);					    /*  AA    */
}  /*  end of classify */
har line[MAXLINE], title[MAXLINE], id[25], *ptr;
   char pattern[3*MAXLINE], counts[3*MAXLINE], ac[10], filename[12];
   char repeats[3*MAXLINE], pdbs[3*MAXLINE];
   FILE *flis;
/* FILE *fpat;           Removed pattern file */

   nseq = npat = 0;
   pattern[0] = title[0] = id[0] = counts[0] = repeats[0] = pdbs[0] = '\0';
   done = NO;
   db = type_dbs(fdat, dbs);
   if (db >= 0 && dbblimps-3.9/protomat/uextract.c000064400001460000012000000430130774502755700170410ustar00jorjastaff00000400000027/*=====================================================================*/
/*(C) Copyright 1991-2001 by Fred Hutchinson Cancer Research Center    */
/*        uextract.c   Un-indexed extract from GENBANK, EMBL, .UNI     */
/*   Reads through ENTIRE list of requested entries for each db entry. */
/*     USE: uextract lisname dbname [-f -ofilename]                    */
/*        dbname = name of database file, program will determine its type
	  lisname = name of a file containing a list of entries to
	    be extracted.  For the various file types this should be:
	      GENBANK:  LOCUS name (FASTA type 1)
	      EMBL:     ID name (FASTA type 3)
	      PIR:	ENTRY name (NBRF/CODATA format, FASTA type 2))
	      VMS:	name immediately following the ; on the first line.
			(NBRF/VMS format, FASTA type 5)
	      UNI:      name immediately following the > on the first line.
			(FASTA type 0)
           -f => extract fragments (not extracted by default)
           -ofilename => put all sequences in file filename (extracted
                         to separate files by default)
           -n => don't execute motifj (executed by default if MOTIF
                 is on title line of .lis file
           -l => don't execute motifj but make .lst file
           -k => like -l but take fewer sequences

    * The "lisname" file should have a title line starting with ">".
      The second line may contain the name of a directory where the
      extracted sequences will be stored; it will be created if it
      does not exist. Subsequent lines should contain the sequence
      entry IDs, one per line. EG:
		>PS00094 ;Cytosine methylases
		c:\proteins\PS00094\
		MTB1_BACSH
		MTB1_BACSU
		MTB1_BREEP

     * One output file is created for each entry in "universal" format
	(>title $, then sequence, then *). The name of the file
	is the 1st 8 characters of the entry name followed by .dna for
	GENBANK and by .pro for EMBL and UNI. EG: "MTB1$BAC.pro".
	NOTE FOR DOS: IF THE ENTRY NAME IS > 8 CHARACTERS THE FILE NAME
	MAY NOT BE UNIQUE SINCE IT IS TRUNCATED!!
     * Another file with a ".lst" extension is created containing the
       names of sequences in lisname which were found and do not appear
       to be fragments (the word FRAGMENT does not appear in the
       description for the sequence). In addition, if the IDs. in the
       lisname  file are of SWISS-PROT format, aaaa$aaaaa, then only
       the longest of all the sequences with the same characters before
       the $ and with the first three characters following the $ the
       same is written to the .lst file. For example, if lisname contains
       MTB1$BACSU and MTB1$BACSH and MTB1$BREEP, and MTB1$BACSU is longer
       than MTB1$BACSH, then MTB1$BACSU and MTB1$BREEP will be written
       to .lst, but not MTB1$BACSH. See lst_list().
     * A statistics file named "uextract.dat" is created.
  KNOWN PROBLEMS:  *If input database is not sorted by ID, may miss some
		    requested entries.
		   *If input list file has extension .lst, overwrites it.
		   *VMS format does not have fragment information.
--------------------------------------------------------------------------*/
/*
 2/19/95  Don't create directory if filename is specified.
          Don't activate -n if filename is specified, works okay now.
	  Don't write .lst or rewrite .lis files if -n (don't run motif)
11/14/95  Added usage;  update title signif, etc. before writing .lis/.lst
 6/ 6/98  Added Version; print ids of sequences NOT found.
 7/26/98  Always rewrite .lis file
 8/11/98  Added -l option: writes .lst file but doesn't execute motifj
	  Only rewrite .lis file if -n or -l
 8/24/99  Fix problem with MOTIFJ on separate line when -l
 2/21/00  Changed lst_list() to print id->full_entry name
 >>>>>>>>>>>>>>>>>>> BLIMPS 3.4 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 6/25/00 Changed lis_list() to print id->full_entry
 6/12/01 Added -k option; like -l but modified lst_list() to put fewer
	 sequences in .lst file
 5/23/03 Bugs in lst_list() - e.g. when full_entry=P81137 
				but entry=BTR1_MANSE|P81137
=========================================================================*/
#include 
#include 
#include 
#include "motifj.h"

int get_ids();
int lst_list();
int lis_list();
/*--------------  Routines from motmisc.o --------------------------*/
void init_dbs();
void kr_itoa();
int type_dbs();
int extract_seqs();
struct db_id *makedbid();
char *dir_unix();
struct split_name *split_names();

char Version[12] = " 2/21/00.1";
char Pros[FNAMELEN];

/*======================================================================*/
int main(argc, argv)
int argc;
char *argv[];
{
   char infile[FNAMELEN], lisfile[FNAMELEN], title[MAXLINE], stemp[MAXLINE];
   char foutname[FNAMELEN], stitle[MAXLINE];
   char lstname[FNAMELEN], *temp, *ptr;
   char runtype[3], signif[5], dups[5], distance[5];
   struct db_info *dbs[MAXDB];
   struct db_id *ids, *id;
   int arg, totseqs, nids, test, totlst, reseqs, frag, motif, lstflag, i;
   int fewer;
   FILE *fin, *flis, *flst, *fdat, *fout;
   struct split_name *lissplit;

   printf("\nUEXTRACT %s: (C) Copyright 1991-2000 by\n", Version);
   printf(" Fred Hutchinson Cancer Research Center\n");
   if (argc < 3)
   {
      printf("USAGE: uextract   [-f -o -n]\n");
      printf("        = file listing sequence names to extract\n");
      printf("                   in PROTOMAT format\n");
      printf("         = sequence database\n");
      printf("       -f          to extract FRAGMENTs\n");
      printf("       -o to have all sequences put in \n");
      printf("       -n          to NOT execute motifj or create .lst file\n");
      printf("       -l          to NOT execute motifj but create .lst file\n");
      printf("       -k          to NOT execute motifj but create .lst file ");
      printf("                   with fewer sequences than -l\n");
   }
/*-------------  arg 1.  List of entries to extract ---------------------*/
   if (argc > 1)
      strcpy(lisfile, argv[1]);
   else
   {
      printf("\nEnter name of file containing list of entries to extract: ");
      gets(lisfile);
   }
   if ( (flis=fopen(lisfile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", lisfile);
      exit(-1);
   }
   lissplit=split_names(lisfile);
/*----------------- arg 2 database name --------------------------------*/
   if (argc > 2)
      strcpy(infile, argv[2]);
   else
   {
      printf("\nEnter name of database file to extract entries from: ");
      gets(infile);
   }
   if ( (fin=fopen(infile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", infile);
      exit(-1);
   }
/*----------------- args 3+ extract fragments---------------------------*/
   frag = fewer = NO;
   foutname[0] = '\0';
   motif = lstflag = YES;
   if (argc > 3)
   {
      for (arg=3; arg < argc; arg++)
      {
         if (argv[arg][0] == '-')
         {
            switch(argv[arg][1]) /* no space allowed after '-' */
            {  
               case 'f': frag = YES; break;
               case 'o': strcpy(foutname, argv[arg]+2); break;
               case 'n': motif = lstflag = NO; break;
               case 'l': motif = NO; break;
               case 'k': motif = NO; fewer = YES; break;
               default: break;
            }
         }
      }
   }
   if (strlen(foutname))
   {
/*    motif = NO;		 motifj won't work with this option */
      if ( (fout=fopen(foutname, "w+t")) == NULL)
      {
         printf("\nCannot open file %s\n", foutname);
         exit(-1);
      }
      else
         printf("\nExtracting all sequences to %s", foutname);
   }
   else fout = NULL;

/*-------------  First line of extract file may have a title ----------*/
   fgets(title, MAXLINE, flis);
   if (strlen(title) && title[0] != '>')
   {
      title[0] = '\0';
      rewind(flis);
   }
   else       /*  Don't print the MOTIFJ= part, confuses people ! */
   {
      strcpy(stitle, title);  ptr = strstr(stitle, "MOTIFJ=[");
      if (ptr != NULL) stitle[strlen(stitle)-strlen(ptr)] = '\0';
      else stitle[strlen(stitle) - 1] = '\0';		/* get rid of \n */
      printf("\n%s", stitle);
/*      if (fout != NULL) fprintf(fout, "%s\n", stitle);  gibbsj loops! */
   }
/*------------Second line may have a directory name --------------*/
   Pros[0] = '\0';
   if (getcwd(Pros, FNAMELEN) != NULL) strcat(Pros, "/");           /*DOS*/
   fgets(stemp, MAXLINE, flis);
   if (strlen(stemp) && stemp[0] != '>' && strstr(stemp, "/") != NULL) /*DOS*/
   {
      strcpy(Pros, stemp); Pros[strlen(stemp)-1] = '\0';   /* get rid of nl */
      if (fout == NULL)
         strcpy(Pros,dir_unix(stemp));      /* create the directory if nec. */
   }

/*--------------- Get extract list --------------------------------------*/
   ids = makedbid();
   nids = get_ids(flis, ids);
   fclose(flis);
   printf("\n%d sequences requested for extract from %s", nids, infile);
   if (fout == NULL)
      printf("\n  and deposit into directory %s", Pros);
   else
      printf("\n  and deposit into file %s", foutname);

/*------------------- Extract the sequences ---------------------------*/
   if (nids > 0)
   {
      init_dbs(dbs);		       /* load database infor. */
      totseqs = extract_seqs(nids, dbs, fin, ids, Pros, fout, frag);
   }
   else  totseqs = 0;
   printf("\n%d sequences extracted\n",  totseqs);
   if (totseqs < nids)
   {
      printf("The following sequences were not found:\n");
      i = totseqs;
      id = ids->next;
      while (id != NULL)
      {
         if (id->found == NO)
         {
             i++;
             printf("%s\n", id->entry);
         }
         id = id->next;
      }
   }
   fclose(fin);

/*======================================================================*/
/*---- Rewrite the .lis file ------------------------------------
      if ( (flis=fopen(lisfile, "w+t")) == NULL)
      {
	 printf("\nCannot open file %s for update\n", lisfile);
      }
      else
      {
	 if (strlen(title) > 2) fprintf(flis, "%s", title);
	 if (strlen(Pros) > 2)  fprintf(flis, "%s\n", Pros);
	 reseqs = lis_list(flis, ids);
	 printf("\n%d entries re-written to %s\n", reseqs, lisfile);
	 fclose(flis);
      }
*/

   /*-----------If they want to run motif, do a lot of stuff now ------*/
   if ((motif || lstflag) && totseqs > 0)
   {
      /*--------  Make the .lst file in the current directory----------*/
      lstname[0] = '\0';
      strncat(lstname, lisfile+lissplit->dir_len, lissplit->name_len);
      lstname[lissplit->name_len] = '\0';
      strcat(lstname, ".lst");
      if ( (flst=fopen(lstname, "w+t")) == NULL)
      {
	 printf("\nCannot open file %s\n", lstname);
	 exit(-1);
      }
      if (strlen(title) > 2) fprintf(flst, "%s", title);
      if (strlen(Pros) > 2)  fprintf(flst, "%s\n", Pros);
      totlst = lst_list(fewer, flst, ids);
      printf("\n%d entries written to %s\n", totlst, lstname);
      fclose(flst);

      if (motif)
      {
         /*-----  Update the title line for the .lis file ------------*/
         /*  NOTE: should do this in the .lst file, too, but requires totlst */
         /*   See if any info. from PROTOMOT; just use runtype & dups    */
         temp = strstr(title, "MOTIFJ=[");
         if (temp != NULL)
         {
            ptr = strtok(temp, "[");
            ptr = strtok(NULL, ",");
            strcpy(runtype, ptr);
            ptr = strtok(NULL, ",");
            strcpy(signif, ptr);
            ptr = strtok(NULL, ",");
            strcpy(dups, ptr);
            test = atoi(dups);
            if (test < 0) test = 0;		/* Default is zero dups */
            kr_itoa(test, dups, 10);
            ptr = strtok(NULL, "]");
            strcpy(distance, ptr);
         }
         else				/* use defaults */
         {
            strcpy(runtype, "4");
            strcpy(dups, "0");
         }
         /*----  redo distance & signif;  don't use PROTOMOT stuff!---*/
         strcpy(distance, "17");		/* Force distance=17 */
         /*--     totlst=#seqs in .lst; totseqs=#seqs in .lis     --*/
         if (strcmp(runtype, "4") == 0)
	       test = (int) ((totlst+1)/2) + 1; /*  start at NUMSEQS/2 +1 */
         else test = totlst;
         if (test <= MINSEQS)  test = MINSEQS + 1;
         kr_itoa(test, signif, 10);
         /* Re-write MOTIFJ=[] stuff in title now!   */
/*>>>>>  be sure stitle doesn't already have \n !!!  */
         sprintf(title, "%s MOTIFJ=[%s,%s,%s,%s];$\n", 
               stitle, runtype, signif, dups, distance);
      }  /* end of if motif */

      /*---- Rewrite the .lis file ------------------------------------*/
      if ( (flis=fopen(lisfile, "w+t")) == NULL)
      {
	 printf("\nCannot open file %s for update\n", lisfile);
      }
      else
      {
	 if (strlen(title) > 2) fprintf(flis, "%s", title);
	 if (strlen(Pros) > 2)  fprintf(flis, "%s\n", Pros);
	 reseqs = lis_list(flst, ids);   /* why flst here ? */
	 printf("\n%d entries re-written to %s\n", reseqs, lisfile);
	 fclose(flis);
      }

      /*================Execute motifj now================================*/
      if (motif)
      {
         /*--------------Write stats to the .dat file --------------------*/
         if ( (fdat=fopen("uextract.dat", "a")) != NULL)
         {
            fprintf(fdat, "%s %d %d %s %s %s\n",
	        lisfile, totseqs, totlst, signif, dups, distance);
            fclose(fdat);
         }
         /*------Execute motifj----------------------------------------*/
         /*------motifj will read either a list of sequences or a file
            of sequences if the file name is preceded with a "-" --------*/
         if (fout == NULL) strcpy(stemp, lstname);
         else
         {  strcpy(stemp, "-"); strcat(stemp, foutname);
            fclose(fout);
         }
         execlp("motifj", "motifj", runtype, stemp,
		signif, dups, distance, NULL);
      }  /* end of if motif */
   }  /*  end of if motif or lstflag  */

   exit(0);
}  /*  end of main */

/*======================================================================
   Build the .lst file for motifj:
     The sequences in the .lis file are all included EXCEPT:
	1. If one was not extracted (id->found=NO)
	2. If one was found to be a fragment (id->frag=1)
	3. If two or more sequences appear to be from SWISS-PROT
	   (id contains a  _) and their ids are identical before the
	   _ and for 3 characters following the _, only the longest of
	   the group is included.                                    
        4. If fewer == YES, modifies 3 to compare just before _
======================================================================*/
int lst_list(fewer, flst, ids)
int fewer;
FILE *flst;
struct db_id *ids;
{
   struct db_id *id, *save;
   char sid[80], tid[80], sid1[80];
   int maxlen, nlst, doll;

   sid1[0] = sid[0] = '\0';
   nlst = 0;
   id = ids->next;				/* initialize 1st set */
   /*----  Skip to first non-fragment, non-P sequence ----*/
   while (id != NULL && 
          (id->frag || !id->found || strcmp(id->ps, "P")==0)) 
                 id = id->next;
   if (id == NULL) return(0);   /*  No .lst sequences */

   strcpy(sid, id->full_entry);  maxlen = id->len;  save=id;
   /*-----  Copy up to $ or _, plus 3 more characters ---------*/
/*>>>>  Note, assuming the Swiss id comes first if compound
	entry name, should break it up at | points.
	Also, this doesn't work at all unless the ids are sorted
	by full_entry, not entry; see motmisc.c:check_entry()
<<<<<*/
   strcpy(sid1, sid);
   /*  doll = #chars before $ or _ */
   doll = strcspn(sid1, "$_");
   if (fewer == NO)
   {  if ( (doll+4) < strlen(sid1) ) sid1[doll+4] = '\0'; }
   else
   {  sid1[doll] = '\0'; }
   /*---- Now do the rest of the entries -------------------*/
   while (id != NULL &&
             (id->frag || !id->found || strcmp(id->ps, "P")==0)) 
                   id=id->next;
   while (id != NULL)
   {
      strcpy(tid, id->full_entry);
      doll = strcspn(tid, "$_");
      if (fewer == NO)
      {   if ( (doll+4) < strlen(tid) ) tid[doll+4] = '\0';  }
      else
      {   tid[doll] = '\0'; }
      if ((save != id) && (strcmp(tid, sid1) != 0))      /*  New set */
      {
	 nlst += 1;
	 /*  Print the previous set (save) */
	 fprintf(flst, "%-20s", save->full_entry);
	 if (strlen(save->ps)) fprintf(flst, "  PS=%s", save->ps);
	 if (save->len > 0) fprintf(flst, "  LENGTH=%-6d", save->len);
	 fprintf(flst, "\n");
	 save->lst = YES;
	 strcpy(sid, id->full_entry);        /*  Initialize the next set */
	 save = id;
	 strcpy(sid1, tid);
	 maxlen = id->len;
      }
      else if (strcmp(tid, sid1) == 0 && id->len > maxlen)
      {
	 strcpy(sid, id->full_entry); save = id;
	 maxlen = id->len;
      }
      /*----  Skip to next non-fragment, non-P sequence ------*/
      id = id->next;
      while (id != NULL && 
             (id->frag || !id->found || strcmp(id->ps, "P")==0)) 
                id = id->next;
   }
   nlst += 1;
   /*  Print the last set */
   fprintf(flst, "%-20s", sid);
   if (strlen(save->ps)) fprintf(flst,"  PS=%s", save->ps);
   if (save->len > 0) fprintf(flst,"  LENGTH=%-6d", save->len);
   fprintf(flst,"\n");
   save->lst = YES;

   return(nlst);

}   /*  end of lst_list */
/*======================================================================*/
int lis_list(flis, ids)
FILE *flis;
struct db_id *ids;
{
   struct db_id *id;
   int nlis;

   nlis = 0;
   id = ids->next;
   while (id != NULL)
   {
       nlis += 1;
       fprintf(flis, "%-20s", id->full_entry);
       if (strlen(id->ps)) fprintf(flis, "  PS=%s", id->ps);
       if (id->len > 0 ) fprintf(flis, "  LENGTH=%-6d", id->len);
       if (id->frag)     fprintf(flis, "  FRAGMENT");
       if (id->lst)      fprintf(flis, "  LST");
       if (strlen(id->pir)) fprintf(flis, " PIR=%s", id->pir);
       fprintf(flis, "\n");
       id = id->next;
   }
   return(nlis);
}   /*  end of lis_list */
   }
   else fout = NULL;

/*-------------  First line of extract file may have a title ----------*/
   fgets(title, MAXLINE, flis);
   if (strlen(title) && title[0] != '>')
   {
      title[0] = '\0';
      rewind(flis);
   }
   else       /*  Don't print the MOTIFJ= part, confuses people ! */
   {
      strcpy(stitle, title);  ptr = strstr(stitle, "MOTIFJ=[");
      if (ptr != NULL) stitle[strlen(stitle)-strlen(ptr)] = '\0';
      else stitle[strlen(stitle) - 1] = '\0';		/* get rid of \n */
   blimps-3.9/protomat/universa.c000064400001460000012000000200770774502755700170430ustar00jorjastaff00000400000027/*=====================================================================*/
/*(C) Copyright 1991, Fred Hutchinson Cancer Research Center           */
/*        universa.c   Convert GENBANK, PIR or EMBL to universal format*/
/*    USE:  universa db_filename uni_filename                          */
/*    Universal format resembles FASTA type 0, but includes features to
      support GenePro format:
       1st line is title starting with ">" and ending with "$"
       Sequence starts on second line and ends with "*"                */
/*---------------------------------------------------------------------*/
/*   10/7/90   Changed EMBL $ to %                                     */
/*   10/13/90  db_info memory allocation changed.                      */
/*   10/29/90  Fixed bug with title when multiple description lines.   */
/*    1/10/91  Changed to filter out CRs for UNIX.                     */
/*   11/23/91  Comments & copyright. Changed to use motmisc.o          */
/* >>>>>>>>>>>>Blocks 5.0 and Blocks 6.0 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
      8/11/93  Limit title line to MAXTITLE characters. 
		Still has $ and * for patmat.
   >>>>>>>>>>>>Blocks 6.2, 7.0, 7.2 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
     11/28/93  Problem missing fragments if word FRAGMENT past MAXTITLE
               characters
   >>>>>>>>>>>>Blocks 8.x, 9.x <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
     12/29/96  Put PROSITE group on title line if SwissProt db, dropped $
		at end of title. Added -s option for short title & no * at
                end of sequence (why is this still needed?)
      6/ 6/98  For EMBL format, put AC as well as ID on title line
      6/10/98  Never put * at end of sequence.
      1/27/99  No blank lines after sequences
      9/22/99  For EMBL format, put multiple ACs on title line;
		don't duplicate ID line (trembl)
=======================================================================*/

#include "motifj.h"

void init_dbs();              /* from motmisc */
int type_dbs();               /* from motmisc */
int convert();

/*======================================================================*/
void main(argc, argv)
int argc;
char *argv[];
{
   FILE *fin, *fout;
   char infile[50], outfile[50], defname[50], *ptr;
   struct db_info *dbs[MAXDB];
   int totseqs;
   int short_title;

   printf("UNIVERSA: (C) Copyright 1991,");
   printf(" Fred Hutchinson Cancer Research Center\n");
   if (argc < 2)
   {
      printf("USAGE:  universa db_file uni_file [-s]\n");
      printf("           db_file = input database (EMBL, GB, PIR)\n");
      printf("           uni_file = output file\n");
      printf("           -s flag => short title (no description)\n");
   }
   if (argc > 1)
      strcpy(infile, argv[1]);
   else
   {
      printf("\nEnter name of file to convert: ");
      gets(infile);
   }
   if ( (fin=fopen(infile, "r")) == NULL)
   {
      printf("\nCannot open file %s\n", infile);
      exit(-1);
   }
   if (argc > 2)
      strcpy(outfile, argv[2]);
   else
   {
      strcpy(defname, infile);
      ptr = strtok(defname, ".");  strcat(ptr, ".uni");
      printf("\nEnter name of output file [%s]: ", defname);
      gets(outfile);
      if (strlen(outfile) < 2)
	 strcpy(outfile, defname);
   }
   if ( (fout=fopen(outfile, "w+")) == NULL)
   {
      printf("\nCannot open file %s\n", outfile);
      exit(-1);
   }
   /* optional flag for short title  */
   short_title = NO;
   if (argc > 3 && strncmp(argv[3], "-s", 2) == 0) short_title = YES;

   init_dbs(dbs);

/*---------------------------------------------------------------------*/
   totseqs = convert(dbs, fin, fout, short_title);
   printf("\n%d sequences processed\n", totseqs);

   fclose(fin);  fclose(fout);
   exit(0);
}  /*  end of main */

/*======================================================================*/
int convert(dbs, fin, fout, short_title)
struct db_info *dbs[];
FILE *fin, *fout;
int short_title;
{
   int nseq, i, db, ilen, frag;
   char line[MAXLINE], title[MAXLINE], temp[MAXLINE], *ptr;
   char id[20], acc[MAXLINE], desc[MAXLINE], start[MAXLINE];

   nseq = 0;
   db = -1;
/*---------  Figure out what type of input file it is ------------------*/
   db = type_dbs(fin, dbs);
   if (db >= 0 && db < MAXDB)
   {
      printf("\nProcessing input file as %s", dbs[db]->type);
      do
      {
/*------------  Put together the title line ----------------------------*/
/*---- Collects all ->start and ->desc lines until the next ->seq line -*/
	 if (strncmp(line, dbs[db]->start, strlen(dbs[db]->start)) == 0)
	 {
	    nseq += 1;
            id[0] = acc[0] = start[0] = desc[0] = '\0';
	    ptr = strtok(&line[dbs[db]->title_offset], " ");
	    strcpy(start, ptr);
            if (strlen(ptr) > 19) ptr[19] = '\0';
	    strcpy(id, ptr);		/* save the id for later */
	    while(fgets(line, MAXLINE, fin) != NULL &&
	       strncmp(line, dbs[db]->seq, strlen(dbs[db]->seq)) != 0)
	    {
	       if (strncmp(line, dbs[db]->desc, strlen(dbs[db]->desc)) == 0 &&
                   !short_title &&
                   strlen(title) + strlen(line) < MAXLINE )
	       {
		  strcat(desc, &line[dbs[db]->title_offset]);
		  desc[strlen(desc)-2] = '\0';         /* get rid of CRLF */
	       } /* end of ->desc  */
	       if (strncmp(line, dbs[db]->acc, strlen(dbs[db]->acc)) == 0 &&
                   !short_title &&
                   strlen(title) + strlen(line) < MAXLINE )
	       {
		  strcat(acc, &line[dbs[db]->title_offset]);
		  acc[strlen(acc)-2] = '\0';         /* get rid of CRLF */
                  if (db == EMBL)
                  {
		     /*  AC   O87740; Q47256;  */
                     temp[0] = '\0';
                     ptr = strtok(acc, "; \n\r\t");
                     while (ptr != NULL)
                     {
                        if (strcmp(ptr, id) != 0)  /* don't repeat the id */
                        {
                           strcat(temp, "|");
			   strcat(temp, ptr);
                        }
		        ptr = strtok(NULL, "; \n\r\t");
                     }
                     strcpy(acc, temp);
                  }
	       } /* end of ->acc  */
               if (db == EMBL &&
	           (strncmp(line, "DR   PROSITE", 12) == 0) &&
                   (strlen(title) + 10 < MAXLINE)  )
	       {
                  strcpy(temp, title); strcat(temp, " | ");
                  strncat(temp, &line[14], 7);
                  temp[strlen(title)+10] = '\0';
                  strcpy(title, temp);
               }  /* end of PROSITE */
	    }   /*  end of descriptive stuff */

            /*--------------Put together the title--------------------*/
            if (acc) 
            {
               if (db == EMBL)  /* already has |; put id first */
               { sprintf(title, "%s%s %s\n", start, acc, desc); }
               else
               { sprintf(title, "%s|%s %s\n", acc, start, desc); }
            }
            else
            { sprintf(title, "%s %s\n", start, desc); }

            frag = NO;
            if (strstr(title, "FRAGMENT") != NULL ||
                strstr(title, "fragment") != NULL)   frag = YES;
	    if (strlen(title) >= MAXTITLE)
            {
                title[MAXTITLE] = '\0';
                /*  If "FRAGMENT" got chopped off, put it back  */
                if (frag && strstr(title, "FRAGMENT") == NULL &&
                        strstr(title, "fragment") == NULL)
                {
                   if (strlen(title) >= (MAXTITLE-11) ) 
                      title[MAXTITLE-11] = '\0';
                   strcat(title, " (FRAGMENT)");
                }
            }
	    fprintf(fout, ">%s\n", title);

/*------ Process the sequence ------------------------------------------*/
	    while(!feof(fin) && fgets(line, MAXLINE, fin) != NULL &&
	       strncmp(line, dbs[db]->end, strlen(dbs[db]->end)) != 0)
	    {
               for (i=0; iseq_offset]);
	    }  /*  end of sequence */
/*            if (!short_title) fprintf(fout, "\n");   was "*\n" */
	 }  /*  end of start of entry */
      }  while (!feof(fin) && fgets(line, MAXLINE, fin) != NULL);

   }

   return(nseq);
}  /* end of convert */
=====*/
void main(argc, argv)
int argc;
char *argv[];
{
   FILE *fin, *fout;
   char infile[50], outfile[50], defname[50], *ptr;
   struct db_info *dbs[MAXDB];
   int totseqs;
   int short_title;

   printf("UNIVERSA: (C) Copyright 1991,");
   printf(" Fred Hutchinson Cancer Research Center\n");
   if (argc < 2)
   {
      printf("USAGE:  universa db_file uni_file [-s]\n");
      printf("           db_file = input database (EMBL, GB, PIR)\n");
 blimps-3.9/protomat/Makefile.Linux000064400001460000012000000043520774502756700176000ustar00jorjastaff00000400000027# Protomat Makefile for Sun Solaris 2.6
#   Type "make install" to compile all programs and move them to ../bin
#   Type  "make blksort" to compile blksort program 
CC = gcc
CFLAGS = -Wall -O2 -c
CL = gcc
LFLAGS = -lm -o
RM = /bin/rm -f
MV = /bin/mv -f
#
install:	clean all
clean:		
	$(RM) *.o blksort getblock getseq multimat motifj motomat uextract blosum blastdat
all:		blksort getblock getseq multimat motifj motomat uextract blosum blastdat
#
#	blksort: Analyze results of a BLOCKS search
blksort:	blksort.o motmisc.o
		$(CL) blksort.o motmisc.o $(LFLAGS) blksort
		mv blksort ../bin
#	getblock: Retrieve BLOCKs
getblock:	getblock.o motmisc.o
		$(CL) getblock.o motmisc.o $(LFLAGS) getblock
		mv getblock ../bin
#	getseq: Retrieve a sequence
getseq:		getseq.o motmisc.o
		$(CL) getseq.o motmisc.o $(LFLAGS) getseq
		mv getseq ../bin
#	multimat: Analyze results of a MATRIX search
multimat:	multimat.o motmisc.o
		$(CL) multimat.o motmisc.o $(LFLAGS) multimat
		mv multimat ../bin
#	motifj: Make blocks using Ham Smith's motif algorithm
motifj:		motifj.o motmisc.o
		$(CL) motifj.o motmisc.o $(LFLAGS) motifj
		mv motifj ../bin
#	motomat: Assemble blocks from motifj
motomat:	motomat.o motmisc.o
		$(CL) motomat.o motmisc.o $(LFLAGS) motomat
		mv motomat ../bin
#	uextract: Extract protein families from prosite.dat
uextract:	uextract.o motmisc.o
		$(CL) uextract.o motmisc.o $(LFLAGS) uextract
		mv uextract ../bin
#	blosum: Make substitution matrices from blocks
blosum:		blosum.o motmisc.o
		$(CL) blosum.o motmisc.o $(LFLAGS) blosum
		mv blosum ../bin
#	blastdat: Read blast output
blastdat:	blastdat.o motmisc.o
		$(CL) blastdat.o motmisc.o $(LFLAGS) blastdat
		mv blastdat ../bin
#
blksort.o:	blksort.c motifj.h
		$(CC) $(CFLAGS) blksort.c
getblock.o:	getblock.c motifj.h
		$(CC) $(CFLAGS) getblock.c
getseq.o:	getseq.c motifj.h
		$(CC) $(CFLAGS) getseq.c
multimat.o:	multimat.c motifj.h
		$(CC) $(CFLAGS) multimat.c
motifj.o:	motifj.c motifj.h
		$(CC) $(CFLAGS) motifj.c
motomat.o:	motomat.c motifj.h
		$(CC) $(CFLAGS) motomat.c
uextract.o:	uextract.c motifj.h
		$(CC) $(CFLAGS) uextract.c
blosum.o:	blosum.c motifj.h
		$(CC) $(CFLAGS) blosum.c
blastdat.o:	blastdat.c motifj.h
		$(CC) $(CFLAGS) blastdat.c
#
motmisc.o:	motmisc.c motifj.h
		$(CC) $(CFLAGS) motmisc.c

#
#
blimps-3.9/protomat/Makefile.Sun_intel000064400001460000012000000046621062462114000204160ustar00jorjastaff00000400000027# Protomat Makefile for Sun Solaris 2.6
#   Type "make install" to compile all programs and move them to ../bin
#   Type  "make blksort" to compile blksort program 
CC = /usr/sfw/bin/gcc
CFLAGS = -Wall -O2 -c
CL = gcc
LFLAGS = -lm -o
RM = /bin/rm -f
MV = /bin/mv -f
#
install:	clean all
clean:		
	$(RM) *.o blksort getblock getseq multimat motifj motomat uextract blosum blastdat
all:		blksort getblock getseq multimat motifj motomat uextract blosum blastdat
#
#	blksort: Analyze results of a BLOCKS search
blksort:	blksort.o motmisc.o
		$(CL) blksort.o motmisc.o $(LFLAGS) blksort
		mv blksort ../bin
#	getblock: Retrieve BLOCKs
getblock:	getblock.o motmisc.o
		$(CL) getblock.o motmisc.o $(LFLAGS) getblock
		mv getblock ../bin
#	getseq: Retrieve a sequence
getseq:		getseq.o motmisc.o
		$(CL) getseq.o motmisc.o $(LFLAGS) getseq
		mv getseq ../bin
#	multimat: Analyze results of a MATRIX search
multimat:	multimat.o motmisc.o
		$(CL) multimat.o motmisc.o $(LFLAGS) multimat
		mv multimat ../bin
#	motifj: Make blocks using Ham Smith's motif algorithm
motifj:		motifj.o motmisc.o
		$(CL) motifj.o motmisc.o $(LFLAGS) motifj
		mv motifj ../bin
#	motomat: Assemble blocks from motifj
motomat:	motomat.o motmisc.o
		$(CL) motomat.o motmisc.o $(LFLAGS) motomat
		mv motomat ../bin
#	uextract: Extract protein families from prosite.dat
uextract:	uextract.o motmisc.o
		$(CL) uextract.o motmisc.o $(LFLAGS) uextract
		mv uextract ../bin
#	blosum: Make substitution matrices from blocks
blosum:		blosum.o motmisc.o
		$(CL) blosum.o motmisc.o $(LFLAGS) blosum
		mv blosum ../bin
#	blastdat: Read blast output
blastdat:	blastdat.o motmisc.o
		$(CL) blastdat.o motmisc.o $(LFLAGS) blastdat
		mv blastdat ../bin
#	lislis: Compare two lists of sequences
lislis:		lislis.o motmisc.o
		$(CL) lislis.o motmisc.o $(LFLAGS) lislis
		mv lislis ../bin
#
blksort.o:	blksort.c motifj.h
		$(CC) $(CFLAGS) blksort.c
getblock.o:	getblock.c motifj.h
		$(CC) $(CFLAGS) getblock.c
getseq.o:	getseq.c motifj.h
		$(CC) $(CFLAGS) getseq.c
multimat.o:	multimat.c motifj.h
		$(CC) $(CFLAGS) multimat.c
motifj.o:	motifj.c motifj.h
		$(CC) $(CFLAGS) motifj.c
motomat.o:	motomat.c motifj.h
		$(CC) $(CFLAGS) motomat.c
uextract.o:	uextract.c motifj.h
		$(CC) $(CFLAGS) uextract.c
blosum.o:	blosum.c motifj.h
		$(CC) $(CFLAGS) blosum.c
blastdat.o:	blastdat.c motifj.h
		$(CC) $(CFLAGS) blastdat.c
lislis.o:	lislis.c motifj.h
		$(CC) $(CFLAGS) lislis.c
#
motmisc.o:	motmisc.c motifj.h
		$(CC) $(CFLAGS) motmisc.c

#
#
blimps-3.9/protomat/Makefile.OSX000064400001460000012000000050571042724465700171450ustar00jorjastaff00000400000027# Protomat Makefile for Sun Solaris
#   Type "make install" to compile all programs and move them to ../bin
#   Type  "make blksort" to compile blksort program 
#
#	Solaris
#CC = /opt/SUNWspro/bin/cc
#CFLAGS = -O -c
#CFLAGS = -g -c
#CL = /opt/SUNWspro/bin/cc
#
#	Linux/OSX
CC = /usr/bin/gcc-3.3
#CC = /usr/bin/gcc-4.0
CFLAGS = -Wall -O2 -c
CL = gcc
#
LFLAGS = -lm -o
RM = /bin/rm -f
MV = /bin/mv -f
#
install:	clean all
clean:		
	$(RM) *.o blksort getblock getseq multimat motifj motomat uextract blosum blastdat
all:		blksort getblock getseq multimat motifj motomat uextract blosum blastdat
#
#	blksort: Analyze results of a BLOCKS search
blksort:	blksort.o motmisc.o
		$(CL) blksort.o motmisc.o $(LFLAGS) blksort
		mv blksort ../bin
#	getblock: Retrieve BLOCKs
getblock:	getblock.o motmisc.o
		$(CL) getblock.o motmisc.o $(LFLAGS) getblock
		mv getblock ../bin
#	getseq: Retrieve a sequence
getseq:		getseq.o motmisc.o
		$(CL) getseq.o motmisc.o $(LFLAGS) getseq
		mv getseq ../bin
#	multimat: Analyze results of a MATRIX search
multimat:	multimat.o motmisc.o
		$(CL) multimat.o motmisc.o $(LFLAGS) multimat
		mv multimat ../bin
#	motifj: Make blocks using Ham Smith's motif algorithm
motifj:		motifj.o motmisc.o
		$(CL) motifj.o motmisc.o $(LFLAGS) motifj
		mv motifj ../bin
#	motomat: Assemble blocks from motifj
motomat:	motomat.o motmisc.o
		$(CL) motomat.o motmisc.o $(LFLAGS) motomat
		mv motomat ../bin
#	uextract: Extract protein families from prosite.dat
uextract:	uextract.o motmisc.o
		$(CL) uextract.o motmisc.o $(LFLAGS) uextract
		mv uextract ../bin
#	blosum: Make substitution matrices from blocks
blosum:		blosum.o motmisc.o
		$(CL) blosum.o motmisc.o $(LFLAGS) blosum
		mv blosum ../bin
#	blastdat: Read blast output
blastdat:	blastdat.o motmisc.o
		$(CL) blastdat.o motmisc.o $(LFLAGS) blastdat
		mv blastdat ../bin
#	lislis: Compare two .lis files
lislis:		lislis.o motmisc.o
		$(CL) lislis.o motmisc.o $(LFLAGS) lislis
		mv lislis ../bin
#
blksort.o:	blksort.c motifj.h
		$(CC) $(CFLAGS) blksort.c
getblock.o:	getblock.c motifj.h
		$(CC) $(CFLAGS) getblock.c
getseq.o:	getseq.c motifj.h
		$(CC) $(CFLAGS) getseq.c
multimat.o:	multimat.c motifj.h
		$(CC) $(CFLAGS) multimat.c
motifj.o:	motifj.c motifj.h
		$(CC) $(CFLAGS) motifj.c
motomat.o:	motomat.c motifj.h
		$(CC) $(CFLAGS) motomat.c
uextract.o:	uextract.c motifj.h
		$(CC) $(CFLAGS) uextract.c
blosum.o:	blosum.c motifj.h
		$(CC) $(CFLAGS) blosum.c
blastdat.o:	blastdat.c motifj.h
		$(CC) $(CFLAGS) blastdat.c
lislis.o:	lislis.c motifj.h
		$(CC) $(CFLAGS) lislis.c
#
motmisc.o:	motmisc.c motifj.h
		$(CC) $(CFLAGS) motmisc.c

#
#
blimps-3.9/protomat/README.OSX000064400001460000012000000006411042724515000163440ustar00jorjastaff000004000000275/6/2006 Mac/OSX compile notes

Can't compile programs that use built-in math.h with either gcc-3.3 or 
gcc-4.0, e.g.

make blosum
/usr/bin/gcc-3.3 -Wall -O2 -c blosum.c
In file included from /usr/include/math.h:26,
                 from blosum.c:65:
/usr/include/architecture/ppc/math.h:349: error: parse error before "double"
make: *** [blosum.o] Error 1

Had to move "#include " from blosum.c to motifj.h 
blimps-3.9/protomat/ccc000075500001460000012000000003141056462463100154760ustar00jorjastaff00000400000027#      Compile one program with blimps
#	Usage to compile program.c:   cccb 
set b = ..
set CC = /opt/SUNWspro/bin/cc
#set CC = /opt/sfw/bin/gcc
$CC -fast -I$b/include -L$b/lib -o $1 $1.c 

exit
blimps-3.9/protomat/Makefile.Sun_sparc000064400001460000012000000050031056464152700204170ustar00jorjastaff00000400000027# Protomat Makefile for Sun Solaris 2.6
#   Type "make install" to compile all programs and move them to ../bin
#   Type  "make blksort" to compile blksort program 
#
#	Solaris
CC = /opt/SUNWspro/bin/cc
CFLAGS = -O -c
CL = /opt/SUNWspro/bin/cc
#
#	Linux
#CC = gcc
#CFLAGS = -Wall -O2 -c
#CL = gcc
#
LFLAGS = -lm -o
RM = /bin/rm -f
MV = /bin/mv -f
#
install:	clean all
clean:		
	$(RM) *.o blksort getblock getseq multimat motifj motomat uextract blosum blastdat
all:		blksort getblock getseq multimat motifj motomat uextract blosum blastdat
#
#	blksort: Analyze results of a BLOCKS search
blksort:	blksort.o motmisc.o
		$(CL) blksort.o motmisc.o $(LFLAGS) blksort
		mv blksort ../bin
#	getblock: Retrieve BLOCKs
getblock:	getblock.o motmisc.o
		$(CL) getblock.o motmisc.o $(LFLAGS) getblock
		mv getblock ../bin
#	getseq: Retrieve a sequence
getseq:		getseq.o motmisc.o
		$(CL) getseq.o motmisc.o $(LFLAGS) getseq
		mv getseq ../bin
#	multimat: Analyze results of a MATRIX search
multimat:	multimat.o motmisc.o
		$(CL) multimat.o motmisc.o $(LFLAGS) multimat
		mv multimat ../bin
#	motifj: Make blocks using Ham Smith's motif algorithm
motifj:		motifj.o motmisc.o
		$(CL) motifj.o motmisc.o $(LFLAGS) motifj
		mv motifj ../bin
#	motomat: Assemble blocks from motifj
motomat:	motomat.o motmisc.o
		$(CL) motomat.o motmisc.o $(LFLAGS) motomat
		mv motomat ../bin
#	uextract: Extract protein families from prosite.dat
uextract:	uextract.o motmisc.o
		$(CL) uextract.o motmisc.o $(LFLAGS) uextract
		mv uextract ../bin
#	blosum: Make substitution matrices from blocks
blosum:		blosum.o motmisc.o
		$(CL) blosum.o motmisc.o $(LFLAGS) blosum
		mv blosum ../bin
#	blastdat: Read blast output
blastdat:	blastdat.o motmisc.o
		$(CL) blastdat.o motmisc.o $(LFLAGS) blastdat
		mv blastdat ../bin
#	lislis: Compare two lists of sequences
lislis:		lislis.o motmisc.o
		$(CL) lislis.o motmisc.o $(LFLAGS) lislis
		mv lislis ../bin
#
blksort.o:	blksort.c motifj.h
		$(CC) $(CFLAGS) blksort.c
getblock.o:	getblock.c motifj.h
		$(CC) $(CFLAGS) getblock.c
getseq.o:	getseq.c motifj.h
		$(CC) $(CFLAGS) getseq.c
multimat.o:	multimat.c motifj.h
		$(CC) $(CFLAGS) multimat.c
motifj.o:	motifj.c motifj.h
		$(CC) $(CFLAGS) motifj.c
motomat.o:	motomat.c motifj.h
		$(CC) $(CFLAGS) motomat.c
uextract.o:	uextract.c motifj.h
		$(CC) $(CFLAGS) uextract.c
blosum.o:	blosum.c motifj.h
		$(CC) $(CFLAGS) blosum.c
blastdat.o:	blastdat.c motifj.h
		$(CC) $(CFLAGS) blastdat.c
lislis.o:	lislis.c motifj.h
		$(CC) $(CFLAGS) lislis.c
#
motmisc.o:	motmisc.c motifj.h
		$(CC) $(CFLAGS) motmisc.c

#
#
blimps-3.9/protomat/cccg000075500001460000012000000005401056464063400156470ustar00jorjastaff00000400000027#      Compile one program with blimps
#	Usage to compile program.c:   cccb 
set CC = /opt/SUNWspro/bin/cc
#set CC = /opt/sfw/bin/gcc
#$CC -g -I$b/include -L$b/lib -o $1 $1.c -lblocks -lmatrix -lsequences -lfrequency -lpssm -lprotomat -lfiles -lmemory -loptions -lgcode -lerrors -lversion -lstrutil -lsl -lm
$CC -g motmisc.o -o $1 $1.c 

exit
blimps-3.9/www/000075500001460000012000000000001041775157100140025ustar00jorjastaff00000400000027blimps-3.9/www/addseqs.html000064400001460000012000000026040775500604700163200ustar00jorjastaff00000400000027
Add Sequences to Blocks

      Add Sequences to Blocks
      


      


      

Add sequences to blocks
aligns a set of Blocks with one or more protein sequences, saving
the best score only for each alignment. It adds each protein
sequence to the blocks if the best alignments are in the correct
order and non-overlapping, re-weights and re-calibrates each block.

      
You can make blocks from unaligned protein sequences with
Block Maker.
      
If you need to convert another multiple alignment to
BLOCKS format, use the
Multiple Alignment Processor or the
Block Formatter.
      

      

Enter your Blocks in 
BLOCKS format:
      


      
Enter your protein sequences in 
FASTA format:
      



      



      


      
Blocks home

      
Contact us
      
Page last modified on August 2003

blimps-3.9/www/biased_blocks.html000064400001460000012000000050430775500606700174620ustar00jorjastaff00000400000027

Biassed Blocks Finder



      Identifying biassed blocks
      

      at the 
Fred Hutchinson Cancer Research Center BLOCKS WWW server.

      

Compositionally biassed blocks are made up of sequence segments rich 
in a few amino acids or short repeats. 
Biassed blocks are not
neccesarily misaligned. Some conserved protein regions are rich in 
charged residues, like basic-zipper transcription factors, or in hydrophobic
amino acids, like transmembranal regions.
However, blocks biassed toward the same amino acid(s) can give a significant 
LAMA (block to block alignment) 
score, even without being biologically related.

      
Biassed blocks have a high number of columns similar to one another.
Such a block can be identified by comparing all of its columns with
each other, clumping those columns sharing high pairwise scores, and counting 
the number of columns in the largest clump.

      
Two parameters are used: 
which pairwise column score is considered "high" and
what fraction of columns in the largest clump is considered "high".
The column comparison measure used is the normalized sum of products (p).
p(A,B) is the sum of A(i)*B(i) for all i amino acids (20) in block 
columns A and B (actually PSSM
columns).
About 5% of the blocks in the Blocks+ (10 June 2000) database were judged
biassed using the default parameters of 0.50 for the cutoff pairwise column
score and 25% of columns in the largest clump of columns.

      



Paste your block(s) below and . 
The blocks must be in the
BLOCK format.
You can reformat multiple sequence alignments to that format
here)

      




      





      

      


      


LAMA Searcher Help

      

[Blocks home] 
[Block Searcher]
[Block Maker]
[Get Blocks]
[Blocks Formatter]
[LAMA Searcher]


      
Contact us 
      
Page last modified June 2000



blimps-3.9/www/biassed_blocks.html000064400001460000012000000050430775500606700176450ustar00jorjastaff00000400000027

Biassed Blocks Finder



      Identifying biassed blocks
      

      at the 
Fred Hutchinson Cancer Research Center BLOCKS WWW server.

      

Compositionally biassed blocks are made up of sequence segments rich 
in a few amino acids or short repeats. 
Biassed blocks are not
neccesarily misaligned. Some conserved protein regions are rich in 
charged residues, like basic-zipper transcription factors, or in hydrophobic
amino acids, like transmembranal regions.
However, blocks biassed toward the same amino acid(s) can give a significant 
LAMA (block to block alignment) 
score, even without being biologically related.

      
Biassed blocks have a high number of columns similar to one another.
Such a block can be identified by comparing all of its columns with
each other, clumping those columns sharing high pairwise scores, and counting 
the number of columns in the largest clump.

      
Two parameters are used: 
which pairwise column score is considered "high" and
what fraction of columns in the largest clump is considered "high".
The column comparison measure used is the normalized sum of products (p).
p(A,B) is the sum of A(i)*B(i) for all i amino acids (20) in block 
columns A and B (actually PSSM
columns).
About 5% of the blocks in the Blocks+ (10 June 2000) database were judged
biassed using the default parameters of 0.50 for the cutoff pairwise column
score and 25% of columns in the largest clump of columns.

      


      

Paste your block(s) below and . 
The blocks must be in the
BLOCK format.
You can reformat multiple sequence alignments to that format
here)

      




      





      

      


      


LAMA Searcher Help

      

[Blocks home] 
[Block Searcher]
[Block Maker]
[Get Blocks]
[Blocks Formatter]
[LAMA Searcher]


      
Contact us 
      
Page last modified June 2000



blimps-3.9/www/blalign.html000064400001460000012000000017300775500610500162760ustar00jorjastaff00000400000027
Re-format Blocks as an Alignment

      Re-format Blocks as an Alignment
      


      


      

You can make blocks from unaligned protein sequences with
Block Maker.
      

      

Enter your Blocks in 
BLOCKS format:
      





      
Select an output alignment format





      



      


      
Blocks home

      
Contact us
      
Page last modified on August 2003

blimps-3.9/www/block_formatter.html000064400001460000012000000047400775501212600200470ustar00jorjastaff00000400000027BLOCK Formatter

       BLOCK Formatter
      

      at the 
Fred Hutchinson Cancer Research Center BLOCKS WWW server.

      



Block Formatter will reformat a multiple alignment to the 
BLOCK format and present a
graphical representation (sequence logo) 
and a scoring matrix of it.
      

      


      
After 
filling the form
you can .
      
If you wish to later resubmit you can 
.
      

      


      ID           
Accession     Distance from previous block, minmax
Description  
Align. method Align. width Number of sequences

Multiple alignment:
Sequence      Start
names         positions  Sequences (must be filled; one sequence per line 
                                      or FASTA format)
      


 

      


      
[Blocks home] 
[Block Searcher]
[Block Maker]
[Get Blocks]
[Formatter Help]

      
Page last modified on August 1996

      
Shmuel Pietrokovski

      

blimps-3.9/www/blocks_format.html000064400001460000012000000132730774527345600175360ustar00jorjastaff00000400000027
Blocks Format

       Format of a Block
      



      ID   short_identifier; BLOCK
AC   block_number; distance from previous block = (min,max)
DE   description
BL   xxx motif; width=w; seqs=s; 99.5%=n1; strength=n2
sequence_id  (offset) sequence_segment  sequence_weight
.
.
.
//
      

ID line starts a block entry and contains a short identifier for the group
of sequences from which the block was made.
If the block was taken from InterPro, it will be the InterPro group ID.
The identifier is terminated by a semi-colon, and the word "BLOCK"
indicates the entry type.
      

AC line contains the block number, a seven-character group number for
sequences from which the block was made, followed by a letter (A-Z) 
indicating the order of the block in the sequences.
If the group has only one block, the letter is omitted.
If the block was made from InterPro group IPRnnnnnn, the block number
is IPBnnnnnna.
If the block was converted from Terri Attwood's Prints Database the
block number is PRnnnnna. 
min,max =  minimum,maximum number of amino acids from previous block for
sequences in this block. For the first block in the group, the distance from
the beginning of the sequences.
      

DE line contains a description of the group of sequences from which
the block was made. If the block was taken from InterPro, it will be
a slightly edited version of the InterPro description.
      

BL line contains information about the block:
      
xxx =  the amino acids in the spaced triplet found by MOTIF upon
which the block is based.
      
w =  width of the sequence segments (columns) in the block.
      
s =  number of sequence segments (rows) in the block.
      
n1 =  raw calibration score; 99.5th percentile score of true
negative sequences. Raw search scores are normalized by
dividing by this score and multiplying by 1000.
      
n2 =  median normalized score of known true positive sequences as
documented in InterPro.
      

Following the BL line are lines for each sequence with
a segment in the block. The segments may be clustered with clusters
separated by blank lines.
Each segment line contains a sequence identifier,
the offset from the beginning of the sequence
to the block in parentheses, the sequence segment, and a weight for the
segment. The weights are normalized so that
the most distant segment has a weight of 100.
      

// line terminates a block entry.

      
Current Blocks Database Release

      
About the Blocks Database

      

      Other Multiple Alignment Formats
      

      FASTA Format
      
Each sequence in the multiple alignment starts with a FASTA
title line containing the sequence name followed by the
aligned sequence residues with dashes representing gaps:

      >JC2395
NVSDVNLNK---YIWRTAEKMK---ICDAKKFARQHKIPESKIDEIEHNSPQDAAE----
-------------------------QKIQLLQCWYQSHGKT--GACQALIQGLRKANRCD
IAEEIQAM
>KPEL_DROME
MAIRLLPLPVRAQLCAHLDAL-----DVWQQLATAVKLYPDQVEQISSQKQRGRS-----
-------------------------ASNEFLNIWGGQYN----HTVQTLFALFKKLKLHN
AMRLIKDY
>FASA_MOUSE
NASNLSLSK---YIPRIAEDMT---IQEAKKFARENNIKEGKIDEIMHDSIQDTAE----
-------------------------QKVQLLLCWYQSHGKS--DAYQDLIKGLKKAECRR
TLDKFQDM

      


      

      CLUSTAL/STOCKHOLM Format
      
ClustalW Site.
      
The first non-blank line must contain the word "CLUSTAL" or "STOCKHOLM".
Sequences are interleaved on separate lines with gaps represented
by dashes. Each sequence line starts with the sequence name which is
separated from the aligned sequence residues by spaces or tabs.
Each set of interleaved sequence segments is separated by one or more
blank lines. Lines containing sequence conservations symbols (CLUSTAL)
or "//" (STOCKHOLM) are ignored.

      
(Please note: Some WWW sites post-process Clustal output so that
it has a different format than in this example; in this case use
FASTA format).

      CLUSTAL W(1.60) multiple sequence alignment



JC2395          NVSDVNLNK---YIWRTAEKMK---ICDAKKFARQHKIPESKIDEIEHNSPQDAAE----
KPEL_DROME      MAIRLLPLPVRAQLCAHLDAL-----DVWQQLATAVKLYPDQVEQISSQKQRGRS-----
FASA_MOUSE      NASNLSLSK---YIPRIAEDMT---IQEAKKFARENNIKEGKIDEIMHDSIQDTAE----


JC2395          -------------------------QKIQLLQCWYQSHGKT--GACQALIQGLRKANRCD
KPEL_DROME      -------------------------ASNEFLNIWGGQYN----HTVQTLFALFKKLKLHN
FASA_MOUSE      -------------------------QKVQLLLCWYQSHGKS--DAYQDLIKGLKKAECRR


JC2395          IAEEIQAM
KPEL_DROME      AMRLIKDY
FASA_MOUSE      TLDKFQDM




      


      

      MSF Format
      
Any comments at the beginning of the file are terminated with a line
starting with two slashes.
Sequences are interleaved on separate lines with gaps represented
by periods. Each sequence line starts with the sequence name which is
separated from the aligned sequence residues by white space:

      //


                1                                                   50
JC2395          NVSDVNLNK. ..YIWRTAEK MK...ICDAK KFARQHKIPE SKIDEIEHNS 
KPEL_DROME      MAIRLLPLPV RAQLCAHLDA L.....DVWQ QLATAVKLYP DQVEQISSQK 
FASA_MOUSE      NASNLSLSK. ..YIPRIAED MT...IQEAK KFARENNIKE GKIDEIMHDS

		51                                                 100
JC2395		PQDAAE.... .......... .......... .....QKIQL LQCWYQSHGK
KPEL_DROME	QRGRS..... .......... .......... .....ASNEF LNIWGGQYN.
FASA_MOUSE	IQDTAE.... .......... .......... .....QKVQL LLCWYQSHGK

                101
JC2395		T..GACQALI QGLRKANRCD IAEEIQAM
KPEL_DROME	...HTVQTLF ALFKKLKLHN AMRLIKDY
FASA_MOUSE	S..DAYQDLI KGLKKAECRR TLDKFQDM



      
      [Blocks home]


blimps-3.9/www/blocks_release.html000064400001460000012000000122070776050313200176420ustar00jorjastaff00000400000027
Current BLOCKS Database Release


      Current Release of BLOCKS
      


      
               BLOCKS Database Version 14.0, October 2003
      
       Copyright 2003 by Fred Hutchinson Cancer Research Center
      
              1100 Fairview AV N, A1-162, Seattle, WA 98109


      
Version 14.0 of the BLOCKS Database consists of 24,294 blocks representing
4944 groups documented in InterPro 6.0 keyed to SWISS-PROT 41.0 and 
TrEMBL 23.0 obtained from the 
InterPro server .
      
The BLOCKS Database is based on InterPro entries with sequences from
SWISS_PROT
and
TrEMBL
and with cross-references to
PROSITE 
and/or
PRINTS
and/or
SMART,
and/or
PFAM
entries.

      
The BLOCKS Database was constructed by the PROTOMAT system 
(S Henikoff & JG Henikoff, "Automated assembly of protein blocks for
database searching", NAR (1991) 19:6565-6572)
using the MOTIF algorithm
(HO Smith, et al, "Finding sequence motifs in groups of functionally
related proteins", PNAS (1990) 87:826-830)
as implemented in
Block Maker.

      
To avoid using possible false positive sequences added to the
InterPro entries automatically (without human oversight),
BLOCKS were made for each InterPro entry using just the sequences
in SWISS-PROT, and then TrEMBL sequences were added if they fit the
resulting BLOCKS model.

      
InterPro 6.0 consisted of 7751 entries. The 4944 entries of these
represented in BLOCKS 14.0 were selected as follows:
      

       7751
-1906 entries with fewer than 3 SWISS-PROT sequences eligible for PROTOMAT (1)
 -901 entries with no PROSITE, PRINTS, SMART or PFAM component (2)
 -156 entries participating in InterPro parent/child relationships (3)
 4788

+ 204 entries PRINTS-only entries with fewer than 3 SWISS-PROT sequences (4)
 4992


 1354 blocks entries taken from PRINTS (4)


 3638 entries processed by PROTOMAT
  - 4 entries with too many sequences to process with PROTOMAT
  - 6 entries for which PROTOMAT failed to find blocks
  -38 entries for which final blocks were obviously useless (5)

 3590 blocks entries made by PROTOMAT


NOTES:
(1) PROTOMAT requires at least 3 sequences to make blocks. To be more
confident that the sequences used are actually members of the InterPro
protein family, we used only sequences from SWISS-PROT. Then, to reduce
redundancy, we use only the longest SWISS-PROT sequence among those
with the same gene name (characters before the "_" in the SWISS-PROT ID)
and similar organism name (first three characters following the "_").
For example, if an InterPro group included SWISS-PROT sequences named
AANT_HDVAM|P25989     LENGTH=214
AANT_HDVD3|P29996     LENGTH=195   
AANT_HDVWO|P29997     LENGTH=205   
only AANT_HDVAM would be used by PROTOMAT.

(2) InterPro now contains entries from several other sources. However,
these four sources tend to define a protein family in terms most amenable
to the BLOCKS model which is short, highly conserved regions. In
particular, PROTOMAT will generally produce unsatisfactory results for
groups comprised of a few, long, globally alignable sequences.

(3) Several InterPro entries are arranged into parent/child hierarchies
where all the sequences in a child entry are included in the parent
entry. Since PROTOMAT will tend to find the same blocks for the parent
and children, each major branch of a hierarchy is represented by only
one BLOCKS entry.

(4) Because the PRINTS model is the same as the BLOCKS model and PRINTS is
a curated collection of alignments, the PRINTS blocks were used directly 
for InterPro entries with only a PRINTS component as long as the PRINTS blocks 
had at least three sequences from any source. Then additional sequences
were added from TrEMBL if they fit the PRINTS model.

(5) These entries tend to be sites (e.g. IPR000886, IPB001216),
repeats (e.g. IPR000479, IPR001473) and viral proteins (e.g. IPR000208,
IPR000752).

      

      
Please note: The PROSITE pattern is not used in any way to make the 
BLOCKS Database and BLOCKS made from an InterPro PROSITE group may or 
may not contain the PROSITE pattern. 
Similarly, the SMART and PFAM multiple alignments are not used
in any way to make the BLOCKS Database and BLOCKS made from an
InterPro PROSITE, SMART or PFAM group may or may not overlap with the
multiple alignments in those databases.


      

      BLOCKS without compositionally biased blocks
      
To avoid the over-representation of compositionally biased blocks in
search results, this subset of the BLOCKS Database excludes several
biased blocks. It may give better results,
especially with DNA queries.


      
BLOCKS home


      
Contact us 
      
Page last modified October 2003

blimps-3.9/www/blocks_search.html000064400001460000012000000120561040612057700174700ustar00jorjastaff00000400000027
Block Search

       Block Searcher
      

      at the 
Fred Hutchinson Cancer Research Center Blocks WWW server.

      
Search your protein or DNA sequence against a
Blocks Database.
 [Help]
[Example of output]

      




      

    • 
Enter your email address if you want the 
results through email :
      



      

    • 
 Select database to search:
  

      We recommend searching both Blocks and Prints. Blocks has
automatically-generated blocks, while Prints has hand-crafted blocks.


      

    • 
Optionally select cutoff expected value:



    • 
Optionally select amount of output:



    • 
Optionally force query sequence type:



      

    • 
Additional optional search parameters for a DNA query:

  
        
  
      • 
  Strands to search:
  

  
      • 
  Genetic code:
  
  
      



      

    • 
Enter your protein or DNA 
query sequence in 
FASTA,
EMBL or
 GENBANK format:

      




      



      
Response time will vary depending on query sequence length and type
and may take several minutes. Our system can process a maximum of about
25 amino acids per second. This means a protein query 300 amino 
acids in length will take at least 12 seconds while a DNA query 1100 
nucleotides in length translated in 6 frames will take at least 1.5 minutes.
Please be patient, or supply an email address.


      • 



      
You can also search Blocks using different algorithms with
Reverse PSI-BLAST, 
IMPALA, 
Ematrix or 
Identify.

      You can search other protein family collections with
InterPro,
CD-Search or
eBLOCKS.

      

      

[Blocks Home] 
[RPS-BLAST Searcher]
[IMPALA Searcher]
[Block Maker]
[Get Blocks]
[LAMA Searcher]



      
Contact us 
      
Page last modified Mar 2006


EM">results through email :
      



      

    • 
 Select database to search:
  

      We recommend searching both Blocks and Prints. Blocks has
automatiblimps-3.9/www/cobbler.html000064400001460000012000000026220775500620400162770ustar00jorjastaff00000400000027
Cobbler Sequence

      Cobbler Sequence
      


      


      

COBBLER 
aligns a set of Blocks with a protein sequence
and embeds a consensus representation of the Blocks in
the sequence, which can then be used to search sequence
databases using 
BLAST,
and other sequence searching programs.
Block Maker makes a
COBBLER sequence automatically, but this page can be used
if you want to embed your blocks in a different sequence.
If you need to convert another multiple alignment to
BLOCKS format, use the
Multiple Alignment Processor or the
Block Formatter.

      

Enter your Blocks in 
BLOCKS format:
      


      
Enter your protein sequence in 
FASTA format:
      



      



      


      
Blocks home

      
Contact us 
      
Page last modified on Dec 1999

blimps-3.9/www/codehop.html000064400001460000012000000400321040405306200162720ustar00jorjastaff00000400000027

CODEHOP




      

      


      CODEHOP:
      COnsensus-DEgenerate Hybrid Oligonucleotide Primers
      		
CODEHOP mascot

      

      _______________________
      

      




      PCR primers designed from protein multiple sequence alignments
      

        
  
      • Getting started
        • 
  
      • Full Help file
        • 
  
      • The CODEHOP algorithm
  
      • The CODEHOP manuscript
  
      • 
Genes identified using CODEHOP

        
  
      • The input should be a set of local multiple alignments (blocks) of a 
group of related protein sequences. The alignments must be in 
  Blocks Database format, such as in Block Maker
        •  output.
  
      •  Ungapped parts of Clustal- or FASTA-formatted global multiple 
alignments can be automatically turned into blocks by the Blocks 
multiple alignment processor. You can also manually reformat 
multiple sequence alignments with the 
 Blocks formatter.
        •  
  
      •  The output of all these programs contains links that send the 
  resulting blocks to this page. 
  
      •  If your sequences align globally, you will get better multiple 
alignment results from Clustal
than from the motif finders used by Block Maker.
  
      • Blocks are processed using sequence weights (the numbers
following each sequence segment). To emphasize particular sequences
in the block(s) manually adjust the sequence weights. Increase the
number to give a sequence more weight.


      


      

      Paste your block(s) below:



      

      

      

      


      


      Core (degenerate 3' region)
- degeneracy
[default=128]:


      


      
- strictness
[default=0.0]:


      


      Clamp
(non-degenerate 5' region)
- temperature
[default=60.0]:


      


      
- poly-nuc
[default=5]:


      


      Primer concentration [in nM,
default=50nM]:

([K+]=50mM)
      


      


      
Genetic code



      
Codon usage table
(scroll for more choices):

      


      By default, up to 3 of the least degenerate primers in an 
overlapping set
are shown.
      

      

      
Show the

least degenerate, or show all overlapping primers.


      

      

By default, the 3' base of the primer must be an invariant position,
regardless of the core strictness setting.

      Use core strictness for the 3' base.



      

      
Force the 
core/clamp boundary to be a codon boundary.



      Use the most common codons in the 
clamp. 

      

      

      


      


      

      


[Blocks home]
[CODEHOP help]
[Getting started]
[CODEHOP program]


      

Contact us 
      
Page last modified Mar 2003
      




blimps-3.9/www/contact.html000064400001460000012000000024451034532463400163240ustar00jorjastaff00000400000027
Blocks Contact

      
Blocks WWW Server Contact Form

      

      


      
We will try to respond to your questions within one working day.


        

        

      • 
Please enter your email address: 

        

      • 
Please enter your name: 


      • 

        
Select a topic:
  


      • 

        
Enter your question or comment:



      • 




      

      


      
[Blocks Home] 
[Get Blocks]
[Block Searcher]
[Block Maker]
[Codehop]


      
Page last modified Apr 2003

blimps-3.9/www/diy.html000064400001460000012000000022730775500624300154610ustar00jorjastaff00000400000027
Do-It-Yourself Block Search

      Do-It-YourSelf Block Search
      


      


      

Do-It-Yourself Block Search 
aligns a set of Blocks with a protein or DNA sequence.

      
You can make blocks from unaligned protein sequences with
Block Maker.
      
If you need to convert another multiple alignment to
BLOCKS format, use the
Multiple Alignment Processor or the
Block Formatter.
      

      

Enter your Blocks in 
BLOCKS format:
      


      
Enter your protein or DNA sequence in 
FASTA format:
      



      



      


      
Blocks home

      
Contact us
      
Page last modified on August 2003

blimps-3.9/www/impala.html000064400001460000012000000034650775452710000161420ustar00jorjastaff00000400000027
Search BLOCKS with IMPALA

       Search BLOCKS with IMPALA
      

      at the 
Fred Hutchinson Cancer Research Center Blocks WWW server.
      


      
IMPALA  is provided by the
NCBI BLAST Group.

      




      

    • 
 Select database to search:
  


      

    • 
Optionally select cutoff expected value:



      

    • 
Check to filter
 your protein query sequence with seg:


      


      

    • 
Enter your protein query sequence in
FASTA format:
      


      


      



      


      
[Blocks Home]
[Block Searcher]

      
Contact us 
      
Page last modified on Mar 2003


blimps-3.9/www/index.html000064400001460000012000000070561040611740000157700ustar00jorjastaff00000400000027

Blocks WWW Server


      
Blocks WWW Server

      

      

A service for biological sequence analysis at the 
Fred Hutchinson Cancer Research Center 
in Seattle, Washington, USA.

      
Visit the
Blocks mirror site at the
Weizmann Institute of Science in Israel.

      

      Blocks-Based Tools
      



      

      Related Tools
      



      
Contact us

      
Acknowledgements

      
Copyright



      
Page last modified 15 March 2006


//bioinformatics.weizmann.ac.il/">Weizmann Institute of Science in Israel.

      

      Blocks-Based Tools
      


      • 
blimps-3.9/www/make_blocks.html000064400001460000012000000072471040612116600171410ustar00jorjastaff00000400000027
Block Maker

       Block Maker
      

      at the 
Fred Hutchinson Cancer Research Center 
BlockS WWW server.

      



Block Maker finds conserved blocks in a group of
two or more unaligned protein sequences, which are assumed to be related,
using two different algorithms.
      
If you already have a multiple alignment, please use the
Multiple Alignment Processor
instead.
      

At least two related protein sequences must be provided 
to make blocks.
Each sequence must have a unique name of 10 characters or less.
If you have the accession numbers of some sequences you would like to use,
Batch Entrez can create a file for you in 
FASTA format.

      
If you have a file a sequences in a format other than FASTA, you can convert
them to FASTA format at the
EBI conversion tool.

      
It may take several minutes to
process your sequences. If you are not prepared to wait for a response,
or have more than 25 sequences or more than 15,000 amino acids,
please provide an email address and your
results will be returned to you in two messages. The second
message contains your blocks in 
Blocks Database format,
and you can copy and paste these into the
Multiple Alignment Processor
to get
Logos and
Trees,
to search sequence database using
Cobbler 
or
Mast,
and to predict PCR primers using CODEHOPs.

      
Enter your email address if you want the results through email:
      

      

Enter a short description of your group of sequences:
      

      

Enter the name of a file containing your protein sequences:
      

      
-or-
      
Enter your protein sequences in a single format (e.g. 
FASTA):
      



      



      
Note: It may take several minutes to compute the results:
Please be patient.


      
You might be interested in trying other
multiple sequence alignment methods,
including ClustalW, MAP and PIMA, at the Human Genome Center at the Baylor 
College of Medicine, 
Multiple EM for Motif Elicitation
at the San Diego Supercomputer Center 
and the
Gibbs Motif Sampler
at the Wadsworth Center.


      

      
[Blocks home] 
[Block Searcher]
[Block Maker]
[Get Blocks]
[LAMA Searcher]

      

      
Contact us 
      
Page last modified on Oct 2003


ks/process_blocks.html">Multiple Alignment Processor
to get
Logos and
Trees,
to search sequence database using
Cobbler 
or
Mast,
and to predictblimps-3.9/www/narrow.html000064400001460000012000000045730775500776100162170ustar00jorjastaff00000400000027
Narrow PSSMs

      
Blocks WWW Server

      

      
A service for biological sequence analysis at the
Fred Hutchinson Cancer Research Center
in Seattle, Washington, USA.

      




      

This page will convert a narrow
block ,
frequency or
weight 
PSSM to
BLIMPS and 
MAST format
and then search it vs 
Swiss-Prot using
BLIMPS.

      
The conversion is done as follows:
      

        

      • If a block is input, equal sequence weights are used.

      • If a block is input, amino acid frequencies are computed for each position.

      • If a block or frequency PSSM is input, minimal pseudo counts are
added to the actual counts; just enough to allow log-odds to be computed.
For a block, 1 pseudo-count per 10,000 real counts is computed using a substitution matrix.
For a frequency PSSM, 10,000 real counts and 1 pseudo-count are assumed
and the pseudo-count is computed using background frequencies.

      • If a block or frequency PSSM is input, the expected values for the
odds ratios are taken from Swiss-Prot and the log base e (scale in nats) 
of the odds ratios is computed.

      • This PSSM is output in MAST format.

      • This PSSM is converted to a positive matrix and output in BLIMPS format.



        
If you have a multiple alignment, you can 
reformat it 
as a 
BLOCK.

        

Select a query type:
        



        
Enter the name of a file containing your query:
        

        
-or-
        
Enter your query:
        




        



        


        
Contact us 
        
Page last modified on Mar 2003

blimps-3.9/www/oligo_melt.html000064400001460000012000000012730774312726500170320ustar00jorjastaff00000400000027
Oligo Melting Temperatures

        Oligo Melting Temperatures
        




        

Select DNA concentration in nM [blank=50nM]:

        
PRIMER3 uses 50nM and NAR uses 0.10nM
        
[K+] is fixed at 50mM

        

Enter your DNA oligo sequence 5' to 3':
        



        



        


        
You may also want to try
MELTING 

        

Contact us 
        
Page last modified on Mar 2003

blimps-3.9/www/rpsblast.html000064400001460000012000000037570775452714400165450ustar00jorjastaff00000400000027
Search BLOCKS with Reverse PSI-BLAST

         Search BLOCKS with Reverse PSI-BLAST
        

        at the 
Fred Hutchinson Cancer Research Center Blocks WWW server.
        


        
RPS-BLAST  is provided by the
NCBI BLAST Group.

        




        

      • 
 Select database to search:
  


        

      • 
Optionally select cutoff expected value:



        

      • 
Check to filter
 your protein query sequence with seg:


        


        

      • 
Enter your protein query sequence in
FASTA format:
        


        


        



        


        
[Blocks Home]
[Block Searcher]
[Block Maker]
[Get Blocks]
[LAMA Searcher]



        
Contact us 
        
Page last modified on Mar 2003

blimps-3.9/www/bin/000075500001460000012000000000001041775053600145525ustar00jorjastaff00000400000027blimps-3.9/www/bin/LAMA_alignment.sh000075500001460000012000000012330774335017300176610ustar00jorjastaff00000400000027#!/bin/sh

#  run show_aligned_blocks
#  modified from LAMA_logos


   cat << EOM
Content-type: text/html


LAMA blocks alignment

        Alignment of $2 and $5
        

        EOM

#  "2>&1" in order to redirect stderr to stdout
./show_aligned_blocks $1 $2 $3 $4 $5 $6 $7 2>&1

echo "
        "
echo ""

exit 0

if [ $3 -gt 55 -o $6 -gt 55 ]
then
   cat << EOM
Content-type: text/html

LAMA logos alignment error

        LAMA logos alignment error
        
At present logos alignment is only shown for regions in the first
55 positions of the blocks. Sorry.
EOM
   exit 1
else
   echo Content-type: application/postscript
   echo 
fi

exit
blimps-3.9/www/bin/LAMA_logos.csh000075500001460000012000000045270775576023700172130ustar00jorjastaff00000400000027#!/bin/csh
#                        1         2     3       4        5      6      7
#	LAMA_logos.csh       
#   Executed by htmlize_LAMA.c which is executed by LAMA_searcher.c
#
#  The files makelogob, colors, marks, wave and default.amino.frq must be in
#  the current directory

unalias rm
limit coredumpsize 1k

set TMP = ../tmp
set BIN = "."
set DNAME = "$$"
set ALIGNLOGOS = "$BIN/align_two_logos.csh"
setenv GS_LIB /opt/sfw/share/ghostscript
setenv LD_LIBRARY_PATH /usr/openwin/lib:/usr/dt/lib:/usr/lib:/usr/ucblib:/opt/sfw/lib:/usr/local/lib

set path = ($path /opt/sfw/bin)



#>>>> where is the 55 limit used???  matrix_logob? <<<<
if ($3 > 55 || $6 > 55) then
   echo "Content-type: text/html"
   echo ""

   echo "LAMA logos alignment error"
   echo "
        LAMA logos alignment error
        "
   echo "At present logos alignment is only shown for regions in the first 55 positions of the blocks. Sorry."
   exit 1
endif


# make logo of first block - creates files logo.1$$, symvec.1$$, etc.
# Compute character width in matrix_logob so it is the same for both
# Really need the exact block widths here ...
if ($3 > $6) then
   @ maxwidth = ($3 + $7)
else
   @ maxwidth = ($6 + $7)
endif
if ( $maxwidth < 55) then
   @ maxwidth = 55
endif
#echo $maxwidth

set DB = $1
set BLKNAME = $2
$BIN/blimps-bin/matrix_logob $DB $BLKNAME 1$DNAME $maxwidth > /dev/null

# make logo of second block

set DB = $4
set BLKNAME = $5
$BIN/blimps-bin/matrix_logob $DB $BLKNAME 2$DNAME $maxwidth > /dev/null

# pass logo files to align_two_logos so that their offset will be positive 

if ($3 > $6) then
   @ offset =  ($3 - $6)
   $ALIGNLOGOS logo.1$DNAME logo.2$DNAME $offset > $TMP/$$.ps
else
   @ offset = ($6 - $3)
   $ALIGNLOGOS logo.2$DNAME logo.1$DNAME $offset > $TMP/$$.ps
endif

rm logo.[1-2]$DNAME symvec.[1-2]$DNAME makelogop.[1-2]$DNAME colors.[1-2]$DNAME

if ( ! (-e $TMP/$$.ps) ) then
   echo "Content-type: text/html"
   echo ""
   echo "LAMA logos alignment error"
   echo "
        LAMA logos alignment error
        "
else
   convert $TMP/$$.ps $TMP/$$.gif
   if ( -e $TMP/$$.gif ) then
      echo "Content-type: image/gif"
      echo ""
      cat $TMP/$$.gif
#     rm $TMP/$$.gif
   else
      echo "Content-type: application/postscript"
      echo ""
      cat $TMP/$$.ps
   endif
#  rm $TMP/$$.ps
endif

exit 0



blimps-3.9/www/bin/LAMA_search.sh000075500001460000012000000110130775575505000171530ustar00jorjastaff00000400000027#!/bin/sh 

#	debug options are -vx
# If a two arguments are passed to the shell it should be a blocks database
# and a valid block name in the database
# It will be placed in the DB_query_block text box. 
# If only one argument is passed to the shell it should be a name of a file
# with correctly formatted block(s). The content of the file will be read into
# the User_query_block text area.
# 3/97 Pass name of blocks database (don't assume blocks.dat)

#	limit core dump size
ulimit -c 0
#	limit execution time to 1 hour = 3600 secs
#ulimit -t 3600

blocks=blocks

#	Get the query
query=""
#	$1 is always a file name, make sure it exists
if [ $# -gt 0 -a -f "$1" -a -r "$1" ]
then
   if [ $# -gt 1 ]
   then
     # There is a block number given
     query=`./blimps-bin/retblock $1 $2 -n`
   else
     # there is no block number given
       query=`cat $1`
    fi
fi

#####
##
##  Common HTML text
##
#####

cat << EOM
Content-type: text/html

LAMA Search

        

Block vs Block Searcher using LAMA
        

        (Local Alignment of Multiple Alignments) 
?
        

        at the 
Fred Hutchinson Cancer Research Center Blocks WWW server.

        
Search a block against a
database of blocks
or compare pairs of blocks.




        
A typical LAMA search against the Blocks or Prints Database will
take 15-20 minutes or more, depending on the number of query blocks.
If you choose not to receive the results via email,
please be patient.

        
Enter your email address if you want the results through email:
        

        


        
After filling in the rest of the form below you can 
. 
 form.

        

EOM

#####
##
##  User specified target data section
##
#####

if [ "$0" = "`pwd`/LAMA_search_userdb.sh" ]
then
#####
##  User target data HTML text
#####

  # This is the script that the user uses to input their own target data

  cat << EOM
Additional options
        
Output Level


        
Score Cutoff Level
(0 = default) 

        

Enter block(s) target data (use the 
BLOCK format; 
reformat multiple sequence alignments 
here)
        
or search the available databases of blocks:

        



        

EOM

else
#####
##  Database as target data HTML text
#####
  # This is the script that the user uses to use the given databases

cat << EOM

Select the database to search:
        
Blocks Database
  or
Prints Database

or Supply your own target data 
O.

        

EOM

fi




#####
##
##  Common HTML text
##
#####

cat << EOM

Enter block(s) query (use the  
BLOCK format; 
reformat multiple sequence alignments 
here):

        



        




        
A search may take 15-20 minutes: Please be patient.

        



        


LAMA Searcher Help

        
[Blocks Home] 
[Block Searcher]
[Block Maker]
[Get Blocks]

        
[Multiple Alignment Processor]
[Biassed Block Checker]


        
Page last modified Jan 1999

        
Shmuel Pietrokovski

        

EOM
blimps-3.9/www/bin/LAMA_search_userdb.sh000075500001460000012000000112770775575547300205440ustar00jorjastaff00000400000027#!/bin/sh

blocks=blocks

# If a first argument passed to the shell it should be a valid block name in
# the Blocks Database (BL#####[@], 3 is a digit and @ a letter). It will be
# placed in the DB_query_block text box. 
# If a second argument is passed to the shell it should be a name of a file
# with correctly formatted block(s). The content of the file will be read into
# the User_query_block text area.
# The shell should either receive no arguments, one argument only 
# (for example in links from get_block pages), or two arguments where the
# first one is empty (for example in links from make_block output page).

# check to see if a second argument has been passed and if its a file that
# could be read

if [ "$1" = "" ]
then
  # there is no block number given
  if [ $# > 1 -a -f "$2" -a -r "$2" ]
  then
    query=`cat $2`
  else
    query=""
  fi

else
  # There is a block number given
  query=`./extblock_stdout ./blocks.dat $1`
fi



#####
##
##  Common HTML text
##
#####

cat << EOM
Content-type: text/html

LAMA Search

        

Block vs Block Searcher using LAMA
        

        (Local Alignment of Multiple Alignments) 
?
        

        at the 
Fred Hutchinson Cancer Research Center Blocks WWW server.

        
Search a block against a
database of blocks
or compare pairs of blocks.
        

        


        

Enter your email address if you want the results through email:
        

        


        
After filling in the rest of the form below you can 
. 
 form.

        
Depending on the server usage, the delay for the answer may vary from
one request to another one.
        
Please be patient.
        

        

EOM




#####
##
##  User specified target data section
##
#####

if [ "$0" = "`pwd`/LAMA_search_userdb.sh" ]
then
#####
##  User target data HTML text
#####

  # This is the script that the user uses to input their own target data

  cat << EOM
Additional options
        
Output Level


        
Score Cutoff Level
(0 = default) 

        

Enter block(s) target data (use the 
BLOCK format; 
reformat multiple sequence alignments 
here)
        
or search the available databases of blocks:

        



        

EOM

else
#####
##  Database as target data HTML text
#####
  # This is the script that the user uses to use the given databases

cat << EOM

Select the database to search:
        
Blocks Database
  or
Prints Database

or Supply your own target data 
O.

        

EOM

fi




#####
##
##  Common HTML text
##
#####

cat << EOM

Enter block(s) query (use the  
BLOCK format; 
reformat multiple sequence alignments 
here):

        



        




        
Depending on the server usage, the delay for the answer may vary from
one request to another one.
        
Please be patient.
        

        

        


        


LAMA Searcher Help

        

[Blocks home] 
[Block Searcher]
[Block Maker]
[Get Blocks]
[format a block]
[check for biassed blocks]
[LAMA Searcher]


        
Page last modified August 1996

        
Shmuel Pietrokovski <pietro@sparky.fhcrc.org>

        

EOM
blimps-3.9/www/bin/addseqs.csh000075500001460000012000000006610775204477300167120ustar00jorjastaff00000400000027#!/bin/csh
#	Search given sequence vs given blocks
#	$1=blocks file, $2=sequence file, $3=output file
set bindir = ./
set tmp = ../tmp/$$

unalias mv
unalias cp
unalias rm

#	Add sequences
$bindir/blimps-bin/addseqs $1 $2 $tmp.add >& $3
#	Re-weight sequences
$bindir/blimps-bin/blweight $tmp.add $tmp.blw P M >& /dev/null
#	Re-calibrate
$bindir/calibrate.csh $tmp.blw $1.add >& /dev/null


rm $tmp.add $tmp.blw >& /dev/null

exit(0)
blimps-3.9/www/bin/addseqs.pl000075500001460000012000000056270774503561400165530ustar00jorjastaff00000400000027#!/usr/bin/perl

# Execute addseqs.csh & process the output
#	Try to add new sequences to existing blocks

#	Set file permissions to rw-rw----
system("umask 006");

$program = "./addseqs.csh";
$tmp = "../tmp";

select(STDOUT); $| = 1;

print "Content-type: text/html\n\n";
print "Do-It-Yourself Block Search Results\n";
print "
        Do-It-Yourself Block Search Results
        ";
print "
        ";


if ( $ENV{"REQUEST_METHOD"} ne "POST" ) {
   print "This script should be referenced with a METHOD of POST\n";
   exit;
}

read (STDIN, $QUERY_STRING, $ENV{"CONTENT_LENGTH"});
%names = &parse_query($QUERY_STRING);


#	Get the blocks & write it to a file
if ($names{blocks} eq "") {
   print "
        Error
         Please enter some blocks.
        \n";
   exit;
}
$blk = "$tmp/$$.blk";
open(BLK, ">$blk");
print BLK $names{blocks};
close(BLK);

#	Get the sequence & write it to a file
if ($names{sequence} eq "") {
   print "
        Error
         Please enter some protein sequences.
        \n";
   exit;
}
$seq = "$tmp/$$.seq";
open(SEQ, ">$seq");
print SEQ $names{sequence};
close(SEQ);

#=========================================================================
#	Run shell now

$addseqs = "$tmp/$$.addseqs";
open(ERR, "$program $blk $seq $addseqs 2>&1 |");
wait;
while ($_ = ) { print; }
close(ERR);

select(STDOUT); $| = 1;

print "
        [Addseqs Output]
        \n";
print "[DIY Search] ";
print "[About DIY]
        \n";
print "[Add Sequences] ";
print "[About Add Sequences]
        \n";
print "
        \n";


open(ADD, "<$blk.add");
while ($_ = ) { print; }
close(ADD);


#-------------------------------------------------------------------------
exit (0);

#-------------------------------------------------------------------------
#
# parameter: a string that is the html QUERY_STRING environment variable
# returns: an associative array of name/value pairs.  The name is the key.
sub parse_query {
  local($query_string) = @_;
  local(%ans, @q, $pair);
#print $query_string;
  # break up into individual name/value lines
  @q = split(/&/, $query_string);

  foreach $pair (@q) {
    # break the name/value pairs up
    # use split rather than regular expressions because the value may have
    #  newlines in it
    split(/=/, $pair, 2);

    # change '+' to ' '
    $_[1] =~ s/\+/ /g;

    # change the escaped characters (has to be after the split on '&' and '=')
    $_[1] =~ s/%(..)/pack("c",&hextodec("$1"))/eg;

    $ans{$_[0]} = $_[1];
  }

  return %ans;
}

# parameter: a hex representation of a number (doesn't need to be a string)
# returns: the decimal representation of the number
sub hextodec {
  unpack("N", pack("H8", substr("0" x 8 . shift, -8)));
}



blimps-3.9/www/bin/addseqs.sh000075500001460000012000000032650775205276000165450ustar00jorjastaff00000400000027#!/bin/sh
#               addseqs.sh 
#
blocks=""
if [ $# -gt 0 -a -f "$1" ]
then
      blocks=`cat $1`
fi
#  From the  to  is ~blocks/www/addseqs.html
#       with the blocks TEXTAREA modified to insert $blocks

cat << EOM
Content-type: text/html



Add Sequences to Blocks

        Add Sequences to Blocks
        


        


        

Add sequences to blocks
aligns a set of Blocks with one or more protein sequences, saving
the best score only for each alignment. It adds each protein
sequence to the blocks if the best alignments are in the correct
order and non-overlapping, re-weights and re-calibrates each block.

        
You can make blocks from unaligned protein sequences with
Block Maker.
        
If you need to convert another multiple alignment to
BLOCKS format, use the
Multiple Alignment Processor or the
Block Formatter.
        

        

Enter your Blocks in 
BLOCKS format:
        


        
Enter your protein sequences in 
FASTA format:
        



        



        


        
Blocks home

        
Contact us
        
Page last modified on August 2003



EOM

exit
blimps-3.9/www/bin/align_two_logos.csh000075500001460000012000000055320774335020200204410ustar00jorjastaff00000400000027#!/bin/csh 

# join two logo files to show one beneath the other

# Checking input argument

# How many arguments passed to the shell ?
  set arguments = `echo $* | wc -w`

  if ($arguments != 3) then
     echo "$0 fname_logo1.ps  fname_logo2.ps offset"
     echo "This shell needs the file names of two logo files and the offset of their alignment"
     echo "The second logo will be moved forward, so that the offset must be positive."
     echo "You may have to switch the order of the logo files to achieve this."
     exit
  endif

# Are the first two arguments files with data 
  if (!(-e $1) || -z $1) then
     echo "First argument ($1) is not an existing file with data !"
     exit
  endif

  if (!(-e $2) || -z $2) then
     echo "Second argument ($2) is not an existing file with data !"
     exit
  endif


# checking if the third argument is a (reasonable) positive integer.
  if (`echo $3 | sed 's/^[0-9][0-9]*$/+int/'` != "+int") then
     echo "Third argument (logos offset) doesn't look like a positive integer !"
     echo "The second logo will be moved forward, realtive to the first, so that the offset must be positive."
     echo "You may have to switch the order of the logo files to achieve this."
     exit
  endif
  if ($3 > 1000) then
     echo "Logos offset ($3) seems too big."
     exit
  endif


# find the line number of the end of the logo-caption lines in the first file
  @ endcaption1 = (6 + `grep -n create $1 | grep -v "{" | awk '-F:' '{print $1}'`)
# copy first file up to end of logo caption
  head -$endcaption1 $1 

# increment by one the line number so that the rest of the file would be copied later
  @ endcaption1 = ($endcaption1 + 1)


# write a 'translate' command to precede the second logo caption
  echo '     0 -1 linemove barheight mul mul translate' 


# find the line number of the end of the logo-caption lines in the second file
  @ endcaption2 = (6 + `grep -n create $2 | grep -v "{" | awk '-F:' '{print $1}'`)
# copy second caption
  head -$endcaption2 $2 | tail -4 


# find the line number of the end of the logo lines in the first file
  set endlogo = `grep -n endline $1 | grep -v "{" | awk '-F:' '{print $1}'`

# write first logo file from the end of the caption up to the end of the logo
  head -$endlogo $1 | tail +$endcaption1 


# find the line numbers of the start and end of the logo lines in the second file
  set startlogo = `grep -n startline $2 | grep -v "{" | awk '-F:' '{print $1}'`
  @ startlogo = ($startlogo + 1)
  set endlogo = `grep -n endline $2 | grep -v "{" | awk '-F:' '{print $1}'`


# write "startline" command
  echo "startline % line number 2"


# create logos offset by adding "shift" commands to file
  set index = $3 
  while ($index > 0)
     @ index = ($index - 1)
     echo "shift" 
  end


# write second logo lines
 head -$endlogo $2 | tail +$startlogo 


# write "endpage" command 
  echo "endpage" 

 exit
blimps-3.9/www/bin/blalign.pl000075500001460000012000000044370775573242500165420ustar00jorjastaff00000400000027#!/usr/bin/perl

# Execute blalign.csh & process the output

#	Set file permissions to rw-rw----
system("umask 006");

$program = "./blalign.csh";
$tmp = "../tmp";
$bin = "./blimps-bin";

select(STDOUT); $| = 1;

print "Content-type: text/html\n\n";
print "Re-format Blocks as Alignment\n";
print "
        Re-format Blocks as Alignment
        ";
print "
        ";


if ( $ENV{"REQUEST_METHOD"} ne "POST" ) {
   print "This script should be referenced with a METHOD of POST\n";
   exit;
}

read (STDIN, $QUERY_STRING, $ENV{"CONTENT_LENGTH"});
%names = &parse_query($QUERY_STRING);


#	Get the blocks & write them to a file
if ($names{blocks} eq "") {
   print "
        Error
         Please enter some blocks.
        \n";
   exit;
}
$blk = "$tmp/$$.blk";
open(BLK, ">$blk");
print BLK $names{blocks};
close(BLK);

#	Get the output format type
if ($names{style} eq "") {
   print "
        Error
         Please select an output format.
        \n";
   exit;
}
#print "style=$names{style}\n";

#=========================================================================
#	Run blalign now

system("$bin/blalign $blk $names{style} > $tmp/$$.out");

select(STDOUT); $| = 1;

open(OUT, "< $tmp/$$.out");
while ($_ = ) { print; }
close(OUT);


#-------------------------------------------------------------------------
exit (0);

#-------------------------------------------------------------------------
#
# parameter: a string that is the html QUERY_STRING environment variable
# returns: an associative array of name/value pairs.  The name is the key.
sub parse_query {
  local($query_string) = @_;
  local(%ans, @q, $pair);
#print $query_string;
  # break up into individual name/value lines
  @q = split(/&/, $query_string);

  foreach $pair (@q) {
    # break the name/value pairs up
    # use split rather than regular expressions because the value may have
    #  newlines in it
    split(/=/, $pair, 2);

    # change '+' to ' '
    $_[1] =~ s/\+/ /g;

    # change the escaped characters (has to be after the split on '&' and '=')
    $_[1] =~ s/%(..)/pack("c",&hextodec("$1"))/eg;

    $ans{$_[0]} = $_[1];
  }

  return %ans;
}

# parameter: a hex representation of a number (doesn't need to be a string)
# returns: the decimal representation of the number
sub hextodec {
  unpack("N", pack("H8", substr("0" x 8 . shift, -8)));
}



blimps-3.9/www/bin/blalign.sh000075500001460000012000000024261014216721000165070ustar00jorjastaff00000400000027#!/bin/sh
#               blalign.sh 
#
blocks=""
if [ $# -gt 0 -a -f "$1" ]
then
      blocks=`cat $1`
fi
#  From the  to  is ~blocks/www/blalign.html
#       with the blocks TEXTAREA modified to insert $blocks

cat << EOM
Content-type: text/html


Re-format Blocks as an Alignment

        Re-format Blocks as an Alignment
        




        

You can make blocks from unaligned protein sequences with
Block Maker.
        

        

Enter your Blocks in 
BLOCKS format:
        





        
Select an output alignment format





        



        


        
Blocks home

        
Contact us
        
Page last modified on August 2003


EOM
exit

Re-format Blocks as an Alignment

        Re-format Blocks as an Alignment
        




        

You can make blocks from unablimps-3.9/www/bin/bm_format.pl000075500001460000012000000367351003106120100170460ustar00jorjastaff00000400000027#!/usr/bin/perl
#
#	bm_format.pl 
#	Formats Block Maker output in 
#-----------------------------------------------------------------------
#  5/16/03 Separated from makeblocks.pl
#  8/25/03 Added blalign.sh links
#  8/27/03 Added diy.sh links
#  3/26/04 Run LAMA & SIFT in a blank window
#-----------------------------------------------------------------------
$tmp = "../tmp/bm";

if (@ARGV >= 0) {  $id = $ARGV[0]; }
else { exit(-1); }

$prefix = "$tmp/$id/$id";

#=========================================================================
# htmlize the output, which is mostly written to separate files

print "Content-type: text/html\n\n";
print "Block Maker results\n";

#print "prefix=$prefix\n";

if (-s "$prefix.err")
{
   print "
        ";
   open(ERR, "<$prefix.err");
   while ($err = ) { print "$err"; $nerr++; }
   close(ERR);
   exit(-1);
}

if (-s "$prefix.warn")
{   print "Check for Warnings before re-submitting"; }

print "
        Block Maker Results
        \n
        \n\n";

#=========================================================================
print "
        BLOCKS from MOTIF
        \n";

#	Print the blalign output 
open(ALN, "<$prefix.maln");
while ($alnrec = )
{ print $alnrec; }
close(ALN);

if (-s "$prefix.mblks") 
{
# print "
        ";
  print "
        ";

  print "";
  print "";
  print "";
  print "";
  print "";
  print "";
  print "\n";

  print "";
  print "";
  print "";
  print "";
  print "\n";
#
  # The blockmap name must match what's in the mapfile
  open(GREP, "grep \"^>\" $prefix.mblks.mapfile |");
  $map_rec = ;
  ($mapname) = $map_rec =~ m/^>(\S+)/;
  print "";
  print "";
  print "";
  print "";
  print "\n";

#
  print "";
  print "";
  print "";
# print "";
  print "";
  print "";
  print "";
  print "";
  print "\n";

#
  print "";
  print "";
   print "";
   print "\n";

#
  print "";
  print "";
  print "";
  $group = "MotifBlocks";
  print "";
  print "";
  print "\n";

#
  print "";
  print "";
#
  print "";
  print "\n";

  print "\n";
  print "\n";
#
  print "";
  print "";
#
  print "";
  print "";
  print "\n";
#

  print "
        Formatted BLOCKS[BLOCKS format][MAST Searchable format][COBBLER Sequence][About COBBLER][Re-format]
        Logos[Postscript][PDF][GIF]
        Maps





)
  { print $maprec; }
  close(MAP);
  print "\">\n";
  print "[Text Map][Map Positions]
        Tree";
  print "
        


)
  {
#    $trerec =~ s/(\W)/sprintf("%%%02X", ord($1))/eg;
     print $trerec;
  }
  close(TRE);
  print "\">)
  { print $blkrec; }
  close(BLK);
  print "\">";
  print ")
  { print $seqrec; }
  close(SEQ);
  print "\">
        \n";
  print "        		[Data][XBitmap][Postscript][PDF][GIF][Newick]
        Structures

        


)
   { print $blkrec; }
   close(BLK);
   print "\">)
   { print $seqrec; }
   close(SEQ);
   print "\">
        		(takes several minutes)
        Search using BLOCKS as query[LAMA][About LAMA][MAST][About MAST]
        Search using COBBLER sequence as query[)
  { 
     #   don't print the title line
     if (!($seqrec =~ m/^>/))  { print $seqrec; }
  }
  close(SEQ);
  print "\">BLAST][)
  {
     #   don't print the title line
     if (!($seqrec =~ m/^>/))  { print $seqrec; }
  }
  close(SEQ);
  print "\">PSI-BLAST]
        Search these Blocks[DIY Search]
        Primers[CODEHOP]
        Substitutions in Blocks[SIFT]
        ";
}  # end of mblks

print "
        \n";

#===========================================================================
print "
        ";
print "
        BLOCKS from GIBBS
        \n" ;

#	Print the blalign output 
open(ALN, "<$prefix.galn");
while ($alnrec = )
{ print $alnrec; }
close(ALN);

if (-s "$prefix.gblks") 
{
# print "
        ";
  print "
        ";

  print "";
  print "";
  print "";
  print "";
  print "";
  print "";
  print "\n";

  print "";
  print "";
  print "";
  print "";
  print "\n";
#
  # The blockmap name must match what's in the mapfile
  open(GREP, "grep \"^>\" $prefix.gblks.mapfile |");
  $map_rec = ;
  ($mapname) = $map_rec =~ m/^>(\S+)/;
  print "";
  print "";
  print "";
  print "";
  print "\n";

#
  print "";
  print "";
  print "";
# print "";
  print "";
  print "";
  print "";
  print "";
  print "\n";

#
  print "";
  print "";
   print "";
   print "\n";

#
  print "";
  print "";
  print "";
  $group = "MotifBlocks";
  print "";
  print "";
  print "\n";

#
  print "";
  print "";
#
  print "";
  print "\n";

  print "\n";
  print "\n";
#
#
  print "";
  print "";
#
  print "";
  print "";
  print "\n";
#

  print "
        Formatted BLOCKS[BLOCKS format][MAST Searchable format][COBBLER Sequence][About COBBLER][Re-format]
        Logos[Postscript][PDF][GIF]
        Maps

        




)
  { print $maprec; }
  close(MAP);
  print "\">
        \n";
  print "        		[Text Map][Map Positions]
        Tree";
  print "
        


)
  {
#    $trerec =~ s/(\W)/sprintf("%%%02X", ord($1))/eg;
     print $trerec;
  }
  close(TRE);
  print "\">)
  { print $blkrec; }
  close(BLK);
  print "\">";
  print ")
  { print $seqrec; }
  close(SEQ);
  print "\">
        \n";
  print "        		[Data][XBitmap][Postscript][PDF][GIF][Newick]
        Structures

        


)
   { print $blkrec; }
   close(BLK);
   print "\">)
   { print $seqrec; }
   close(SEQ);
   print "\">
        		(takes several minutes)
        Search using BLOCKS as query[LAMA][About LAMA][MAST][About MAST]
        Search using COBBLER sequence as query[)
  { 
     #   don't print the title line
     if (!($seqrec =~ m/^>/))  { print $seqrec; }
  }
  close(SEQ);
  print "\">BLAST][)
  {
     #   don't print the title line
     if (!($seqrec =~ m/^>/))  { print $seqrec; }
  }
  close(SEQ);
  print "\">PSI-BLAST]
        Search these Blocks[DIY Search]
        Primers[CODEHOP]
        Substitutions in Blocks[SIFT]
        ";

}  # end of gblks

print "
        \n";

#-------------------------------------------------------------------------
print "
        [BLOCKS home]\n";
exit(0);

;

#
  print "Search using blimps-3.9/www/bin/bm_htmlize-map.pl000075500001460000012000000043570775501363500200330ustar00jorjastaff00000400000027#!/usr/bin/perl
#
#	bm_htmlize-map.pl - /blocks-bin/ version
#		Can't use btest's version becuase wants "../tmp"
# Htmlize a block map drawing (from block_vis) and insert links to sequences
# (in the NCBI Entrez WWW database) and blocks (in file file.blocks).
# Script can work either as filter or just with arguments.
#
# Invocation: htmlize-map.pl file.vis file.maps
#             htmlize-map.pl file.maps < file.vis
#
# Written by Ross Morgan-Linial

# Get the block number
$blocknum = pop @ARGV;

# HTML header tags
print '', "\n";
print 'Block map', "\n"; 
print '', "\n";
print '
        ', "\n";

# Various constant bits of code, to make them easy to change.
# The second command-line argument gets incorporated into $blockurl.
$tagstart = '';
$blockurl = '/blocks-bin/showblock.sh?' . $blocknum . '+';
$sequenceurl = 'http://www3.ncbi.nlm.nih.gov:80/htbin-post/Entrez/query?uid=';
$options = '&form=6&db=p&Dopt=g';

# Loop over all the input lines
while (<>) {
    # Change '&', '<' and '>' for HTML 
    s/\&/\&/g;
    s/\/\>/g;

    # Match a line containing actual data.
    # This is highly sensitive to the block_vis output format.
    if (/^(\s*)([\w\d]+)(\s+\(?[ \d]+\)?\s*)([^ \n]*)(.*)/) {
        # Print the first part (sequence name & length)
#       print $1, $tagstart, $sequenceurl, $2, $options, $tagend, $2, '', $3;
        print "$1 $2 $3";

        # Save the map visualization in the magic variable $_
        $_ = $4;

        # Save the extra stuff
        $extra = $5;

        # Bracket the blocks with WWW links
        # We need to set $family, below, before doing this
#       s"(([A-Z])\2*)"$tagstart$blockurl$family$2$tagend$1"g;

        # Reintroduce the newline removed in the regexp above
        print $_, $extra, "\n";
    }
    else { 
        # The block family accession need to be found before the above is done.
        # The accesion is identified as 7 non-whitespace chars at the 
        # begining of a line followed by ": " string.
        if (/^(\S{7}): /) {
            $family = $1;
        }

        # Print the line unchanged
        print;
    }
}

# Close HTML tags
print '
        ', "\n";
print '', "\n";
print '', "\n";

exit(0);
blimps-3.9/www/bin/bm_map.csh000075500001460000012000000033410774510415300165060ustar00jorjastaff00000400000027#!/bin/csh
# map.csh  
# views one or more block maps - blockmkr version (see MAP_VIEW)
#  Requires programs block_vis & htmlize-map.pl in same directory
#  Assumes blocks corresponding to mapfile are in mapfile:r (but they aren't)
#
# Written by Ross Morgan-Linial


# content type for the WWW browser 
echo Content-type: text/html
echo ""

# No arguments
if ($#argv <= 0) then
    echo "Error: no arguments"
    exit 1
endif

# One argument
if ($#argv <= 1) then
    # get blocks file name - the map structure file name without its suffix
    set blocks_file = "$1:r"

    if (-f "$1") then           # file exists
        if (-z "$1") then       # file is empty, for cases like PRINTS where we 
                                # currently have no map files and create an
                                # empty file
            echo "Sorry, block map not available."
            exit 0 
        endif
        # Draw map (first argument is map structure) and 
        # pipe through HTMLIZE_MAP (argument is the name of blocks file)
	./block_vis $1 -c10 | ./bm_htmlize-map.pl $blocks_file 
    else
        echo "Error: input file not found."
    endif

    # done
    exit 0
endif

# Two or more arguments
set MAP_VIEW=/blocks-bin/map.csh

# HTML header tags
echo ''
echo 'Block maps'
echo ''

# Calculate the  parameters
@ width = 100 / $#argv
@ leftover = $width + 100 - $width * $#argv

# print the frameset commands
printf '\n'

# print the frames
foreach input ($argv[1-])
    echo \
end

# close the HTML tags
echo ''
echo ''
echo ''

# done
exit 0
blimps-3.9/www/bin/bm_mast.sh000075500001460000012000000031650775205315700165430ustar00jorjastaff00000400000027#!/bin/sh
#		mast.sh  
#	Set up the mast search, requires POST
#	NOTE: See the mast form at
#	http://meme.sdsc.edu/meme/website/mast.html
#	NOTE: Don't use blocks version because blk2pssm was already run
#		and catfile.sh location has to be blocks-bin

#
if [ $2 ]; then
  AC=$2
else
  AC="Blocks"
fi
if [ $1 ]; then

# ./blimps-bin/blk2pssm $1 $1.pssm M > /dev/null 2>&1
  echo "Content-type: text/html"
  echo
  echo "";
  echo "Blocks to Mast";
  echo "
        ";
  echo "MAST Search of Blocks Database Blocks
        ";
  echo "";
  echo "";
  echo "
        ";
  echo "MAST searches blocks against a sequence database at SDSC.
        ";
  echo "Results are returned via EMAIL.
        ";
  echo "See the MAST PSSM";
  echo "made from the blocks.
        ";

  echo "
        ";
  echo "Enter your complete EMAIL address for MAST search results:\n";
  echo " ";
# echo "";
#		No spaces, slashes, etc allowed in "inline_name" ...
  echo "";
  echo "";
  echo "
        \n";

#	mast.in is edited from the mast.html form, remove the above fields
  cat ./mast.in
fi

#\rm $1.pssm > /dev/null 2>&1
#
exit
blimps-3.9/www/bin/calibrate.csh000075500001460000012000000007471001174535300172010ustar00jorjastaff00000400000027#!/bin/csh
#		calibrate.csh blks-in blks-out
#
set NSEQ = 80000
set NRES = 29085965
set frq = ../docs/default.amino.frq
set bin = ./

unalias rm
unalias mv

#       Make matrices and observed frequency files
$bin/blimps-bin/blk2pssm $1 $1.mats B 3 >& /dev/null
$bin/blimps-bin/blk2pssm $1 $1.obsf B 21 >& /dev/null
#               writes $1.dat
$bin/blimps-bin/pssmdist $1.mats $1.obsf $frq $NSEQ $NRES $1 >& /dev/null
$bin/blimps-bin/pssmBL $1.dat $1 $2 >& /dev/null
rm $1.dat

exit(0)
blimps-3.9/www/bin/catfile.sh000075500001460000012000000001720774335017400165220ustar00jorjastaff00000400000027#!/bin/sh
#		catfile 

echo Content-type: text/html
echo

echo "
        "
if [ $1 ]; then
	cat $1
fi
echo "
        "
blimps-3.9/www/bin/cathtml.sh000075500001460000012000000002070774335017400165460ustar00jorjastaff00000400000027#!/bin/sh
#		cathtml 

#echo Content-type: text/html
#echo

echo "
        "
if [ $1 ]; then
	cat $1
fi
echo "
        "

exit
blimps-3.9/www/bin/catpdf.sh000075500001460000012000000001540774335017400163540ustar00jorjastaff00000400000027#!/bin/sh
#		catpdf.sh 

echo Content-type: application/pdf
echo

if [ $1 ]; then
	cat $1
fi
exit
blimps-3.9/www/bin/cobbler.csh000075500001460000012000000010020775204510100166460ustar00jorjastaff00000400000027#!/bin/csh
#	Embed blocks in a provided sequence
#	$1=blocks, $2=sequence, $3=cobbler
set bindir = ./
set tmp = ../tmp/$$
#	Make cobbler sequence = $tmp.cob
   echo "TY	2"	     > $tmp.cf
   echo "BL	$1"   >> $tmp.cf
   echo "SQ	$2"    >> $tmp.cf
   echo "OU	$3"    >> $tmp.cf
   echo "SU	$bindir/default.iij" >> $tmp.cf
   echo "FR	$bindir/default.amino.frq" >> $tmp.cf
   echo "QM	$bindir/default.qij" >> $tmp.cf
   echo "TR	10" >> $tmp.cf
   $bindir/blimps-bin/cobbler $tmp.cf >& /dev/null
   rm $tmp.cf
exit(0)
blimps-3.9/www/bin/cobbler.pl000075500001460000012000000103360774503611100165210ustar00jorjastaff00000400000027#!/usr/bin/perl

# Execute cobbler.csh & process the output

#	Set file permissions to rw-rw----
system("umask 006");

$program = "./cobbler.csh";
$tmp = "../tmp";

select(STDOUT); $| = 1;

print "Content-type: text/html\n\n";
print "Cobbler Results\n";
print "
        Cobbler Results
        ";
print "
        ";


if ( $ENV{"REQUEST_METHOD"} ne "POST" ) {
   print "This script should be referenced with a METHOD of POST\n";
   exit;
}

read (STDIN, $QUERY_STRING, $ENV{"CONTENT_LENGTH"});
%names = &parse_query($QUERY_STRING);


#	Get the blocks & write it to a file
if ($names{blocks} eq "") {
   print "
        Error
         Please enter some blocks.
        \n";
   exit;
}
$blk = "$tmp/$$.blk";
open(BLK, ">$blk");
print BLK $names{blocks};
close(BLK);

#	Get the sequence & write it to a file
if ($names{sequence} eq "") {
   print "
        Error
         Please enter a protein sequence.
        \n";
   exit;
}
$seq = "$tmp/$$.seq";
open(SEQ, ">$seq");
print SEQ $names{sequence};
close(SEQ);

#=========================================================================
#	Run shell now


$cob = "$tmp/$$.cob";
open(ERR, "$program $blk $seq $cob 2>&1 |");
wait;
while ($_ = ) { print; }
close(ERR);

select(STDOUT); $| = 1;

open(COB, "<$cob");
@input = ;

print "
        To do a Blast search, copy the cobbler sequence below ";
print "then click on a Blast link\n
        ";

#	Print sequence for blast search, skip title line
#print "[[Blast Search]\n";

#	Print sequence again for gap-blast search
#print "[[Gap-Blast Search]\n";

#	Print sequence again for psi-blast search
#print "[Psi-Blast Search]\n";

#	Print it to the screen, including title line
print "\n\n";
$i = 0;
while ($i < @input) {
  print @input[$i];
  ++$i;
}
close(COB);
print "
        ";

print "[Blast Search]\n";
print "[Gap-Blast Search]\n";
print "[Psi-Blast Search]\n";

#-------------------------------------------------------------------------
exit (0);

#-------------------------------------------------------------------------
#
# parameter: a string that is the html QUERY_STRING environment variable
# returns: an associative array of name/value pairs.  The name is the key.
sub parse_query {
  local($query_string) = @_;
  local(%ans, @q, $pair);
#print $query_string;
  # break up into individual name/value lines
  @q = split(/&/, $query_string);

  foreach $pair (@q) {
    # break the name/value pairs up
    # use split rather than regular expressions because the value may have
    #  newlines in it
    split(/=/, $pair, 2);

    # change '+' to ' '
    $_[1] =~ s/\+/ /g;

    # change the escaped characters (has to be after the split on '&' and '=')
    $_[1] =~ s/%(..)/pack("c",&hextodec("$1"))/eg;

    $ans{$_[0]} = $_[1];
  }

  return %ans;
}

# parameter: a hex representation of a number (doesn't need to be a string)
# returns: the decimal representation of the number
sub hextodec {
  unpack("N", pack("H8", substr("0" x 8 . shift, -8)));
}



blimps-3.9/www/bin/cobbler.sh000075500001460000012000000032560774527224300165330ustar00jorjastaff00000400000027#!/bin/sh
#		cobbler.sh 
#
blocks=""
if [ $# -gt 0 -a -f "$1" ]
then
      blocks=`cat $1`
fi
#  From the  to  is ~blocks/www/cobbler.html
#	with the blocks TEXTAREA modified to insert $blocks

cat << EOM
Content-type: text/html




Cobbler Sequence

        Cobbler Sequence
        




        

COBBLER 
aligns a set of Blocks with a protein sequence
and embeds a consensus representation of the Blocks in
the sequence, which can then be used to search sequence
databases using 
BLAST,
and other sequence searching programs.
Block Maker makes a
COBBLER sequence automatically, but this page can be used
if you want to embed your blocks in a different sequence.
If you need to convert another multiple alignment to
BLOCKS format, use the
Multiple Alignment Processor or the
Block Formatter.

        

Enter your Blocks in 
BLOCKS format:
        


        
Enter your protein sequence in 
FASTA format:
        



        



        


        
Blocks home

        
Contact us 
        
Page last modified on Dec 1999






EOM
blimps-3.9/www/bin/colors000064400001460000012000000034130774505301000157700ustar00jorjastaff00000400000027* Color scheme for logos of proteins (for the MakeLogo program).
* The colors are based on the divisions discussed on the usenet
* and given to me by Irit Orr. Modification according to division of Joel
* Sussman. The differences from Sussman's division are -
* Met in a group by itself (not with Pro), Ala with hydrophobic (not with Gly),
* Tyr with aromatics (not with Asn and Gln), His with Arg and Lys (not by
* itself), and charged aa separated to positive and negative.
* Shmuel Pietrokovski. June 94'
* 
* Red for acidic amino acids; Glu, Asp
D 1 0 0
d 1 0 0
E 1 0 0
e 1 0 0
*
*Blue for basic amino acids; Lys, Arg, His
K 0 0 1 
k 0 0 1 
R 0 0 1 
r 0 0 1 
H 0 0 1 
h 0 0 1 
*
*White for polar OH/SH amino acids; Ser, Thr, Cys
* White would not be seen onthe background so it is light grey
C 0.8 0.8 0.8
c 0.8 0.8 0.8
S 0.8 0.8 0.8
s 0.8 0.8 0.8
T 0.8 0.8 0.8
t 0.8 0.8 0.8
*
*Green for amide amino acids; Asn and Gln
N 0 0.8 0.4
n 0 0.8 0.4
Q 0 0.8 0.4
q 0 0.8 0.4
*
*Yellow (sulphur) for Metionine
M 1 0.9 0
m 1 0.9 0
*
*Black for hydrophobic amino acids; Ala, Val, Leu, Ile
*(Black is the opposite of white and so if white is for hydrophilic
*hydroxyl amino acids black is a natural for hydrophobic ones)
*A
*a
*V
*v
*L
*l
*I
*i
*
*Orange for aromatic amino acids; Tyr, Phe, Trp
*(since "orange" sounds a little like "aromatic" and
*oranges are aromatic (if that suits you better))
Y 1 0.6 0
y 1 0.6 0
F 1 0.6 0
f 1 0.6 0
W 1 0.6 0
w 1 0.6 0
*
*Purple for proline; Pro
*(since both have "prl" in them)
P 0.7 0 1
p 0.7 0 1
*
*Grey for glycine; Gly
*(since both start with "g" and grey is sort of blah-like glycine)
G 0.5 0.5 0.5
g 0.5 0.5 0.5
*
*All other letters light blue so they would stand out
B 0 1 1
b 0 1 1
J 0 1 1
j 0 1 1
O 0 1 1
o 0 1 1
U 0 1 1
u 0 1 1
X 0 1 1
x 0 1 1
Z 0 1 1
z 0 1 1
blimps-3.9/www/bin/codehop.csh000075500001460000012000000005740775202213500166760ustar00jorjastaff00000400000027#!/bin/csh
#      codehop.csh   
#
#  Make codehops from a set of blocks
#
unalias rm
unalias mv
#
#
#setenv BLIMPS_DIR /usr/local/blimps
#	Want $BLIMPS_DIR/docs/
setenv BLIMPS_DIR ../
#
if ( -e $1 ) then
   ./blimps-bin/codehop $1 $3 >& $$.tmp
   ./htmlize-codehop $$.tmp >& $2
   rm $$.tmp
#  
else
   echo "Cannot open blocks file $1."
endif
#
exit(0)
blimps-3.9/www/bin/codehop.pl000075500001460000012000000104530775200024200165240ustar00jorjastaff00000400000027#!/usr/bin/perl
#			codehop.pl

# Execute codehop & process the output

#	Set file permissions to rw-rw----
system("umask 006");

#	Location of codon usage tables
$codon_dir = '../docs/';

$program = './codehop.csh';
$htmlize = './htmlize-codehop';
$bdir = '../tmp/';
$blocks = $bdir.$$.'.blks';
$out = $bdir.$$.'.pride';
$err = $bdir.$$.'.err';

# output the beginning text to be used on all pages
print "Content-type: text/html\n\n";
print "CODEHOP Results\n";
#print "
        ";


if ( $ENV{"REQUEST_METHOD"} ne "POST" ) {
   print "This script should be referenced with a METHOD of POST\n";
   exit;
}

#	Get the parameter info
#	codonuse	-Ccodonuse
#	gcode		-Ggenetic_code
#	core_degen	-Dcore_degen
#	core_strict	-Score_strict
#	clamp_strict	-Lclamp_strict
#	clamp_temp	-Tclamp_temp
#	polyx		-Apolyx
#	clamp_conc	-Nclamp_conc
#	verbose		-V 
#	outoligo	-O
#	rose		-R
#	most		-M
#       begin	        -B
#
read (STDIN, $QUERY_STRING, $ENV{"CONTENT_LENGTH"});
#print $QUERY_STRING;

%names = &parse_query($QUERY_STRING);

#	Get the blocks & write them to a file for codehop
if ($names{blocks} eq "") {
   print "
        Error
         Please enter a block.
        \n";
   exit;
}
open(BLK, ">$blocks");
print BLK $names{blocks};
print BLK "\n";
close(BLK);

#	Make a string of the other parameters
$parameters = '';
$rose = ''; $most = ''; $verbose = ''; $outoligo = ''; $begin = '';
if ($names{gcode} ne "")
{  $parameters = $parameters.' -G'.$names{gcode}; }
if ($names{codonuse} ne "")
{  $parameters = $parameters.' -C'.$codon_dir.$names{codonuse};
   $codon = '-C'.$codon_dir.$names{codonuse};  }
else
{  $parameters = $parameters.' -C'.$codon_dir.'human.codon.use';
   $codon = '-C'.$codon_dir.'human.codon.use';  }
#
if ($names{core_degen} ne "")
{  $parameters = $parameters.' -D'.$names{core_degen}; }
if ($names{core_strict} ne "")
{  $parameters = $parameters.' -S'.$names{core_strict}; }
if ($names{clamp_strict} ne "")
{  $parameters = $parameters.' -L'.$names{clamp_strict}; }
if ($names{clamp_temp} ne "")
{  $parameters = $parameters.' -T'.$names{clamp_temp}; }
if ($names{polyx} ne "")
{  $parameters = $parameters.' -A'.$names{polyx}; }
if ($names{clamp_conc} ne "")
{  $parameters = $parameters.' -N'.$names{clamp_conc}; }
#		Checkboxes
if ($names{rose} eq "TRUE")
{  $parameters = $parameters.' -R';  $rose = '-R'; }
if ($names{most} eq "TRUE")
{  $parameters = $parameters.' -M'; $most = '-M';  }
if ($names{verbose} eq "TRUE")
{  $parameters = $parameters.' -V'; $verbose = '-V'; }
if ($names{outoligo} ne "")
{  $parameters = $parameters.' -O'.$names{outoligo}; }
if ($names{begin} eq "TRUE")
{  $parameters = $parameters.' -B'; $begin = '-B'; }


#print "$parameters\n";

#=========================================================================
#	Run codehop now
#  NOTE: Following are unreliable, perl executes sh -c, sometimes hangs
#open(OUT, "$program $blocks $parameters  2>&1 | $htmlize |");
#open(ERR, "$program $blocks $out '$parameters' 2>&1 |");
#wait;
#while ($_ = ) {
#   print;
#}
#close(ERR);

print "
        ";
system("$program $blocks $out '$parameters' > $err 2>&1");
open (ERR, "<$err");
while ($_ = ) { print; }
close(ERR);
print "
        ";

#	Make sure group can remove these files
system("chmod -f 660 ../tmp/$$.*");
#system("rm $err");
#
open (OUT, "<$out");
while ($_ = ) { print; }
close(OUT);


#print "
        ";
exit;

#-------------------------------------------------------------------------
#
# parameter: a string that is the html QUERY_STRING environment variable
# returns: an associative array of name/value pairs.  The name is the key.
sub parse_query {
  local($query_string) = @_;
  local(%ans, @q, $pair);
#print $query_string;
  # break up into individual name/value lines
  @q = split(/&/, $query_string);

  foreach $pair (@q) {
    # break the name/value pairs up
    # use split rather than regular expressions because the value may have
    #  newlines in it
    split(/=/, $pair, 2);

    # change '+' to ' '
    $_[1] =~ s/\+/ /g;

    # change the escaped characters (has to be after the split on '&' and '=')
    $_[1] =~ s/%(..)/pack("c",&hextodec("$1"))/eg;

    $ans{$_[0]} = $_[1];
  }

  return %ans;
}

# parameter: a hex representation of a number (doesn't need to be a string)
# returns: the decimal representation of the number
sub hextodec {
  unpack("N", pack("H8", substr("0" x 8 . shift, -8)));
}

blimps-3.9/www/bin/codehop.sh000075500001460000012000000350131002633632100165200ustar00jorjastaff00000400000027#!/bin/sh
#		codehop.sh 
#
blocks=""
if [ $# -gt 0 -a -f "$1" ]
then
      blocks=`cat $1`
fi
#  From the  to  is ~blocks/www/codehop.html
#	with the blocks TEXTAREA modified to insert $blocks

cat << EOM
Content-type: text/html





CODEHOP




        

        


        CODEHOP:
        COnsensus-DEgenerate Hybrid Oligonucleotide Primers
        		
CODEHOP mascot

        

        _______________________
        

        




        PCR primers designed from protein multiple sequence alignments
        

          
  
        • Getting started
          • 
  
        • Full Help file
          • 
  
        • The CODEHOP algorithm
  
        • The CODEHOP manuscript
  
        • 
Genes identified using CODEHOP

          
  
        • The input should be a set of local multiple alignments (blocks) of a 
group of related protein sequences. The alignments must be in 
  Blocks Database format, such as in Block Maker
          •  output.
  
        •  Ungapped parts of Clustal- or FASTA-formatted global multiple 
alignments can be automatically turned into blocks by the Blocks 
multiple alignment processor. You can also manually reformat 
multiple sequence alignments with the 
 Blocks formatter.
          •  
  
        •  The output of all these programs contains links that send the 
  resulting blocks to this page. 
  
        •  If your sequences align globally, you will get better multiple 
alignment results from Clustal
than from the motif finders used by Block Maker.
  
        • Blocks are processed using sequence weights (the numbers
following each sequence segment). To emphasize particular sequences
in the block(s) manually adjust the sequence weights. Increase the
number to give a sequence more weight.


        


        

        Paste your block(s) below:



        

        

        

        


        


        Core (degenerate 3' region)
- degeneracy
[default=128]:


        


        
- strictness
[default=0.0]:


        


        Clamp
(non-degenerate 5' region)
- temperature
[default=60.0]:


        


        
- poly-nuc
[default=5]:


        


        Primer concentration [in nM,
default=50nM]:

([K+]=50mM)
        


        


        
Genetic code



        
Codon usage table
(scroll for more choices):

        


        By default, up to 3 of the least degenerate primers in an 
overlapping set
are shown.
        

        

        
Show the

least degenerate, or show all overlapping primers.


        

        

By default, the 3' base of the primer must be an invariant position,
regardless of the core strictness setting.

        Use core strictness for the 3' base.



        

        
Force the 
core/clamp boundary to be a codon boundary.



        Use the most common codons in the 
clamp. 

        

        

        


        


        



[Blocks home]
[CODEHOP help]
[Getting started]
[CODEHOP program]


        
Contact us 
        
Page last modified Feb 2001
        








EOM
r

      \n") {	# All sources have been searched, we
					# can now sort and print the entire
					# hit list array.
		print @hit_list[ sort byscores $[..$#hit_list ];
		print "$line";
	} elsif ($line eq "\n") {
		# End of one "hit" listing, save in the hit array.
		$output_hit .= $line;
		push ( @hit_list, $output_hit );
		push ( @scores, $score );
		$output_hit = "";
	} else {	# more stuff for the same hit
		$output_hit .= $line;
	}
}

sub do_wais {

    $src = $default_src;
    # if 'PATH_INFO' has a non-null value, then use it as the name of the
    # WAIS source to search, otherwise will default to $default_src.
    $path_extension = $ENV{'PATH_INFO'};
    if ($path_extension =~ /^\/(.+)$/) { $src = $1; }
    $kidofwaisREF = $ENV{'SCRIPT_NAME'} . "/$src";
    @Sources = ( $src );	# Initialize array of sources to search
    if ( $use_Source_table ) {	# Read in the Source table info into
				# associative array.
	open (INDEX_TITLES, $Source_table) || last;
	while () {
		chop;
		next if /^\s*#/;	# skip comments
		next if /^\s*$/;	# skip blank lines
		($src_name, $remainder) = split(/~/, $_, 2);
		$src_array{$src_name} = $remainder;
	}
	close (INDEX_TITLES);
	($src_title, $src_multiple, $src_prefix, $file_title_table, $sources,
	   $go_to_url, $go_to_title) = split(/~/, $src_array{$src});
	if ($src_title ne "") {
		$openingTitle = "Search of $src_title";
		$closingTitle = "Search results from $src_title";
	}
	$src_multiple && (@Sources = split(/,/, $sources)); # Store the sources
    }							    # to be searched.

    do { &send_index; return; } unless defined @ARGV; # No search terms yet.

    local(@query) = @ARGV;
    local($pquery) = join(" ", @query);
    # NCSA's HTTPD puts backslashes in front of "funny" or "dangerous"
    # characters in the input supplied thru argv. In the case of search terms
    # for WAIS, this can screw up the search (parens and "*" get backslashed
    # and then don't work correctly). So remove the backslashes, AND the
    # potentially "dangerous" characters ( ; ` ! ).
    $pquery =~ tr/!\;\`\\//d;		# just in case, get rid of ;`! and \
    @query = split(' ',$pquery);	# and recreate query word array
    $query_plus = join("+", @query);

    print "Content-type: text/html\n\n"; # Start the "html" doc to be returned

    print "\n$closingTitle\n";
    print "\n
      ", $closingTitle, "
      \n";
    print "\n
      \n";

#@@@@@
    print "[Getblock]   ";
    print "[Return to BLOCKS Home Page]
      ";

    print "Note that you can enter a new query in the search term box \n";
    print "from this screen/page without having to go back.\n";
    if ($use_Source_table && $go_to_url) {
	print "Another option is to \n";
	print "go to the $go_to_title.\n";
    }

    local($hits, $score, $headline, $lines, $bytes, $type, @types, $date);
    $DEBUG && do { open (LOG, ">>$debugLOG") || die "can't open log";};

    foreach $src (@Sources) {	# Search each indicated index for the terms
      ($src_prefix, $file_title_table) = (split(/~/, $src_array{$src}))[2,3];
      open(WAISQ, "-|") || exec ($waisq, "-c", $waisd, "-s", $waisd, "-m",
		$max_hits, "-f", "-", "-S", "$src.src", "-g", @query);
      while () {
	$DEBUG && print LOG $_;
        /:score\s+(\d+)/ && ($score = $1);
        /:number-of-lines\s+(\d+)/ && ($lines = $1);
        /:number-of-bytes\s+(\d+)/ && ($bytes = $1);
        /:type "(.*)"/ && (push (@types, $1));
        /:headline "(.*)"/ && ($headline = $1);#%%%%
        /:date "(\d+)"/ && ($date = $1, $hits++, &docdone);
      }
      close(WAISQ);
      $total_hits += $hits;
      $hits = 0;
    }
    #&print_it ("\n");	# signal to print out hit array if we've been
				# building it (for multiple sources).
    if ($total_hits == 0) {
        print "
      \n";
	print "No items found that match your search query. You can enter \n";
	print "another query in the search term box if you want \n";
	print "to try searching for something else. If you would like to \n";
	print "see a description of the search options again, you can \n";
	print "go back to the main search page \n";
	print "for this index.\n";
	print "
      \n";
    } elsif ($total_hits >= $max_hits) {
	print "
      The following are the first $total_hits items that match \n";
	print "your query \`$pquery\'. Note that there may be more \n";
	print "items that match that are not shown (the search is limited \n";
	print "to $max_hits matches). You might want to further qualify \n";
	print "your search (use AND and NOT) to limit the matches. \n";
	print "
        \n";
	&print_it ("
      \n");
    } else {
	print "
      The following $total_hits item(s) match your query \n";
	print "\`$pquery\':\n";
	print "
        \n";
	&print_it ("
      \n");
    }

    print "\n";	# End the "html" doc being returned
}

sub docdone {	# Called for each "hit" returned by waisq
    local($endfile,$path_to_file,$file_proper,$file_ext,$multi_type,$alt_count);
    if ($headline =~ /Search produced no result/) {
	if ($src_multiple) {  # don't print source listing if
	   $hits--;           # multi-index search
	}
	else {
           print "
      \n";
	   print "No items found that match your search query. You can enter \n";
	   print "another query in the search term box if you want \n";
	   print "to try searching for something else. If you would like to \n";
	   print "see a description of the search options again, you can \n";
	   print "go back to the main search page \n";
	   print "for this index.\n";

	   # Hack to exit after the above is printed (since we are using only
           # one DB this should be OK) -- BJA
           exit(0);  # added by BJA
	}
    } elsif (($headline =~ /^Information on database:/) ||
			($headline =~ /^Catalog for database:/)) {
	$hits--;
    } else {	# this is a "real" hit
	($endfile, $path_to_file) = split(' ', $headline);
        if ($path_to_file ne "") { # Not indexed with -t url, so headline of
				   # form:  "filename /path/to/file/"
		# Multitype indexed files will probably have this form, as at
		# least I can't get "-t url" to coexist with "-M type,type"
		$the_full_File = $theFile = $path_to_file.$endfile;
#		$theFile =~ s/^.*$wwwDocpath//i; # changed by BJA
		$theFile = $endfile;
#		$url_to_use = $serverURL.$theFile;  # changed by BJA
		$url_to_use = $serverURL.$cgibin.'/getblock.pl?'.$endfile;
	} else { # should have been indexed as "-t url", so headline of form
		 # http://your_server_url/path/to/actual/file
	
		# get the string to munge
		$theFile = $url_to_use = $headline;

		# parse out the file name (remove the server URL from the front)
		$theFile =~ s/^.*$serverURL//i;
	
		# concatenate the "wwwDocpath" variable with the file name
		$the_full_File = $wwwDocpath.$theFile;
	}

	$last_period = rindex($theFile, ".");	# need filename without .ext if
	if ($last_period > 0) {			# it turns out to be multitype
		$file_proper = substr($theFile, 0, $last_period);
		$file_ext = substr($theFile, $last_period + 1);
	}
	$doc_title = $theFile;
	$type  = &type_file ($theFile); # also modifies $url_to_use if flag
					# $use_hilite is set and right filetype
	$src_multiple && ($doc_title = "$src_prefix $doc_title");
	if ($bytes < 1000) { $calc_bytes = "< 1 Kbyte"; }
	else { $calc_bytes = int(($bytes + 500)/1000) . " Kbytes"; }

	# this is what is printed on each line -- BJA
        &print_it ("
    • $doc_title");
        # changed the output to remove the type specification -- BJA
	&print_it (&block_info($doc_title));
	&print_it ("
      ");
	&print_it ("\n");

	if (($#types > 0) && ($file_proper ne "")) {  # Multitype indexing
	  $alt_count = 0;			      # offer alternatives
	  foreach $multi_type (@types) {
		next if $multi_type eq $file_ext; # skip, already listed
		&print_it ("
      ...Alternate Types Available: ") if $alt_count == 0;
		$alt_count ++;
		$theFile = "$file_proper.$multi_type";
		$url_to_use = $serverURL.$theFile;
		$type  = &type_file ($theFile);
		&print_it ("$type, ");
	  } # end foreach $multi_type
	}
	&print_it ("
      • \n");
    }
    $score = $headline = $lines = $bytes = $type = $date = '';
    $file_proper = $file_ext = '';
    @types = ();
}

sub block_info {
    local($block) = @_;
    local($tmp, $grp_rec, $grp_ac, $grp_id, $grp_de);

    $tmp = $grp_ac = $grp_id = $grp_de = "";
    if ($show_block_description) {

        if ($block =~ m/^PR/) {
           open(GREP, "grep \"^$block\" $printsdb |");
        }
        else  {
           open(GREP, "grep \"^$block\" $blocksdb |");
        }
        while($grp_rec = )
        {
           ($grp_ac, $grp_id, $grp_de) = split(/\s+/, $grp_rec);
        }
        close(GREP);
        if ($grp_ac eq $block)
	{ $tmp = " 
       ".$grp_id." ".$grp_de; }
    }
    $tmp;
}

open (STDERR,"> /dev/null");
eval '&do_wais';

				 last SUFFIX;
				};
		/\.gz$/i	&& do {
				 $type = "compressed file";
				 last SUFFIX;
				};
		/\.au$/i	&& do {
				 $type = "Sun audio file";
				 last SUFFIX;
				};
		/\.hqx$/i	&& do {
				 $type = "Binhex file";
				 last SUFFIX;
				};
		/\.tar$/i	&& do {
				 $type = "tar'red file";
				 last SUFFIX;
				};
#		$type = "Unknown type"; # "fall tblimps-3.9/www/bin/logo.csh000075500001460000012000000056631013375520100162130ustar00jorjastaff00000400000027#!/bin/csh
#
#		logo.csh  
#		 = ps | pdf | gif
#	Makes postscript logos & converts them to gif format
#  The files colors, marks, wave and default.amino.frq must be in
#  the current directory
#	

set TMP = ../tmp
#/opt/sfw/share/ghostscript/6.52/lib/gs_fonts.ps
#/opt/sfw/esp/share/ghostscript/7.05/lib/gs_fonts.ps
setenv GS_LIB /opt/sfw/share/ghostscript

setenv LD_LIBRARY_PATH /usr/openwin/lib:/usr/dt/lib:/usr/lib:/usr/ucblib:/opt/sfw/lib:/usr/local/lib
set path = ($path /opt/sfw/bin)

#---------Make all the logos----------------------------------------------
unalias rm
unalias cp
\cp colors colors.$$

#   This creates one logo PS file for each block in the file $1
#	They have odd names - logo.$$
if ( ($#argv > 0) && (-e $1) ) then
   ./blimps-bin/matrix_logob $1 - $$ > /dev/null
else
   echo "Content-type: text/html"
   echo ""
   echo "Logo error: Input file $1 not found"
   exit
endif
#		matrix_logob used to remove these files
rm colors.$$* symvec.$$* makelogop.$$* >& /dev/null

#-------------------------------------------------------------------------
#	See if any logo files were created
#	If so, merge them all into one big postscript file
set logos = (logo.$$*)
if ($#logos < 1) then
	echo "Content-type: text/html"
	echo ""
	echo "Logo error: No logos produced"
	exit
endif

#-------------------------------------------------------------------------
#	Show the logos
if ($#argv < 2) then
   set type = "gif"
else
   set type = $2
endif
if ($type == "ps") then
   echo "Content-type: application/postscript"
   echo ""
   cat logo.$$*
   rm logo.$$* >& /dev/null
else
   if ($type == "pdf") then
      foreach logo ($logos)
	convert -crop 612x300\!+0+0 ps:$logo pdf:$TMP/$logo.pdf
	rm -f $logo
      end
      echo "Content-type: application/pdf"
      echo ""
      set logos = ($TMP/logo.$$*.pdf)
      montage +frame +shadow +label -geometry 612x300\!+0+0 -tile 1x$#logos $logos $TMP/$$.logos.pdf
      cat $TMP/$$.logos.pdf
      rm $TMP/$$.logos.pdf $TMP/logo.$$*.pdf >& /dev/null
   else
      #	Crop off blank bottom & convert to gif format
      #	Logos are about 612 pixels wide by 792 pixels high
      foreach logo ($logos)
	convert -crop 612x300\!+0+0 ps:$logo $logo.gif
	rm -f $logo
      end

      #-------------------------------------------------------------------------
      #	Group them on a page; it may be a long page
      set logos = (logo.$$*.gif)
      montage +frame +shadow +label -geometry 612x300\!+0+0 -tile 1x$#logos $logos $TMP/$$.logos.gif
      rm -f logo.$$*.gif

      if (-e $TMP/$$.logos.gif) then
         #---------------Now show the combined logos ----------------------
         echo "Content-type: image/gif"
         echo "" 
         cat $TMP/$$.logos.gif
      else
         echo "Content-type: text/html"
         echo ""
         echo "Logo error: No gif file produced"
      endif

#-------------------------------------------------------------------------

   endif
endif
exit(0)
blimps-3.9/www/bin/makeblocks.pl000075500001460000012000000232240774527012700172330ustar00jorjastaff00000400000027#!/usr/bin/perl
#       makeblocks.pl
#	executes protomat.csh
#
#  2/ 9/98 Added pdf versions of trees
#  2/12/98 Moved codehop link to blocks/bin/codehop.sh; removed flush of
#	   stdout, caused output problems...
#  3/ 8/98 Possibly get sequences from a file. general_parse()
#  5/27/98 Gapped blast link
#  11/20/98 Fixed bug with semicolons in general_parse()
#           Changed blocks-bin to blockmkr-bin
#	    Relative file name for $tmp
#  12/ 7/98 drawgram.csh instead of drawgram.*.sh|csh & newick.sh
#           logo.csh instead of logo.*.sh|csh
#   7/20/99 Link to proweb's 3dmotifs
#   6/ 6/00 Fixed Gibbs Blast links
#   8/27/01 3dblocks changes
#  11/29/01 Fixed Blast links
#   5/13/02 Be sure input sequences have different titles
#   7/19/02 Fix proweb 3dblocks link (runs on separate system now)
#           Add proweb tree viewer link
#           Fix blastp links
#   8/14/02 Output in separate target windows
#           Link to file with hints on saving output
#   9/17/02 3dblocks link again (are METHOD & SAVE parameters used?)
#   1/ 3/03 Make proweb treeviewer link a button
#   1/ 6/03 Pass proweb treeviewer blocks & pros
#   4/16/03 Added proweb block mapper
#   4/23/03 User reports Gibbs format problem (?), major format changes
#   4/28/03 Don't use $r.out file
#   5/ 9/03 Execute protomat.csh instead of processmail.sh
#   5/ 9/03 Put htmlize stuff in bm_format.pl
#=========================================================================
#
# "constants" and variables
#	Assume are executing in ~/bin subdirectory
$tmp = "../tmp/bm";
$www_address = "WWW";


#	Be sure files and directories are created with rw-rw---- permissions
system("umask 006");

# output the beginning text to be used on all pages
print "Content-type: text/html\n\n";
print "Block Maker results\n";

# check that this is a POST submission
if ( $ENV{"REQUEST_METHOD"} ne "POST" ) {
    print "This script should be referenced with a METHOD of POST.\n";
    exit;
}
#	Check nixlist; IP addresses with a record of bad behavior
$ipaddr = $ENV{"REMOTE_ADDR"};
$nixstatus = system("./nixcheck.pl $ipaddr");
if ($nixstatus != 0)  {  exit(-1);  }

#print "
      ";
#print "
      ";
#print "HOST:$ENV{\"REMOTE_HOST\"}
      ";
#print "ADDR:$ENV{\"REMOTE_ADDR\"}
      ";
#print "USER:$ENV{\"REMOTE_USER\"}
      ";
#print "IDENT:$ENV{\"REMOTE_IDENT\"}
      ";
#print "$ENV{\"CONTENT_TYPE\"}";
#print "
      ";

#	Now multipart/form-data
#if ($ENV{"CONTENT_TYPE"} ne "application/x-www-form-urlencoded") {
#    print "This script can only be used to decode form results. \n";
#    exit;
#}


# get the QUERY_STRING environment variable and the name/value pairs
read (STDIN, $QUERY_STRING, $ENV{"CONTENT_LENGTH"});


# debug
#print "
      \n";
#print "
      \n";
#print $QUERY_STRING ;
#print "
      \n";
#exit;

#%names = &parse_query($QUERY_STRING);
%names = &general_parse($ENV{"CONTENT_TYPE"}, $QUERY_STRING);

#debug
#print "
      \n";
#while (($key, $val) = each %names) {
#   print "key:$key\nval:$val\n";
#   $n = length($key); print " $n\n";
#   $loc = index($key, "address");
#   if ($loc >= 0) {$address = $val; }
#   $loc = index($key, "desc");
#   if ($loc >= 0) {$desc = $val; }
#}

#print "
      \n";
#print "address:$names{address}\n";
#print "address:$address\n";
#print "desc:$names{desc}\n";
#print "desc:$desc\n";
#print "seqfile:$names{seqfile}\n";
#exit;


#
if ($names{desc} eq "")
{ $names{desc} = "unknown"; }

# check that there is sequence data
$temp = $names{sequences};
$temp =~ s/\s//g;
$n1 = length($temp);
$temp = $names{seqfile};
$temp =~ s/\s//g;
$n2 = length($temp);
if ($n1 <= 0 && $n2 <= 0)
{
    print "
      Error
      
	Please provide at least two protein sequences.
      \n";
    exit;
}


# get $id
$id = $$;
system("mkdir -p $tmp/$id");
system("chmod -f 770 $tmp/$id");
$prefix = "$tmp/$id/$id";

$mail_flag = 0;
if ($names{address} ne "") { $return = $names{address}; $mail_flag = 1; }
else                       { $return = $www_address;    }
#	This file still looks like an email message
$seq_file = "$prefix.in";
open(SEQ, ">$seq_file");
print SEQ "From $return\n";
print SEQ "From: $return\n";
print SEQ "Reply-To: $return\n";
print SEQ "Subject: $names{desc}\n";
print SEQ "\n";

#	Notice that the sequences can come from both sources
#	Neither will ever eq "" because of whitespace ...
if  ($names{seqfile} ne "" )
{ print SEQ $names{seqfile}; }
if  ($names{sequences} ne "" )
{ print SEQ $names{sequences}; }
print SEQ "\n";
close SEQ;



#=========================================================================
# run protomat.csh, creates several output files in $prefix
#	This flush causes everything printed until OUT is referenced
#	again to be printed ... that is, stuff after the wait is printed
#	before it finishes waiting. It only seems to wait for stuff from
#	OUT and continues to process other statements. 
#	If email, queue it and exit
print "
      ";
if ($mail_flag)
{
   system("./add_queue_entry.pl MAKER_queue ./protomat.csh $prefix $return");
   print "Your results will be emailed to $return\n";
}
else
{
   print "Making your blocks, please wait...\n";
   select(STDOUT); $| = 1;
   system("./protomat.csh $prefix $return 2>&1 /dev/null");
}

#===========================================================================
$nerr = 0;
open(ERR, "<$prefix.err");
while ($err = ) { print "$err"; $nerr++; }
close(ERR);
if ($nerr > 0) { exit(-1); }

print "Your results will be available for approximately 24 hours ";
print "here.
      \n";

exit(0);

#=========================================================================
#-------------------------------------------------------------------------
# parameter: a string that is the html QUERY_STRING environment variable
# returns: an associative array of name/value pairs.  The name is the key.
sub parse_query {
  local($query_string) = @_;
  local(%ans, @q, $pair);

  # break up into individual name/value lines
  @q = split(/&/, $query_string);

  foreach $pair (@q) {
    # break the name/value pairs up
    # use split rather than regular expressions because the value may have
    #  newlines in it
    split(/=/, $pair, 2);

    # change '+' to ' '
    $_[1] =~ s/\+/ /g;

    # change the escaped characters (has to be after the split on '&' and '=')
    $_[1] =~ s/%(..)/pack("c",&hextodec("$1"))/eg;

    $ans{$_[0]} = $_[1];
  }

  return %ans;
}

# parameter: a hex representation of a number (doesn't need to be a string)
# returns: the decimal representation of the number
sub hextodec {
  unpack("N", pack("H8", substr("0" x 8 . shift, -8)));
}

#-------------------------------------------------------------------------
# $names = &general_parse($ENV{CONTENT_TYPE}, $QUERY_STRING);
# parameters:	CONTENT_TYPE
#		QUERY_STRING
# returns: an associative array of name/value pairs.  The name is the key.

# CONTENT_TYPE: application/x-www-form-urlencoded
# QUERY_STRING: key1=val1&key2=val2

# CONTENT_TYPE: multipart/form-data; boundary=
# QUERY_STRING: 
#		Content-Disposition: form-data; name="key1"
#		
#		val1
#		
#		Content-Disposition: form-data; name="key2"
#		
#		val2
#		

sub general_parse {
  local($content_type, $query_string) = @_;
  local(%ans, @q, $pair, $loc, $boundary, $temp, $temp1);

  if ($content_type eq "application/x-www-form-urlencoded")
  {
     # break up into individual name/value lines
     @q = split(/&/, $query_string);

     foreach $pair (@q) {
       # break the name/value pairs up
       # use split rather than regular expressions because the value may have
       #  newlines in it
       split(/=/, $pair, 2);

       # change '+' to ' '
       $_[1] =~ s/\+/ /g;
   
       # change the escaped characters (must be after the split on '&' and '=')
       $_[1] =~ s/%(..)/pack("c",&hextodec("$1"))/eg;

       $ans{$_[0]} = $_[1];
     }

  }
  else
  {
     $loc = index($content_type, "boundary=");
     if ($loc > 0)
     { 
        $temp = substr($content_type, $loc+9);
#		Why is this necessary? (boundary= doesn't match actual)
	$boundary = "--".$temp;
#print "$query_string\n";
#print "boundary=$boundary\n";
        # break up into individual name/value lines
        @q = split(/$boundary/, $query_string);
        foreach $pair (@q) {
          # break the name/value pairs up
#print "pair=$pair\n";
          $loc = index($pair, "name=");
	  $temp = substr($pair, $loc+5);
#	  $loc = index($temp, "\n\n");
 	  $loc = index($temp, "\n");
	  $temp1 = substr($temp, $loc+2);
#print "temp=$temp\ntemp1=$temp1\n";
#		Get rid of stuff after the name; including semicolon if any
	  $loc_semi = index($temp, ";");
	  $loc_eol = index($temp, "\n");
	  $loc = $loc_eol;
          if ($loc_semi > 0 && $loc_semi < $loc) {$loc = $loc_semi; }
	  if ($loc > 0) { $temp = substr($temp, 0, $loc); }
#		Get rid of quotes around the name
          $temp =~ s/\"//g;
#		Still has a trailing whitespace character ...
          $temp =~ s/\s//g;
#		Need to strip leading/ending whitespace off of $temp1,
#		but be careful not to strip off internal CRs
	  if ($temp ne "seqfile" && $temp ne "sequences")
 	  { $temp1 =~ s/\s//g; }
#		MAC file lines end in just \r, no \n, so makelis won't find all
#		of the sequences; DOS file lines end in \r\n, UNIX in \n.
	  if ($temp eq "seqfile")
#	  { $temp1 =~ s/\r/\n/g; $temp1 =~ s/\n\n/\n/g; }
#		Change \r\n to \n and then \r to \n
 	  { $temp1 =~ s/\r\n/\n/g; $temp1 =~ s/\r/\n/g; }
#         print "temp=$temp\ntemp1=$temp1\n";
	  if ($temp ne "") { $ans{$temp} = $temp1; }
        }
     }
     else
     {  print "Cannot parse $content_type\n"; }
  }
  return %ans;
}

# parameter: a hex representation of a number (doesn't need to be a string)
# returns: the decimal representation of the number
sub hextodec {
  unpack("N", pack("H8", substr("0" x 8 . shift, -8)));
}

blimps-3.9/www/bin/makecs.sh000075500001460000012000000021000774335017600163510ustar00jorjastaff00000400000027#!/bin/sh
#   11/16/94 Changed to search mats.dat instead of blocks.dat   JGH
#   12/19/95 Changed to search blocks.dat with Blocks 9.0

cat > $1.cs << _END_
ERror_level		2			-- only WARNINGs and higher
SQuence			$1.seq			-- the query sequence
DBase			../data-blocks/blocks.dat	-- the BLOCKS database
DBase			../data-prints/prints.noBL	-- PRINTS but not BLOCKS
DBase			../data-pfam/pfam.dat
DBase			../data-prodom/prodom.dat
DBase			../data-domo/domo.dat
OUtput_file		$1.out			-- the output file
STrands_to_search	2			-- if DNA, search both strands
FRequency		./default.amino.frq
REpeats_allowed		yes			-- repeats are allowed
NUmber_to_report	0			-- have blimps judge
COnversion_method	3			-- the conversion method
OP alts: 5.0 default.qij :alts
//
Note: Anything after the second whitespace delimited field in an entry
      is ignored.  Anything after the // is ignored.
Note: The search type is not needed.  A sequence vs a database is a 
      Blocks search.
Note: Only the first two characters are needed for the field key.  The
      case of the characters does not matter.
_END_


blimps-3.9/www/bin/maketree.csh000075500001460000012000000046000775204735000170520ustar00jorjastaff00000400000027#!/bin/csh
#      maketree.csh    Make a tree from a set of blocks
#	 = dat (data), xbm (xbitmap), ps (postscript),
#		 pdf (pdf), new (newick), gif
#	 is optional, calls drawgram.csh if provided
#	creates :r.treefile & displays it in  format
#   where  is a file containing the blocks to be processed
#   Attempts to find nseq from :r.seqs
#	Used by process_blocks.pl
#--------------------------------------------------------------------------
#  7/19/02 Check for and save $r.treefile
#  1/ 3/03 Replace clustalw with quicktree
#
unalias rm
unalias mv
limit cputime 5m

#
#  If $1 = /howard/btest/tmp/AA.blks, then $r = /howard/btest/tmp/AA
#
if ( -e $1 ) then
   set r = $1:r

   #  Try to find out how big the tree is
   if ( -e $r.seqs ) then
       @ nseq = (`grep -c ">" $r.seqs`)
   else
       @ nseq = 0
   endif

   #   See if the tree is already made
   if ( !(-e $r.treefile) ) then
      #		Make tree file using quicktree
      ./blimps-bin/blalign $1 -h > $r.hblks
      if ( -e $r.hblks ) then
         @ nchar = (`wc -m $r.hblks | awk '{print $1}'`)
         @ nerr = (`grep -c "ERROR in block" $r.hblks`)
#echo "nseq=$nseq nchar=$nchar nerr=$nerr"
         if ($nerr == 0) then
            # 	Bootstrap if not too many seqs (same limit as protomat.csh)
            if (($nseq > 0 && $nseq <= 100) || ($nseq == 0 && $nchar <= 25000)) then
               @ nboot = 100
               (./quicktree -in a -out t -kimura -boot $nboot $r.hblks > $r.treefile) >& $r.err
            else
               (./quicktree -in a -out t -kimura $r.hblks > $r.treefile) >& $r.err
            endif
            if ( !(-e $r.treefile) || (-z $r.treefile)) then
               echo "quicktree failed to make a tree" >> $r.treefile
               cat $r.err >> $r.treefile
            endif
         else
            echo "Failed to make a tree due to block errors" >> $r.treefile
            grep "ERROR in block" $r.hblks >> $r.treefile
         endif  # end of nerr
      endif  # end of if hblks
#     rm $r.hblks $r.err >& /dev/null
   endif      # end of if no treefile
#  
else
   echo "Cannot open blocks file $1 to make a tree." >> $r.treefile
   exit
endif
#
#------------------Make plotfile & display the tree -------------------

if ($#argv < 2) then 
   exit(0)
else
   set type = $2
endif
if ( -e $r.treefile ) then
	./drawgram.csh $r.treefile $type
endif

exit(0)
blimps-3.9/www/bin/marks000064400001460000012000000000000774505301700156000ustar00jorjastaff00000400000027blimps-3.9/www/bin/mast.csh000075500001460000012000000007110775205237300162210ustar00jorjastaff00000400000027#!/bin/csh
#		mast.csh 
#	For narrow.pl; does a local mast search vs swiss
#	Because can't set -ev at SDSC
#
unalias rm
unalias mv
unalias cp

#echo "1=$1"

set bin = .
set db = /d3/databases/swiss/swiss.uni

echo "Your search is running ... please wait"

#	Now execute mast
/usr/local/bin/mast $1 -d $db -ev 100 -stdout -text -brief -nostatus >& $1.mout

$bin/htmlize-swiss.pl $1.mout 

#echo Content-type: text/html
#echo
#cat $1.mout

exit(0)
blimps-3.9/www/bin/mast.in000064400001460000012000000246510774506113200160530ustar00jorjastaff00000400000027

       

  
      
    
      Sequence database to search:
      

   
           
     

  
      
     
       OPTIONS 
      

  
      
    
       
      Scale motif display threshold
       by sequence length; recommended for
      nucleotide searches

    
      Description
      of your motifs:
      

  
      
    
       
      
      Use individual sequence composition 
      
      in E- and p-value calculation

          		
      
      Display sequences with E-value below:
      

  
      
    
       
      Text output format

    
      Rank
      of the first match returned: 
	
	
	
  
      
    
    
      
      Ignore motifs if E-value above:
      

  
      
     
       DNA-ONLY OPTIONS 
      

  
      
    
       
      Search nucleotide database
      with protein motifs

    
      Treatment of 
      reverse complement strands: 
       

    
      
       
      

    
      
      
              
        

      



      
Click here for 
more information 
on MAST.


      
Return to 
MEME SYSTEM introduction.


      
Please send comments and questions to:
tbailey@sdsc.edu.


      




blimps-3.9/www/bin/mast.sh000075500001460000012000000030710775205317700160630ustar00jorjastaff00000400000027#!/bin/sh
#		mast.sh  
#	Set up the mast search, requires POST, requires mast.in file
#	NOTE: See the mast form at
#	http://meme.sdsc.edu/meme/website/mast.html

#
if [ $2 ]; then
  AC=$2
else
  AC="Blocks"
fi
if [ $1 ]; then

  ./blimps-bin/blk2pssm $1 $1.pssm M > /dev/null 2>&1
  echo "Content-type: text/html"
  echo
  echo "";
  echo "Blocks to Mast";
  echo "
      ";
  echo "MAST Search of Blocks Database Blocks
      ";
  echo "";
  echo "";
  echo "
      ";
  echo "MAST searches blocks against a sequence database at SDSC.
      ";
  echo "Results are returned via EMAIL.
      ";
  echo "See the MAST PSSM";
  echo "made from the blocks.
      ";

  echo "
      ";
  echo "Enter your complete EMAIL address for MAST search results:\n";
  echo " ";
# echo "";
#		No spaces, slashes, etc allowed in "inline_name" ...
  echo "";
  echo "";
  echo "
      \n";

#	mast.in is edited from the mast.html form, remove the above fields
  cat ./mast.in
fi

#	Keep for display
#\rm $1.pssm > /dev/null 2>&1
#
exit
blimps-3.9/www/bin/mastpssm.sh000075500001460000012000000031120775205324100167520ustar00jorjastaff00000400000027#!/bin/sh
#		mast.sh  
#	Set up the mast search, requires POST
#	NOTE: See the mast form at
#	http://meme.sdsc.edu/meme/website/mast.html
#	NOTE: Don't use mast.sh version because blk2pssm was already run <<<

#
if [ $2 ]; then
  AC=$2
else
  AC="Blocks"
fi
if [ $1 ]; then

# ./blocks-bin/blk2pssm $1 $1.pssm M > /dev/null 2>&1
  echo "Content-type: text/html"
  echo
  echo "";
  echo "Blocks to Mast";
  echo "
      ";
  echo "MAST Search of Blocks Database Blocks
      ";
  echo "";
  echo "";
  echo "
      ";
  echo "MAST searches blocks against a sequence database at SDSC.
      ";
  echo "Results are returned via EMAIL.
      ";
  echo "See the MAST PSSM";
  echo "made from the blocks.
      ";

  echo "";
  echo "Enter your complete EMAIL address for MAST search results:\n";
  echo " ";
# echo "";
#		No spaces, slashes, etc allowed in "inline_name" ...
  echo "";
  echo "";
  echo "
      \n";

#	mast.in is edited from the mast.html form, remove the above fields
  cat ./mast.in
fi

#\rm $1.pssm > /dev/null 2>&1
#
exit
blimps-3.9/www/bin/matrix.csh000075500001460000012000000011750775177637100166000ustar00jorjastaff00000400000027#!/bin/csh
#		matrix.csh 
#	For narrow.pl; does a blimps search vs swiss
#
unalias rm
unalias mv
unalias cp

#echo "1=$1"

set bin = .
set db = /d3/databases/swiss/swiss.uni
setenv BLIMPS_DIR /usr/local/blimps

echo "Your search is running ... please wait"

#	Now execute blimps
echo "MA $1" > $1.cs
echo "DB $db" >> $1.cs
echo "OU $1.bout" >> $1.cs
echo "TY AA" >> $1.cs
echo "ER 3" >> $1.cs
echo "RE no" >> $1.cs
echo "NU 1000" >> $1.cs
echo "FR $bin/default.amino.frq" >> $1.cs
echo "OP alts: 5.0 $bin/default.qij :alts" >> $1.cs
echo "//" >> $1.cs
$bin/blimps $1.cs >& /dev/null

$bin/htmlize-swiss.pl $1.bout 

exit(0)
blimps-3.9/www/bin/model.csh000075500001460000012000000014700774507167400163670ustar00jorjastaff00000400000027#!/bin/csh
#	model.run        = seqs in fasta format
#	Fix Gibbs9_95 model based on min seq len
#	   Expects MINIMUM indicated in input file title line.
#          Always specify blocks 8 wide, Gibbs will "column sampling",
#	   possibly resulting in wider blocks.
#
#	< 36 	1 motif
#	36-85	2 motifs
#	86-135	3
#	136-185	4
#	186-235	5
#	236-285	6
#		etc. to max of 26 motifs allowed by Gibbs program
#
set minlen = (`grep " MINIMUM" $1 |  awk '{print $2}'`)
#echo $minlen
@ l = $minlen
#echo $l
if ($l < 36) then
   set model = 8
else
         set model = "8,8"
	 @ n = 2
         @ x = $l
         @ x -= 35
         @ x -= 50
         while ($n < 26 && $x > 0)
            set model = "$model,8" 
#           echo $x $model
            @ x -= 50
	    @ n += 1
         end
endif
echo $model
exit(0)

blimps-3.9/www/bin/narrow.csh000075500001460000012000000003450775204516300165670ustar00jorjastaff00000400000027#!/bin/csh
#		narrow.csh  
#
unalias rm
unalias mv
unalias cp

#echo "1=$1"
#echo "2=$2"

set bin = .

#	Creates PSSMs in $2.mast and $2.blimps
#	Believes format type in $1
$bin/blimps-bin/narrow $1 $2

exit(0)
blimps-3.9/www/bin/narrow.pl000075500001460000012000000146120774503577100164350ustar00jorjastaff00000400000027#!/usr/bin/perl

#	pssm.pl
# Execute pssm.csh & display the output

#	Set file permissions to rw-rw----
system("umask 006");
#	Don't like to hard-code file names this way ...
$tmpdir = "../tmp/$$";
system("mkdir $tmpdir");

$bin = ".";

# output the beginning text to be used on all pages
print "Content-type: text/html\n\n";
print "Narrow PSSM Results\n";


if ( $ENV{"REQUEST_METHOD"} ne "POST" ) {
   print "This script should be referenced with a METHOD of POST\n";
   exit;
}

read (STDIN, $QUERY_STRING, $ENV{"CONTENT_LENGTH"});
#%names = &parse_query($QUERY_STRING);
%names = &general_parse($ENV{"CONTENT_TYPE"}, $QUERY_STRING);

$err = "$tmpdir/err";
$fin = "$tmpdir/fin";
#	$mast & $blimps are created by jcooper
$mast = "$fin.mast";
$blimps = "$fin.blimps";
$bout = "$fin.bout";
$mout = "$fin.mout";

#	Get the program name
#if ($names{program} eq "") {
#   print "
      Error
       Please select a searching program.
      \n";
#   exit;
#}

#	Problem here; $names{qfile} always has some \n's, never empty ...
$qftemp = $names{qfile};
$qftemp =~ s/\s//g;
$qutemp = $names{query};
$qutemp =~ s/\s//g;
#	Get the query & write it to a file
if ($qutemp eq "" && $qftemp eq "")
{
         print "
      Error
       Please enter a query.
      \n";
         exit;
}

#  create a file of the input
open(FIN, ">$fin");
#	Problem here; $names{qfile} always has some \n's, never empty ...
if ($qftemp ne "")
{ print FIN $names{qfile}; }
elsif ($qutemp ne "")
{ print FIN $names{query}; }
print FIN "\n";
close(FIN);

#=========================================================================
#	Run shell now

#print "Your search is running, please wait ...
      ";
#	Try to flush stdout so they see the above message
select(STDOUT); $| = 1;

system("$bin/narrow.csh $names{type} $fin > $err 2>&1");

print "
      Narrow PSSM Results
      ";

print "
      ";
open(ERR, "<$err");
while ($_ = )
{
  print;
}
close(ERR);
print "
      ";


print "[Input] ";
print "
      ";

print "[BLIMPS PSSM] ";
print "[BLIMPS Search]  ";
print "
      BLIMPS search vs Swiss-Prot will take several minutes to complete";
print "
      ";

print "[MAST PSSM] ";
$group = "NarrowBlock";
print "[MAST Search at SDSC]  ";
print "[About MAST] ";
print "
      MAST search results vs several popular databases are returned via email from SDSC";
print "
      Use a large E-value cutoff for narrow PSSMs";
#print "
      ";


#print "[return to top]
      ";
#-------------------------------------------------------------------------
exit (0);

#=========================================================================

#-------------------------------------------------------------------------
#  NOTE: Not really general, does special stuff for names{query}
#	 and for names{sequences}
# $names = &general_parse($ENV{CONTENT_TYPE}, $QUERY_STRING);
# parameters:	CONTENT_TYPE
#		QUERY_STRING
# returns: an associative array of name/value pairs.  The name is the key.

# CONTENT_TYPE: application/x-www-form-urlencoded
# QUERY_STRING: key1=val1&key2=val2

# CONTENT_TYPE: multipart/form-data; boundary=
# QUERY_STRING: 
#		Content-Disposition: form-data; name="qfile"; filename="file.name"
#		
#		
#		
#		Content-Disposition: form-data; name="sequences"
#		
#		
#		

sub general_parse {
  local($content_type, $query_string) = @_;
  local(%ans, @q, $pair, $loc, $boundary, $temp, $temp1);

#print "
      $content_type\n\n";
#print "query_string:\n$query_string\n\n";

  if ($content_type eq "application/x-www-form-urlencoded")
  {
     # break up into individual name/value lines
     @q = split(/&/, $query_string);

     foreach $pair (@q) {
       # break the name/value pairs up
       # use split rather than regular expressions because the value may have
       #  newlines in it
       split(/=/, $pair, 2);

       # change '+' to ' '
       $_[1] =~ s/\+/ /g;
   
       # change the escaped characters (must be after the split on '&' and '=')
       $_[1] =~ s/%(..)/pack("c",&hextodec("$1"))/eg;

       $ans{$_[0]} = $_[1];
     }

  }
  else
  {
     $loc = index($content_type, "boundary=");
     if ($loc > 0)
     { 
        $temp = substr($content_type, $loc+9);
#	Why is this necessary? (boundary= sometimes doesn't match actual?)
 	$boundary = "--".$temp;
#       $boundary = $temp;
#print "boundary=$boundary\n\n";
        # break up into individual name/value lines
        @q = split(/$boundary/, $query_string);
        foreach $pair (@q) {
          # break the name/value pairs up
#print "pair=$pair\n\n";
          $loc = index($pair, "name=");
	  $temp = substr($pair, $loc+5);
#	  $loc = index($temp, "\n\n");
 	  $loc = index($temp, "\n");
	  $temp1 = substr($temp, $loc+2);
#print "1 temp=$temp\n";
#		Get rid of stuff after the name
#	Need to look for a ; before the first \n ... <<< find another way!
	  $loc1 = index($temp, ";");
          $loc = index($temp, "\n");
          if ($loc1 > 0 && $loc1 < $loc) { $loc = $loc1; }
 	  if ($loc > 0) { $temp = substr($temp, 0, $loc); }
#print "2 loc=$loc temp=$temp\n";
#		Get rid of quotes around the name
          $temp =~ s/\"//g;
#print "3 temp=$temp\n";
#		Still has a trailing whitespace character ...
          $temp =~ s/\s//g;

#		Need to strip leading/ending whitespace off of $temp1,
#		but be careful not to strip off internal CRs in "query"
#		and "sequences"
#print "4 temp=$temp\ntemp1=$temp1\n";
	  if ($temp ne "qfile" && $temp ne "query")
 	  { $temp1 =~ s/\s//g; }

#		MAC file lines end in just \r, no \n;
#		DOS file lines end in \r\n; UNIX in \n.
#		mablock uses fgets() which requires \n.
#		Change \r\n to \n, then change \r to \n
 	  if ($temp eq "qfile" || $temp eq "query")
  	  { $temp1 =~ s/\r\n/\n/g;  $temp1 =~ s/\r/\n/g; }
#print "temp=$temp\ntemp1=$temp1\n";
	  if ($temp ne "") { $ans{$temp} = $temp1; }
        }
     }
     else
     {  print "Cannot parse $content_type\n"; }
  }
#print "
      ";
  return %ans;
}

# parameter: a hex representation of a number (doesn't need to be a string)
# returns: the decimal representation of the number
sub hextodec {
  unpack("N", pack("H8", substr("0" x 8 . shift, -8)));
}

>]  ";
print "[About MAST] ";
print "
      MAST searchblimps-3.9/www/bin/newick.sh000075500001460000012000000003660774335017600164020ustar00jorjastaff00000400000027#!/bin/sh
#		newick.sh 
#	Cat the treefile for mime type newick

if [ -f "$1" ]; then
      echo Content-type: application/newick
      echo
      cat "$1"
else
      echo Content-type: text/html
      echo
      echo "No tree file"
fi
blimps-3.9/www/bin/oligo_melt.csh000075500001460000012000000002430775204652700174130ustar00jorjastaff00000400000027#!/usr/bin/csh 
#		oligo_temp.csh   
#
#	oligo_temp  
./blimps-bin/oligo_melt $1 $2 > $3
unalias rm
rm $1
exit
blimps-3.9/www/bin/oligo_melt.pl000075500001460000012000000044740774503602700172570ustar00jorjastaff00000400000027#!/usr/bin/perl

# Execute oligo_temp & process the output

#	Set file permissions to rw-rw----
system("umask 006");

$program = "./oligo_melt.csh";
$tmp = "../tmp";

select(STDOUT); $| = 1;

print "Content-type: text/html\n\n";
print "Oligo Melting Temperature Results\n";
print "
      Oligo Melting Temperature Results
      ";
print "
      ";


if ( $ENV{"REQUEST_METHOD"} ne "POST" ) {
   print "This script should be referenced with a METHOD of POST\n";
   exit;
}

read (STDIN, $QUERY_STRING, $ENV{"CONTENT_LENGTH"});
%names = &parse_query($QUERY_STRING);

if ($names{clamp_conc} eq "") { $conc = 50; }
else { $conc = $names{clamp_conc}; }

#	Get the sequence & write it to a file
if ($names{sequence} eq "") {
   print "
      Error
       Please enter an oligo sequence.
      \n";
   exit;
}
$seq = "$tmp/$$.seq";
open(SEQ, ">$seq");
print SEQ ">oligo 5' to 3'\n";
print SEQ $names{sequence};
print SEQ "\n";
close(SEQ);

#=========================================================================
#	Run shell now

$out = "$tmp/$$.out";

open(ERR, "$program $seq $conc $out 2>&1 |");
wait;
while ($_ = ) { print; }
close(ERR);

select(STDOUT); $| = 1;

open(OUT, "<$out");
while ($_ = ) { print; }
close(OUT);

print "
      ";

#-------------------------------------------------------------------------
exit (0);

#-------------------------------------------------------------------------
#
# parameter: a string that is the html QUERY_STRING environment variable
# returns: an associative array of name/value pairs.  The name is the key.
sub parse_query {
  local($query_string) = @_;
  local(%ans, @q, $pair);
#print $query_string;
  # break up into individual name/value lines
  @q = split(/&/, $query_string);

  foreach $pair (@q) {
    # break the name/value pairs up
    # use split rather than regular expressions because the value may have
    #  newlines in it
    split(/=/, $pair, 2);

    # change '+' to ' '
    $_[1] =~ s/\+/ /g;

    # change the escaped characters (has to be after the split on '&' and '=')
    $_[1] =~ s/%(..)/pack("c",&hextodec("$1"))/eg;

    $ans{$_[0]} = $_[1];
  }

  return %ans;
}

# parameter: a hex representation of a number (doesn't need to be a string)
# returns: the decimal representation of the number
sub hextodec {
  unpack("N", pack("H8", substr("0" x 8 . shift, -8)));
}



blimps-3.9/www/bin/pdbmast.pl000075500001460000012000000117150774503576000165560ustar00jorjastaff00000400000027#!/usr/bin/perl
#		pdbmast.pl  
#		(replaces pdbfile.pl)
#	Insert links for pdbmast.dat entries
#---------------------------------------------------------------------------
#  7/19/02 fix 3dblocks link
#  2/18/03 More elaborate 3motif link, etc.
#  2/19/03 New format for blk2pdb.dat entries
#	Each line has: 
#  [_]  
#  3/ 9/03 Added MMDB links
#---------------------------------------------------------------------------

print "Content-type: text/html\n\n";
print "\n";

if ( @ARGV < 2 )
{
   print "USAGE: pdbmast.pl  \n";
   exit(-1);
}
$pdbmast = "$ARGV[0]";
$lastac = "$ARGV[1]";
#print "pdbmast=$pdbfile\n";
#print "lastac=$lastac\n";
open(PDB, "<$pdbmast") || die("pdbfile.pl: Could not open $pdbfile\n");
#while ($pdb_rec = )
#{ print "$pdb_rec"; }
#close(PDB);
#exit;

$ac = $lastblk = "";
while ($pdb_rec = )
{
   ($pdb_ac, $pdb_pdb, $pdb_all, $pdb_order) = split(/\s+/, $pdb_rec);
   if ($pdb_pdb =~ m/\_/)
   {   ($pdb, $chain) = $pdb_pdb =~ m/(\S+)\_(\S*)/; }
   else
   { $pdb = $pdb_pdb; $chain = ""; }
   if ($ac eq "")
   {
      if ($pdb_rec =~ m/^IPB/)
      {   
         $ac = substr($pdb_rec, 0, 9);  
         if ($lastac =~ m/^${ac}/ && length($lastac) > 9)
         {  $lastblk = substr($lastac, 9, 1); }
      }
      else
      {   
         $ac = substr($pdb_rec, 0, 7);  
         if ($lastac =~ m/^${ac}/ && length($lastac) > 7)
         {  $lastblk = substr($lastac, 7, 1); }
      }
#print "ac=$ac lastblk=$lastblk\n";
      print "Structure Links for $ac\n";
      print "
      Structure Links for $ac
      \n";

      print "
        ";
      print "
      • Structures found by searching ";
      print "$ac";
      print " blocks vs PDB with ";
      print "MAST";
      print "
        \n";

      print "\n";
      print "";
      print "\n";
      print "\n";
      print "\n";
      print "\n";
      print "\n";
      print "\n";
      print "";
   }

   if ($ac ne "")
   {
      print "";

      print "\n";

      print "\n";

      print "\n";

      print "\n";

      print "\n";

      print "\n";

      print "";
   }
}   # end of pdbmast
close(PDB);

if ($ac eq "")
{
   print "ERROR: Problem reading $pdbmast\n";
   close(PDB);
   exit(-1);
}


print "
        All Blocks in HitBlocks in Order3D BlocksProtein Data BankMolecules R USEntrez Structure Database
        ";
      if ($pdb_all == 1) { print "Yes"; }
      else               { print "No";  }
      print "";
      if ($pdb_order == 1) { print "Yes"; }
      elsif ($pdb_all == 1 && $pdb_order == 0) { print "No";  }
      else { print "   ";  }
      print "";
#	&mast=yes&CUTOFF=0.0001   (searches the cobbler seq with blast now)
      print "$pdb_pdb\n";
      print "";
      print "$pdb_pdb\n";
      print "";
      print "$pdb_pdb\n";
      print "";
      print "$pdb_pdb\n";
      print "
        \n";
print "
        \n";

#===============3motif stuff==============================================
print "
      • ";
print "Go to 3Motif at Stanford ";
#print "Requires Chime ";
print " (Requires Chime)
        \n";
print " 3Motif finds and displays structures for each block individually:
        \n";
print "
          ";
if ($lastblk ne "")
{
   for ($blk = "A"; $blk le $lastblk; $blk++)
   {
print "
        • ${ac}${blk}\n";
   }
}
else
{
print "
        • ${ac}\n";
}
print "
        ";

print "
      ";
print "\n";

exit(0);

blimps-3.9/www/bin/printscs.sh000075500001460000012000000007640774335017600167710ustar00jorjastaff00000400000027#!/bin/sh

#	Like makecs, but search prints database instead of blocks

cat > $1.cs << _END_
ERror_level		2			-- only WARNINGs and higher
SQuence			$1.seq			-- the query sequence
DBase			../data-prints/prints.dat	-- the BLOCKS database
OUtput_file		$1.out			-- the output file
STrands_to_search	2			-- if DNA, search both strands
REpeats_allowed		yes			-- repeats are allowed
NUmber_to_report	0			-- have blimps judge
COnversion_method	3			-- the conversion method
OP alts: 5.0 default.qij :alts
//

blimps-3.9/www/bin/process_blocks.pl000075500001460000012000000336411003106161700201170ustar00jorjastaff00000400000027#!/usr/bin/perl
#		process_blocks.pl (executed by www/process_blocks.html)
#
#	NOTE: Would have to input the sequences that went into
#	making the blocks in order to make a cobbler sequence.
#	Also have to input sequences in order to add sequences to blocks.
#--------------------------------------------------------------------------
#  7/19/02 Fix 3dblocks link; add tree viewer link
#  8/14/02 Put logos, etc. in separate window
#  8/29/02 Use hidden fields for 3dblocks because
#          sometimes the input is too big for Apache on www.proweb.org
#  1/ 3/03 Use hidden fields for treeviewer
#  1/ 8/03 Pass treeviewer blocks & seqs
#  4/14/03 Proweb block map
#  8/27/03 Added DIY search
#  8/30/03 Added minwidth & maxwidth
#  3/26/04 Run LAMA & SIFT in a blank window
#--------------------------------------------------------------------------
#
$ID = $$;

$bin = ".";
$tmp = "../tmp";
#		These files are removed after use
$blin = "$tmp/$ID.blin";
$blks = "$tmp/$ID.blks";
$cblks = "$tmp/$ID.cblks";
$seqs = "$tmp/$ID.seqs";
$err = "$tmp/$ID.err";
$out = "$tmp/$ID.out";
#		These files are left
$wblks = "$tmp/$ID.wblks";
$tree = "$tmp/$ID.treefile";
#	htmlize-map.pl expects this format!
$map = "$wblks.map";
$pssm = "$tmp/$ID.pssm";
$mast = "$tmp/$ID.mast";

#	Be sure files and directories are created with rw-rw---- permissions
#system("umask 006");

# output the beginning text to be used on all pages
print "Content-type: text/html\n\n";
print "Block Information\n";


# check that this is a POST submission

if ( $ENV{"REQUEST_METHOD"} ne "POST" ) {
    print "This script should be referenced with a METHOD of POST. \n";
    exit;
}

#if ($ENV{"CONTENT_TYPE"} ne "application/x-www-form-urlencoded") {
#    print "This script can only be used to decode form results. \n";
#    exit;
#}


# get the QUERY_STRING environment variable and the name/value pairs
read (STDIN, $QUERY_STRING, $ENV{"CONTENT_LENGTH"});
%names = &general_parse($ENV{"CONTENT_TYPE"}, $QUERY_STRING);

# check that there are blocks
if ($names{seqfile} eq "" && $names{sequences} eq "") {
    print "
      Error
      Please enter some blocks.
      \n";
    exit;
}

#	Get rid of everything but numbers
#print "minwidth=$names{minwidth} maxwidth=$names{maxwidth}\n";
$names{minwidth} =~ s/\D//g;
$names{maxwidth} =~ s/\D//g;
$minwidth = 10;
if ($names{minwidth} > 0) { $minwidth = $names{minwidth}; }
$maxwidth = 55;
if ($names{maxwidth} >= $minwidth) { $maxwidth = $names{maxwidth}; }


#  create a file of the input multiple alignment
#  Notice input from both sources will be concatenated
open(BLK, ">$blin");
if ($names{seqfile} ne "")
{  print BLK $names{seqfile}; }
if ($names{sequences} ne "")
{  print BLK $names{sequences};   }
print BLK "\n";
close(BLK);

#  Be sure blocks are in the correct format: puts output in
#	$tmp/$ID.blks = $blks and $tmp/$ID.seqs 
#>>>> empty .seqs file when blocks input?
#  Can handle blocks, fasta and clustal format multiple alignments
#  Adds sequence weights as well, but in floating point format
#print "minwidth=$minwidth maxwidth=$maxwidth\n";
system("$bin/blimps-bin/mablock $blin $tmp/$ID B $minwidth $maxwidth > $err 2>$err");

#	Check that $blks has non-zero size
if (-s "$blks") 
{
   #  calibrate the blocks for diy searching
   system("$bin/calibrate.csh $blks $cblks > /dev/null");
   #  create a file of PB-weighted blocks
   # NOTE: Should give them the option of using existing weights (if any)
   #       or other weighting schemes
   system("$bin/blimps-bin/blweight $cblks $wblks P M > /dev/null");

   #  create the PSSM files == $pssm & $mast
   system("$bin/blimps-bin/blk2pssm $wblks $pssm B > /dev/null");
   system("$bin/blimps-bin/blk2pssm $wblks $mast M > /dev/null");

   #  create the treefile == $tree
   system("$bin/maketree.csh $wblks > /dev/null");

   #  create the map file == $map
   system("$bin/blimps-bin/makeblockmap $wblks $map > /dev/null 2>&1");

   #  remove unnecessary files
#  system("rm $blin $blks $tmp/$ID.seqs");
}

#=========================================================================
#	Assuming here that all the other files got made if $wblks has
#	non-zero size
if (-s "$wblks") 
{
  print "
      Block Information
      \n";
# print "";
  print "
      ";
  open(OUT, "cat $out |");
  while ($_ = ) { print; }
  close(OUT);	
  print "
      ";

  print "
      Sequence-Weighted Blocks:
      ";
  print "[Blocks Format] ";
  print "[Blimps PSSM] ";
  print "[MAST PSSM] ";
  print "[About PSSMs] ";
  print "
      ";
  # The blockmap name must match what's in the mapfile
  open(GREP, "grep \"^>\" $map |");
  $map_rec = ;
  ($mapname) = $map_rec =~ m/^>(\S+)/;
  print "
      Map:     
      ";
  print "





)
  { print $maprec; }
  close(MAP);
  print "\">
        \n";
  print "[Text Map]  \n";
  print "[Map Positions]  \n";
  print "[About Maps]";

  print "
      Logos:     
      ";
  print "[Postscript] ";
  print "[PDF] ";
  print "[GIF] ";
  print "[About logos]\n ";

  print "
      Tree:     
      ";
  print "

      


)
  { print $trerec; }
  close(TRE);
  print "\">)
  { print $blkrec; }
  close(BLK);
  print "\">)
  { print $seqrec; }
  close(SEQ);
  print "\">
      \n";
  print "[XBitmap] ";
  print "[Postscript] ";
  print "[PDF] ";
  print "[GIF] ";
  print "[NEW] ";
  print "[Data] ";
  print "[About trees]\n";

#	Don't have a cobbler sequence to send to 3dblocks.cgi
# print "&SEQ=";
  print "
      Structures (takes several minutes):
      ";
  print "

      



)
  { print $blkrec; }
  close(BLK);
  print "\">
      \n";
  print "  [About 3D Blocks]\n";

  print "
      Multiple alignment search:
      ";
  print "[LAMA] ";
  print "[About LAMA]   ";
  print "";
  $group = "UserBlocks";
  print "[MAST] ";
  print "[About MAST]\n";

  print "
      COBBLER sequence and single sequence search:
      ";
  print "[COBBLER] ";
  print "[About COBBLER]\n";

  print "
      Search these blocks:
      ";
  print "[DIY Search] ";
  print "[About DIY]\n";

  print "
      Primers:
      ";
  print "[CODEHOP] ";
  print "[About CODEHOP]\n";

  print "
      Substitutions:
      ";
  print "[SIFT] ";
  print "[About SIFT on Blocks]\n";

}
else 
{ 
  print "
      Problem processing input:
      ";
  open(ERR, "cat $err |");
  while ($_ = ) { print; }
  close(ERR);	
  print "\n
      <\PRE>Please refer to "; 
  print "[acceptable formats].";
}

print "
      \n";

exit(0);

#=========================================================================
# parameter: a string that is the html QUERY_STRING environment variable
# returns: an associative array of name/value pairs.  The name is the key.
sub parse_query {
  local($query_string) = @_;
  local(%ans, @q, $pair);

  # break up into individual name/value lines
  @q = split(/&/, $query_string);

  foreach $pair (@q) {
    # break the name/value pairs up
    # use split rather than regular expressions because the value may have
    #  newlines in it
    split(/=/, $pair, 2);

    # change '+' to ' '
    $_[1] =~ s/\+/ /g;

    # change the escaped characters (has to be after the split on '&' and '=')
    $_[1] =~ s/%(..)/pack("c",&hextodec("$1"))/eg;

    $ans{$_[0]} = $_[1];
  }

  return %ans;
}

#-------------------------------------------------------------------------
#  NOTE: Not really general, does special stuff for names{seqfile}
#	 and for names{sequences}
# $names = &general_parse($ENV{CONTENT_TYPE}, $QUERY_STRING);
# parameters:	CONTENT_TYPE
#		QUERY_STRING
# returns: an associative array of name/value pairs.  The name is the key.

# CONTENT_TYPE: application/x-www-form-urlencoded
# QUERY_STRING: key1=val1&key2=val2

# CONTENT_TYPE: multipart/form-data; boundary=
# QUERY_STRING: 
#		Content-Disposition: form-data; name="seqfile"; filename="file.pros"
#		
#		
#		
#		Content-Disposition: form-data; name="sequences"
#		
#		
#		

sub general_parse {
  local($content_type, $query_string) = @_;
  local(%ans, @q, $pair, $loc, $boundary, $temp, $temp1);

#print "
      $content_type\n\n";
#print "query_string:\n$query_string\n\n";

  if ($content_type eq "application/x-www-form-urlencoded")
  {
     # break up into individual name/value lines
     @q = split(/&/, $query_string);

     foreach $pair (@q) {
       # break the name/value pairs up
       # use split rather than regular expressions because the value may have
       #  newlines in it
       split(/=/, $pair, 2);

       # change '+' to ' '
       $_[1] =~ s/\+/ /g;
   
       # change the escaped characters (must be after the split on '&' and '=')
       $_[1] =~ s/%(..)/pack("c",&hextodec("$1"))/eg;

       $ans{$_[0]} = $_[1];
     }

  }
  else
  {
     $loc = index($content_type, "boundary=");
     if ($loc > 0)
     { 
        $temp = substr($content_type, $loc+9);
#	Why is this necessary? (boundary= sometimes doesn't match actual?)
#	$boundary = "--".$temp;
        $boundary = $temp;
#print "boundary=$boundary\n\n";
        # break up into individual name/value lines
        @q = split(/$boundary/, $query_string);
        foreach $pair (@q) {
          # break the name/value pairs up
#print "pair=$pair\n\n";
          $loc = index($pair, "name=");
	  $temp = substr($pair, $loc+5);
#	  $loc = index($temp, "\n\n");
 	  $loc = index($temp, "\n");
	  $temp1 = substr($temp, $loc+2);
#print "1 temp=$temp\n";
#		Get rid of stuff after the name
#	Need to look for a ; before the first \n ... <<< find another way!
	  $loc1 = index($temp, ";");
          $loc = index($temp, "\n");
          if ($loc1 > 0 && $loc1 < $loc) { $loc = $loc1; }
 	  if ($loc > 0) { $temp = substr($temp, 0, $loc); }
#print "2 loc=$loc temp=$temp\n";
#		Get rid of quotes around the name
          $temp =~ s/\"//g;
#print "3 temp=$temp\n";
#		Still has a trailing whitespace character ...
          $temp =~ s/\s//g;

#		Need to strip leading/ending whitespace off of $temp1,
#		but be careful not to strip off internal CRs in "seqfile:
#		and "sequences"
#print "4 temp=$temp\ntemp1=$temp1\n";
	  if ($temp ne "seqfile" && $temp ne "sequences")
 	  { $temp1 =~ s/\s//g; }

#		MAC file lines end in just \r, no \n;
#		DOS file lines end in \r\n; UNIX in \n.
#		mablock uses fgets() which requires \n.
#		Change \r\n to \n, then change \r to \n
 	  if ($temp eq "seqfile")
  	  { $temp1 =~ s/\r\n/\n/g;  $temp1 =~ s/\r/\n/g; }
#print "temp=$temp\ntemp1=$temp1\n
      ";
	  if ($temp ne "") { $ans{$temp} = $temp1; }
        }
     }
     else
     {  print "Cannot parse $content_type\n"; }
  }
  return %ans;
}

# parameter: a hex representation of a number (doesn't need to be a string)
# returns: the decimal representation of the number
sub hextodec {
  unpack("N", pack("H8", substr("0" x 8 . shift, -8)));
}

blimps-3.9/www/bin/protomat.csh000075500001460000012000000275711000053557200171220ustar00jorjastaff00000400000027#!/bin/csh
#      protomat.csh  
#	where prefix = directory and name of .in file, e.g.
#		../tmp/bm/15319/15319 for ../tmp/bm/15319/15319.in
#		which contains the input file made by makeblocks.pl
#	and return = email address, use WWW for web output
#----------------------------------------------------------------------------
#  1/ 8/97  Change clustalw option from -tree to -bootstrap
#  6/ 4/97  -bootstrap=100, or depends on nseq
#  7/ 7/97  Get $IN_WWW flag from processmail, if $IN_WWW reduce cputime,
#	    if > 25 sequences print warning 
#  8/ 7/97  Added block map files
#  8/25/97  Reduced number of bootstraps
# 10/ 4/97  Set #bootstraps=100 because clustalw doesn't normalize
#	    intermediate values making them difficult to interpret
# 10/25/97  Write warnings to the .warn file
#  1/19/98  Stop if > 250 sequences
#  7/15/98  Don't try to run Gibbs if min seq length < 8
#  8/ 5/98  Check for empty tree files & remove them so drawgram doesn't loop
#  1/12/99  Send trees back with searchable PSSMs.
#  9/ 2/99  Changes for clustalw 1.75
# 12/ 9/99  Changes for clustalw 1.80
#  6/ 6/00  Changes for revised motomat; all blocks in one file
#  7/16/01  Require at least 3 seqs
#  1/22/03  2nd arg is return address, mail results here (no longer
#		using processmail.sh)
#  1/23/03  Use quicktree instead of clustalw
#  4/23/03  Write blalign output to a file; don't want to use $r.out any more
#		except for error messages
#  5/ 9/03  Run makelis
#  8/28/03  Add calibration
#----------------------------------------------------------------------------
set prefix = $1
set return = $2
#umask 002
umask 006
unalias rm
unalias mv
set bindir = .
set NSEQ = 80000
set NRES = 29085965
set frq = ./default.amino.frq
#	Limit CPU time more severely for WWW executions
limit coredumpsize 1k
limit datasize 32m
if ($return == "WWW") then
   limit cputime 30m
else
   limit cputime 240m
endif
set minseq = 3
set maxseq = 250
set wwwchar = 20000
set maxchar = 100000

#    Split up the input file name
#  If $1 = ../tmp/bm/AA/AA, then $r = ../tmp/bm/AA/AA and $t = AA
#  motomat dumps all its files into the current directory, which
#   will be /home/blocks/bin/

set r = $prefix:r
set t = $r:t
rm -f $t.blks >& /dev/null
touch $r.err

#  makelis reads $prefix.in and writes $prefix.lis, .pros, .seqlen, .err, .warn
./blimps-bin/makelis $prefix $return


#	Find out how many sequences and characters there are
set nseq = (`grep -c "^>" $r.pros`)
if ( $nseq < $minseq ) then
   echo "ERROR: Block Maker requires at least 3 sequences" >> $r.err
   echo "       Use a pairwise alignment algorithm for 2" >> $r.err
   exit(-1)
endif
if ( $nseq > $maxseq ) then
   echo -n "ERROR: Your input has $nseq sequences which" >> $r.err
   echo " exceeds Block Maker's limit of $maxseq sequences" >> $r.err
   rm $r.pros
   exit(-1)
endif
if ( ($nseq > 100) || ($nseq > 25 && $return == "WWW") ) then
   echo -n "WARNING: Execution may not complete because of CPU time" >> $r.warn
   echo " limit with $nseq sequences." >> $r.warn
   if ( $return == "WWW" ) then
      echo "The CPU time limit is greater using the email option."
   endif
   echo " " >> $r.warn
endif
set nchar = (`wc -l $r.pros | awk '{print $1}'`)
if ($nchar > $maxchar) then
   echo -n "ERROR: Your input has $nchar characters which" >> $r.err
   echo " exceeds Block Maker's limit of $maxchar characters." >> $r.err
   rm $r.pros
   exit(-1)
   else 
      if (($return == "WWW") && ($nchar > $wwwchar)) then
         echo -n "ERROR: Your input has $nchar characters which" >> $r.err
         echo " exceeds Block Maker's WWW limit of $wwwchar characters." >> $r.err
	 echo " Please supply an email address." >> $r.err
         rm $r.pros
         exit(-1)
       endif
endif

#=============================================================================
#	Make blocks from the proteins (motifj executes motomat)
#	NOTE: motifj writes $t.motifj.pros with MINIMUM seq len marked for gibbs
#	For dups:  motifj 4 -$r.pros 0 dups 17 (0 seqs => n/2 to start)
$bindir/blimps-bin/motifj 4 -$r.pros >& /dev/null
#  Run motomat again so sequences aren't clumped/re-ordered
$bindir/blimps-bin/motomat $t.mot 1 1 -10  >& /dev/null
if ( -e $t.blks ) then
   #  Calibrate blocks
   #       Make matrices and observed frequency files
   $bindir/blimps-bin/blk2pssm $t.blks $t.mats B 3 >& /dev/null
   $bindir/blimps-bin/blk2pssm $t.blks $t.obsf B 21 >& /dev/null
   #               writes pssmdist.dat
   $bindir/blimps-bin/pssmdist $t.mats $t.obsf $frq $NSEQ $NRES >& /dev/null
   #	This is bad, should change pssmdist.c to name the file
   mv pssmdist.dat $t.dist
   $bindir/blimps-bin/pssmBL $t.dist $t.blks $t.cblks >& /dev/null
   rm $t.dist

#  Add weights to blocks
   $bindir/blimps-bin/blweight $t.cblks $r.mblks P M >& /dev/null
#	Produce a "multiple alignment"
   echo "              **BLOCKS from MOTIF**" > $r.maln
   $bindir/blimps-bin/blalign $r.mblks >> $r.maln
#	Make cobbler sequence = $r.mcob
   echo "TY	2"	     > $r.cf
   echo "BL	$r.mblks"   >> $r.cf
   echo "DB	$r.pros"    >> $r.cf
   echo "OU	$r.mcob"    >> $r.cf
   echo "SU	default.iij" >> $r.cf
   $bindir/blimps-bin/cobbler $r.cf >& /dev/null
else
   echo "ERROR: No blocks produced by MOTIF" >> $r.err
endif
#
#   	Clean up
rm motomat.err $t.mot $t.plt $t.blks $t.cblks >& /dev/null
#
#===========================================================
#	Make blocks using Gibbs now  
#
set minlen = (`grep " MINIMUM" $t.motifj.pros |  awk '{print $2}'`)
if ($minlen < 8) then
   echo "ERROR: Minimum sequence length is 8 for GIBBS" >> $r.err
   echo "ERROR: No blocks produced by GIBBS" >> $r.err
else
   #	Model heuristic; needs MINIMUM sequence length from $t.motifj.pros
   set model = (`$bindir/model.csh $t.motifj.pros`)
   $bindir/gibbs $t.motifj.pros $model -f -s3 >& $r.gblks

   #	Convert gibbs output for motomat
   grep ">" $r.lis > $t.temp
   cat $t.motifj.pros.sn >> $t.temp
   $bindir/blimps-bin/blk2mot $t.motifj.pros $t.temp $t.mot
   $bindir/blimps-bin/motomat $t.mot 1 1 -15 >& /dev/null
   if ( -e $t.blks ) then
      #  Calibrate blocks
      #       Make matrices and observed frequency files
      $bindir/blimps-bin/blk2pssm $t.blks $t.mats B 3 >& /dev/null
      $bindir/blimps-bin/blk2pssm $t.blks $t.obsf B 21 >& /dev/null
      #               writes pssmdist.dat
      $bindir/blimps-bin/pssmdist $t.mats $t.obsf $frq $NSEQ $NRES >& /dev/null
      #	This is bad, should change pssmdist.c to name the file
      mv pssmdist.dat $t.dist
      $bindir/blimps-bin/pssmBL $t.dist $t.blks $t.cblks >& /dev/null
      rm $t.dist

      #  Add weights to blocks
      $bindir/blimps-bin/blweight $t.cblks $r.gblks P M >& /dev/null
      #  	Make multiple alignment
      echo "              **BLOCKS from GIBBS**" > $r.galn
      $bindir/blimps-bin/blalign $r.gblks >> $r.galn
      #	Make cobbler sequence = $r.gcob
      echo "TY	2"	     > $r.cf
      echo "BL	$r.gblks"   >> $r.cf
      echo "DB	$r.pros"    >> $r.cf
      echo "OU	$r.gcob"    >> $r.cf
      echo "SU	default.iij" >> $r.cf
      $bindir/blimps-bin/cobbler $r.cf >& /dev/null
   else
      #  $r.gblks contains the Gibbs output now 
      cat $r.gblks >> $r.err
      echo "ERROR: No blocks produced by GIBBS" >> $r.err
      rm $r.gblks
   endif
endif
#
#---------------------------------------------------------------------------
#	Format PSSMs for MAST searches & make tree files & map files
if (-e $r.mblks) then
   $bindir/blimps-bin/blk2pssm $r.mblks $r.mmast M >& /dev/null
   #	Make block map files
   #	Need lengths of the sequences in the blocks - makelis creates $r.lis
   $bindir/blimps-bin/makeblockmap $r.mblks $r.mblks.mapfile -L$r.lis >& /dev/null
   #	Make tree files
   $bindir/blimps-bin/blalign $r.mblks -h > $r.fmblks
   if ($nseq < 3) then
      echo "Need at least 3 sequences to make a tree" >> $r.warn
   else
      if ( $nseq < 100) then
         @ nboot = 100
         (./quicktree -in a -out t -kimura -boot $nboot $r.fmblks > $r.mtree) >& $r.mout
      else
         (./quicktree -in a -out t -kimura $r.fmblks >& $r.mtree) >& $r.mout
      endif
   endif
#	If quicktree failed, get rid of the empty output file
   set nlin = 0
   if (-e $r.mtree) then
      set nlin = (`wc -l $r.mtree | awk '{print $1}'`)
   endif
   if ($nlin == 0) then
	rm $r.mtree >& /dev/null
        cat $r.mout >> $r.warn
   endif
   rm $r.mout
endif
#	Do the same for Gibbs
if (-e $r.gblks) then
   $bindir/blimps-bin/blk2pssm $r.gblks $r.gmast M >& /dev/null
   #
   $bindir/blimps-bin/makeblockmap $r.gblks $r.gblks.mapfile -L$r.lis >& /dev/null
   #	Make tree files
   $bindir/blimps-bin/blalign $r.mblks -h > $r.fgblks
   if ($nseq < 3) then
      echo "Need at least 3 sequences to make a tree" >> $r.warn
   else
      if ( $nseq < 100) then
         @ nboot = 100
         (./quicktree -in a -out t -kimura -boot $nboot $r.fgblks > $r.gtree) >& $r.gout
      else
         (./quicktree -in a -out t -kimura $r.fgblks >& $r.gtree) >& $r.gout
      endif
   endif
#	If quicktree failed, get rid of the empty output file
   set nlin = 0
   if (-e $r.gtree) then
      set nlin = (`wc -l $r.gtree | awk '{print $1}'`)
   endif
   if ($nlin == 0) then
	rm $r.gtree >& /dev/null
        cat $r.gout >> $r.warn
   endif
   rm $r.gout
endif

#---------------------------------------------------------------------------
#	Cat the blocks format blocks to the output in case they
#	want to do a search
if (-e $r.mblks) then
   echo "      **BLIMPS Searchable BLOCKS from MOTIF**" >> $r.search
echo "======================CUT HERE==============================" >> $r.search
   cat $r.mblks | tr '\015' ' ' >> $r.search
echo "======================CUT HERE==============================" >> $r.search
endif

if (-e $r.gblks) then
   echo "      **BLIMPS Searchable BLOCKS from GIBBS**" >> $r.search
echo "======================CUT HERE==============================" >> $r.search
   cat $r.gblks | tr '\015' ' '>> $r.search
echo "======================CUT HERE==============================" >> $r.search
endif

if (-e $r.mmast) then
   echo "      **MAST Searchable PSSMS from MOTIF**" >> $r.search
echo "======================CUT HERE==============================" >> $r.search
   cat $r.mmast | tr '\015' ' ' >> $r.search
echo "======================CUT HERE==============================" >> $r.search
endif

if (-e $r.gmast) then
   echo "      **MAST Searchable PSSMS from GIBBS**" >> $r.search
echo "======================CUT HERE==============================" >> $r.search
   cat $r.gmast | tr '\015' ' ' >> $r.search
echo "======================CUT HERE==============================" >> $r.search
endif

#		Show the trees
if (-e $r.mtree) then
   echo "      **CLUSTALW tree from MOTIF**" >> $r.search
echo "======================CUT HERE==============================" >> $r.search
   cat $r.mtree >> $r.search
echo "======================CUT HERE==============================" >> $r.search
endif

if (-e $r.gtree) then
   echo "      **CLUSTALW tree from GIBBS**" >> $r.search
echo "======================CUT HERE==============================" >> $r.search
   cat $r.gtree >> $r.search
echo "======================CUT HERE==============================" >> $r.search
endif


#------------------------------------------------------------------------------
#	Mail back the results if not working from WWW
if ($return != "WWW" && $return != "OLD") then
   #	Prepare the output file emailed to user
   cat $r.warn $r.err > $r.blk
   echo "Results available for 24 hours at" >> $r.blk
   echo "http://blocks.fhcrc.org/blocks-bin/bm_format.pl?$t" >> $r.blk
   echo "" >> $r.blk
   cat $r.maln >> $r.blk
   echo "" >> $r.blk
   cat $r.galn >> $r.blk
   /usr/bin/mailx -s "BlockMaker Results" -r "blocks@fhcrc.org" $return < $r.blk
   /usr/bin/mailx -s "BlockMaker Searchable Formats" -r "blocks@fhcrc.org" $return < $r.search
endif

#
#
#
#   	Clean up; leave $r.mblks and $r.gblks for logos link
#		  leave $r.mblks.mapfile & $r.gblks.mapfle for map link
#		  leave $r.mmast and $r.gmast for mast link
#		  leave $r.mtree and $r.gtree for tree link
#		  may also want to leave .mcob & .gcob ...
rm $t.*

exit(0)

set minseq = 3
set maxseq = 250
set wwwchar = 20000
set maxchar = 100000

#    Split up the input file name
#  If $1 = ../tmp/bm/AA/AAblimps-3.9/www/bin/pssm.sh000075500001460000012000000004440774335017600161010ustar00jorjastaff00000400000027#!/bin/sh 

blockfile=`echo $QUERY_STRING | awk '-F&' '{print $0}' | awk -F= '{print $1}'| sed 's/\%2F/\//g'`

echo Content-type: text/html
echo

cat << EOM

PSSM

                   Alignment positions ==>
||Amino acid score
\/

EOM

./blk_to_PSSM $blockfile 

echo "
      "


blimps-3.9/www/bin/sift.sh000075500001460000012000000053640775205300100160550ustar00jorjastaff00000400000027#!/bin/sh
#               sift.sh 
#
fasta=""
if [ $# -gt 0 -a -f "$1" ]
then
	./blimps-bin/blalign $1 -f > $1.fas
	fasta=`cat $1.fas`
fi
#  From the  to  is ~btest/www/codehop.html
#       with the blocks TEXTAREA modified to insert $blocks

cat << EOM
Content-type: text/html



SIFT:Submit aligned sequences

      

SIFT: Submit aligned sequences
      

      

      
Submit your query sequence along with other protein sequences that are aligned to it for SIFT.  Your query sequence is the sequence that you would like prediction on (i.e. the sequence in which you have introduced the amino acid substitutions).  
The query sequence should be first in the alignment.
  The alignment must correspond to the length of your query sequence (i.e. no gaps in your query sequence in the alignment).
Partial sequences should be flanked by Xes at the beginning and end of the sequence so that those positions are not considered gaps (and hence have liberal prediction).
[More info]
      

      

      
Entering sequences 
      
Enter your query sequence aligned with related sequences. These sequences are assumed to be functional, and is what SIFT will base its prediction on. The normal (functional) query sequence should appear first. 

      

      
Enter the name of the file containing your aligned sequences 

[clustal, msf, or fasta format].


      

      -or-

      
Paste in your aligned sequences 

[clustal, msf, or fasta format].
      


      

      

      
Optional fields
      

      
Entering substitutions.
      
Enter the substitutions that occur in the query sequence.
      

      
Enter the name of file containing substitutions of interest:
[format]:

      


      

      -or-

      
Enter the substitutions of interest:
[format]:

      


      
Account for Gaps

      
  If your alignment is especially gapped, turn this off.
      

      



      

      
Questions or comments?
      
Contact us 
      



EOM
exit
blimps-3.9/www/bin/rpsblast.csh000075500001460000012000000013620775205252700171130ustar00jorjastaff00000400000027#!/bin/csh
#	rpsblast.csh    
#	 = plus-psi|minus-psi|prints-psi
#	if  = blplus; go to $test directory
#
#echo 1=$1 2=$2 3=$3 4=$4
setenv BLASTFILTER /usr/local/filter
setenv NCBI /usr/local/blast
#setenv LD_LIBRARY_PATH /usr/lib:/usr/ucblib:/opt/local/lib
#
unalias cp
unalias rm

umask 006
chmod 660 $1
#	blast programs are intolerant of format deviations
./blimps-bin/fastaseqs $1 $1.fas >& /dev/null
if ($4 == 'T') then
   $BLASTFILTER/seg $1.fas -x > $1.imp
else
   cp $1.fas $1.imp
endif

if ($2 == "blplus" || $2 == "blminus" || $2 == "prints") then
#  $NCBI/rpsblast -i $1.imp -d ../impala/$2 -e $3 -z 0 -F $4
   $NCBI/rpsblast -i $1.imp -d ../impala/$2 -e $3 -z 0 
endif

rm $1 $1.fas $1.imp
#
exit(0)
blimps-3.9/www/bin/rpsblast.pl000075500001460000012000000273240776251005700167550ustar00jorjastaff00000400000027#!/usr/bin/perl

#	rpsblast.pl
# Execute rpsblast & display the output

#	Set file permissions to rw-rw----
system("umask 006");
$bin = "./";
$tmpdir = "../tmp";
$bdir = "../";
$ipbdir = "$bdir/data-blocks";
$prdir = "$bdir/data-prints";
$pfdir = "$bdir/data-pfam";
$bpdir = "$bdir/data-prodom";
$dmdir = "$bdir/data-domo";


# output the beginning text to be used on all pages
print "Content-type: text/html\n\n";
print "RPS-BLAST Results\n";
if ( $ENV{"REQUEST_METHOD"} ne "POST" ) {
   print "This script should be referenced with a METHOD of POST\n";
   exit;
}

read (STDIN, $QUERY_STRING, $ENV{"CONTENT_LENGTH"});
%names = &general_parse($ENV{"CONTENT_TYPE"}, $QUERY_STRING);

if ($names{database} =~ /minus/) { $db = "blminus"; }
elsif ($names{database} =~ /plus/) { $db = "blplus"; }
elsif ($names{database} =~ /prints/) { $db = "prints"; }
else { $db = "blplus";  }

#print "$names{database} $db\n";
if ($db eq "") { $db = "blplus"; }
#$db = $names{database};
#$db =~ /\s+//g;

if ($names{ex} eq "") { $names{ex} = "5"; }
$ex = $names{ex};

#	Get the sequence & write it to a file
if ($names{sequence} eq "") {
   print "
      Error
       Please enter a query sequence.
      \n";
   exit;
}
$seq = "../tmp/$$.seq";
open(SEQ, ">$seq");
print SEQ $names{sequence};
print SEQ "\n";
close(SEQ);

#	Filter flag, default is not to filter
$filt = "F";
if ($names{filter} eq "T") { $filt = "T"; }

#=========================================================================
#	Run shell now

$out = "../tmp/$$.out";
$arguments = $seq.' '.$db.' '.$ex.' '.$filt;
#print $arguments;
#	Only the first 2 arguments are getting passed this way
system("$bin/rpsblast.csh $seq $db $ex $filt > $out 2>&1");

#	why doesn't umask take care of this?
system("chmod 660 ../tmp/$$.*");

#=========================================================================
#	Format the output

print "\n";
print "Block Searcher RPS-BLAST Results\n";
print "
      Block Searcher RPS-BLAST Results
      \n";

print"
      \n";

$ac = "";
@blist = (); $nblock = 0; $bline = ""; 
open(OUT, "<$out");
while ($_ = )
{
  #   Put links on the list of hits
  if (/^IPB\d\d\d\d\d\d\S*/) {
    s|(^IPB\d\d\d\d\d\d)(\S*)|\1\2|g
  }
  elsif (/^BL\d\d\d\d\d\S*/) {
    s|(^BL\d\d\d\d\d)(\S*)|\1\2|g
  }
  elsif (/^DM\d\d\d\d\d\S*/) {
    s|(^DM\d\d\d\d\d)(\S*)|\1\2|g
  }
  elsif (/^PD\d\d\d\d\d\S*/) {
    s|(^PD\d\d\d\d\d)(\S*)|\1\2|g
  }
  elsif (/^BP\d\d\d\d\d\S*/) {
    s|(^BP\d\d\d\d\d)(\S*)|\1\2|g
  }
  elsif (/^PR\d\d\d\d\d\S*/) {
    s|(^PR\d\d\d\d\d)(\S*)|\1\2|g
  }
  elsif (/^PF\d\d\d\d\d\S*/) {
    s|(^PF\d\d\d\d\d)(\S*)|\1\2|g
  }
  #   Mark the blocks in the alignment
  elsif ($_ =~ m/^>/) 
  {
     @words = split(/\s+/, $_);
     $ac = $words[0]; $ac =~ s/^>//;
     if ($ac =~ m/^IPB/) { $dir = $ipbdir; }
     elsif ($ac =~ m/^PR/) { $dir = $prdir; }
     elsif ($ac =~ m/^PF/) { $dir = $pfdir; }
     elsif ($ac =~ m/^BP/) { $dir = $bpdir; }
     elsif ($ac =~ m/^DM/) { $dir = $dmdir; }
#print "ac=$ac dir=$dir\n";

      # Find >$ac in $dir/cobbler.pros and read cobbler sequence name
      #     & starting aa ">$ac seq_name from xxx to yyy"
      @blist = (); $nblock = 0; $bline = ""; 
      $cob_ac = "";
      open(GREP, "grep \"^>$ac\" $dir/cobbler.pros |");
      while($cob = )
      {
#print "$cob\n";
         ($cob_ac, $cob_seq, $junk1, $cob_start, $junk2, $cob_end)
		= split(/\s+/, $cob);
         $cob_ac =~ s/^>//;
         if ($cob_ac eq $ac)
         {
         # Find >$ac in $dir/maps.dat and read starting & ending locations of
         #     each block for cobbler sequence seq_name
         # NOTE: too slow to read $dir/maps.dat directly, thus getseq
            $mapfile = "$tmpdir/$ac.map";
            system("$bin/blimps-bin/getseq $ac $dir/maps.dat $mapfile > /dev/null");
#           open(MAP, "<$dir/maps.dat");
            open(MAP, "<$mapfile");
            while ( ($map = ) && !($map =~ m/^>$ac/) )
            { ;  }
            if ($map =~ m/^>$ac/)
            {
               @words = split(/\s+/, $map);
               $nblock = $words[1];
               while ( ($map = ) && !($map =~ m/^>/) &&
                 !($map =~ m/^$cob_seq/) )
               { ;  }
               if ($map =~ m/^$cob_seq/)
               {
                  $i = 0;
                  while( ($i < $nblock) && ($map = ) )
                  {
                     ($block, $start, $end) = split(/\s+/, $map);
                     @blist = (@blist, $block, $start, $end);
                     $i++;
#print "$block $start $end\n";
                  }
               }
            }
            close(MAP);
            system("rm -f $mapfile");
         }
      }  # end of cobbler file
#print "cobac=$cob_ac $cob_seq $cob_start $cob_end\n";
  } # end of ^>

  elsif ($_ =~ m/^Sbjct: /) 
  {
  # Read each Sbjct line until next ^> line "Sbjct: "
  #     Subtract (xxx-1) from , compare it with block start/end
  #     If Sbjct line is within a block, insert line afterwards
     $bline = ""; $bpos = 0;
     if ($nblock > 0)
     {
        ($junk1, $sstart, $sseq, $send) = split(/\s+/, $_);
        $bsstart = $sstart + $cob_start - 1;	# Sbjct location in block
        $bsend = $send + $cob_start - 1;	# Sbjct location in block
        $gaps = 59 - ($bsend - $bsstart);	# Number of gaps in Sbjct
        $bline = "$ac";

        # distance between ^Sbjct: and start of sequence varies, us. 11 or 12
        # try to figure out what it is
        $subseq = substr($_, 6, 10);	# 10 chars after ^Sbjct:
        $sublen1 = length($subseq);
#print "subseq=$subseq\n";
        $subseq =~ s/[0-9]//g;		# remove numbers & spaces
#print "subseq=$subseq\n";
        $subseq =~ s/\s+//g;
#print "subseq=$subseq\n";
        $sublen2 = length($subseq);
        $skip = 6 + ($sublen1 - $sublen2); # Sbjct: + numbers & spaces
#print "sublen1=$sublen1 sublen2=$sublen2 skip=$skip\n";

        for ($i=length($ac); $i < $skip; $i++)	# Assumes "^Sbjct: nnn  "
        { $bline = "$bline" . " "; }
        $bpos = $bsstart; $sbjctpos = 0;
        for ($i=0; $i<$nblock; $i++)
        {
           $k = $i * 3;			# 3 elements in @blist
           ($block, $start, $end) = ($blist[$k], $blist[$k+1], $blist[$k+2]);
#print "bsstart=$bsstart bsend=$bsend block=$block start=$start end=$end\n";
           if ($end >= $bpos && $start <= $bsend)	# block touches
           {
              if ($end > $bsend) { $last = $bsend; }
              else { $last = $end; }
              if ($start > $bpos)
              {   
                 # If there are gaps in Sbjct before $start, have to skip over
		 #>>> wrong if gaps within the block <<<
                 $nextgap = index($sseq, "-", $sbjctpos); # -1 if none, else pos
                 if ($nextgap >= 0)
                 {
                    $sublen = $start - $bpos;
                    $subseq = substr($sseq, $sbjctpos, $sublen);
#print "subseq=$subseq\n";
                    $sublen1 = length($subseq);
                    $subseq =~ s/-//g;		# remove the gap characters
                    $sublen2 = length($subseq);
                    $ngaps = $sublen1 - $sublen2; # number of gaps in subseq
#print "start=$start bpos=$bpos sbjctpos=$sbjctpos sublen=$sublen ngaps=$ngaps\n";
                 }
                 for ($pos = $bpos; $pos < $start + $ngaps; $pos++)
                 { $bline = "$bline" . " "; $bpos++; $sbjctpos++; }
                 $bpos -= $ngaps;  # should be true block position
              }
#print "bpos=$bpos end=$end bsend=$bsend last=$last\n";
              for ($pos = $bpos; $pos <= $last; $pos++)
              { $bline = "$bline" . "$block"; $bpos++; $sbjctpos++; }
           }
        }  # end of blocks
        $bline = "$bline" . "\n";
     } # end of if blocks
  }
  print $_;
  if ($bline ne "") { print $bline; $bline = ""; }
}
close(OUT);

print "
      ";
print "
      [return to top]
      ";
#-------------------------------------------------------------------------
exit (0);


#-------------------------------------------------------------------------
# $names = &general_parse($ENV{CONTENT_TYPE}, $QUERY_STRING);
# parameters:	CONTENT_TYPE
#		QUERY_STRING
# returns: an associative array of name/value pairs.  The name is the key.

# WARNING:  Some of this routine is program-dependent!!!

# CONTENT_TYPE: application/x-www-form-urlencoded
# QUERY_STRING: key1=val1&key2=val2

# CONTENT_TYPE: multipart/form-data; boundary=
# QUERY_STRING: 
#		Content-Disposition: form-data; name="key1"
#		
#		val1
#		
#		Content-Disposition: form-data; name="key2"
#		
#		val2
#		

sub general_parse {
  local($content_type, $query_string) = @_;
  local(%ans, @q, $pair, $loc, $boundary, $temp, $temp1);

  if ($content_type eq "application/x-www-form-urlencoded")
  {
     # break up into individual name/value lines
     @q = split(/&/, $query_string);

     foreach $pair (@q) {
       # break the name/value pairs up
       # use split rather than regular expressions because the value may have
       #  newlines in it
       split(/=/, $pair, 2);

       # change '+' to ' '
       $_[1] =~ s/\+/ /g;
   
       # change the escaped characters (must be after the split on '&' and '=')
       $_[1] =~ s/%(..)/pack("c",&hextodec("$1"))/eg;

       $ans{$_[0]} = $_[1];
     }

  }
  else
  {
     $loc = index($content_type, "boundary=");
     if ($loc > 0)
     { 
        $temp = substr($content_type, $loc+9);
#		Why is this necessary? (boundary= doesn't match actual)
	$boundary = "--".$temp;
#print "
      ";
#print "$query_string\n";
#print "boundary=$boundary\n";
        # break up into individual name/value lines
        @q = split(/$boundary/, $query_string);
        foreach $pair (@q) {
          # break the name/value pairs up
#print "pair=$pair\n";
          $loc = index($pair, "name=");
	  $temp = substr($pair, $loc+5);
#	  $loc = index($temp, "\n\n");
 	  $loc = index($temp, "\n");
	  $temp1 = substr($temp, $loc+2);
#print "1temp=$temp\ntemp1=$temp1\n";
#		Get rid of stuff after the name; including semicolon if any
	  $loc_semi = index($temp, ";");
	  $loc_eol = index($temp, "\n");
	  $loc = $loc_eol;
          if ($loc_semi > 0 && $loc_semi < $loc) {$loc = $loc_semi; }
	  if ($loc > 0) { $temp = substr($temp, 0, $loc); }
#		Get rid of quotes around the name
          $temp =~ s/\"//g;
#		Still has a trailing whitespace character ...
          $temp =~ s/\s//g;
#		Need to strip leading/ending whitespace off of $temp1,
#		but be careful not to strip off internal CRs
#>>>>>       Following line is program-dependent !!!
	  if ($temp ne "dbfile" && $temp ne "sequence" && $temp ne "database")
 	  { $temp1 =~ s/\s//g; }
#		MAC file lines end in just \r, no \n, so makelis won't find all
#		of the sequences; DOS file lines end in \r\n, UNIX in \n.
	  if ($temp eq "seqfile")
#	  { $temp1 =~ s/\r/\n/g; $temp1 =~ s/\n\n/\n/g; }
#		Change \r\n to \n and then \r to \n
 	  { $temp1 =~ s/\r\n/\n/g; $temp1 =~ s/\r/\n/g; }
#print "2temp=$temp\ntemp1=$temp1\n";
	  if ($temp ne "") { $ans{$temp} = $temp1; }
        }
     }
     else
     {  print "Cannot parse\n";  
        print "content_type=$content_type\n";
        print "query_string=$query_string\n";
     }
  }
  return %ans;
#print "
      ";
}   # end of general_parse
#-------------------------------------------------------------------------
# parameter: a hex representation of a number (doesn't need to be a string)
# returns: the decimal representation of the number
sub hextodec {
  unpack("N", pack("H8", substr("0" x 8 . shift, -8)));
}

blimps-3.9/www/bin/showblock.sh000075500001460000012000000022630775501400600171030ustar00jorjastaff00000400000027#!/bin/sh

#  A shell to show a block in a html format using the retblock program
#  and unix shell commands. 
#  Usage showblock.sh blocks_file_name block_accession.
#  The block header, sequence weights and end string ("//") are removed.

RETBLOCK=./blimps-bin/retblock

if [ $# -ne 2 ]
then
   cat << EOM
Content-type: text/html


Extract block error

      Extract block error
      
Wrong number of arguments given. There should be two arguments: the blocks file name and the accession code of the required block(s).

EOM
   exit 1
else
cat << EOM
Content-type: text/html


Block(s) $2

      EOM
fi

DB=$1
BLKNAME=$2

# extract block. remove header lines (except for the block accession), the last 3 chars in each remaining line (the sequence weights) and the "\\" string with "--".
$RETBLOCK $DB $BLKNAME -n | grep -v "ID   " | grep -v "DE   " | grep -v "BL   "| sed -e 's|^AC   ||' -e 's|...$||g' -e 's|; distance.*$||' -e 's|//$||'

#>>> $status is set by csh, but apparently not by sh
#if [ $status -ne 0 ]
#then
#cat << EOM
#
      
#Could not extract block $2. Sorry.
#
#EOM
#   exit 1
#else
cat << EOM

      

EOM
#fi

exit 0

blimps-3.9/www/bin/tree.csh000075500001460000012000000026230774335020400162120ustar00jorjastaff00000400000027#!/bin/csh
#      tree.csh 		Make a tree from a set of blocks
#	creates .treefile
#   where  is a file containing the blocks to be processed
#
unalias rm
unalias mv
limit cputime 5m
#
set mach = `uname -n`
#  If $1 = /howard/btest/tmp/AA.blks, then $r = /howard/btest/tmp/AA
#
if ( -e $1 ) then
#
   set r = $1:r
#	Make clustalw tree file
   ./blalign $1 -f > $r.fblks
   if ( -e $r.fblks ) then
      set nseq = (`grep -c ">" $r.fblks`)
      if ( $nseq <= 25 || $mach == muller) then
#		always use 100 bootstraps
         @ nboot = 100
#        echo "      **CLUSTALW tree (bootstrap=$nboot)**" >> $r.treefile
#		drawgram requires bootlabels=node (default is branch)
         ./clustalw $r.fblks -bootstrap=$nboot -bootlabels=node -kimura >& /dev/null
         if (-e $r.phb) then
#           cat $r.phb >> $r.treefile
            mv $r.phb $r.treefile
         else
            echo "clustalw failed to make a tree" > $r.treefile
         endif
      else
#        echo "      **CLUSTALW tree (no bootstrap)**" >> $r.treefile
         ./clustalw $r.fblks -tree -kimura >& /dev/null
         if (-e $r.ph) then
#           cat $r.ph >> $r.treefile
            mv $r.ph $r.treefile
         else
            echo "clustalw failed to make a tree" >> $r.treefile
         endif
      endif
      rm $r.fblks
   endif
#  
else
   echo "Cannot open blocks file $1 to make a tree." >> $r.treefile
endif
#
exit(0)
blimps-3.9/www/bin/wave000064400001460000012000000000000774505302500154240ustar00jorjastaff00000400000027blimps-3.9/www/bin/getblock.pl000075500001460000012000000251221040611562600166770ustar00jorjastaff00000400000027#!/usr/bin/perl

# getblock.pl

#	Set file permissions to rw-rw----
system("umask 006");

select(STDOUT); $| = 1;

print "Content-type: text/html\n\n";
print "Blocks Information\n";

if (@ARGV > 0 ) { $group = $ARGV[0]; }
else
{
   read (STDIN, $QUERY_STRING, $ENV{"CONTENT_LENGTH"});
   %names = &parse_query($QUERY_STRING);
   $group = $names{group};
}
#	Strip off any alpha chars at end
$group =~ s/[A-Z]$//;
#print "group=$group\n";
if ($group eq "")
{
   print "
      ERROR: Please enter a Blocks family (e.g. IPB001525).
      \n";
   exit(-1);
}
$blocks_flag = 0;
$prints_flag = 0;
if ($group =~ m/^IPB/) { $blocks_flag = 1; }
elsif ($group =~ m/^IPR/) { $group =~ s/^IPR/IPB/; $blocks_flag = 1; }
elsif ($group =~ m/^PR/) { $prints_flag = 1; }
if ($blocks_flag == 0 && $prints_flag == 0)
{
   print "
      ERROR: $group is not a recognized Blocks family.
      \n";
   exit(-1);
}

#print "
      Get Block $group
      \n";
#print "\n";
print "
      Blocks Information for $group
      \n";


#=========================================================================
   
print "
      \n";
if ( $blocks_flag )
{
   $ipr = $group; $ipr =~ s/^IPB/IPR/;
   $bdir = "../data-blocks";
   $maptype = "IPB";
}
elsif ( $prints_flag )
{
   $bdir = "../data-prints";
   $maptype = "PR";
}
$head = "$bdir/bhead";
$blks = "$bdir/blks/$group.blks";
$map = "$bdir/maps/$group.map";
$tree = "$bdir/trees/$group.tree";
$cob = "$bdir/cobs/$group.cob";
$pdbs = "$bdir/pdbs/$group.pdb";
$pros = "$bdir/pros/$group.pros";

#	Read the blocks into memory to get the DE and list of ACs
open (IN, "<$blks");
@blocks = ;
close(IN);
$id = $de = "";
@acs = ();
foreach $in_rec (@blocks)
{
   if ($in_rec =~ m/^AC   /)
   {
     ($ac) = $in_rec =~ m/^AC   (\S+)/;
     $ac =~ s/;//g;
     @acs = (@acs, $ac);
   }
   elsif ($id eq "" && $in_rec =~ m/^ID   /)
   {
     ($id) = $in_rec =~ m/^ID   (\S+)/;
     $id =~ s/;//g;
   }
   elsif ($de eq "" && $in_rec =~ m/^DE   /)
   {
     ($de) = $in_rec =~ m/^DE   (.+)/;
   }
}
#----------------------------------------------------------------------
#  Start printing
print "Blocks Information for $group\n";
if ($#acs < 0)
{
   print "
      ERROR: No blocks found for $group.
      \n";
   exit(-1);
}

print "
      $group: $id
      \n";
print "
      $de
      \n";

print "
      \n";
print "
        \n";
print "
      •  Introduction\n";

foreach $ac (@acs)
{
   print "
      •  Block number ", $ac, "\n";
}

print "
        \n";
if ($blocks_flag)
{
   print "
      • ";
   print "InterPro entry  $ipr" ;
   print " (source of sequences used to make blocks)\n";
}
elsif ($prints_flag)
{
   print "
      • ";
   print "PRINTS Entry  $group";
   print " (source of blocks)\n";
}

print "
        \n";
print "
      • Block Maps.";
print "[Graphical Map]";
print "     [Text Map]";
print "     [Map Positions]";
print "     [About Maps]";

print "
        \n";
print "
      • Logos.";
print "[About Logos]";
print "
        Select display format: ";
if (-e "../logos/$group.gif")
{  
   print "[GIF] \n"; 
   print "[PDF] ";
}
else
{  
   print "[GIF] ";
   print "[PDF] ";
}
print "[Postscript] ";

#	Some groups with < 4 seqs don't have trees
if ( -s "$tree" )	# $ntree > 0 ???
{
print "
        \n";
print "
      • Tree from blocks alignment. ";
print "[About Trees]  ";
print "[About ProWeb TreeViewer]  ";
print "
        [Data]  ";
print " [ProWeb TreeViewer] ";
print "[XBitmap]  ";
print "[GIF] ";
print "[PDF] ";
print "[Postscript]  ";
#print "[Newick] ";
}

if (!(-z $pdbs))
{
   print "
      • Structures\n";
}

print "
        ";
print "
      • Search blocks vs other databases:
        ";

print "
        ";
print "
      • ";
print "CODEHOP";
print " to design PCR primers from blocks";
print "     [About CODEHOP]";

print "
        ";
print "
      • ";
print "SIFT";
print " to predict amino acid substitutions in blocks";
print "     [About SIFT]";
print "
        \n";

print "
        ";
print "
      • ";
print "Re-format";
print " blocks as a multiple alignment ";
print "
        \n";

#
print "
      \n";
print "      \n";
print "
      \n";

#------------------------------------------------------------------------
# Header
print "
      ";
open (IN, "<$head");
foreach $in_rec ()  { print "$in_rec"; }
close (IN);

print "
      [Return to top]
      \n";

#-----------------------------------------------------------------------
# Output Blocks
foreach $in_rec (@blocks)
{
  if ($in_rec =~ m/^ID   /)
  {  $id_rec = $in_rec;   }
  elsif ($in_rec =~ m/^AC   /)
  {
     $ctemp = $in_rec;
     ($ac) = $ctemp =~ m/^AC   (\S+)/;
     $ac =~ s/;//g;
     print "
      Block ", $ac, "";
     print "
      \n";
     print "$id_rec";
     print "$in_rec";
  }
  elsif ($in_rec =~ m/^DE   / || $in_rec =~ m/^BL   /)
  {  print "$in_rec";  }
  else
  {
    $ctemp = $in_rec;
    $ctemp =~ s/\s+//g;
    if ($ctemp eq "") { print "$in_rec"; }	#  blank line
    elsif ($in_rec =~ /\s*\S+\ +\(/) 		#  sequence?
    {
      ($in_rec =~ /^\s*(\S+)/) && ($sid = $1) if $in_rec =~ /\s*\S+\ +\(/;
      #	Assume we have a sequence name == $sid; could be "id|ac", 
      #	if so, use just	the ac part in the link
      @bar = split(/\|/, $sid);
      if (@bar[1] ne "") {$sid = @bar[1]; }
      $in_rec =~ s|(\s*)(\S+)(.*)|\1\2\3| if  $in_rec =~ /\s*\S+\ +\(/;
      print $in_rec;
    }  # end of sequence line
    else { print $in_rec; }	#  unknown line
  }
}  # end of blocks file
close(IN);
print "
      [Return to top]
      \n";

#-------------------------------------------------------------
# Output the COBBLER sequence
#  Read it into memory
open (IN, "<$cob");
@cobseq = ;
close(IN);

print "
      COBBLER sequence (region containing Blocks only)
      \n";

print "To do a BLAST search, copy the cobbler sequence";
print " below then click on a BLAST link
      \n";

#	Print sequence for blast search
print "[Blast Search]\n";

#	Print sequence again for gap-blast search
print "[Gap-Blast Search]\n";

#	Print sequence again for psi-blast search
print "[PSI-Blast Search]\n";

#	Print sequence to the screen
print "
      ";
foreach $in_rec (@cobseq)
{ print "$in_rec"; }
print "
      [Return to top]
      \n";
print "";

#-------------------------------------------------------------------------
exit (0);

#-------------------------------------------------------------------------
#
# parameter: a string that is the html QUERY_STRING environment variable
# returns: an associative array of name/value pairs.  The name is the key.
sub parse_query {
  local($query_string) = @_;
  local(%ans, @q, $pair);
#print $query_string;
  # break up into individual name/value lines
  @q = split(/&/, $query_string);

  foreach $pair (@q) {
    # break the name/value pairs up
    # use split rather than regular expressions because the value may have
    #  newlines in it
    split(/=/, $pair, 2);

    # change '+' to ' '
    $_[1] =~ s/\+/ /g;

    # change the escaped characters (has to be after the split on '&' and '=')
    $_[1] =~ s/%(..)/pack("c",&hextodec("$1"))/eg;

    $ans{$_[0]} = $_[1];
  }

  return %ans;
}

# parameter: a hex representation of a number (doesn't need to be a string)
# returns: the decimal representation of the number
sub hextodec {
  unpack("N", pack("H8", substr("0" x 8 . shift, -8)));
}
bases:
      


      

      
Blocks home


      
Contact us 
      
Page last modified Nov 2003

blimps-3.9/www/papers.html000064400001460000012000000244421037442141200161560ustar00jorjastaff00000400000027
Blocks Manuscripts

      Blocks Manuscripts
      


      
S. Henikoff & J.G. Henikoff, "Automated assembly of protein blocks
for database searching", Nucl. Acids Res. 19:6565-6572 (1991).

      
PubMed

Postscript

PDF


      
S. Henikoff & J.G. Henikoff,
"Amino acid substitution matrices from protein blocks" Proc 
Natl. Acad. Sci. USA, 89:10915-10919 (1992).

      
PubMed

Postscript

PDF


      
S. Henikoff & J.G. Henikoff,
"Performance evaluation of amino acid substitution matrices" 
Proteins 17:49-61 (1993).

      
PubMed

Postscript

PDF


      
S. Henikoff & J.G. Henikoff,
"Protein family classification based on searching a database
of blocks." Genomics 19:97-107 (1994). 

      
PubMed

Postscript

PDF


      
S. Henikoff & J.G. Henikoff,
"A Protein Family Classification Method for Analysis of Large
DNA Sequences." Proceedings of the 27th Ann. Hawaii Intl. Conf. on
System Sciences pp. 265-274 (1994).

      
Postscript

PDF


      
S. Henikoff & J.G. Henikoff,
"Position-based sequence weights" J. Mol. Biol. 243:574-578 (1994).

      
PubMed

Postscript

PDF


      
S. Henikoff, J.G. Henikoff, W.J. Alford & S. Pietrokovski,
"Automated construction and graphical presentation of
protein blocks from unaligned sequences". Gene-COMBIS, Gene 163 (1995) GC17-26.

      
PubMed

Gene-COMBIS Article

Postscript

PDF


      
S. Pietrokovski, J.G. Henikoff & S. Henikoff, "The Blocks database -
a system for protein classification" NAR 24:197-200 (1996).

      
PubMed

NAR Article

Postscript

PDF


      
Jorja G. Henikoff and Steven Henikoff, "Using substitution probabilities
to improve position-specific scoring matrices", CABIOS 12:135-143(1996).

      
PubMed

Postscript

PDF


      
S. Pietrokovski, "Searching Databases of Conserved Sequence Regions by
Aligning Protein Multiple-Alignments", NAR 24:3836-3845 (1996).

      
PubMed

NAR Article 

Postscript

PDF


      
Jorja G. Henikoff and Steven Henikoff, "Blocks database and its applications",
Meth. Enzymol. 266, 88-105 (1996).

      
PubMed

Postscript

PDF


      
J.G. Henikoff, S. Pietrokovski & S. Henikoff, "Recent enhancements to the
blocks database servers", Nucl. Acids Res. 25:222-226 (1997). 

      
PubMed

NAR Article

Postscript

PDF


      
S. Henikoff & J.G. Henikoff, "Embedding strategies for effective use of
information from multiple sequence alignments", Protein Science 6:698-705
 (1997).

      
PubMed

Postscript

PDF


      
S. Henikoff, S. Pietrokovski & J.G. Henikoff, "Superior performance in
protein homology detection with the Blocks Database servers",
Nucl. Acids Res. 26:309-312 (1998). 

      
PubMed

NAR Article

Postscript

PDF


      
T.M.Rose, E.R.Schultz, J.G.Henikoff, C.M.McCallum & S. Henikoff,
"Consensus-degenerate hybrid oligonucleotide primers for amplification
of distantly-related sequences", Nucl. Acids Res. 26:1628-1635 (1998).

      
PubMed

NAR Article

Postscript

PDF


      
J.G. Henikoff, S. Henikoff &  S. Pietrokovski, "New features
of the Blocks Database servers", Nucl. Acids Res. 27:226-228 (1999). 

      
PubMed

NAR Article

PDF


      
S. Henikoff, J.G. Henikoff & S. Pietrokovski, "Blocks+: A non-redundant database
of protein alignment blocks derived from multiple compilations",
Bioinformatics 15:471-9 (1999).

      
PubMed

Bioinformatics Article

PDF



      
J.G. Henikoff, E.A. Greene, S. Pietrokovski & S.Henikoff, "Increased coverage
of protein families with the blocks database servers", 
Nucl. Acids Res. 28:228-230 (2000). 

      
PubMed

NAR Article



      
S. Henikoff and J.G. Henikoff, "Amino acid substitution matrices",
Adv. Protein Chem. 54:73-97 (2000).

      
PubMed

PDF


      
P.C. Ng, J.G. Henikoff & S. Henikoff, "PHAT: a transmembrane-specific
substitution matrix" Bioinformatics 16:760-6 (2000).

      
PubMed

Bioinformatics Article

PDF

      
P.C. Ng & S. Henikoff
"SIFT: Predicting amino acid changes that affect protein function",
NAR, 31.13:3812-3814 (2003).

      
PDF

      
T.M Rose, J.G. Henikoff & S. Henikoff
"CODEHOP PCR Primer Design",
NAR, 31.13:3763-3766 (2003).

      
PDF


blimps-3.9/www/blocks_biblio.html000064400001460000012000000104551015320043000174460ustar00jorjastaff00000400000027
BLOCKS Bibliography

      BLOCKS Bibliography
      

      

Blocks papers in  Postcript and PDF format.


      
The current references for the Blocks Database are:

      

        

      • 
J.G. Henikoff, E.A. Greene, S. Pietrokovski & S. Henikoff, "Increased
coverage of protein families with the blocks database servers",
Nucl. Acids Res. 28:228-230 (2000).

        
MEDLINE

NAR Article


        

      • 
S. Henikoff, J.G. Henikoff & S. Pietrokovski, "Blocks+: A non-redundant
database of protein alignment blocks dervied from multiple compilations",
Bioinformatics 15(6):471-479 (1999).

        
MEDLINE

PDF


      




      
If you use the Block Searcher as a tool in your
published research, we ask that you cite:

      

        

      •  
S. Henikoff & J. G. Henikoff, 
"Protein family classification based on searching a database
of blocks", Genomics 19:97-107 (1994). 

        
MEDLINE

Postscript

PDF

      


      
If you use the Block Maker as a tool in your
published research, we ask that you cite:

        

        

      •  
S. Henikoff, J. G. Henikoff, W. J. Alford & S. Pietrokovski, 
"Automated construction and graphical presentation of protein blocks
from unaligned sequences", Gene-COMBIS, Gene 163 (1995) GC 17-26.

        
MEDLINE

Gene-COMBIS Article

Postscript

PDF

      

      

If you use LAMA as a tool in your published research, we ask
that you cite:

      

        

      • 
S. Pietrokovski, "Searching Databases of Conserved Seqeuence Regions by
Aligning Protein Multiple-Alignments", Nucl. Acids Res. 24:3836-3845 (1996).

        
MEDLINE

NAR Article

Postscript

PDF

      

If you use CODEHOP as a tool in your published research, we ask
that you cite:

      

        

      • 
T.M. Rose, E.R. Schultz, J.G. Henikoff, C.M. McCallum & S. Henikoff,
"Consensus-degenerate hybrid oligonucleotide primers for
amplification of distantly-related sequences", Nucl. Acids Res. 26:1628-1635
(1998).

        
MEDLINE

NAR Article

Postscript

PDF

      

If you use SIFT as a tool in your published research, we ask
that you cite:

      

        

      • 
P.C. Ng and S. Henikoff, "SIFT: Predicting deleterious substitutions",
Genome Res. 11:863-874 (2001).

        
MEDLINE

PDF

      


      
[Blocks Home]


      
Contact us 
      
Page last modified Nov 2004

 Genomics 19:97-107 (1994). 

      
MEDLINE



LAMA help


      


      What does LAMA do?
      
LAMA (Local Alignment of Multiple Alignments) is a program for comparing 
protein multiple sequence alignments with each other. The program can search 
databases of such multiple alignments. The search is for sequence 
similarities between conserved regions of protein families.
The method is sensitive, detecting weak sequence 
relationships between protein families. Sequence similarities 
beyond the range of conventional sequence database searches can be 
detected by the method.
      


      What can LAMA do for me?
      
LAMA can identify protein families similar to your protein(s) of interest
and protein motifs similar to conserved regions in your protein(s). The
information known about these similar families and motifs can help you
identify the function and structure of your protein and locate critical
conserved regions in your protein(s). This can direct you in
designing experiments to test your hypotheses.
      

LAMA compares multiple sequence alignments of proteins. 
If you have only a single protein sequence you first need to 
find other members of its family. The protein sequences also need to 
be multiply aligned. The Content of input
section explains how to find related sequences and align them.
      


      How does LAMA align blocks?
      
The multiple alignments are first transformed into position specific 
scoring matrices (PSSMs). Each column in 
the PSSM corresponds to a position in the 
alignment and has the amino acid distribution of that position. The 
transformation into the PSSM is done with position-based sequence weights 
(Henikoff & Henikoff, 1994a) 
and odd ratios between the amino acid frequencies 
observed in the multiple alignments and the frequencies expected 
from protein databases 
(Henikoff & Henikoff, 1995). 
The transformation corrects possible overrepresentation of some 
sequences by sequence weighting and considers the background 
frequencies of the amino acids. 
The method was tested and calibrated with ungapped local multiple alignments 
(blocks) from the 
Blocks Database
.
       

The matrices are treated as sequences of columns, enabling 
their alignment with one another. To use algorithms developed for
aligning single sequences we need a measure for comparing pairs of 
matrix columns. This corresponds to the substitution matrices 
(PAM, BLOSUM etc.) used in single-sequence alignments. The
measure used in our method to score the similarity between pairs of 
matrix columns is the Pearson correlation coefficient (r): 

where A(i) and B(i) are the values of amino acid i in columns A and B, 
respectively, and /A and /B
are the means of the values in columns A and B.
The correlation score ranges from 1 for columns with identical 
amino acid distributions to -1 for columns with opposite 
distributions (in each column only 10 amino acids occur and 
those 10 amino acids are different in the two compared 
columns).
      

The score of a block-to-block alignment is the sum of the scores from 
comparing the corresponding columns in the two block matrices: 
      


      Local alignment of blocks.
Positions 2 to 7 from block A aligned with positions 4 to 9 from 
block B. A column comparison score, s(Xn*Ym), is calculated for 
each pair of positions (A2*B4 to A7*B9). The score of the alignment 
of the two segments, S, is the sum of the column comparison scores.

      

 The alignment is done using the Smith-Waterman algorithm for optimal 
local alignments. No gaps are allowed since the aligned objects are 
short conserved sequence regions. All alignments above the cutoff score 
are reported for each pair of compared blocks. There may be cases where parts
of one long block are similar to several blocks:

      	AAAAAAAAAAAAAAAAAAA
	 BBB       CCCCCC

      



      Input for LAMA
      


      Content of input
      
 LAMA can compare any multiple alignment if it is in the correct format.
However, the 
column comparison measure and 
the significance estimation of the scores
are appropriate for protein sequence blocks - ungapped conserved multiple 
alignments. The use of other types of multiple alignments, such as global 
multiple alignments that include many gaps, may give misleading results.
For example, the resulting alignments may not be optimal or their 
significance different from what the output suggests.

      

 If you only have a single protein sequence or want to find more protein
sequences related to yours you can search the sequence databases.
One way to do this on the WWW is using the 

BLAST program to search the
NCBI sequence databases. 
Links to other search methods can be found at 
the Baylor College of Medicine Human Genome Center

Search Launcher site.
      

 The BlockMaker WWW site can be used
for finding blocks in your group of related protein sequences. There are 
various other methods for making protein multiple sequence alignments. 
Among these are the 

MEME system,

Gibbs sampling programs, 
the 
MACAW interactive program, and
the 
CLUSTAL-W progressive multiple alignment program. 
Several of these methods are available through the 

multiple sequence alignment page 
at the Baylor College of Medicine Human Genome Center.

      

Multiple alignments submitted to the program should be of conserved, 
relatively ungapped, protein sequence regions. A few gaps in the 
alignment are acceptable. The more sequences are in the alignment the 
better. In general, avoid alignments with less than 4 sequences.

      



      Format of input
      
LAMA only accepts input in the 
Block format. Other multiple
alignments can be 
reformatted to the Block format. If you are not sure of your 
multiple alignment or just have a group of related
sequences you can use the 
BlockMaker program for 
finding blocks in the sequences. Note that to avoid biassed sequence 
representation blocks include sequence weights.
      


      Output options
      

        

      • Output level
         
The standard output displays pairs of 
blocks with alignment scores above a 
Z score cutoff. When both target and query blocks are given 
by the user there are options for also seeing the 
column scores composing the alignment score 
for every reported alignment and the PSSMs
of all the compared blocks.
        


      • Score cutoff
        
The default cutoff value is 5.6 Z scores. When both target and query 
blocks are given by the user different cutoffs can be specified. 
Giving a lower value will allow reporting of weaker alignments. 
Alignments with low values can occur by chance between unrelated 
blocks. Raising the cutoff score may exclude potentially genuine 
alignments. The expected number of 
occurrences should be used to 
evaluate the alignment scores.

      
Some of the examples included in this document
illustrate the use of the options.
      



      Output from LAMA
      


      Content and format of output:
      

      
LAMA version 1.00 October 96.

Minimal length of reported alignments   4
Score cutoff is 5.6 Z score units (in the top 7.7e-05 percentile of chance scores)


                                            alignment     Z-score  expected number for 
block 1   from:to       block 2   from:to   length                 searching 5000 blocks
BL01063B   20 :  46 and BL00042B    3 :  29 (27) score  39 ( 7.2  1.3e-02) [alignment Logos?]
BL01063B    5 :  39 and BL00324C    3 :  37 (35) score  27 ( 6.1  1.5e-01) [alignment Logos?]
BL01063B   12 :  47 and BL00622     8 :  43 (36) score  33 ( 8.2  0.0e+00) [alignment Logos?]
BL01063B   10 :  46 and BL00894A    1 :  37 (37) score  26 ( 5.7  3.2e-01) [alignment Logos?]
BL01063B    4 :  42 and BL01043A    2 :  40 (39) score  29 ( 8.1  0.0e+00) [alignment Logos?]

      

The program version and execution parameters head the search output. 
Only alignments longer than the minimal length will 
be reported. The significance of very short alignments (fewer than 4 
positions) 
cannot be reliably estimated. Alignments with scores equal or above 
the score cutoff will be reported. 
The score cutoff is specified as a Z score. 
Z score is 
the number of standard deviations between the score and the mean score. 
The mean score and the standard deviations 
were calculated for the random scores from the alignment of a large number 
of shuffled unbiassed blocks (7 million block pairs; 
see first supplement).
The Z score is related to the percentile of the score 
in the shuffled blocks scores. This dependence is not linear but sigmoidal
(see second supplement).
      
For each reported alignment the program shows the names of the two 
aligned blocks, 
their position relative to one another,
the alignment length,
the score, 
and the expected number
of such scores when searching a given number of blocks. 
The expected number is for chance (random) 
alignments of unbiassed blocks. 
It is calculated from the score percentiles between the shuffled 
unbiassed blocks.
In this example the expected number is for searching 5000 blocks. 
Blocks from the 
Blocks Database
and from the
Prints database 
will be linked to the database entries. The "alignment" link 
(alignment) 
shows the alignment of the two blocks. This can also be seen by 
following the "logos" 
(Logos) 
link that shows the sequence logos 
of aligned pairs of blocks.
Sequence logos are graphical representations 
of the blocks. 
For example, 
here 
(PostScript viewer required) the logo of block 
BL00622
is shifted 4 positions relative to the logo of block 
BL01063B
so that their similar segments (8-43 and 12-47) are aligned. 
Indeed, these segments both contain helix-turn-helix DNA binding motifs.

      
When both query and target blocks are provided by the user the 
output can also contain the column scores 
of each reported alignment and the PSSMs 
of every compared block.

      
Pay attention to any error or warning messages. Most will probably 
have to do with the format of the input.

      


      Evaluating LAMA alignment scores
      
The alignment score is the average of the 
column scores in the alignment multiplied by 100. 
Since the column scores have a range of -1 to 1 the alignment score 
will range from -100 to 100. An alignment score of 46 means 
that on average the aligned positions had a correlation coefficient
of 0.46. The significance of the alignment score depends on the 
length of the compared blocks. Alignments between longer blocks 
will tend to be longer and have higher scores. 
The Z score and 
expected number let us estimate the 
significance of the scores 
and to compare alignments of different lengths. 
The higher the Z score the less likely the alignment is due
to chance. How unlikely depends on the number of blocks searched.
The more blocks searched the greater the probability to find chance 
high scores. For example, the output of the calibration with the 
shuffled blocks contained 7 million 
scores but no alignments with Z scores greater than 8.3 . 
Hence an alignment with a score equal or higher than that Z score 
is unlikely by chance in a comparable or smaller number 
of alignments. The expected number shows this directly. 
The expected number is shown for searching 5000 blocks since version 9.1 of the
Blocks Database
contains 3300 blocks. For example, searching this release of 
the Blocks Database and finding an alignment expected to appear 
1.8e-01 times (0.18) suggests that this alignment is not due to chance.
Alignments with expected occurrences of 7.5e-03 or even 0 are almost
certainly genuine (or due to biassed blocks,
see below).
      

 A relation between two families by a single pair of blocks with a
high Z score is termed a single hit.
However, protein families often have a number of blocks. 
A multiple hit is when two or more block pairs 
from the same two families are similar:

                                                     multiple hit
     Family 1, blocks 1A, 1B, 1C, 1D.         1A=2B + 1D=2C
     Family 2, blocks 2A, 2B, 2C.

      
We expect the order of the blocks in the hit to be the same in both 
families (in this example 1A -> 1D and 2B -> 2C).
      


 Individual block pairs with Z scores likely by chance 
by themselves can still indicate a genuine relation if they 
are in a multiple hit. While the shuffled blocks scores contained 
no single hit with Z score above 8.3, there were no multiple hit 
with Z scores less than 5.6 . Hence genuine relationships can also 
be indicated by several alignments whose Z scores are 
individually expected to occur by chance.
      

When comparing blocks against a database the Z score cutoff is set as 5.6, 
corresponding to expected occurrence rate of 0.385 per searching 5000 blocks.
When both query and target blocks are provided other cutoffs can be 
chosen.

      

False positive (high score but no relation) and false negative 
(low score but genuine relation) hits are still possible and
biological knowledge and common sense should be used. 
Compositionally 
biassed blocks (consisting of sequence segments rich in a few amino 
acids or short repeats) are a common cause for false positive hits. 
You can check if a block is biassed here.
False negative hits can be caused by misalignment in the blocks .

      

Each entry in the 
Blocks Database
version 8.6 (3174 blocks from 858 protein families)
was searched against the other entries in the database. 
All block pairs with Z scores larger than 5.6 were saved. 
Protein families related by more then one saved score were
considered as multiple hits and alignments with Z scores 
above 8.3 as single hits. This resulted in 141 pairs of families. 
Eighty percent of these were 
identified as genuine relationships (true positives) according to the 
family descriptions, by sharing common sequences, or by detailed 
examination. Compositional bias was responsible for another eight percent 
of the high scores. The remaining twelve percent of the high scores could 
not be classified as either genuine or false based on available evidence.
      



      
Distribution of top scoring family pairs

      Relation typeGenuine(1)Biassed
      Composition      		UnknownTotal
      

      Multiple block hits- independent(2)
        24 
        -
        1 
        25 
      

                         - repeats(3)
        11 
        6 
        9 
        26 
      

                         - inner repeats(4)
        15 
        4 
        2 
        21 
      

      Single block hits
        63
        1
        5
        69
      

      Total
       113
       11
       17
       141
      

      Fraction
        80%
        8%
       12%
      

      

      

      (1) Genuine relations were identified by the families prosite descriptions,
    detailed analysis of the literature or by sharing common sequences 
    (22 of the single and independent-multiple hits).
(2) An independent multiple hit is two different protein families 
    related by two or more different block pairs.
(3) A repeat multiple hit is two different protein families where a 
    block from one family is similar with two or more blocks from the 
    other family.
(4) An inner-repeat multiple hit is a case where the similarities are 
    between blocks from the same family.

      


      Examples
      

        

      • Flavoproteins FAD binding and catalytic sites
        
     A comparison of all the Blocks Databases v8.6 entries with each other 
found the following hit between FAD flavoprotein subunits from two 
oxidoreductase enzyme complexes, BL00504 - succinate dehydrogenases 
(Sdh) and fumarate reductases (Frd) and BL00677 - D-amino oxidases (DAO):

                                                    alignment     Z-score  expected number for
block 1   from:to       block 2   from:to   length                 searching 5000 blocks
BL00504A    2 :  20 and BL00677A    2 :  20 (19) score  51 (10.0  0.0e+00) [logos ?]

        
A comparison with a lower cutoff found another hit supporting the first one:

        BL00504D    3 :  35 and BL00677D   17 :  49 (33) score  26 ( 5.5  5.1e-01) [logos ?]

        

Sequence annotations and a literature search revealed that block BL00504A 
is the FAD-binding site and BL00504D is the active site (Birch Machin 
et al., 1992) of the Sdh/Frd flavoproteins. Block BL00677A is 
the FAD-binding site of the DAO proteins. The FAD AMP-binding sites in 
both families are beta-alpha-beta ADP binding folds and were already 
noted as such (Birch-Machin et al., 1992; Schulz et al., 1982). 
This explains the first hit. 

        
     The DAO BL00677D block has a conserved histidine important for 
enzymatic activity of pig DAO (Miyano et al., 1991). This histidine 
is aligned with a conserved and essential histidine in the Sdh/Frd 
flavoproteins catalytic site (Birch-Machin et al., 1992; Schroder 
et al., 1991). Other positions in these aligned regions are also 
similar (column scores 0.31 to 0.98). The dissimilar positions have 
column scores close to zero (0.04 to -0.14). This finding suggests 
that the active site of DAO flavoproteins is in the BL00677D region with 
the conserved histidine as the crucial residue.

        
      BLAST and FASTA searches of the SwissProt protein database could 
not identify this similarity. No sequence from one family identified 
any sequence from the other family. Optimal local alignments of all the 
sequence pairs from the two families had scores expected by chance. 
Searching the Blocks Database with the sequences from the two families 
identified the relation between the families with 6 Sdh/Frd flavoproteins 
sequences (multiple hits with 98.1 to 76.2 percentiles of scores with 
shuffled sequence queries and P values of 8.4*10-3 to 1.1*10-1) but not 
with the other two sequences from that family or any of the sequences 
from the DAO family (single hits with less then 60.0 score percentiles).

        


        Suggested catalytic site of DAO flavoproteins.
A, positions 17-49 of DAO flavoproteins (block BL00677D) aligned with
the catalytic region of Sdh/Frd flavoproteins (positions 3-35 of block
BL00504D). The histidines important for the enzymes catalytic activity
are outlined (the histidine in sequence DHSA_BACSU is misaligned due to
a two aa insertion). The start and end coordinates flank the sequences.
B, the column scores of the alignment.

        

        

Birch-Machin, M. A., Farnsworth, L., Ackrell, B. A., Cochran, B., Jackson, S.,
 Bindoff, L. A., Aitken, A., Diamond, A. G. & Turnbull, D. M. (1992). 
The sequence of the flavoprotein subunit of bovine heart succinate 
dehydrogenase. J. Biol. Chem. 267, 11553-11558.
        
Miyano, M., Fukui, K., Watanabe, F., Takahashi, S., Tada, M., Kanashiro, M. & 
Miyake, Y. (1991). Studies on Phe-228 and Leu-307 recombinant mutants of 
porcine kidney D-amino acid oxidase: expression, purification, and 
characterization. J. Biochemistry 109, 171-177.
        
Schroder, I., Gunsalus, R. P., Ackrell, B. A., Cochran, B. & Cecchini, G. 
(1991). Identification of active site residues of Escherichia coli fumarate 
reductase by site-directed mutagenesis. J. Biol. Chem. 266, 
13572-13579.
        
Schulz, G. E., Schirmer, R. H. & Pai, E. F. (1982). FAD-binding site of 
glutathione reductase. J. Mol. Biol. 160, 287-308.

        

      • Snake toxins and the CD59 extracellular domain
        

Conserved regions from snake toxins and the CD59 extracellular domain were found
similar to each other. The alignment score is not very striking but the two families 
seem be quite dissimilar. What is the connection between snake toxins, small 
extracellular proteins that bind to nerve receptors, and the CD59 domain, a domain 
that is found in one or more copies on GPI-linked cell surface glycoproteins ? 
a closer look at the alignment was taken by requesting to see the column scores.
These scores are shown above the score line for each of the 12 alignment positions 
(8,3 to 19,14):

        Column scores for optimal alignment of BL00272B and BL00983B -
  8, 3   9, 4  10, 5  11, 6  12, 7  13, 8  14, 9  15,10  16,11  17,12  18,13 19,14
 0.262  0.169  0.138  0.286  0.995  1.000  0.368  0.224  0.986 -0.067  1.000 1.000
BL00272B    8 :  19 and BL00983B    3 :  14 (12) score  53 ( 6.5  6.0e-02) [logos ?]

        

 Five of the positions [(12,7), (13.8), (16,11), (18,13) and (19,14)]
have very high column scores (0.986-1.000) 
indicating identical and almost identical amino acid distribution in these
column pairs. The other positions contribute less to the alignment score
and position (12,17) has a slightly negative score, actually detracting from
the alignment.
        
Upon requesting to see the PSSMs of the blocks (below) or their aligned 
logos (link to 'logos' above) you will note 
that 3 of the alignment positions contributing to the score are highly 
conserved cysteine residues. This raises the possibility of identical 
patterns of disulphide bonds in both regions. We might give this 
alignment more attention since disulphide bonds are known to be well
conserved even between distantly related sequences. 
 More information can be found by following the block links to the
Blocks Database 
entries. Each family is accompanied by its 
InterPro 
annotation and the multiple alignment each block can be 
viewed as a graphical 
sequence logo. 
The structures of both proteins 
are known and confirm their relation. (The 
SWISS-3DIMAGE 
was the source for these images of the structures.)

        

        PSSM of BL00272B

  |                                       1   1   1   1   1   1   1   1   1   1
  |   1   2   3   4   5   6   7   8   9   0   1   2   3   4   5   6   7   8   9
--+----------------------------------------------------------------------------
A |   0   0   0  13   0   3   0   0   1   0   2   0   0   0   1   0   2   0   0
C |  87  12  12  11   0   0   0   0  21   0   6 100 100   0   0   0   0  99   0
D |   0   0   3   2  11   9   3   2   6   0   0   0   0   3   0  82  10   0   2
E |   0   5   2   8   3   5   2   9   4   6   9   0   0   7   0   5   5   0   0
F |   2   3   9   0   0   2   6   4   2   2   0   0   0   0   0   0   0   0   0
G |   1   1   1   1   3   0  24   8   7   0   0   0   0   2   3   0   1   0   2
H |   0   0   2   0   0   4   2   0   4   0  13   0   0   6   0   0   0   0   0
I |   0   0   4   0   2   1   0  17   7  30   3   0   0   0   6   0   0   0   0
K |   0   3  22   4  30   3   8   5  17   0  24   0   0  16   1   0  36   0   0
L |   0   0   1   0   1   3   8   3   0  14   5   0   0   0   0   0   2   0   0
M |   0   0   0   0  11   2   9   0   3   0   3   0   0   0   0   0   0   0   0
N |   0   0   0   5   2   7   2   2   2   0   2   0   0  16   0  13  22   1  96
P |   6  65   9   2   3  23   6   8   2   5   0   0   0   0   0   0   0   0   0
Q |   0   2   6   0   0   1   0   1   6   0   8   0   0   3   0   0   0   0   0
R |   0   2   4  15   8   2   6   6   2   3   8   0   0  10   0   0  19   0   0
S |   1   4   4   6  13   3   0   4   6   2   1   0   0  19  16   0   0   0   0
T |   3   4  14   5   5   5   1   5   0   4   3   0   0  18  72   0   0   0   0
V |   0   0   3  28   5   1   0  19   1  22   6   0   0   0   0   0   1   0   0
W |   0   0   0   0   0  22   0   0   0   0   0   0   0   0   0   0   0   0   0
X |   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
Y |   0   0   5   0   3   2  23   7   9  11   7   0   0   0   0   0   2   0   0
- |   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0


PSSM of BL00983B

  |                                       1   1   1   1   1
  |   1   2   3   4   5   6   7   8   9   0   1   2   3   4
--+--------------------------------------------------------
A |   0   0   0   0   0   0   0   0   0   0   0   0   0   0
C |   0   0   0   0   0   0  91 100   0   0   0   0 100   0
D |   0   0   0   0   0   0   0   0   0   0  76   0   0   0
E |   0  17  29   0  20   0   0   0   0  42   0   0   0   0
F |   0   0   0   0   0   0   0   0   0   0   0   0   0   0
G |  10   0   0   0   0   0   0   0  10   0   0   0   0   0
H |   0   0   0   0   0  39   0   0   0   0   0   0   0   0
I |  25   0   0   0   0   0   0   0   0   0   0   0   0   0
K |   0   0   0  30   0   0   0   0  28  23   0   0   0   0
L |   0   0  48   0   0   0   0   0   0   9   0 100   0   0
M |   0   0   0   0   0   0   0   0   0   0   0   0   0   0
N |  25  23   0  13   0   0   0   0   0   0  24   0   0 100
P |   0   0   0   0   0   0   0   0   0   0   0   0   0   0
Q |   0  15   0   0   0  13   0   0  29   0   0   0   0   0
R |   0  12   0  12   0   0   0   0  24   0   0   0   0   0
S |   0  20   0  11   0  18   0   0   9  12   0   0   0   0
T |  23  13   0  23  35  10   0   0   0  14   0   0   0   0
V |  16   0  22  11   0   8   9   0   0   0   0   0   0   0
W |   0   0   0   0   0   0   0   0   0   0   0   0   0   0
X |   0   0   0   0   0   0   0   0   0   0   0   0   0   0
Y |   0   0   0   0  45  13   0   0   0   0   0   0   0   0
- |   0   0   0   0   0   0   0   0   0   0   0   0   0   0


        
("X" specifies unknown amino acids.)

        

      • IS30 transposases DNA-binding domain
        

        Excision and insertion of bacterial insertion sequence elements (IS)
require the activity of a transposase protein sometimes encoded by the
ISs. The IS30 transposase family (Dong et al., 1992) is represented by
five blocks in BLOCKS 8.6. A region of 21 positions from the first block
had high scores (Z scores 6.7 to 8.8) only to helix-turn-helix
DNA-binding motifs (hth) from four protein families (see the
figure in the
next example).
Hth DNA binding motifs occur in many proteins that bind specific DNA
sequences (Pabo & Sauer, 1992).
        
        BLAST searches of the SwissProt protein database with the IS30
sequences did not identify any protein with known hth region. Searching
the Blocks Database with the IS30 sequences gave high scores with hth
blocks for two of the sequences (98.1 and 93.1 percentiles of scores
with shuffled sequence queries (Henikoff & Henikoff, 1994)). The other
two sequences had low scores with hth blocks (30.8 and 18.1 score
percentiles) and higher scores with non-hth blocks. However, each of the
transposases putative DNA binding regions was detected by the method of
Dodd and Egan (Dodd & Egan, 1990) as an almost certain hth domain.
        
        Classification of the first IS30 block as a hth motif is supported by
the finding that the N-terminal region of an IS30 transposase,
containing the putative hth DNA-binding region, binds the IS30 element
(Stalder et al., 1990).
        



        Hth-like region in IS30 transposases.
Block BL01043A of the IS30 transposases family. The regions similar to
the hth motifs in the block to block searches are underlined. The start
and end coordinates flank the sequences. The diagram shows the suggested
position of the hth motifs found by the hth  algorithm (Dodd & Egan, 1990). 
The algorithm scores for hth motifs were 5.19 standard deviation
units (SD), corresponding to 100% probability for TRA1_STRSL, 5.95 SD
and 100% for TRA4_BACFR, 4.13 SD and 90% for TRA8_ALCEU, and 5.72 SD and
100% for TRA8_ECOLI.

        

Dodd, I. B. & Egan, J. B. (1990). Improved detection of helix-turn-helix
DNA-binding motifs in protein sequences. Nucl. Acid. Res. 18, 5019-5026.
        

Dong, Q., Sadouk, A., van der Lelie, D., Taghavi, S., Ferhat, A.,
Nuyten, J. M., Borremans, B., Mergeay, M. & Toussaint, A. (1992).
Cloning and sequencing of IS1086, an Alcaligenes eutrophus insertion
element related to IS30 and IS4351. J. Bacteriol. 174, 8133-8138.
        

Henikoff, S. & Henikoff, J. G. (1994). Protein family classification
based on searching a database of blocks. Genomics 19, 97-107.
        

Pabo, C. O. & Sauer, R. T. (1992). Transcription factors: structural
families and principles of DNA recognition. Annu. Rev. Biochem. 61,
1053-1095.
        

Stalder, R., Caspers, P., Olasz, F. & Arber, W. (1990). The N-terminal
domain of the insertion sequence 30 transposase interacts specifically
with the terminal inverted repeats of the element. J. Biol. Chem. 265,
3757-3762.
        


        

      • Hth motifs in the Blocks Database
        

     In comparing the entries in the Blocks Database v8.6 among 
themselves all fourteen hth blocks had high scores with two or more 
other hth blocks (Figure). 
The two high scoring non-hth blocks could be 
distinguished by relating to single hth block and having lower scores 
relative to the ones between the hth blocks. The blocks are from four 
types of protein families - bacterial regulatory proteins, homeobox 
domain proteins, sigma bacterial transcription initiation factors and IS 
transposases. Manual inspection of the Prosite annotation of the protein 
families in the Blocks Database and of blocks themselves found no 
other hth blocks in the database.
        
     The hth blocks included different number of sequences, from 4 to 185. 
There was no correlation between the number of sequences in a block and 
its relation to other blocks. This suggests that even blocks with 4-6 
sequences can give a correct representation of conserved protein domains. 
More than 90% of the blocks in the database used had more than four 
sequences. This fraction is increasing with each release (>94% in BLOCKS 
9.0) as the number of new protein sequences is higher than the number of 
new protein families (Green et al., 1993; Koonin et al., 
1995; Koonin et al., 1994).
        

     Hth blocks illustrate the problem of distinguishing genuine 
relationships from chance ones and suggest a solution. Two of the hth 
blocks (BL00622 and BL01063B) lie below the threshold for detection 
single-hit relations (Z score >=8.3, bold lines in 
Figure). Protein 
families with hth-motifs usually have no other common blocks to support the 
relation between the hth blocks. However, hth motifs are found in several 
protein families. These hth blocks all have high scores with each other, but 
not all these scores are high enough to identify genuine relationships by 
themselves. Nevertheless, blocks with a number of such scores to known hth 
blocks can be identified as hth blocks too. The two non-hth blocks have high 
scores to single hth blocks, and do not form part of the connected graph. An 
analogous strategy is the basis for detecting weak similarities in 
single-sequence alignments using the BLAST3 program (Altschul & Lipman, 1990).

        



        High scores of helix-turn-helix DNA binding blocks.
All 14 hth blocks found in BLOCKS 8.6 and their high scoring relationships 
with each other (true positives) and with other blocks (false positives, 
outward pointing lines). Each block had different sequences except two pairs 
of homeobox blocks that had common sequences (BL00027 with BL00032B and with 
BL00035B). Lines show scores above the 5.6 Z score cutoff. Thick lines 
correspond to scores above the 8.3 Z score cutoff. BRP - bacterial 
regulatory proteins.
        

        

Since all the hth blocks are similar to one another we examined how well 
would one composite hth block identify other hth blocks. The 

ecmot database (Koonin et al., 1995) contains such a 

composite hth block, with 609 sequence segments from many hth families. 
The graphical representation 
(logo) of this block 
illustrates the conservation in each of its positions. This and the 
avoidance of particular amino acids at specific positions can also be seen in 
the PSSM of block EC0157.
This block had high scores with 18 blocks in Blocks Database v8.6 
(Table). 
Fourteen of those are the hth blocks discussed above. All the 
hth blocks had high to extremely high scores, the lowest one expected to 
occur 3.2e-3.
         
(Here you will find block 
EC0157 in a format you can use in a 
LAMA search.)
        

The four blocks at the end of the table have significantly lower scores 
(Z 5.6-6.5). These are non-hth blocks but their similarity to the 
composite hth block can be explained. Two of the blocks are from 
bacterial regulatory proteins families, occurring C-terminal to the hth 
motifs. One is a hth-similar region from the araC family (Brunelle & 
Schleif, 1989) and the other corresponds to the 
hth helix3 and DNA 
binding hinge helix in the E.coli lac repressor protein (Lewis et 
al., 1996). Another block is from the S3 ribosomal proteins (BL00548A). 
This protein binds RNA, and it is interesting to note the recent report 
of the RNA binding activity by a hth domain (Dubnau & Struhl, 1996). The 
last non-hth block is from L-lactate dehydrogenase (LDH) proteins. LDHs 
do not bind DNA but the 
crystal structure of the detected region 
(alpha-2f to Beta-G) is a helix-turn followed by a helix or strand in 
different proteins (Abad Zapatero et al., 1987; Grau et al., 1981; Iwata 
& Ohta, 1993).
        



        

Blocks similar to composite hth block EC0157

        

        Protein family (1)
        Z  score
        

        'Homeobox' domain proteins
        18.4
        

        'Homeobox' antennapedia-type proteins
        13.2
        

        'POU' domain proteins
        11.7
        

        BRP crp family
        12.1
        

        BRP gntR family
        12.4
        

        BRP lysR family
        14.4
        

        BRP lacI family (2)
        11.7
        

        BRP luxR family
        12.4
        

        BRP arsR family
         8.0
        

        BRP deoR family
         8.7
        

        BRP tetR family
        14.1
        

        Sigma-54 factors family
         7.8
        

        Sigma-70 factors ECF subfamily
         8.3
        

        Transposases, IS30 family
        11.2
        

        

        BRP araC family
         6.5
        

        BRP lacI family (2)
         6.6
        

        Ribosomal S3 proteins
         5.8
        

        L-lactate dehydrogenase family
         5.8
        


        

        (1) The family Blocks Database entry numbers are in the previous figure 
    except for BRP araC family - BL00041, L-lactate dehydrogenase - BL00064D 
    and Ribosomal protein S3 proteins - BL00548A.
    The non-hth blocks are separated at the end of the table.
(2) Two blocks from the lacI hth family are similar to the composite hth block -
    block BL00356A, the hth region, and block BL00356B, the following
    DNA-binding hinge region.

        

     Identifying all the hth regions in the Blocks Database illustrates 
the potential of the multiple alignment comparison method as an aid for 
annotating protein-family databases. Besides identifying the function of 
unknown regions, the approach outlined in this example can be useful in 
annotating databases that generate the multiple alignments automatically. 
Multiple alignments of characterized protein motifs (such as the hth, 
nucleotide binding folds or leucine zipper) could be used to identify other 
multiple alignments containing these motifs.
        

Altschul, S. F. & Lipman, D. J. (1990). Protein database searches for multiple alignments. Proc. Natl. Acad. Sci. USA 87, 5509-5513.
        

Abad Zapatero, C., Griffith, J., Sussman, J. & Rossmann, M. (1987). 
Refined crystal structure of dogfish M4 apo-lactate dehydrogenase. 
J Mol Biol 198, 445-467.
        

Brunelle, A. & Schleif, R. (1989). Determining residue-base interactions 
between AraC protein and araI DNA. J Mol Biol 209, 607-622.
        

Dubnau, J. & Struhl, G. (1996). RNA recognition and translational 
regulation by a homeodomain protein. Nature 379, 694-699.
        

Grau, U., Trommer, W. & Rossmann, M. (1981). Structure of the active 
ternary complex of pig heart lactate dehydrogenase with S-lac-NAD at 2.7 
A resolution. J Mol Biol 151, 289-307.
        

Green, P., Lipman, D., Hillier, L., Waterston, R., States, D. & Claverie, J. M. 
(1993). Ancient conserved regions in new gene sequences and the protein databases. 
Science 259, 1711-1716.
        

Iwata, S. & Ohta, T. (1993). Molecular basis of allosteric activation of 
bacterial L-lactate dehydrogenase. J Mol Biol 230, 21-27.
        

Koonin, E., Tatusov, R. & Rudd, K. (1995). Sequence similarity analysis of 
Escherichia coli proteins: functional and evolutionary implications. 
Proc Natl Acad Sci USA 92, 11921-11925.
        

Koonin, E. V., Bork, P. & Sander, C. (1994). Yeast chromosome III: 
new gene functions. EMBO J. 13, 493-503.
        

Lewis, M., Chang, G., Horton, N. C., Kercher, M. A., Pace, H. C., 
Schumacher, M. A., Brenan, R. G. & Lu, P. (1996). Crystal Structure of 
the Lactose Operon Repressor and Its Complexes with DNA and Inducer. 
Science 271, 1247 1254.
        

        

      



      Supplements
      
To calibrate the LAMA scores the 
Blocks Database
was purged from biassed blocks, the PSSMs of 
the remaining blocks were each shuffled and then compared against the 
blocks from the unshuffled database. The best score from each of
the resulting 7 million comparisons was saved. These scores are due to chance
and were used to estimate the significance of alignment scores between blocks.
The mean and variance of chance alignments depend on the length of the 
compared blocks. Longer blocks will give longer alignments and higher scores
by chance alone. Grouping the chance scores by the length of the shorter 
block in each comparison gave very similar score distributions. The mean 
and standard deviation of each group was used to transform each score into
a Z score. The percentiles of all these Z scores was
then calculated. These percentiles are used to estimate the 
expected number each score should appear not due 
to genuine relationship.
      

Following are links to tables with this data. Note that the scores in the
tables are the raw scores of the alignments. The scores shown in the LAMA
output are normalized by dividing the raw score by the alignment length.


      


      Credits and citation
      
The multiple alignment comparison method and LAMA program were developed by
Shmuel Pietrokovski 
in the lab of Steve Henikoff at the 
Fred Hutchinson Cancer Research Center, 
Seattle.
      
An article describing the method and its uses
      
"Searching Databases of Conserved Sequence Regions by 
 Aligning Protein Multiple-Alignments"
      
appeared in

Nucleic Acids Research 24(19) 3836-3845 (October 96'). 
This article should be cited in research using this method.
      

      
[Blocks home] 
[Block Searcher]
[Block Maker]
[Get Blocks]
[format a block]
[check for biassed blocks]
[LAMA Searcher]

      
Page last modified January 1997 
(thanks for Liz G.Wiz for useful comments)


      
Shmuel Pietrokovski

      

LAST3 program (Altschul & Lipman, 1990).

      



      High scores of helix-turn-helix DNA binding blocks.
All 14 hth blimps-3.9/www/help/PSSM_def.html000064400001460000012000000014310774357760500172330ustar00jorjastaff00000400000027PSSM definition

      What is a PSSM ?
      

 A PSSM is a Position Specific Scoring Matrix. A profile is one type of PSSM. 
PSSMs enable the scoring of multiple alignments with sequences, structures etc. 
There are a number of ways to convert a multiple alignment, such as a block, 
into a PSSM. The conversion can use the multiple alignment sequence weights, 
the expected number of amino acids and the frequencies of unobserved amino 
acids (pseudocounts).
      

More information on PSSMs can be found in the 
Blocks Bibliography.
      

 Lastly, PSSM is pronounced "possum".
      

      
Page last modified May 1996

      
Shmuel Pietrokovski

      

blimps-3.9/www/help/PSSM_pict.html000064400001460000012000000002010774357760500174260ustar00jorjastaff00000400000027
possum

      
Didelphis virginiana
      
(photo courtesy of J. Sabl).
      


blimps-3.9/www/help/about_addseqs.html000064400001460000012000000015030774527306400204430ustar00jorjastaff00000400000027
About Adding Sequences to Blocks

      About Adding Sequences to Blocks
      



      
A protein sequence is added to a set of
Blocks
using the
Blimps
alignment algorithm based on the best single alignment
of the sequence with each of the blocks. These best
alignments must be in the correct order and non-overlapping,
which is stricter than 
searching
the sequence against the blocks.
      
After sequences are added to the blocks, they are re-weighted
and re-calibrated.


      

      
Contact us
      
Blocks home

      
Page last modified August 2003

blimps-3.9/www/help/about_blimps.html000064400001460000012000000026540774527307500203170ustar00jorjastaff00000400000027
About Blimps

      About Blimps
      



      Blimps Searching Program
      


The Blimps (blocks improved searcher) searching program can be used
to search a protein or DNA sequence against a database of blocks, or
the reverse. Each block is converted to a position-specific scoring 
matrix (PSSM). A PSSM has as many columns as there are positions in
the block, and 20 rows, one for each amino acid. Each PSSM entry is
a numeric score based on the ratio of the observed frequency of an 
amino acid in a block column to its expected overall frequency in a
large protein database. The observed frequencies are weighted for
sequence redundancy and pseudo-counts are added to compensate for
unobserved amino acids.

      
During a search, a block is aligned with a sequence at all possible
positions and an alignment score is computed by adding the PSSM scores
from every column of the block. If the sequence is DNA, BLIMPS translates
it in all six reading frames and scores all six translated sequences.

      
J.G. Henikoff and S. Henikoff, "Blocks Database and Its Applications",
Methods in Enzymology (1996) 266:88-105.


      

      

Blimps FTP Site
      
Contact us
      
Blocks home
      


      
Page last modified August 2003

 and 20 rows, one for each amino acid. Each PSSM entry is
a numeric score based on tblimps-3.9/www/help/about_blocks.html000064400001460000012000000046630775501027700203020ustar00jorjastaff00000400000027
About Blocks

      A Little About Blocks...
      


Blocks are multiply aligned ungapped segments corresponding to the
most highly conserved regions of proteins.
Block Searcher, 
Get Blocks and
Block Maker are aids to
detection and verification of protein sequence homology. They compare
a protein or DNA sequence to a database of protein blocks
(current version),
retrieve blocks, and create new blocks, respectively. 


      

      The Blocks Database
      
The blocks for the
Blocks Database
are made automatically by looking for the most highly
conserved regions in groups of proteins documented in
InterPro.

The blocks created by Block Maker are created in the same manner as the
blocks in the Blocks Database but with sequences provided by the user.
Results are reported in a multiple sequence alignment format without 
calibration and in the standard
Block format for searching. 
      

More information is available at 
Block Searcher Help and at
Block Maker Help.
See the Blocks Bibliography for references.

      


      The Prints Database in Blocks Format
      

The Blocks WWW Server optionally searches a complete 
version of Terri Attwood's 
Prints Database in Blocks format using the Blimps searching program.
Although this service is not available from the Blocks email server,
a subset of Prints blocks not represented in the Blocks
Database is always searched.
Because Prints includes blocks from more than 300 families not
represented in the Blocks Database, and because different methods are
used to construct blocks for families represented in both databases,
we recommend searching both databases.
Please visit the

Prints Protein Motif Fingerprint Database Site
for more information and to retrieve entries.



      
Blocks home


      
Contact us 
      
Page last modified Jan 2002

blimps-3.9/www/help/about_cobbler.html000064400001460000012000000027070774527253500204400ustar00jorjastaff00000400000027
About COBBLER

      About COBBLER
      



      COBBLER Sequences Displayed by Blocks and Block Maker
      

COBBLER means COnsensus Biasing By Locally
 Embedding Residues.

      
A single sequence is selected from a set of blocks and enriched by
replacing the conserved regions delineated by the blocks by consensus
residues derived from the blocks. Embedding consensus residues improved
performance with readily available single sequence query searching
programs, such as BLAST and FASTA, in comprehensive tests.

      


S. Henikoff and J.G. Henikoff, "Embedding strategies for effective use
of information from multiple sequence alignments", Protein Science (1997)
6:698-705.
MEDLINE


      
The COBBLER sequence used with 
PSI-BLAST
has produced excellent results, such as those reported by
Thelen, et al for
Rad1/PCNA.
[Cell article]
[PubMed entry]



      

      
Blocks home


      
Contact us 
      
Page last modified Feb 2000

blimps-3.9/www/help/about_colors.html000064400001460000012000000022010774357760600203230ustar00jorjastaff00000400000027
BLOCKS Sequence Logo colors

      About sequence logo colors:
      

      

The amino acid colors in sequence logos help visualize the chemical and 
physical properties of specific positions and areas in the Block. 
Amino acids each have a number of different properties. 
Thus there are several ways to group amino acids.

      

In the file defining the colors of the logo characters, lines that begin with 
an asterisk [*] are comment lines. Other lines define a character color. 
Each such line contain 4 parameters - the character defined and its red, green 
and blue (RGB) components defining its color. The RGB values are real values 
between 0 and 1. A value of 0 means black and a value of 1 means the most 
bright. Characters which are not defined will be black.

      

You can view the color files used:

      

      


      
Contact us 
      
Page last modified on July 1995

blimps-3.9/www/help/about_diy.html000064400001460000012000000011540774527247700176150ustar00jorjastaff00000400000027
About DIY Blocks Search

      About DIY Blocks Search
      



      
The Do-it-yourself Blocks Searcher allows you to align a protein
or translated DNA sequence with your own
Blocks
using the
Blimps
searching program. More than one high-scoring alignment may be
reported for each block.


      

      
Contact us
      
Blocks home

      
Page last modified August 2003

blimps-3.9/www/help/about_impala.html000064400001460000012000000074600776273176100202740ustar00jorjastaff00000400000027
IMPALA at the Blocks Server

       IMPALA at the Blocks Server
      
      IMPALA
(Integrating Matrix Profiles And Local Alignments) is a program
that searches a protein query sequence against a multiple alignment database
represented as a collection of 
PSI-BLAST 
checkpoint files.
IMPALA has been implemented on the Blocks Server to search a blocks database,
such as Blocks.
Although the Blocks Searcher performs a similar type
of search and both utilize position-specific scoring matrix (PSSM)
representations of the Blocks Database, there are differences between IMPALA
and the Blocks Searcher in the PSSMs used, in the alignments reported,
and in the
calculation of statistics that can lead to somewhat different
results. Therefore, any marginal similarity detected with one searching
program should be confirmed using the other. We have found that 
both programs generally detect true positive hits but they
tend to report different false positives,
and so any hit not detected by both searching programs
should be regarded with caution.


      
      Blocks are ungapped multiple alignments representing the most highly
conserved regions of proteins. Whereas the Block Searcher scores individual
blocks separately and then combines the scores for blocks in a family,
IMPALA scores the set of blocks for a family as a whole
so a hit is for the whole family, not for an individual block.
For instance, the Block Searcher aligns and scores the query sequence versus 
each of the six PSSMs representing the six blocks (IPB001525A-F) for the C5 DNA
methyltransferase family (IPB001525) 
in Blocks, while IMPALA 
aligns and scores a single PSSM representing the full set of blocks. 


      
	To make the checkpoint file PSSM representation of
a family for IMPALA on the Block Server,
PSI-BLAST 
is applied to the full set of sequences for the family
using the COBBLER
(Consensus Biasing By Locally Embedding Residues)
embedded sequence as query, iterating until convergence. 
The COBBLER sequence is a single representative sequence for the family
stretching from 10 residues upstream of the
first block to 10 residues downstream of the last block,
with consensus residues in block positions.


      
	Since IMPALA scores not only the blocks but also regions between them, 
its alignments may extend beyond the blocks.
The resulting BLAST-like output gives scores and expected values,
This differs from the Block Searcher
which provides expected values for individual blocks as well as an overall
expected value for the family, and alignments to the individual blocks.

	In theory, the Block Searcher
should be more specific and IMPALA more sensitive. However, other differences
complicate any simple comparison, including differences in implementation of
the searching algorithms, and differences in the methods used for calculating
PSSM column scores.


      
      We thank the 
NCBI BLAST group,
especially
Alejandro Schäffer
for making IMPALA available for searching the Blocks databases.


      
Reference:

      

Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin,
L. Aravind, Stephen F. Altschul, "Software to Match a Protein Sequence 
Against a Collection of PSI-BLAST-Constructed Position-Specific Score 
Matrices", manuscript.

      

[Blocks Home]
[Impala Searcher]
[Block Searcher]



blimps-3.9/www/help/about_logos.html000064400001460000012000000061620775500640100201360ustar00jorjastaff00000400000027
Sequence Logos

      Sequence Logos
      
 A sequence logo is a graphical representation of aligned
sequences where at each position the size of each residue is proportional to
its frequency in that position and the total height of all the residues in the
position is proportional to the conservation (information content) of the 
position
(
TD Schneider & RM Stephens, "Sequence Logos: A New Way to Display
Consensus Sequences", NAR 18:6097-6100 (1990) ). 
      

      

Tom Schneider's Sequence Logos site

      
  
      Logos from Related Sequences, Blocks, and Multiple Alignments
      
Blocks can be displayed as logos to examine sequence 
conservation.
Start with a set of related sequences or a multiple alignment in Blocks, Clustal or FASTA-alignment format. For a set of related
sequences, get a ClustalW alignment using either the 
EBI Clustal or the 
BCM Search Launcher multiple sequence alignment site for
global multiple alignments from which blocks are made, or use 
Block Maker to make blocks directly. Clustal-generated alignments
are copied and pasted into the 
Multiple Alignment Processor window in Clustal (include the word 'CLUSTAL' from the heading) or
FASTA-alignment format, and choose 'Submit the sequences'. The processor carves out blocks from fully-ungapped regions that are
at least 10 residues wide and provides an automatic link for making logos from
the full set of blocks. 
Get Blocks (for Blocks/Prints Database entries) and Block Maker (which uses Motif or Gibbs sampling) 
provides blocks that are ready to go. In each case, there are links to 
view logos or other displays. 

      
The logo for a block is computed from the position-specific
scoring matrix
(PSSM)
 that is used to score the block against a
query sequence. The PSSM is based on sequence-weighted counts
of each amino acid in each column of the block normalized by
dividing by the expected frequency of each amino acid in a protein
sequence database.
(
S. Henikoff, J. G. Henikoff, W. J. Alford & S. Pietrokovski, "Automated
construction
and graphical presentation of protein blocks from unaligned sequences",
Gene-COMBIS,
Gene 163 (1995) GC 17-26).

      

Tom Schneider's makelogo program is used to create the sequence logo from the
PSSM.
The logo is in PostScript or PDF format.
The amino acids in the logo are
colored
according to their chemical and physical characteristics.

      
[Blocks Home]

      
Contact us 
      
Page last modified January 15, 1998

blimps-3.9/www/help/about_maps.html000064400001460000012000000006030774527316000177540ustar00jorjastaff00000400000027
About Block Maps

      About Block Maps
      


  
      Block Maps Displayed by Blocks and Block Maker
      

  The maps display the Block alignments 






      

      
Blocks home


      
Contact us 
      
Page last modified Aug 1997

blimps-3.9/www/help/about_rpsblast.html000064400001460000012000000021770774527320200206530ustar00jorjastaff00000400000027
RPS-BLAST at the Blocks Server

       RPS-BLAST at the Blocks Server
      

RPS-BLAST: Reversed Position Specific Blast

RPS-BLAST is one of the 
BLAST
series of searching programs from NCBI. It reverses the popular
PSI-BLAST
search by comparing a protein query with a database
of PSI-BLAST checkpoint files made from multiple alignments of
protein families. Here the checkpoint files are made from the
Blocks and Prints alignments, and are the same files searched with
the similar
IMPALA 
searching program also from NCBI. RPS-BLAST should be
somewhat faster than IMPALA since it uses the 
BLAST heuristics
while IMPALA does full dynamic programming.

RPS-BLAST output closely mimics output of BLASTP family programs and
should be compatible with SEALS BLAST parsers.

Send suggestions, comments, complaints to blast-help@ncbi.nlm.nih.gov


cks Server

RPS-BLAST: Reversed Position Specific Blast

RPS-BLAST is one of the 
BLAST
series of searching programs from NCBI. It reverses the popular
PSI-BLAST
search by comparing a protein query with a database
of PSI-BLAST checkpoint files made from multiple ablimps-3.9/www/help/about_trees.html000064400001460000012000000107420775500643400201420ustar00jorjastaff00000400000027
Trees from Blocks

      About Trees from Blocks
      


  
      Generation and Display of Trees from Related Sequences, Blocks, and Multiple Alignments
      
A set of blocks can also be used to construct and display a neighbor-joining tree for examination of
possible subfamily relationships. Because blocks represent the most highly conserved regions of proteins,
misaligned regions are avoided, and so trees from blocks should be of high quality. Bootstrap resampling
percentages are supplied to aid in evaluating the significance of each branch.

       
Start with a set of related sequences or a multiple alignment in Blocks, Clustal or FASTA-alignment format. For a set of related
sequences, get a ClustalW alignment using either the EBI Clustal or the BCM Search Launcher multiple sequence alignment site for
global multiple alignments from which blocks are made, or use 
Block Maker to make blocks directly. Clustal-generated alignments
are copied and pasted into the 
Multiple Alignment Processor window in Clustal (include the word 'CLUSTAL' from the heading) or
FASTA-alignment format, and choose 'Submit the sequences'. The processor carves out blocks from fully-ungapped regions that are
at least 10 residues wide and provides an automatic link for making a tree from
the full set of blocks. 
Get Blocks (for Blocks Database entries) and Block Maker (which uses Motif or Gibbs sampling) provides blocks that are ready to go. In each case, there are links to various displays of neighbor-joining trees. 

      

      How Trees are made
      
 The neighbor-joining trees are made from the Block alignments using a routine in Clustal W
  [Clustal ftp site].
  The Kimura correction for multiple substitutions is applied.
  If there are not too many sequences, 100 bootstrap values are
  calculated. The output from Clustal W is a tree file in Newick
  or New Hampshire format which can be read by most tree display
  programs.
  ( Excerpts from Clustal documentation ).


      Clustal W versions 1.7+ will not make a tree with fewer than four
sequences.


      NOTE: Before attempting to display a tree, look at the Clustal W
output by selecting [Data] format to check for error messages.
Common problems that can cause Clustal W to fail are: non-unique
sequence names (the first 10 characters of each name should be unique)
and sequence title lines that start with ">P1;" which causes Clustal W
to assume the sequences are in PIR format instead of FASTA format.


      
  The the drawgram program from the
  PHYLIP
  package is used to format the tree for display.
  Resolution is calculated according to number of sequences in the tree
  using values that give satisfactory images viewed with NetScape on a Mac:
  Here are the drawgram parameters used:


           resolution = num_seqs * 25 + 50

     "X"          # X - 'X bitmap (XBM)'
     "N"          # N - No preview
     $resolution  # XBM horizontal resolution
     $resolution  # XBM vertical resolution
     "1"          # Tree growth, toggle to horizontal
     "2"          # Style of tree
     "P"          # P for Phenogram style
     "4"          # Angle of labels
     "90"         # labels 90 degrees to the tree
     "8"          # Stem-length/tree-depth
     "0"          # 0 stem won't show
     "Y"          # Y(es) to accept choices 

      


      
The trees can also be displayed locally using any program that accepts
input in Newick format, such as those listed below.
To activate this feature in your browser (such as Netscape), enter these
"helper application" parameters (substitute your application program
for treetool):

      Type: application/newick
Suffix:  treefile, tre
Application:  treetool %s

      

Tree display programs include
NJplot, 
TreeView and
Treetool.


      

      
Blocks home


      
Contact us 
      
Page last modified Aug 1999

blimps-3.9/www/help/email.html000064400001460000012000000067310774357760700167340ustar00jorjastaff00000400000027
Blocks Searcher Email Server Options

      Blocks Searcher Email Server Options
      

Please note: The Blocks Searcher Email Server will soon be
discontinued. For searching a few queries, supply your email address
on the
Block Searcher form.
Here is a
sample perl script
to do bulk searches.
      

      
Blocks Email Searcher: 
blocks@blocks.fhcrc.org

      Examples of the new options follow.


      
Please note: Please send clear text only.


      
Please note: Effective 2 May 2002 the #SQ option is required.


      
Please note: Default options will be used
if the message consists solely of a sequence.


      
Please note: If you want to put comments in the message,
start them with # in the first column and put them before the
sequence, being careful not to start your comment with any of
the reserved words listed below. Nothing should follow the sequence.


      
Searching options:

        


      • 
Database to search:
        

        #DB PLUS(default) | MINUS(PLUS without biased blocks) | PRINTS

        


      • 
Query sequence type:
        

        #TY AUTO(default) | AA | DNA 

        


      • 
For DNA queries, strands to search:
        

        #ST BOTH(default) | FORWARD | REVERSE or   2 | 1 | -1

        


      • 
For DNA queries, genetic code to use for translation:
        

        #GE 0(default) to 8

        


      

Post-processing options:

        


      • 
Output type:
        

        #OU ALL(default) | SUM | GFF | OLD | RAW

        


      • 
Output format:
        

        #FO TEXT(default) | HTML

        


      • 
Expected value cutoff:
        

        #EX n (default=5)

        


      

Sequence definition (required):

        

        #SQ
Sequence in fasta or other common formats.
WARNING: Everything after #SQ is treated as sequence, so do not
append any signature, etc.

        

      


      
Examples:


      
1. Old defaults; result of just mailing sequence
with no lines beginning with "#":
#DB plus
#TY auto
#ST 2
#GE 0
#OU old
#FO text
#SQ
>SPRE_RAT SEPIAPTERIN REDUCTASE (EC 1.1.1.153) (SPR) 
MEGGRLGCAV CVLTGASRGF GRALAPQLAG LLSPGSVLLL SARSDSMLRQ LKEELCTQQP
GLQVVLAAAD LGTESGVQQL LSAVRELPRP ERLQRLLLIN NAGTLGDVSK GFLNINDLAE
VNNYWALNLT SMLCLTTGTL NAFSNSPGLS KTVVNISSLC ALQPFKGWGL YCAGKAARDM
LYQVLAVEEP SVRVLSYAPG PLDTNMQQLA RETSMDPELR SRLQKLNSEG ELVDCGTSAQ
KLLSLLQRDT FQSGAHVDFY DI

2. New searching/post-processing defaults
#DB plus
#TY auto
#ST 2
#GE 0
#EX 5
#OU all
#FO text
#SQ
>SPRE_RAT SEPIAPTERIN REDUCTASE (EC 1.1.1.153) (SPR) 
MEGGRLGCAV CVLTGASRGF GRALAPQLAG LLSPGSVLLL SARSDSMLRQ LKEELCTQQP
GLQVVLAAAD LGTESGVQQL LSAVRELPRP ERLQRLLLIN NAGTLGDVSK GFLNINDLAE
VNNYWALNLT SMLCLTTGTL NAFSNSPGLS KTVVNISSLC ALQPFKGWGL YCAGKAARDM
LYQVLAVEEP SVRVLSYAPG PLDTNMQQLA RETSMDPELR SRLQKLNSEG ELVDCGTSAQ
KLLSLLQRDT FQSGAHVDFY DI

3. New searching/post-processing options
#DB prints
#TY DNA
#ST 1
#GE 1
#EX 3
#OU sum
#FO html
#SQ
gi|8133541|gb|AW507376.1|AW507376 EST00092 Rattus
ACATCATGGCTCTGACTTGGGTTAAGCTCTTGGCACCAATGTCCTGACAGGAATGCTGGATGCCAGCAAT
CAAATAAGGGACAAACTTGTGGATAGACCCTTTGTCCTGCACTGCCCCTGAAACTCCTTGGGCCACTTTG
ATCTTGTCAGCTTCACTGAAATATCGGTTCTGGCTGCTGAGGTGTTTGTCAAGTACATCAAGGAAAAATA
CCCCAATCTCCAGGTCATCGGAGGCAATGTAGTCACTGCTGCTCAAGCCAAGAACCTCATCGACGCAGGT
GTGGACGCTCTGCGAGTCGGCATGGGAAGTGGTTCCATCTGCATCACCCAGGAAGTGTTGGCCTGTGGGC
GACCCCAAGCAACAGCAGTATACAAGGTCTCTGAGTATGCCCGTCGCTTCGGTGTCCCTGGTATTGCTGA
TGGAGGAAT

      

blimps-3.9/www/help/biased_list.html000064400001460000012000000111751040211130700200640ustar00jorjastaff00000400000027
Blocks Biased Blocks

      Blocks Biased Blocks
      
Below is a list of the groups excluded from Blocks 14.2 (Mar 2006)
because one or more blocks representing each group were judged 
compositionally biased based on the
Biased Block Checker
with column score cutoff = 0.50 and maximum clump size = 35%
of the total columns.

      
These may not be the only biased blocks in
the database. If others are causing you problems, please 
contact us.
      

      IPB000034
IPB000046
IPB000076
IPB000104
IPB000108
IPB000116
IPB000142
IPB000144
IPB000161
IPB000200
IPB000202
IPB000221
IPB000228
IPB000314
IPB000316
IPB000347
IPB000354
IPB000356
IPB000363
IPB000372
IPB000381
IPB000383
IPB000423
IPB000434
IPB000469
IPB000480
IPB000492
IPB000518
IPB000519
IPB000545
IPB000563
IPB000586
IPB000617
IPB000631
IPB000647
IPB000705
IPB000714
IPB000735
IPB000775
IPB000817
IPB000869
IPB000893
IPB000921
IPB000935
IPB000966
IPB000967
IPB000972
IPB000976
IPB001007
IPB001008
IPB001026
IPB001053
IPB001095
IPB001105
IPB001118
IPB001151
IPB001169
IPB001195
IPB001219
IPB001234
IPB001313
IPB001318
IPB001355
IPB001368
IPB001376
IPB001389
IPB001396
IPB001397
IPB001399
IPB001418
IPB001432
IPB001435
IPB001442
IPB001445
IPB001450
IPB001458
IPB001475
IPB001489
IPB001513
IPB001521
IPB001634
IPB001671
IPB001672
IPB001673
IPB001681
IPB001704
IPB001729
IPB001740
IPB001749
IPB001778
IPB001817
IPB001841
IPB001859
IPB001904
IPB001908
IPB001935
IPB001947
IPB001954
IPB001965
IPB001970
IPB001973
IPB001976
IPB001988
IPB002006
IPB002031
IPB002045
IPB002049
IPB002079
IPB002090
IPB002105
IPB002122
IPB002144
IPB002147
IPB002153
IPB002154
IPB002170
IPB002185
IPB002232
IPB002238
IPB002240
IPB002243
IPB002244
IPB002246
IPB002247
IPB002248
IPB002249
IPB002250
IPB002251
IPB002253
IPB002255
IPB002260
IPB002261
IPB002264
IPB002268
IPB002270
IPB002274
IPB002281
IPB002318
IPB002322
IPB002360
IPB002366
IPB002367
IPB002369
IPB002383
IPB002395
IPB002396
IPB002426
IPB002442
IPB002445
IPB002455
IPB002461
IPB002463
IPB002494
IPB002552
IPB002565
IPB002597
IPB002713
IPB002888
IPB002906
IPB002914
IPB002919
IPB002929
IPB002945
IPB002952
IPB002953
IPB002954
IPB002955
IPB002958
IPB002960
IPB002978
IPB002989
IPB003022
IPB003023
IPB003025
IPB003026
IPB003027
IPB003046
IPB003047
IPB003050
IPB003058
IPB003060
IPB003061
IPB003066
IPB003071
IPB003072
IPB003073
IPB003077
IPB003078
IPB003124
IPB003202
IPB003267
IPB003271
IPB003272
IPB003273
IPB003276
IPB003279
IPB003290
IPB003303
IPB003341
IPB003446
IPB003449
IPB003482
IPB003505
IPB003517
IPB003532
IPB003536
IPB003538
IPB003541
IPB003548
IPB003549
IPB003550
IPB003551
IPB003553
IPB003563
IPB003566
IPB003569
IPB003572
IPB003606
IPB003616
IPB003623
IPB003861
IPB003868
IPB003882
IPB003884
IPB003904
IPB003905
IPB003908
IPB003909
IPB003915
IPB003926
IPB003927
IPB003929
IPB003932
IPB003933
IPB003934
IPB003935
IPB003936
IPB003938
IPB003948
IPB003949
IPB003969
IPB003976
IPB003977
IPB003978
IPB003980
IPB003981
IPB003982
IPB003983
IPB003984
IPB003986
IPB004006
IPB004051
IPB004053
IPB004054
IPB004059
IPB004062
IPB004064
IPB004066
IPB004068
IPB004069
IPB004073
IPB004115
IPB004116
IPB004153
IPB004169
IPB004214
IPB004227
IPB004286
IPB004295
IPB004326
IPB004339
IPB004350
IPB004828
IPB004931
IPB004977
IPB005016
IPB005028
IPB005358
IPB005385
IPB005386
IPB005387
IPB005388
IPB005391
IPB005393
IPB005396
IPB005401
IPB005403
IPB005404
IPB005405
IPB005407
IPB005409
IPB005410
IPB005420
IPB005422
IPB005435
IPB005445
IPB005446
IPB005448
IPB005449
IPB005451
IPB005452
IPB005458
IPB005466
IPB005535
IPB005612
IPB005634
IPB005649
IPB005819
IPB005826
IPB005827
IPB006024
IPB006030
IPB006031
IPB006057
IPB006079
IPB006081
IPB006207
IPB006552
IPB006572
IPB006581
IPB006599
IPB006706
IPB006712
IPB006714
IPB006718
IPB006757
IPB006782
IPB006792
IPB006794
IPB006796
IPB006845
IPB006970
IPB006975
IPB007064
IPB007086
IPB007149
IPB007199
IPB007282
IPB007455
IPB007643
IPB007671
IPB007672
IPB007688
IPB007689
IPB007718
IPB007738
IPB007829
IPB007836
IPB007932
IPB007958
IPB007980
IPB007991
IPB008021
IPB008036
IPB008056
IPB008065
IPB008068
IPB008071
IPB008075
IPB008083
IPB008087
IPB008109
IPB008112
IPB008115
IPB008119
IPB008120
IPB008123
IPB008128
IPB008129
IPB008155
IPB008211
IPB008212
IPB008351
IPB008386
IPB008412
IPB008440
IPB008532
IPB008550
IPB008736
IPB008779
IPB008782
IPB008883
IPB008904
IPB009147
IPB009243
IPB009254
IPB009317
IPB009621
IPB009733
IPB009806
IPB010011
IPB010012
IPB010257
IPB010307
IPB010465
IPB010500
IPB010515
IPB010527
IPB010528
IPB010571
IPB010613
IPB010790
IPB010798
IPB010800
IPB010851
IPB011443
IPB011651
IPB012484
IPB012532
IPB012565
IPB012573
IPB012576
IPB012627
IPB012631
IPB012980
IPB012980
IPB013221

      
blimps-3.9/www/help/blkprob-aa.html000064400001460000012000000323350774357760600176550ustar00jorjastaff00000400000027Block Searcher Results

      Block Searcher Results
      
Go to hits

      Introduction
      
BLKPROB Version  4/11/99.1
Database=../data-blplus/blocks.dat
        ___________               ___________               ___________ 
       |\ __________\            |___________|            /__________ /|
       | |           |           |           |           |           | |
       | | **********|           |***********|           |********** | |
       | | * BLOCKS  |           |EMAIL & WWW|           |SEARCHER * | |
       | | **********|           |***********|           |********** | |
        \|___________|___________|___________|___________|___________|/
                     |\ __________\         /__________ /|
                     | |  blocks@  |       | http://   | |
                     | |   blocks. |       |  blocks.  | |
                     | |   fhcrc.  |       |  fhcrc.   | |
                     | |   org     |       |  org      | |
                      \|___________|       |___________|/


Here are your search results. The database searched was Blocks+ (19 Mar 99)
which includes: BLOCKS 11.0 consisting of 4034 blocks representing 994 groups
documented in PROSITE 15, plus 2277 blocks from 352 groups documented in
PRINTS 22.0 but not represented in BLOCKS, plus 1083 blocks from 254 groups
documented in PFAM 3.4 but not represented in BLOCKS or PRINTS, plus
1035 blocks from 268 groups documented in PRODOM 36 but not represented in
BLOCKS, PRINTS or PFAM, plus 480 blocks from 127 groups documented in DOMO 2.0
but not represented in BLOCKS, PRINTS, PFAM or PRODOM for a total of 8909
blocks from 1995 groups.  Get more information at http://blocks.fhcrc.org.
If you found the Blocks Searcher useful, please cite:
   S Henikoff & JG Henikoff, "Protein family classification
   based on searching a database of blocks", Genomics 19:97-107 (1994).
==============================================================================
Each hit consists of one or more blocks from a protein group found
in the query sequence. One set of the highest-scoring blocks that are in the 
correct order and separated by distances comparable to the Blocks database is 
selected for analysis. If this set includes multiple blocks the probability 
that the lower scoring blocks support the highest scoring block is reported. 
Maps of the database blocks and query sequence are shown:
AAA represents a block roughly in proportion to its width.
  : represents the minimum distance between blocks in the database.
  . represents the maximum distance between blocks in the database.
< > indicate the sequence has been truncated to fit the page.
The query map is aligned on the highest scoring block. Multiple block hits 
that are consistent with the highest scoring block are separated by colons.
Block hits that are not consistent are mapped below. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database is
shown. The distance between detected blocks is listed as (min, max): for the
database entry followed by the distance in the query. Upper case in the query
indicates at least one occurrence of the residue in that column of the block.

=============================================================================
Note: For searches using DNA queries, "Location" refers to the position
in the query in base pairs from 5' to 3' on the + strand, whereas the map and 
alignment show the translated position in amino acid residues.
============================================================================= 


      [Return to top]
      Hits
      
Query=7UP1_DROME|P16375    STEROID RECEPTOR SEVEN-UP TYPE 1 | PS00031  
Size=543 Amino Acids
Blocks Searched=8909
Alignments Done=5067002
Cutoff Expected Value=  2
==============================================================================
                                                           Anchor   Combined
Family                                     Strand Blocks   E-value  E-value
BL00031 Nuclear hormones receptors DNA-bind   1   2 of 2   9.1e-27  4.9e-52
PR00545 RETINOIC ACID RECEPTOR SIGNATURE      1   6 of 8   1.1e-09  4.3e-22
PR00546 THYROID HORMONE RECEPTOR SIGNATURE    1   2 of 9        11     0.56
PR00307 ADENOVIRUS FIBRE PROTEIN SIGNATURE    1   1 of 7       1.2      1.1
PR00678 PI3 KINASE P85 REGULATORY SUBUNIT S   1   1 of 10      1.6      1.6
BL01114 GPR1/FUN34/yaaH family proteins.      1   1 of 4       1.7      1.6

==============================================================================
>BL00031 2/2 blocks: Nuclear hormones receptors DNA-binding region proteins.
Block    Frame    Location (aa)      Block E-value
BL00031A    0        200-232            9.1e-27
BL00031B    0        234-265            3.6e-24
Other reported alignments:

                         |---   31 amino acids---|
     BL00031 AAAAAAAAAAAAAAAAAAAAAAAAAA........BBBBBBBBBBBBBBBBBBBBBBBBBB
  7UP1_DROME AAAAAAAAAAAAAAAAAAAAAAAAAA:BBBBBBBBBBBBBBBBBBBBBBBBBB

BL00031A    <->A   (4,603):199                      
7UP1_DROME 200     CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNL
                   |||||||||||||||||||||||||||||||||
7UP1_DROME 200     CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNL

BL00031B   A<->B   (0,10):1                        
7UP1_DROME 234     YSCRGSRNCPIDQHHRNQCQYCRLKKCLKMGM
                   ||||||||||||||||||||||||||||||||
7UP1_DROME 234     YSCRGSRNCPIDQHHRNQCQYCRLKKCLKMGM

------------------------------------------------------------------------------
>PR00545 6/8 blocks: RETINOIC ACID RECEPTOR SIGNATURE
Block    Frame    Location (aa)      Block E-value
PR00545A    0        266-280                 51       **biased**
PR00545C    0        335-355              0.066
PR00545E    0        420-440                 36
PR00545F    0        460-477                9.2
PR00545G    0        481-500            1.1e-09
PR00545H    0        508-527            0.00098
Other reported alignments:

                         |---  116 amino acids---|
     PR00545 AAA::..BBBB::..CCCCC:::::.DDDD:::::...EEEEE::::FFFF:GGGG::HHHH
  7UP1_DROME <:::AAA::::::::::::CCCCC::::::::::::::EEEEE::::FFFF:GGGG::HHHH

PR00545A    <->A   (120,271):265     PR00545C   A<->C   (39,55):54           
C41977     227     KREAVQEERQRGKER   C41977     288     SDPVTNICQAADKQLFTLVEW
                    |||||  |                                 |||  |   ||  |||
7UP1_DROME 266     rREAVQrgRvpptQp   7UP1_DROME 335     imgidNICelAarlLFsaVEW

PR00545E   C<->E   (63,80):64           
RRXG_HUMAN 347     FDRVLTELVSKMKDMQMDKSE
                     |   | | | |    |  |
7UP1_DROME 420     hiRifqEqVeKlKalhvDsaE

PR00545F   E<->F   (19,19):19           PR00545G   F<->G   (3,3):3             
RRXA_CHICK 391     PSEVESLREKVYATLEAY   C41977     433     KYPEQPGRFAKLLLRLPALR
                       ||| ||    || |                       || || || ||||||| ||
7UP1_DROME 460     vthiESLqEKsqcaLEeY   7UP1_DROME 481     qYPnQPtRFgKLLLRLPsLR

PR00545H   G<->H   (7,7):7             
C41977     460     EHLFFFKLIGDTPIDTFLME
                   | |||  | | ||| |    
7UP1_DROME 508     EqLFFvrLvGkTPIeTlird

------------------------------------------------------------------------------
>PR00546 2/9 blocks: THYROID HORMONE RECEPTOR SIGNATURE
Block    Frame    Location (aa)      Block E-value
PR00546H    0        367-386                 34
PR00546I    0        434-456                 11
Other reported alignments:

                         |---  125 amino acids---|
     PR00546 AAA:::::BB:::::CCCDDDD:EEEE:FFFF:::..GGGG:HHHH:::::::::IIIII
  7UP1_DROME <:::::::::::::::::::::::::::::::::::::::::HHHH:::::::::IIIII

PR00546H    <->H   (206,435):366       
THA1_HUMAN 244     CEDQIILLKGCCMEIMSLRA
                     ||  ||     |   | |
7UP1_DROME 367     vtDQvaLLrlvwsElfvLnA

PR00546I   H<->I   (45,45):47             
THA1_HUMAN 309     FNLDDTEVALLQAVLLMSTDRSG
                      |  |   | |  |  ||  |
7UP1_DROME 434     lhvDsaEyscLkAivLftTDacG

------------------------------------------------------------------------------
>PR00307 1/7 blocks: ADENOVIRUS FIBRE PROTEIN SIGNATURE
Block    Frame    Location (aa)      Block E-value
PR00307B    0          3-15                 1.2
Other reported alignments:

                         |---  460 amino acids---|
     PR00307 AB:.........C................D:........................EF:::.G
  7UP1_DROME  B

PR00307B    <->B   (18,43):2    
FIBP_ADECG 21      PKPSTQPPFFNDR
                     ||| | ||| |
7UP1_DROME 3       asPSTaPGFFNPR

------------------------------------------------------------------------------
>PR00678 1/10 blocks: PI3 KINASE P85 REGULATORY SUBUNIT SIGNATURE
Block    Frame    Location (aa)      Block E-value
PR00678D    0        416-434                1.6
Other reported alignments:

                         |---  157 amino acids---|
     PR00678 AAA::::::BB::::CCCC::::::DDDEEEE:::::FFFGGGG::::HHHHIIIJJJJ
  7UP1_DROME <::::::::::::::::::::::::DDD

PR00678D    <->D   (186,486):415      
RATP3KA    486     AFNDTIKIFEEQCHPQERY
                   || | | || ||       
7UP1_DROME 416     AFmDhIrIFqEQveklkal

------------------------------------------------------------------------------
>BL01114 1/4 blocks: GPR1/FUN34/yaaH family proteins.
Block    Frame    Location (aa)      Block E-value
BL01114A    0        290-312                1.7       **biased**
Other reported alignments:

                         |---   77 amino acids---|
     BL01114 AAAAAAA:::::.BBBBBBBBBBB:::::::..CCCCCCCCCCCCCDDDDDDDDDDDDDD
  7UP1_DROME AAAAAAA

BL01114A    <->A   (4,85):289             
YD84_YEAST 83      QFANPVPLGLASFSLSCLVLSLI
                   | ||  | | | |       | |
7UP1_DROME 290     QiANgdPmGiAGFnghsyLsSyI

------------------------------------------------------------------------------

6 possible hits reported

      [Return to top]   [Blocks Home]

blimps-3.9/www/help/blkprob-dna.html000064400001460000012000000301300774357760600200250ustar00jorjastaff00000400000027Blocks Search Results

      Blocks Search Results
      

      

      Introduction
      

BLKPROB Version  4/ 8/99.1
Database=../data-blplus/blocks.dat
        ___________               ___________               ___________ 
       |\ __________\            |___________|            /__________ /|
       | |           |           |           |           |           | |
       | | **********|           |***********|           |********** | |
       | | * BLOCKS  |           |EMAIL & WWW|           |SEARCHER * | |
       | | **********|           |***********|           |********** | |
        \|___________|___________|___________|___________|___________|/
                     |\ __________\         /__________ /|
                     | |  blocks@  |       | http://   | |
                     | |   blocks. |       |  blocks.  | |
                     | |   fhcrc.  |       |  fhcrc.   | |
                     | |   org     |       |  org      | |
                      \|___________|       |___________|/


Here are your search results. The database searched was Blocks+ (19 Mar 99)
which includes: BLOCKS 11.0 consisting of 4034 blocks representing 994 groups
documented in PROSITE 15, plus 2277 blocks from 352 groups documented in
PRINTS 22.0 but not represented in BLOCKS, plus 1083 blocks from 254 groups
documented in PFAM 3.4 but not represented in BLOCKS or PRINTS, plus
1035 blocks from 268 groups documented in PRODOM 36 but not represented in
BLOCKS, PRINTS or PFAM, plus 480 blocks from 127 groups documented in DOMO 2.0
but not represented in BLOCKS, PRINTS, PFAM or PRODOM for a total of 8909
blocks from 1995 groups.  Get more information at http://blocks.fhcrc.org.
If you found the Blocks Searcher useful, please cite:
   S Henikoff & JG Henikoff, "Protein family classification
   based on searching a database of blocks", Genomics 19:97-107 (1994).
==============================================================================
Each numbered result consists of one or more blocks from a Prosite group found
in the query sequence. One set of the highest-scoring blocks that are in the 
correct order and separated by distances comparable to the Blocks database is 
selected for analysis. If this set includes multiple blocks the probability 
that the lower scoring blocks support the highest scoring block is reported. 
Maps of the database blocks and query sequence are shown:
AAA represents the first block roughly in proportion to its width.
  : represents the minimum distance between blocks in the database.
  . represents the maximum distance between blocks in the database.
< > indicate the sequence has been truncated to fit the page.
The query map is aligned on the highest scoring block. Multiple block hits 
that are consistent with the highest scoring block are separated by colons.
Block hits that are not consistent are mapped below. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database is
shown. The distance between detected blocks is listed as (min, max): for the
database entry followed by the distance in the query. Upper case in the query
indicates at least one occurrence of the residue in that column of the block.

For interpretation of block hits, you might find it worthwhile to obtain the
full set of blocks and documentation for a group. To do this, send a blank
message to blocks@blocks.fhcrc.org with the subject heading: GET BL????? e.g.,  
'Subject: GET BL00044' (0s are zeros) for full information on this group.
=============================================================================
Note: For searches using DNA queries, "Location" refers to the position
in the query in base pairs from 5' to 3' on the + strand, whereas the map and 
alignment show the translated position in amino acid residues as before.
============================================================================= 


      [Return to top]
      Hits
      
Query=gi|2332305|gb|AA560840|AA560840  vk94e04.r1 Knowles Solter mouse blastocyst B1 M
Size=642 Base Pairs
Blocks Searched=8909
Alignments Done=12815646
Cutoff Expected Value=  2
==============================================================================
                                                           Anchor   Combined
Family                                     Strand Blocks   E-value  E-value
BL50040 Elongation factor 1 gamma chain pro   1   3 of 7   7.9e-32  5.5e-65
DM01181 7 kw 103-1A LACTOYLGLUTATHIONE GLUT   1   1 of 3   4.8e-05  4.6e-05
PF00043 Glutathione S-transferases.           1   1 of 1    0.0028   0.0026
BL00702 Granulocyte-macrophage colony-stimu   1   1 of 4      0.24     0.22
BL00421 Transmembrane 4 family proteins.      1   1 of 5      0.47     0.42
PR00614 NI-FE HYDROGENASE SMALL SUBUNIT SIG   1   1 of 11     0.77     0.71
BL00415 Synapsins proteins.                   1   1 of 19      2.1        2

==============================================================================
>BL50040 3/7 blocks: Elongation factor 1 gamma chain profile.
Block    Frame    Location (bp)   Position p-value
BL50040A    3          6-39             1.7e-14
BL50040B    2        152-227            7.2e-30
BL50040C    1        397-523            1.2e-38
Other reported alignments:

                         |---  186 amino acids---|
     BL50040 AA:::..BBB::::::...CCCCCC::::::::::...DDDDDDDEEEEEEEFFFFF.G
          gi  AA:::::BBB::::::::CCCCCC

BL50040A    <->A   (2,3):1        BL50040B   A<->B   (25,37):37                
EF1G_HUMAN 4       GTLYTYPENWRA   EF1G_HUMAN 53      FPAGKVPAFEGDDGFCVFESNAIAYY
                   ||||||||||||                      ||||||||||||||||||||||||||
gi         2       GTLYTYPENWRA   gi         51      FPAGKVPAFEGDDGFCVFESNAIAYY

BL50040C   B<->C   (47,66):56                                 
EF1G_RABIT 135     VKRILGLLDAHLKTRTFLVGERVTLADITVVCTLLWLYKQVLE
                   ||||||||| |||||||||||||||||||||||||||||||||
gi         133     VKRILGLLDtHLKTRTFLVGERVTLADITVVCTLLWLYKQVLE

------------------------------------------------------------------------------
>DM01181 1/3 blocks: 7 kw 103-1A LACTOYLGLUTATHIONE GLUTATHIONE LYASE.
Block    Frame    Location (bp)   Position p-value
DM01181C    1        367-478            7.5e-12
Other reported alignments:

                         |---   63 amino acids---|
     DM01181 AAAAAAAAAAAAAAAAAAAAAA::::::...BBBBBBBBB::::.CCCCCCCCCCCCCCC
          gi <::::::::::::::::::::::::::::::::::::::::::::CCCCCCCCCCCCCCC

DM01181C    <->C   (112,128):122                         
GTX1_TOBAC 115     GEEQEKDKEEVCEMLKVLDNELKDKKFFVGDKFGFADI
                       |  ||||   |  ||  ||   | ||     |||
gi         123     kqAtEnAKEEVkrILgLLDthLKtRTFlVGErVtLADI

------------------------------------------------------------------------------
>PF00043 1/1 blocks: Glutathione S-transferases.
Block    Frame    Location (bp)   Position p-value
PF00043     2        164-251            4.4e-10
Up to 1 repeats expected:
PF00043     2        167-254            8.5e-07
Other reported alignments:

PF00043     <->
EF1G_HUMAN 57      KVPAFEGDDGFCVFESNAIAYYVSNEELRG
                   ||||||||||||||||||||||||||||||
gi         55      KVPAFEGDDGFCVFESNAIAYYVSNEELRG
           56      VPAFEGDDGFCVFESNAIAYYVSNEELRGS

------------------------------------------------------------------------------
>BL00702 1/4 blocks: Granulocyte-macrophage colony-stimulating factor proteins.
Block    Frame    Location (bp)   Position p-value
BL00702B    1        430-532            3.7e-08
Other reported alignments:

                         |---   60 amino acids---|
     BL00702 AAAAAAAAAAAAAAAAA:::.BBBBBBBBBBBBBBBCCCCCCCCCCCCDDDDDDDDDDDD
          gi <::::::::::::::::::::BBBBBBBBBBBBBBB

BL00702B    <->B   (32,52):143                        
CSF2_PIG   53      MNETVDVVCEMFDPQEPTCVQTRLNLYKQGLRGSL
                          | |       | | | | |||| |  | 
gi         144     LktrTflVgErvtLadiTvVcTlLwLYKQvLepSF

------------------------------------------------------------------------------
>BL00421 1/5 blocks: Transmembrane 4 family proteins.
Block    Frame    Location (bp)   Position p-value
BL00421C    2        479-512            7.3e-08
Other reported alignments:

                         |---  107 amino acids---|
     BL00421 AAAA:::::::..BBBBBBBBB::::::::::..CCC:....D::.........EEEEEEE
          gi <:::::::::::::::::::::::::::::::::CCC

BL00421C    <->C   (132,154):159
C151_HUMAN 149     LQQEFHCCGSNN 
                   ||    |||| | 
gi         160     LQlSVpCCGSiN 

------------------------------------------------------------------------------
>PR00614 1/11 blocks: NI-FE HYDROGENASE SMALL SUBUNIT SIGNATURE
Block    Frame    Location (bp)   Position p-value
PR00614I    1          1-79             1.2e-07
Other reported alignments:

                         |---  112 amino acids---|
     PR00614 AAAAABBBBBB::::.CCCCC:.DDDEEEEEE:.FFFFFGGGGHHHH:IIIIIIJJJKKK
          gi                                                 IIIIII

PR00614I    <->I   (204,283):0                
MBHS_ALCHY 254     RKGYCLYKVGCKGPTTYNACSTTRWNG
                   | | |       || |   ||  |  |
gi         1       RlGpCthtLkigGPsTsvrCSvQRgsG

------------------------------------------------------------------------------
>BL00415 1/19 blocks: Synapsins proteins.
Block    Frame    Location (bp)   Position p-value
BL00415Q    1         40-145            3.3e-07       biased
Other reported alignments:

                         |---  294 amino acids---|
     BL00415 AAABBBCCCDDDEEEFFFGGHHHHIIJJKKKKLLMMMNNNN::OOOPPPQQQRRRSSS
          gi                                                 :QQQ

BL00415Q    <->Q   (594,596):13                        
SYN1_RAT   595     PAGPIRQASQAGPGPRTGPPTTQQPRPSGPGPAGRP
                   |    |   | | |||    |     |  | |   |
gi         14      PstsvRcsvQrGsGPRalrtTplplwPnqPhP*isP

------------------------------------------------------------------------------

7 possible hits reported

      [Return to top]   [Blocks Home]
ound
in the query sequence. One set of the highest-scoring blocks that are in the 
correct order and separated by distances comparable to the Blocks database is 
selected for analysis. If this set includes multiple blocks the probability 
that the lower scoring blocks support the highest scoring block is reported. 
Maps of the database blocks and query sequence are shown:
AAA represents the first block roughly in proportblimps-3.9/www/help/blkprob.html000064400001460000012000000310560774357760700172760ustar00jorjastaff00000400000027
Blocks Search Results

      Blocks Search Results
      

      

      Introduction
      

BLKPROB Version  3/29/99.1
Database=../data-blplus/blocks.dat
        ___________               ___________               ___________ 
       |\ __________\            |___________|            /__________ /|
       | |           |           |           |           |           | |
       | | **********|           |***********|           |********** | |
       | | * BLOCKS  |           |EMAIL & WWW|           |SEARCHER * | |
       | | **********|           |***********|           |********** | |
        \|___________|___________|___________|___________|___________|/
                     |\ __________\         /__________ /|
                     | |  blocks@  |       | http://   | |
                     | |   blocks. |       |  blocks.  | |
                     | |   fhcrc.  |       |  fhcrc.   | |
                     | |   org     |       |  org      | |
                      \|___________|       |___________|/


Here are your search results. The database searched was Blocks+ (19 Mar 99)
which includes: BLOCKS 11.0 consisting of 4034 blocks representing 994 groups
documented in PROSITE 15, plus 2277 blocks from 352 groups documented in
PRINTS 22.0 but not represented in BLOCKS, plus 1083 blocks from 254 groups
documented in PFAM 3.4 but not represented in BLOCKS or PRINTS, plus
1035 blocks from 268 groups documented in PRODOM 36 but not represented in
BLOCKS, PRINTS or PFAM, plus 480 blocks from 127 groups documented in DOMO 2.0
but not represented in BLOCKS, PRINTS, PFAM or PRODOM for a total of 8909
blocks from 1995 groups.  Get more information at http://blocks.fhcrc.org.
If you found the Blocks Searcher useful, please cite:
   S Henikoff & JG Henikoff, "Protein family classification
   based on searching a database of blocks", Genomics 19:97-107 (1994).
==============================================================================
Each numbered result consists of one or more blocks from a Prosite group found
in the query sequence. One set of the highest-scoring blocks that are in the 
correct order and separated by distances comparable to the Blocks database is 
selected for analysis. If this set includes multiple blocks the probability 
that the lower scoring blocks support the highest scoring block is reported. 
Maps of the database blocks and query sequence are shown:
AAA represents the first block roughly in proportion to its width.
  : represents the minimum distance between blocks in the database.
  . represents the maximum distance between blocks in the database.
< > indicate the sequence has been truncated to fit the page.
The query map is aligned on the highest scoring block. Multiple block hits 
that are consistent with the highest scoring block are separated by colons.
Block hits that are not consistent are mapped below. The alignment of the
query sequence with the sequence closest to it in the BLOCKS database is
shown. The distance between detected blocks is listed as (min, max): for the
database entry followed by the distance in the query. Upper case in the query
indicates at least one occurrence of the residue in that column of the block.

For interpretation of block hits, you might find it worthwhile to obtain the
full set of blocks and documentation for a group. To do this, send a blank
message to blocks@blocks.fhcrc.org with the subject heading: GET BL????? e.g.,  
'Subject: GET BL00044' (0s are zeros) for full information on this group.
=============================================================================
Note: For searches using DNA queries, "Location" refers to the position
in the query in base pairs from 5' to 3' on the + strand, whereas the map and 
alignment show the translated position in amino acid residues as before.
============================================================================= 


      [Return to top]
      Hits
      
Query=7UP1_DROME|P16375  STEROID RECEPTOR SEVEN-UP TYPE 1 | PS00031  
Size=543 Amino Acids
Blocks Searched=8909
Alignments Done=5067002
Cutoff Expected Value=  2
==============================================================================
                                                           Anchor   Combined
Family                                            Blocks   E-value  E-value
BL00031 Nuclear hormones receptors DNA-binding r  2 of  2  9.1e-27  4.9e-52
PR00545 RETINOIC ACID RECEPTOR SIGNATURE          6 of  8  1.1e-09  4.3e-22
PR00546 THYROID HORMONE RECEPTOR SIGNATURE        2 of  9       11     0.56
PR00307 ADENOVIRUS FIBRE PROTEIN SIGNATURE        1 of  7      1.2      1.1
PR00678 PI3 KINASE P85 REGULATORY SUBUNIT SIGNAT  1 of 10      1.6      1.6
BL01114 GPR1/FUN34/yaaH family proteins.          1 of  4      1.7      1.6

==============================================================================
>BL00031 2/2 blocks: Nuclear hormones receptors DNA-binding region proteins.
Block    Frame    Location (aa)   Position p-value
BL00031A    0        200-232            1.8e-33
BL00031B    0        234-265              7e-31
Other reported alignments:

                         |---   31 amino acids---|
     BL00031 AAAAAAAAAAAAAAAAAAAAAAAAAA........BBBBBBBBBBBBBBBBBBBBBBBBBB
  7UP1_DROME AAAAAAAAAAAAAAAAAAAAAAAAAA:BBBBBBBBBBBBBBBBBBBBBBBBBB

BL00031A    <->A   (4,603):199                      
7UP1_DROME 200     CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNL
                   |||||||||||||||||||||||||||||||||
7UP1_DROME 200     CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNL

BL00031B   A<->B   (0,10):1                        
7UP1_DROME 234     YSCRGSRNCPIDQHHRNQCQYCRLKKCLKMGM
                   ||||||||||||||||||||||||||||||||
7UP1_DROME 234     YSCRGSRNCPIDQHHRNQCQYCRLKKCLKMGM

------------------------------------------------------------------------------
>PR00545 6/8 blocks: RETINOIC ACID RECEPTOR SIGNATURE
Block    Frame    Location (aa)   Position p-value
PR00545A    0        266-280              1e-05       biased
PR00545C    0        335-355            1.3e-08
PR00545E    0        420-440            7.2e-06
PR00545F    0        460-477            1.8e-06
PR00545G    0        481-500            2.2e-16
PR00545H    0        508-527            1.9e-10
Other reported alignments:

                         |---  116 amino acids---|
     PR00545 AAA::..BBBB::..CCCCC:::::.DDDD:::::...EEEEE::::FFFF:GGGG::HHHH
  7UP1_DROME <:::AAA::::::::::::CCCCC::::::::::::::EEEEE::::FFFF:GGGG::HHHH

PR00545A    <->A   (120,271):265     PR00545C   A<->C   (39,55):54           
C41977     227     KREAVQEERQRGKER   C41977     288     SDPVTNICQAADKQLFTLVEW
                    |||||  |                                 |||  |   ||  |||
7UP1_DROME 266     rREAVQrgRvpptQp   7UP1_DROME 335     imgidNICelAarlLFsaVEW

PR00545E   C<->E   (63,80):64           
RRXG_HUMAN 347     FDRVLTELVSKMKDMQMDKSE
                     |   | | | |    |  |
7UP1_DROME 420     hiRifqEqVeKlKalhvDsaE

PR00545F   E<->F   (19,19):19           PR00545G   F<->G   (3,3):3             
RRXA_CHICK 391     PSEVESLREKVYATLEAY   C41977     433     KYPEQPGRFAKLLLRLPALR
                       ||| ||    || |                       || || || ||||||| ||
7UP1_DROME 460     vthiESLqEKsqcaLEeY   7UP1_DROME 481     qYPnQPtRFgKLLLRLPsLR

PR00545H   G<->H   (7,7):7             
C41977     460     EHLFFFKLIGDTPIDTFLME
                   | |||  | | ||| |    
7UP1_DROME 508     EqLFFvrLvGkTPIeTlird

------------------------------------------------------------------------------
>PR00546 2/9 blocks: THYROID HORMONE RECEPTOR SIGNATURE
Block    Frame    Location (aa)   Position p-value
PR00546H    0        367-386            6.8e-06
PR00546I    0        434-456            2.2e-06
Other reported alignments:

                         |---  125 amino acids---|
     PR00546 AAA:::::BB:::::CCCDDDD:EEEE:FFFF:::..GGGG:HHHH:::::::::IIIII
  7UP1_DROME <:::::::::::::::::::::::::::::::::::::::::HHHH:::::::::IIIII

PR00546H    <->H   (206,435):366       
THA1_HUMAN 244     CEDQIILLKGCCMEIMSLRA
                     ||  ||     |   | |
7UP1_DROME 367     vtDQvaLLrlvwsElfvLnA

PR00546I   H<->I   (45,45):47             
THA1_HUMAN 309     FNLDDTEVALLQAVLLMSTDRSG
                      |  |   | |  |  ||  |
7UP1_DROME 434     lhvDsaEyscLkAivLftTDacG

------------------------------------------------------------------------------
>PR00307 1/7 blocks: ADENOVIRUS FIBRE PROTEIN SIGNATURE
Block    Frame    Location (aa)   Position p-value
PR00307B    0          3-15             2.3e-07
Other reported alignments:

                         |---  460 amino acids---|
     PR00307 AB:.........C................D:........................EF:::.G
  7UP1_DROME  B

PR00307B    <->B   (18,43):2    
FIBP_ADECG 21      PKPSTQPPFFNDR
                     ||| | ||| |
7UP1_DROME 3       asPSTaPGFFNPR

------------------------------------------------------------------------------
>PR00678 1/10 blocks: PI3 KINASE P85 REGULATORY SUBUNIT SIGNATURE
Block    Frame    Location (aa)   Position p-value
PR00678D    0        416-434            3.2e-07
Other reported alignments:

                         |---  157 amino acids---|
     PR00678 AAA::::::BB::::CCCC::::::DDDEEEE:::::FFFGGGG::::HHHHIIIJJJJ
  7UP1_DROME <::::::::::::::::::::::::DDD

PR00678D    <->D   (186,486):415      
RATP3KA    486     AFNDTIKIFEEQCHPQERY
                   || | | || ||       
7UP1_DROME 416     AFmDhIrIFqEQveklkal

------------------------------------------------------------------------------
>BL01114 1/4 blocks: GPR1/FUN34/yaaH family proteins.
Block    Frame    Location (aa)   Position p-value
BL01114A    0        290-312            3.3e-07       biased
Other reported alignments:

                         |---   77 amino acids---|
     BL01114 AAAAAAA:::::.BBBBBBBBBBB:::::::..CCCCCCCCCCCCCDDDDDDDDDDDDDD
  7UP1_DROME AAAAAAA

BL01114A    <->A   (4,85):289             
YD84_YEAST 83      QFANPVPLGLASFSLSCLVLSLI
                   | ||  | | | |       | |
7UP1_DROME 290     QiANgdPmGiAGFnghsyLsSyI

------------------------------------------------------------------------------

6 possible hits reported

      [Return to top]   [Blocks Home]

      
/getblock.sh?BL01114#BL01114">BL01114 GPR1/FUN34/yaaH family proteins.          1 of  4      1.7      1.6

==============================================================================
>BL00031 2/2 blocks: Nuclear hormones receptors DNA-binding region proteins.
Block    Frame    Location (aa)   Position p-value
BL00031A    0        200-232        blimps-3.9/www/help/blocks_format.html000064400001460000012000000132740776273164300204630ustar00jorjastaff00000400000027Blocks Format

       Format of a Block
      



      ID   short_identifier; BLOCK
AC   block_number; distance from previous block = (min,max)
DE   description
BL   xxx motif; width=w; seqs=s; 99.5%=n1; strength=n2
sequence_id  (offset) sequence_segment  sequence_weight
.
.
.
//
      

ID line starts a block entry and contains a short identifier for the group
of sequences from which the block was made.
If the block was taken from InterPro, it will be the InterPro group ID.
The identifier is terminated by a semi-colon, and the word "BLOCK"
indicates the entry type.
      

AC line contains the block number, a seven-character group number for
sequences from which the block was made, followed by a letter (A-Z) 
indicating the order of the block in the sequences.
If the group has only one block, the letter is omitted.
If the block was made from InterPro group IPRnnnnnn, the block number
is IPBnnnnnna.
If the block was converted from Terri Attwood's Prints Database the
block number is PRnnnnna. 
min,max =  minimum,maximum number of amino acids from previous block for
sequences in this block. For the first block in the group, the distance from
the beginning of the sequences.
      

DE line contains a description of the group of sequences from which
the block was made. If the block was taken from InterPro, it will be
a slightly edited version of the InterPro description.
      

BL line contains information about the block:
      
xxx =  the amino acids in the spaced triplet found by MOTIF upon
which the block is based.
      
w =  width of the sequence segments (columns) in the block.
      
s =  number of sequence segments (rows) in the block.
      
n1 =  raw calibration score; 99.5th percentile score of true
negative sequences. Raw search scores are normalized by
dividing by this score and multiplying by 1000.
      
n2 =  median normalized score of known true positive sequences as
documented in InterPro.
      

Following the BL line are lines for each sequence with
a segment in the block. The segments may be clustered with clusters
separated by blank lines.
Each segment line contains a sequence identifier,
the offset from the beginning of the sequence
to the block in parentheses, the sequence segment, and a weight for the
segment. The weights are normalized so that
the most distant segment has a weight of 100.
      

// line terminates a block entry.

      
Current Blocks Database Release

      
About the Blocks Database

      

      Other Multiple Alignment Formats
      

      FASTA Format
      
Each sequence in the multiple alignment starts with a FASTA
title line containing the sequence name followed by the
aligned sequence residues with dashes representing gaps:

      >JC2395
NVSDVNLNK---YIWRTAEKMK---ICDAKKFARQHKIPESKIDEIEHNSPQDAAE----
-------------------------QKIQLLQCWYQSHGKT--GACQALIQGLRKANRCD
IAEEIQAM
>KPEL_DROME
MAIRLLPLPVRAQLCAHLDAL-----DVWQQLATAVKLYPDQVEQISSQKQRGRS-----
-------------------------ASNEFLNIWGGQYN----HTVQTLFALFKKLKLHN
AMRLIKDY
>FASA_MOUSE
NASNLSLSK---YIPRIAEDMT---IQEAKKFARENNIKEGKIDEIMHDSIQDTAE----
-------------------------QKVQLLLCWYQSHGKS--DAYQDLIKGLKKAECRR
TLDKFQDM

      


      

      CLUSTAL/STOCKHOLM Format
      
ClustalW Site.
      
The first non-blank line must contain the word "CLUSTAL" or "STOCKHOLM".
Sequences are interleaved on separate lines with gaps represented
by dashes. Each sequence line starts with the sequence name which is
separated from the aligned sequence residues by spaces or tabs.
Each set of interleaved sequence segments is separated by one or more
blank lines. Lines containing sequence conservations symbols (CLUSTAL)
or "//" (STOCKHOLM) are ignored.

      
(Please note: Some WWW sites post-process Clustal output so that
it has a different format than in this example; in this case use
FASTA format).

      CLUSTAL W(1.60) multiple sequence alignment



JC2395          NVSDVNLNK---YIWRTAEKMK---ICDAKKFARQHKIPESKIDEIEHNSPQDAAE----
KPEL_DROME      MAIRLLPLPVRAQLCAHLDAL-----DVWQQLATAVKLYPDQVEQISSQKQRGRS-----
FASA_MOUSE      NASNLSLSK---YIPRIAEDMT---IQEAKKFARENNIKEGKIDEIMHDSIQDTAE----


JC2395          -------------------------QKIQLLQCWYQSHGKT--GACQALIQGLRKANRCD
KPEL_DROME      -------------------------ASNEFLNIWGGQYN----HTVQTLFALFKKLKLHN
FASA_MOUSE      -------------------------QKVQLLLCWYQSHGKS--DAYQDLIKGLKKAECRR


JC2395          IAEEIQAM
KPEL_DROME      AMRLIKDY
FASA_MOUSE      TLDKFQDM




      


      

      MSF Format
      
Any comments at the beginning of the file are terminated with a line
starting with two slashes.
Sequences are interleaved on separate lines with gaps represented
by periods. Each sequence line starts with the sequence name which is
separated from the aligned sequence residues by white space:

      //


                1                                                   50
JC2395          NVSDVNLNK. ..YIWRTAEK MK...ICDAK KFARQHKIPE SKIDEIEHNS 
KPEL_DROME      MAIRLLPLPV RAQLCAHLDA L.....DVWQ QLATAVKLYP DQVEQISSQK 
FASA_MOUSE      NASNLSLSK. ..YIPRIAED MT...IQEAK KFARENNIKE GKIDEIMHDS

		51                                                 100
JC2395		PQDAAE.... .......... .......... .....QKIQL LQCWYQSHGK
KPEL_DROME	QRGRS..... .......... .......... .....ASNEF LNIWGGQYN.
FASA_MOUSE	IQDTAE.... .......... .......... .....QKVQL LLCWYQSHGK

                101
JC2395		T..GACQALI QGLRKANRCD IAEEIQAM
KPEL_DROME	...HTVQTLF ALFKKLKLHN AMRLIKDY
FASA_MOUSE	S..DAYQDLI KGLKKAECRR TLDKFQDM



      
      [Blocks home]

uence segments (columns) in the block.
      
s =  number of sequence segments (rows) in the block.
      
n1 =  raw calibration score; 99.5th percentile score of true
negative sequences. Raw search scores are normalized by
dividing by this score and multiplying by 1000.
      
n2 =  median normalized score of blimps-3.9/www/help/blocks_release.html000064400001460000012000000124141040507100500205570ustar00jorjastaff00000400000027
Current BLOCKS Database Release


      Current Release of BLOCKS
      


      
               BLOCKS Database Version 14.2, March 2006
      
       Copyright 2006 by Fred Hutchinson Cancer Research Center
      
              1100 Fairview AV N, A1-162, Seattle, WA 98109


      
Version 14.2 of the BLOCKS Database consists of 29,767 blocks representing
6149 groups documented in InterPro 12.0 keyed to SWISS-PROT 48.3 and 
TrEMBL 31.3 obtained from the 
InterPro server .
      
The BLOCKS Database is based on InterPro entries with sequences from
SWISS_PROT
and
TrEMBL
and with cross-references to
PROSITE 
and/or
PRINTS
and/or
SMART,
and/or
PFAM
and/or
ProDom
entries.

      
The BLOCKS Database was constructed by the PROTOMAT system 
(S Henikoff & JG Henikoff, "Automated assembly of protein blocks for
database searching", NAR (1991) 19:6565-6572)
using the MOTIF algorithm
(HO Smith, et al, "Finding sequence motifs in groups of functionally
related proteins", PNAS (1990) 87:826-830)
as implemented in
Block Maker.

      
To avoid using possible false positive sequences added to the
InterPro entries automatically (without human oversight),
BLOCKS were made for each InterPro entry using just the sequences
in SWISS-PROT, and then TrEMBL sequences were added if they fit the
resulting BLOCKS model.

      
Version 14.2 is an incremental update. Additional sequences were added
to 5261 entries in Blocks 14.1, 33 entries were dropped and 449 entries 
were added.
InterPro 12.0 consisted of 12,542 entries. The 6149 entries of these
represented in BLOCKS 14.2 were selected as follows:
      

      
12542
-2850 entries with no PROSITE, PRINTS, SMART, PFAM or ProDom component (1)
-3104 entries with fewer than 3 SWISS-PROT sequences eligible for PROTOMAT (2)
 -293 entries participating in InterPro parent/child relationships (3)
  -29 entries with too many sequences to process with PROTOMAT
  -12 entries for which PROTOMAT failed to find blocks
 -105 entries for which final blocks were obviously useless (5)
 6149


 1372 blocks entries taken from PRINTS (4)


 4777 blocks entries made by PROTOMAT


NOTES:

(1) InterPro now contains entries from several other sources. However,
these five sources tend to define a protein family in terms most amenable
to the BLOCKS model which is short, highly conserved regions. In
particular, PROTOMAT will generally produce unsatisfactory results for
groups comprised of a few, long, globally alignable sequences.

(2) PROTOMAT requires at least 3 sequences to make blocks. To be more
confident that the sequences used are actually members of the InterPro
protein family, we used only sequences from SWISS-PROT. Then, to reduce
redundancy, we use only the longest SWISS-PROT sequence among those
with the same gene name (characters before the "_" in the SWISS-PROT ID)
and similar organism name (first three characters following the "_").
For example, if an InterPro group included SWISS-PROT sequences named
AANT_HDVAM|P25989     LENGTH=214
AANT_HDVD3|P29996     LENGTH=195   
AANT_HDVWO|P29997     LENGTH=205   
only AANT_HDVAM would be used by PROTOMAT.

(3) Several InterPro entries are arranged into parent/child hierarchies
where all the sequences in a child entry are included in the parent
entry. Since PROTOMAT will tend to find the same blocks for the parent
and children, each major branch of a hierarchy is represented by only
one BLOCKS entry.

(4) Because the PRINTS model is the same as the BLOCKS model and PRINTS is
a curated collection of alignments, the PRINTS blocks were used directly 
for InterPro entries with only a PRINTS component as long as the PRINTS blocks 
had at least three sequences from any source. Then additional sequences
were added from TrEMBL if they fit the PRINTS model.

(5) These entries tend to be sites (e.g. IPR000886, IPB001216),
repeats (e.g. IPR000479, IPR001473) and viral proteins (e.g. IPR000208,
IPR000752).

      

      
Please note: The PROSITE pattern is not used in any way to make the 
BLOCKS Database and BLOCKS made from an InterPro PROSITE group may or 
may not contain the PROSITE pattern. 
Similarly, the SMART and PFAM multiple alignments are not used
in any way to make the BLOCKS Database and BLOCKS made from an
InterPro PROSITE, SMART or PFAM group may or may not overlap with the
multiple alignments in those databases.


      

      BLOCKS without compositionally biased blocks
      
To avoid the over-representation of compositionally biased blocks in
search results, this subset of the BLOCKS Database excludes several
biased blocks. It may give better results,
especially with DNA queries.


      
BLOCKS home


      
Contact us 
      
Page last modified March 2006

blimps-3.9/www/help/formatter_help.html000064400001460000012000000136070775500655600206510ustar00jorjastaff00000400000027
Block Formatter Help

      Block Formatter Help
      

Block formatter will format 
a multiple sequence alignment to the 
block format used in the 
Blocks Database. 
You can obtain multiple sequence alignments by various methods. 
A number of 

programs for multiple alignment are available on the WWW. 
One such program is Block Maker. 
It finds ungapped local multiple alignments (blocks) in groups of related 
protein sequences. The BlockMaker output is already in the block format.
      

The minimal input is the 
aligned sequence segments, 
all the other data can be found or given arbitrary values.
      

The header fields

        

      • The ID field is a short 
identifier for sequences in the alignment.
        
Example - "Phosphorylases".
        


      • The Accession field is for the block name
. It should be 7 or 8 characters long. It is recommended that the 
first 7 characters will designate the block family or group and the last 
character will be used to number different blocks in that group 
(using upper case letters A-Z).
        
Examples - "TR1421_A", "TR1421_B", "Transpo".
        


      • The minimal and maximal distance from the 
previous block (or from the beginning of the sequences if this is 
the first block) is the number of amino acids between the block and the 
previous one (or sequences start).
        
Example - "5", "34".
        


      • The Description field is for the 
description of the group of sequences from which the 
block was made.
        
Example - "'Homeobox' domain proteins".
        


      • The Alignment method should shortly describe 
how the alignment was made or found.
        
Examples - "Manual alignment", "MACAW", "ClustalW", "Prot. Sci. 12 p345, 
            87'".
        


      • The alignment width specifies how 
wide (or long) is the alignment.
        
Example - "32".
        


      • The number of sequences is how many 
sequences are in the alignment.
        
Example - "11".
        

      

All the previous fields are optional. Their values could be 
given by the formatting program (either by default or from the multiple 
alignment).
      

The multiple alignment fields
      


        

      • The sequence names should not be 
longer than 10 characters and be unique.
        
Examples - "RECA_ECOLI", "S67853_A", "PCR#543"
        


      • The positions 
of the aligned sequence segment are their offset from the 
begining of the sequence. Every position should be in a separate line. 
Avoid empty lines.
        
Example - "67"

      

 The names and sequence position of each aligned sequence segment in the 
multiple alignment will be given by the program if nothing
is entered in these fields.
      


        

      • This field must be filled.
        
The aligned sequences 
should be in the amino acids single letter code. 
Use "-" for gaps, "X" for unknowns, and "*"
for stop codons. All other characters (numbers, spaces, punctuation marks) 
will be ignored. 
Every segment in the alignment must be the same length and equal to the 
alignment width.
        
Examples - "NAQKLMRYTK", "G--GWTEQL", "ADSEXXHYTT*"
        

The sequences can be given each on a separate line (avoiding empty lines) 
or in the FASTA format. Each sequence in the fasta format is headed by a 
line begining in a '>' character. The string following this character will
be taken as the sequence name. The following lines contain the sequence
until the next sequence header line. Thus you can specify both sequences 
and their name in the sequence field if you use the FASTA format. In this
format a sequence can be in more than one line.
        
The 
readseq
program can transform many sequence formats to the FASTA format.
        

      
Examples 
FASTA format -

      >vde_yeast vacuolar ATPAse 19 aa
DYYGIT
LSDDSD
HQFLLAN

>vde_cantr another yeast
1  NYYGITLAE
10 ETDHQFLLS
19 N
>reci_myctu (sequence can be in lower or upper case)
r a r t f
d l e v e
e l h t l
v a e g 
>reci_mycle (sequence can be on one line or more)
SMNRFDIEVEGNHNYFVDG
>dpi1_theli (only first word in this line is read as sequence name)
EGYVYDLSV
EDNENFLVGF

>dpi2_theli (header lines MUST start with a '>')
EGYV
YDIE
VEET
HRFF
ANN

      
basic format -

      DYYGITLSDDSDHQFLLAN
NYYGITLAEETDHQFLLSN
RARTFDLEVEELHTLVAEG
SMNRFDIEVEGNHNYFVDG
EGYVYDLSVEDNENFLVGF
EGYVYDIEVEETHRFFANN

      

An example of a possible output -


      ID   Inteins; BLOCK
AC   vde_yea; distance from previous block = (98,190)
DE   Protein introns (inteins).
BL   gibbs; width=19; seqs=6;
 vde_yeast ( 430) DYYGITLSDDSDHQFLLAN  90
 vde_cantr ( 447) NYYGITLAEETDHQFLLSN  84
reci_myctu ( 417) RARTFDLEVEELHTLVAEG 100
reci_mycle ( 342) SMNRFDIEVEGNHNYFVDG  95
dpi1_theli ( 513) EGYVYDLSVEDNENFLVGF  83
dpi2_theli ( 367) EGYVYDIEVEETHRFFANN  74
//

      

[Blocks home] 
[Block Searcher]
[Block Maker]
[Get Blocks]
[LAMA Searcher]
[Block formatter]

      
Page last modified August 1996

blimps-3.9/www/help/help.html000064400001460000012000000355340776273161200165650ustar00jorjastaff00000400000027
Block Searcher Help


      
Block Searcher Help
      



      Introduction
      

      
As an aid to detection and verification of protein sequence homology, the 
BLOCKS Searcher compares a protein or DNA sequence to the
current database
of protein blocks. Blocks are short multiply aligned ungapped 
segments corresponding to the most highly conserved regions of proteins. 

      
The rationale behind searching a database of blocks is that information from
multiply aligned sequences is present in a concentrated form, reducing
background and increasing sensitivity to distant relationships.  This
information is represented in a position-specific scoring table or "profile"
(4),
in which each column of the alignment is converted to a column of a table
representing the frequency of occurrence of each of the 20 amino acids.  For
searching a database of blocks, the first position of the sequence is aligned
with the first position of the first block, and a score for that amino acid is
obtained from the profile column corresponding to that position.  Scores are
summed over the width of the alignment, and then the block is aligned with the
next position.  This procedure is carried out exhaustively for all positions
of the sequence for all blocks in the database, and the best alignments
between a sequence and entries in the BLOCKS database are noted.  If a
particular block scores highly, it is possible that the sequence is related to
the group of sequences the block represents.  Typically, a group of proteins
has more than one region in common and their relationship is represented as a
series of blocks separated by unaligned regions.  If a second block for a
group also scores highly in the search, the evidence that the sequence is
related to the group is strengthened, and is further strengthened if a third
block also scores it highly, and so on.


      Return to top 
      


      
WWW form
      

        

      • Select the database to search
        


        

      • Results through email
        
If you enter an email address, your search will be queued and
your results will be emailed in text format. Your results
will also be available in HTML format via a URL that will remain
active for approximately 4 hours.


        

      • Cutoff expected value
        
Select an expected value for the search, the default is 5 hits
expected by chance. The expected value is the combined p-value
(18) multiplied by the number of
alignments done between the query sequence and blocks database
during the search. 


        

      • Amount of output
        
Summary with alignments: Includes a one line 
summary for each hit plus 
details for each blocks included in the hit.  
        
Summary only:A one line
summary is printed for each hit.
        
GFF format:"Gene Finding Features" format proposed by the 
Sanger Centre.
Because of the limitations of this format, the combined E-value cannot
be displayed. Instead, each block included in a hit is displayed individually
with an E-value for that block alone. Protein queries are reported with
strand "+" and frame "0".

        
Old style results: The original "block sort" post-processing
program is used, with statistics based on percentiles.
        
Raw results only: The raw
Blimps 
search results are returned
without any statistics or post-processing to combine blocks from the
same family.
        


        

      • Query sequence type
        
Determine automatically: If the query sequence
contains any occurence of 'E', 'F', 'I', 'L', 'P' or 'Q',
it is assumed to be protein, otherwise, if it consists of
more than 85% 'A', 'C', 'G', 'T', 'U', and 'N", it is
assumed to be DNA, otherwise, it is assumed to be protein.
Problems can arise if the query sequence format is incorrectly
interpreted; for example, the title may be incorrectly combined
with the sequence itself causing a DNA sequence to be
interpreted as protein. Check that the sequence read in is
of the correct type and length before interpreting your 
results.
        

Amino acid: Forces the sequence to be treated as protein
and it will not be translated before searching.
        

DNA: Forces the sequence to be treated as DNA and translated
before searching. Be sure that the sequence length reported 
is correct.


        
Optional search parameters for DNA queries:
        

        

      • Enter query sequence
        

        

      

      Return to top 
      


      Submitting multiple searches
      
If you have a large query sequence or several queries, 
Here is a sample perl script
to do bulk searches.
      


      
The Blocks Email Searcher currently runs on a Sun E250 workstation.
It uses an unsophisticated first-in/first-executed queuing scheme and
can complete an average search of one typical search of 350 amino
acids every two minutes. A DNA search takes longer because the
sequence is translated in all six frames. So a 1000 residue DNA query
will take about the same amount of time as six average amino acid
queries, or about 12 minutes, and a contig of 10,000 residues will take
about two hours. Consequently, if you have more than five searches
to do, we ask that you space them at reasonable intervals depending
on the type and size of your sequences so other people can get searches
processed between yours. The Blocks Searcher is least busy on weekends
and between about 20:00 and 04:00 Pacific coast (USA) time. We
appreciate your considerate use of this service.

      Return to top 
      


      Interpreting results of a search
      
Example using a protein query
      
Example using a DNA query
      

      
Heading
      
Query=Description line from query sequence
      
Size=Number of amino acids for protein query or base pairs for DNA query.
Be sure this number is correct before interpreting your results.
      
Blocks searched=Number of blocks searched with query.
      
Alignments done=Number of alignments done between query and blocks searched. 
this number is used to determine the expected value for each hit.
      
Cutoff expected value=Maximum combined E-value reported.
This is the number of matches expected to be found merely by chance.
      

      
Summary
      
One line is printed per hit, where a hit consists of blocks belonging
to a protein family represented in the database of blocks searched with
combined E-value less than or equal to the cutoff.
      


        

      • 
Strand: 1 for protein or forward strand (frames 1,2,3) of DNA query,
and -1 for reverse strand (frames -1,-2,-3) of DNA query
        

      • 
Blocks x of y: x blocks of a total of y for the family are included in the
hit. Blocks are only included if they appear in the correct order within
the query, and are spaced consistently with those observed in the sequences
from which the blocks were made. 
        

      • 
Anchor E-value: E-value of the "anchor" block for this hit, which is
the block with the lowest position p-value.
        

      • 
Combined E-value: Combined E-value for all of the blocks in the hit
(18). For single block hits, this is about the same
as the Anchor E-value.
        

      


      
Details
      
Detailed information is printed for each hit, including alignments with
the most similar sequence in each block.
      


        

      • 
Frame: 0 for protein query, or 1,2,3,-1,-2,-3 for DNA query.
        
Location: Location of block within query sequence in amino acids for 
protein or base pairs from 5' to 3' on the forward strand for DNA query.

      • 
Block E-value: Expected number of times the score for the alignment of this
block with the query sequence at this position could be seen by chance
given the search space (number of alignments done)
(17, 11).
        

      • 
Bias: If the block has biased composition as determined by
checking the correlation among positions using the
Biased Block Checker,
this fact is noted to the right of the position p-value. If this
is the case, a high-scoring alignment may simply be due to biased
composition of the query sequence.

      • 
Up to n repeats expected:
        
If the family is documented as having repeated domains, this fact
is noted and the location of possible repeats are printed.
        

      • 
Other reported alignments:
        
Alignments of the query with blocks in the family that were not included
in the hit either because they were lower-scoring or because they were
in the wrong order, or because the distance between them and other
blocks in the hit is inconsistent with distances represented in the
blocks database, are printed for reference. The distance criterion may
exclude blocks from the hit erroneously, especially for translated
searching of sequences containing introns.
        

      • 
Map: Following the list of blocks in the hit, a rough map compares
the blocks seen in family members with those seen in the query.
        
AAA represents a block roughly in proportion to its width.
        
  : represents the minimum distance between blocks in the database.
        
  . represents the maximum distance between blocks in the database.
        
< > indicate the sequence has been truncated to fit the page.
        
The query map is aligned on the highest scoring block. Multiple block hits 
that are consistent with the highest scoring block are separated by colons.
Block hits that are not consistent are mapped below.
        


      • 
Alignments: The query sequence in aligned with the family member from
each block in the hit which is most like it; a different family member may be
shown for each block.
The distance between detected blocks is listed as (min, max): for the
database entry followed by the distance in the query. Upper case in the query
indicates at least one occurrence of the residue in that column of the block.

        
Note: For searches using DNA queries, "Location" refers to the position
in the query in base pairs from 5' to 3' on the forward strand, 
whereas the map and 
alignments show the translated position in amino acid residues.

      

      

      Return to top 
      


      Getting documentation for blocks
      
Following up a potentially interesting hit is often aided by examining the
full set of blocks for a group.
Hits are linked to Get blocks.


      

      

      Return to top 
      


      References
      

      If you find the Blocks Searcher useful, please cite:

Henikoff S, Henikoff JG: Protein family classification based on
searching a database of blocks", Genomics 1994, 19:97-107.
[Postscript PDF]

Other references for this work are:

1. Henikoff S, Henikoff JG: Automated assembly of protein blocks for database
searching. Nucleic Acids Res. 1991, 19:6565-6572.
[Postscript PDF]

2. Bairoch A: PROSITE: A dictionary of sites and patterns in proteins. Nucleic
Acids Res. 1992, 20:2013-2018.
[Prosite page]

3. Bairoch A, Boeckmann B: The SWISS-PROT protein sequence data bank. Nucleic
Acids Res. 1992, 20:2019-2022.
[Swiss-Prot page]

4. Henikoff JG and HENIKOFF S: Using substitution probabilities
to improve position-specifiic scoring matrices", CABIOS 1996, 12:135-143.
[Postscript PDF]

5. Wallace JC, Henikoff S: PATMAT: a searching and extraction program for
sequence, pattern, and block queries and databases. CABIOS 1992, 8:249-254.

6. Henikoff S: Detection of Caenorhabditis transposon homologs in diverse
organisms. New Biol. 1992, 4:382-388.

7. Oliver SG et al.: The complete DNA sequence of yeast chromosome III. Nature
1992, 357:38-46.

8. Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E: What's
in a genome? Nature 1992, 358:287.

9. Henikoff S, Henikoff JG: A protein family classifcation method for
analysis of large DNA sequences, Proc. 27th HICSS 1994, p. 265-274.
[Postscript PDF]

10. Henikoff S, Henikoff JG: Position-based sequence weights, J. Mol. Biol.
1994, 243:574-578.
[Postscript PDF]

11. Tatusov RL, Altschul SF, Koonin EV: Detection of conserved segments in
proteins: Iterative scanning of sequence databases with alignment blocks,
PNAS 1994, 91:12091-12095.

12. Henikoff JG, Henikoff S: Using substitution probabilities to improve
position-specific scoring matrices, CABIOS 1996, 12:135-143.

13. Henikoff S, Henikoff JG: Embedding strategies for effective use of
multiple sequence alignment information, 1996, sumbitted for publication.

14. Thompson, JD, Higgins, DG and Gibson, TJ: CLUSTAL W: Improving the
sensitivity of progressive multiple sequence alignment through sequence
weighting, position-specific gap penalties and weight matrix choice,
NAR 1994, 22:4673-4680.
[FTP CLUSTAL W]

15. Saitou, N and Nei, M: The neighbor-joining method: A new method for
reconstructing phylogenetic trees, Mol. Biol. Evol. 1987, 4:406-425.

16. Felsenstein, J: , Cladistics 1989, 5:164-166.
[Phylip page]

17. McLachlan, A.: ,J. Mol. Biol. 1983, 169:15-30.

18. Bailey, T.L. and Gribskov, M.: Combining evidence
using p-values: application to sequence homology searchers, Bioinformatics
1998, 14:48-54.
[Postscript]


      

      Return to top 
      
blimps-3.9/www/help/index.html000064400001460000012000000012100774527412100167220ustar00jorjastaff00000400000027
Blocks Help Files

      
Blocks Help Files

      

      


       Contents: 
      



      

      
Contact us
      
Page last modified on Oct 2003


blimps-3.9/LICENSE000064400001460000012000000127671062460604100141670ustar00jorjastaff00000400000027(C) Copyright 1993-2007, Fred Hutchinson Cancer Research Center

LICENSE -- License and copyright information for BLOCKS and BLIMPS



---------------------------------------------------------------------------
                      FHCRC NONCOMMERCIAL LICENSE
                Fred Hutchinson Cancer Research Center
                         1100 Fairview AV N
                       Seattle, WA  98109-1024


This license may be copied and distributed but may not be modified in
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                               RECITALS:

      A.  Fred Hutchinson Cancer Research Center is a nonprofit
corporation dedicated to investigating the nature and causes of cancer
and methods of cancer prevention and treatment and for conducting
education in all phases of cancer research.

      B.  This license is designed to permit certain activities with
respect to any computer programs to which it applies on the terms
stated in this license.

                         TERMS AND CONDITIONS:

      1.   Definitions.

      "Program" means the computer software and associated
documentation in whatever form or format including source and object
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      "Derivative Work" means any modification, addition, upgrade,
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      "Licensee" means licensee of the Program under this license.

      "FHCRC" means Fred Hutchinson Cancer Research Center.

      2.  License, Copy, Distribute and Create Derivative Work.  FHCRC
hereby grants Licensee and Licensee accepts, subject to the terms and
conditions of this Agreement, a nonexclusive, royalty-free license to
use, copy and sublicense the Program and prepare and sublicense
Derivative Works.  This license is expressly limited as follows:

           a.  All copies of the Program must conspicuously show an
appropriate copyright notice and disclaimer of warranty and must
expressly refer to this license.  In addition, Derivative Works must
conspicuously state that the Program has been modified and the date of
any modification.

           b.  Licensee may not charge any fee or royalty for copies
of the Program or Derivative Work.  Licensee is authorized to
sublicense the Program and any Derivative Work to third parties on a
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otherwise distribute the Program or any Derivative Work.
Notwithstanding the foregoing, Licensee may be reimbursed for any
actual expenses it incurs in reproducing or delivering a copy of the
Program or any Derivative Work.

           c.  This license does not apply to a work written entirely
by Licensee.

           d.  Licensee agrees to make available to any person to whom
it sublicenses this Program or a Derivative Work source code and
object code for the Program or Derivative Work.

           e.  Licensee may not impose any terms in addition to the
terms of this license on any third party to whom it distributes the
Program, any Derivative Work or any copy thereof.

      3.  Reservation of Rights to FHCRC.  FHCRC hereby reserves to
itself all rights of any nature whatsoever with respect to the
Program.  Any Derivative Work created by FHCRC or its employees or
agents is not subject to the terms of this license.

      4.  Termination of license.  This license precludes any copying,
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Derivative Work except as expressly permitted under this license.
Violation of the terms of this license by Licensee will be deemed an
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provided, however, that sublicenses derived from Licensee will remain
in full force and effect provided that any such sublicensees do not
breach the terms of this license.

      5.  Acceptance of Terms of License.  Licensee agrees that by
copying or distributing this Program or by creating, copying or
distributing any Derivative Work, Licensee has agreed to the terms of
this license.

      6.  Limitation of Remedies and Indemnity.  Because this Program
is licensed on a royalty-free basis, FHCRC and any person distributing
this Program or any Derivative Work expressly disclaim all warranties
express or implied including, without limitation, any implied warranty
of merchantability or fitness for a particular purpose.  Neither FHCRC
nor any other party distributing the Program or any Derivative Work
will be liable for any damages arising from or related to the use of
the Program or such Derivative Work, including, without limitation,
incidental or consequential damages caused by the use or inability to
use the Program or loss or damage to data.

      Licensee agrees to indemnify, defend and hold FHCRC harmless
from and against any claims, causes of action, damages, liabilities
and expenses, including without limitation attorney's fees, arising
from or related to Licensee's use, copying or distribution of the
Program or any Derivative Work.

      7.  Severability.  If any provision of this license is held
invalid under any applicable law or for any other reason, such
invalidity shall not effect any other provision of this license that
can be given effect without the invalid provision.

      8.  Notice.  Persons wishing to communicate with FHCRC
concerning this license or the Program should address their
communications as follows:

      Fred Hutchinson Cancer Research Center
      Attn:  Dr. Steven Henikoff
      1100 Fairview AV N, A1-162
      PO Box 19024
      Seattle, WA  98109-1024

---------------------------------------------------------------------------
blimps-3.9/README000064400001460000012000000027561062460611100140350ustar00jorjastaff000004000000275/23/2007 BLIMPS version 3.9 a maintenance update

These are the versions of the programs used to make release 14.3 of
the Blocks Database and that are currently used on our web pages:
http://blocks.fhcrc.org

Installation requires an ANSI C compiler on a UNIX system.

1. Block Searcher, LAMA, CODEHOPs and other utilities:
   cd blimps
   make clean, make depend, make install

2. Block Maker
   cd protomat
   make clean, make depend, make install

3. Compiled programs are placed in the lib/ and bin/ directories
   There are pre-compiled versions for Solaris 9, GNU i686 Linux
   and Mac/OSX in the bin/ and lib/ directories.

4. You need to set the environment variable BLIMPS_DIR to be sure
   the programs run correctly. For example, they look for $BLIMPS_DIR/docs/

5. See the examples/ sub-directory for sample program execution.
   Block Searcher is in examples/blimps/
   Block Maker is in examples/protomat/
   CODEHOP is in examples/codehop/

6. Please read the LICENSE file before using the programs.

7. Maintenance of these programs is funded by:
NIH RO1 GM068488 "Maintenance of blocks-based tools for functional genomics"
7/1/03 to 6/30/07

-------------------------------------------------------------------------
Jorja Henikoff                                     jorja@fhcrc.org
Fred Hutchinson Cancer Research Center             FAX: 206-667-5889
1100 Fairview AV N, A1-162, PO Box 19024           Seattle, WA 98109-1024
-------------------------------------------------------------------------
blimps-3.9/UPDATES000064400001460000012000000125751062460636100142140ustar00jorjastaff00000400000027UPDATES to BLIMPS programs for Version 3.9

=======================================================================
Outstanding issues:
-Problem with sequences.c:read_a_sequence() if sequence file is rewound
or changed between calls because it saves the last record read.
-Need to call read_a_sequence() to eof after a rewind().
-Should add an initialization flag argument to read_a_sequence() to
force initialization of the buffer.
-Problem reading extremely long title lines of fasta formatted sequences
See include/strutil.h:#define EXTRA_LARGE_BUFF 1000
=======================================================================
Changes since version 3.8:
blimps/protxblk		new, lists proteins in blocks
include/protomat.h	increased sequence name length from 18 to 20
blimps/blocks.c		increased sequence name length
blimps/blalign.c	increased sequence name length
blimps/blk2slx.c	increased sequence name length
blimps/blkprob.c	increased sequence name length
blimps/block_vis.c	increased sequence name length
blimps/blweight.c	increased sequence name length,
			correct number of sequences if necessary
blimps/show_aligned_blocks.c		increased sequence name length
blimps/mablock.c	increased sequence name length
blimps/format_block.c	increased sequence name length
blimps/makelis.c	increased sequence name length
protomat/motifj.h	increased sequence name length
protomat/motifj.c	increased sequence name length
protomat/motomat.c	increased sequence name length
protomat/blksort.c	increased sequence name length
protomat/multimat.c	increased sequence name length
protomat/lislis.c	accomodate revised Trembl sequence names

=======================================================================
Changes since version 3.7:
include/protomat.h	increased MAXSEQS
protomat/motifj.h	increased MAXSEQS
protomat/lislis.c	improved sequence name recognition
blimps/addseqs.c	improved sequence name recognition
blimps/blklis.c		new, read blocks and list sequences
blimps/blDR.c		new, rewrite sequences in blocks
bin/osx, lib/osx	pre-compiled versions for Mac/OSX

--------------------------------------------------------------------------
Changes since version 3.6:
include/gcode.h:	add missing commas to gcodes[] table
	affects blimps/gcode.c, blimps/blimps.c and blimps/codehop.c
blimps/block.c, sequences.c: prevent aborts if incomplete blocks
blimps/codehop.h, codehop.c:	fixes for genetic codes, incomplete blocks
blimps/blweight.c:	increased MAXROWS
protomat/motifj.h:	increased MAXSEQS
blimps/papssm.c:	new
blimps/convert.c:	ignore Xs in blocks when computing scoring matrices,
			affects blimps, blk2pssm
lib/libblimps.a:	consolidated all libraries into this one

--------------------------------------------------------------------------
Changes since version 3.5:
docs/default.sij	removed leading spaces, causes load_qij() to abort!
blimps/addseqs.c	compare multi-part sequence names
blimps/blalign.c	added Stockholm output format & made it run faster
blimps/blimps.c		set error level to suppress most warnings
blimps/blk2pssm.c	fixed type argument bug
blimps/blkprob.c	use sprintf() instead of kr_itoa,
			added -C and -H options
blimps/blocks_search.c	new, web page interface 
blimps/cobbler.c	default values for SU,QM,FR
blimps/convert.c	fixed make_alts() problem with types 10,20,21,30
blimps/frequency.c	modified error messages
blimps/LAMA.c		fixed problem with freeing memory too soon
blimps/mablock.c	read Stockholm input format
blimps/makeblockmap.c	longer block family name bug
blimps/makelis.c	sequence name length problem
blimps/makelogob.c,.h	new, makes logos from blocks
blimps/matrix_logob.c	data typing problem (added explicit cast)
blimps/pssmdist.c	new, calculates theoretical PSSM score distribution
blimps/pssmBL.c		new, inserts calibration info from pssmdist in blocks
post-blimps/blksort.c	use sprintf() instead of kr_itoa

----------------------------------------------------------------------------
Changes since version 3.4:
blimps/Makefile.Solaris	changed compile options to access large files
include/protomat.h	added full_entry to struct db_id
include/convert.h	SIFT
include/strutil.h	EXTRA_LARGE_BUFF for wider blocks
include/gcode.h		Updated genetic codes from NCBI
include/protomat.h	Increased MAXSEQS and MAXFREQ

blimps/codehop.h	Updated list of genetic codes
blimps/blocks.c		wider blocks
blimps/protomat.c	updates for multi-part sequence names
blimps/cobbler.c	fixed bug finding LL sequence in read_seq()
blimps/convert.c	added type 22 to block_to_matrix() - almost no pseudos
		  	added type 40 to block_to_matrix() - SIFT
blimps/frequency.c	comments

blimps/blweight.c	wider blocks
blimps/blpssm.c		wider blocks
blimps/mablock.c	new parameters, wider blocks, fasta output
blimps/blk2pssm.c	new parameters for SIFT, etc.
blimps/rank_matrix.c	new program
blimps/bldist.c		new program
blimps/narrow.c		new program
blimps/prints2blocks.c	new program

post-blimps/motifj.h	added acc to struct db_info, increased MAXSEQS & MAXFREQ
post-blimps/motmisc.c	changes for multi-part sequence names
post-blimps/uextract.c	changed lis_list() to print id->full_entry
			added -k option
post-blimps/blksort.c	fixed bug when hit vs blocks with > MAXSEQS seqs

docs/default.sij, default.diri new for SIFT

www/			Blocks Server html files - samples only

=======================================================================
Solaris: Compile to access large (>2gb) files "man lfcompile"
	Change ftell() to ftello() and fseek() to fseeko()
	then
	cc `getconf LFS_CFLAGS` -fast ... -ly